@article {pmid40622509,
year = {2025},
author = {Can, A and Baysal, Ö},
title = {A Chitinase Gene Belonging to Serratia marcescens GBS19 Reveals Horizontal Gene Transfer within Bacterial Strains Besides its Biocontrol Potential Against Myzus persicae.},
journal = {Biochemical genetics},
volume = {},
number = {},
pages = {},
pmid = {40622509},
issn = {1573-4927},
abstract = {Microorganisms produce diverse enzymes with applications in biological control and pest management. Chitinase enzymes degrade chitin, a structural component of insect exoskeletons and fungal cell walls, offering sustainable and environmentally friendly solutions for agricultural pest and pathogen management. This study focused on the chiA gene from our original strain belonging to Serratia marcescens identified using multi locus sequencing and ribosomal DNA analysis, amplified via PCR, cloned into expression vectors, and expressed as a recombinant protein. The chiA enzyme was purified using His-tag affinity chromatography and showed optimal activity at 40 °C and pH 5. The purified chiA enzyme exhibited strong insecticidal activity against Myzus persicae, with an lethal dose50 of 15.8 ppm. The comparative genomic analysis using MUMMER4 and MAUVE, identified horizontal gene transfer (HGT) events and genomic rearrangements within reference strain and our strain GBS19. The recombinant chiA enzyme exhibited 98.4% similarity with reference chiA sequences, highlighting its evolutionary conservation. Molecular docking studies confirmed a binding affinity of - 5.74 kcal/mol between the enzyme and chitin monomers, supported by interaction studies with modeled chitin layer. In addition, we have also predicted the most variable mutations required for enzyme stability and enzymatic activity enhancement in cloned amino acid sequence using protein AI tool, which will also guide us further studies linked to site-directed mutagenesis. This study demonstrates the potential of S. marcescens chitinase as an effective biocontrol agent against Myzus persicae. It underscores the importance of recombinant DNA technology in sustainable agriculture and sheds light on the evolutionary adaptation of chitinase genes through HGT and mutational events.},
}
@article {pmid40621911,
year = {2025},
author = {Yu, J and Gao, J-W and Cao, K and He, D-Y and Xu, L and Fu, G-Y and Sun, C},
title = {Characterization of two novel species of the genus Flagellimonas reveals the key role of vertical inheritance in the evolution of alginate utilization loci.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0091725},
doi = {10.1128/spectrum.00917-25},
pmid = {40621911},
issn = {2165-0497},
abstract = {Flavobacteriaceae is the major participant in the degradation of algal polysaccharides. With diverse polysaccharide utilization loci (PULs) and specific carbohydrate-active enzymes (CAZymes), Flavobacteriaceae strains appear to have different abilities in algal polysaccharide degradation and therefore change their roles in the bacterial community. Here, we identified two novel isolates as two novel species of genus Flagellimonas with the names Flagellimonas alginolytica sp. nov. and Flagellimonas cixiensis sp. nov. Furthermore, the comprehensive genomic comparison of 41 Flagellimonas genomes revealed that Flagellimonas strains were diverse in the CAZymes and PUL profiles and exhibited a preference for polysaccharides derived from brown algae. The evolutionary analysis of alginate utilization loci (AUL) in this genus illuminated that the function genes in AULs, that is, PL7 and PL17, were more reliant on the stable inheritance from ancestors associated with gene duplication and loss rather than horizontal gene transfer (HGT) from outside, and the AUL structures exhibited a trend of simplification which resulted in the incidental decrease in alginate degradation ability. This study highlights the important role of vertical inheritance in the evolution of AULs and proves that the discrepancy in AUL structure can arouse phenotypic differences, providing a new perspective on the evolution of AUL and the niche adaptation mechanism of Flavobacteriaceae strains.IMPORTANCEFlavobacteriaceae play an important role in the marine carbon cycle with their noteworthy ability in algal polysaccharides degradation, which is primarily reliant on diverse polysaccharide utilization loci (PULs). Our study highlights the crucial role of vertical inheritance in the evolution of alginate utilization loci (AUL) in Flagellimonas strains and reveals the AUL structural simplification found in Flagellimonas strains that will lead to the reduction of alginate degradation ability. These insights advance understanding of niche adaptation strategy and related evolutionary mechanisms of Flavobacteriaceae strains.},
}
@article {pmid40619778,
year = {2025},
author = {Bhide, AJ},
title = {Redefining the nitroplast: Recent insights into the endosymbiontto- organelle transition.},
journal = {Journal of biosciences},
volume = {50},
number = {},
pages = {},
pmid = {40619778},
issn = {0973-7138},
mesh = {*Symbiosis/genetics ; Gene Transfer, Horizontal ; Photosynthesis/genetics ; *Plastids/genetics ; Cyanobacteria/genetics ; Rhodophyta/genetics ; Mitochondria/genetics ; Chlorophyta/genetics ; Alphaproteobacteria/genetics ; Biological Evolution ; Evolution, Molecular ; Dinoflagellida/genetics ; },
abstract = {One of the most remarkable events in cellular evolution is the endosymbiosis of α-proteobacteria with a single archaean host cell, a rare evolutionary process, which eventually led to the transformation of symbionts into fully functional mitochondrial organelles in eukaryotes. Evolutionary events related to plants occurred almost 1.6 billion years ago, when eukaryotic heterotrophs acquired a β-cyanobacterium (containing 1B RUBISCO) in what is termed as primary endosymbiosis. Further, this composite cell lineage evolved into three photosynthetic lineages: green algae (plants), red algae and the glaucophytes. Thereafter, a secondary, and tertiary endosymbiosis event occurred giving rise to distinct kinds of green and red-derived photosynthetic plastids, which can be observed in a few haptophytes and dinoflagellates respectively. Eventually, these endosymbionts acquired characteristic cellular properties such as two/multiple envelope membranes and reduction of their genomes through either loss or concerted endosymbiotic gene transfer (EGT) into the nucleus, which ultimately led to the decline of more than three quarters of coding capacity and complete loss of several metabolic pathways. This loss, however, is partly compensated by import of nuclearencoded proteins as well as proteins acquired by horizontal gene transfer (HGT). For most proteins, specific transport mechanisms from nucleus/cytoplasm to organelle exist. The proteins are typically translated as a preprotein with specific signal sequences targeted to the organelle membrane. These membranes harbour receptors, in some cases soluble receptors, for recognition of these signal sequences. Proteins are then internalised using a set of translocation machineries (Gould et al. 2006).},
}
@article {pmid40614847,
year = {2025},
author = {Wang, R and Chen, H and Liu, Y},
title = {Metagenomic insights into the characteristics and co-migration of antibiotic resistome and metal(loid) resistance genes in urban landfill soil and groundwater.},
journal = {Environmental research},
volume = {285},
number = {Pt 1},
pages = {122285},
doi = {10.1016/j.envres.2025.122285},
pmid = {40614847},
issn = {1096-0953},
abstract = {The heavy metals and antibiotic resistance genes (ARGs) in landfills showed a significant correlation; however, the relationship between metal(loid) resistance genes (MRGs) and ARGs in contaminated environments, as well as whether they co-migrate with human pathogenic bacteria (HPB), remains unclear. This study is the first to report the characteristics and co-migration of ARGs and MRGs in the soil and groundwater of aged urban landfill sites. Our findings indicated that quinolone, efflux, and macrolide-lincosamide-streptogramin represented the most abundant ARGs identified. Notably, ARG abundance was higher in groundwater compared to soil, with subtype diversity reflecting a similar trend; however, microbial diversity in soil was greater. Metagenome-assembled genomes data indicated a higher risk of antibiotic-resistant HPB in groundwater. It is imperative to focus on HPB that co-carry ARGs and MRGs alongside mobile genetic elements (MGEs), such as Ralstonia pickettii and Pseudomonas stutzeri. Genes conferring resistance to copper and mercury, as well as MGEs such as qacEdelta and intI1, played a critical role in promoting horizontal gene transfer of antibiotic resistance. MRG may promote ARG migration by affecting the permeability of the cell membrane. Procrustes analysis revealed a strong similarity (87 %) between heavy metals and MRG structures. Variance partitioning analyses demonstrated that both heavy metals and biological factors jointly governed landfill ARGs (96.2 %), exerting a more substantial influence in groundwater than in soil. This study serves as a reference for managing landfill, while emphasizing the importance of addressing the co-migration of MRGs and ARGs in pathogens when controlling the spread of risks.},
}
@article {pmid40612915,
year = {2025},
author = {Vasta, GR and Bianchet, MA},
title = {F-type lectins: Structural and functional aspects, and potential biomedical applications.},
journal = {BBA advances},
volume = {8},
number = {},
pages = {100166},
pmid = {40612915},
issn = {2667-1603},
abstract = {Among the multiple animal lectin families recognized to date, F-type lectins (FTLs), fucose-binding lectins characterized by an FTL domain (FTLD), constitute the most recent lectin family to be identified and structurally characterized. The structure of the FTL from the European eel Anguilla anguilla revealed a novel jellyroll lectin fold (the "F-type" fold) with unique fucose- and calcium-binding sequence motifs. The FTL lectin family comprises proteins that may exhibit single or multiple FTLD, in combination with structurally and functionally distinct domains, and can form oligomeric associations that display high-avidity multivalent binding. Differences in fine carbohydrate specificity among tandemly arrayed FTLDs present in any FTL polypeptide subunit, together with the expression of multiple FTL isoforms in a single individual supports a broad diversity in ligand recognition. Widely distributed in invertebrates, protochordates, ectothermic vertebrates, birds, and monotreme and marsupial mammals, the FTLD is also present in some bacterial proteins and viruses but absent in placental mammals. The taxonomically broad, and discontinuous distribution of the FTLD, suggests an extensive structural and functional diversification of this lectin family, including horizontal gene transfer in viruses and prokaryotic organisms, together with possible gene loss and/or cooption along the lineages leading to the mammals. FTLs' biological roles range from pathogen recognition in innate immunity to fertilization, cell adhesion and cell aggregation, and as bacterial virulence factors, among others. The specificity of FTLs for fucosylated moieties should provide ample opportunities for novel applications in glycan and cell separation, and innovative diagnostic, preventive, and therapeutic approaches in cancer and infectious disease.},
}
@article {pmid40479505,
year = {2025},
author = {Pianezza, R and Scarpa, A and Haider, A and Signor, S and Kofler, R},
title = {Spatiotemporal Tracking of Three Novel Transposable Element Invasions in Drosophila melanogaster over the Last 30 Years.},
journal = {Molecular biology and evolution},
volume = {42},
number = {7},
pages = {},
doi = {10.1093/molbev/msaf143},
pmid = {40479505},
issn = {1537-1719},
support = {NSF-EPSCoR-1826834 and NSF-EPSCoR-2032756//National Science Foundation/ ; P35093 and P34965//Austrian Science Fund (FWF)/ ; },
mesh = {Animals ; *DNA Transposable Elements ; *Drosophila melanogaster/genetics ; Gene Transfer, Horizontal ; Evolution, Molecular ; Genome, Insect ; },
abstract = {Transposable elements (TEs) are repetitive sequences capable of mobilizing within genomes, exerting a significant influence on evolution throughout the tree of life. Using a novel approach that does not require prior knowledge of the sequence of repeats, we identified three novel TE invasions in Drosophila melanogaster: McLE spread between 1990-2000, Souslik between 2009-2012, and Transib1 between 2013-2016. We recapitulate previous findings, revealing that a total of 11 TEs invaded D. melanogaster over the past two centuries. These 11 invasions increased the fly genome by ∼1 Mbp. Using data from over 1,400 arthropod genomes, we provide evidence that these TE invasions were triggered by horizontal transfers, with Drosophila simulans and species of the Drosophila willistoni group acting as putative donors. Through the analysis of ∼600 short-read datasets spanning diverse geographic regions, we reveal the rapidity of TE invasions: Transib1 swiftly multiplied from three isolated epicenters in 2014 to all investigated populations in just 2 years. Our findings suggest that anthropogenic activities, which facilitate the range and population expansions of D. melanogaster, could have accelerated the rate of horizontal transposon transfer as well as the spread of the TEs into the worldwide population. Given the significant impact of TEs on evolution and the potential involvement of humans in their dispersal, our research has crucial implications for both evolution and ecology.},
}
@article {pmid40612392,
year = {2025},
author = {Ma, Y and Lei, Z and Zhang, Y and Liu, Q and Zhang, F and Zu, H and Yang, X and Li, Z and Lu, B},
title = {Tracing the evolutionary trajectory of the IncP-2 plasmid co-harboring bla IMP-45 and bla VIM-1: an outbreak of Pseudomonas aeruginosa co-producing IMP-45 and VIM-1 carbapenemases in China.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1623241},
pmid = {40612392},
issn = {2235-2988},
mesh = {*beta-Lactamases/genetics/metabolism ; *Pseudomonas aeruginosa/genetics/drug effects/enzymology/isolation & purification ; *Plasmids/genetics ; Humans ; China/epidemiology ; *Pseudomonas Infections/epidemiology/microbiology ; *Bacterial Proteins/genetics/metabolism ; *Disease Outbreaks ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Microbial Sensitivity Tests ; Molecular Docking Simulation ; Evolution, Molecular ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {BACKGROUND: Carbapenem-resistant Pseudomonas aeruginosa (CRPA) poses a significant global health risk, particularly for immunocompromised individuals. This study documents an outbreak of CRPA strains co-harboring bla VIM-1 and bla IMP-45 on IncP-2 plasmids in a Chinese tertiary hospital, resulting in poor outcomes for transplant patients.<br><br>METHODS: 17 ST313 VIM-1-IMP-45 CRPA strains were collected from transplant patients, and antibiotic susceptibility was tested via microbroth dilution. Whole genome sequencing (WGS) identified drug resistance and virulence mechanisms, analyzed ST313 P. aeruginosa phylogeny, and traced bla VIM-1 and bla IMP-45 origins. Conjugation experiments were conducted to assess the conjugative potential of the IncP-2 plasmid co-harboring bla VIM-1 and bla IMP-45. Structural and molecular docking studies explored the PBP3 (P527S) mutation's role in aztreonam resistance.<br><br>RESULTS: From February 2022 to July 2024, 17 ST313 VIM-1-IMP-45 CRPA strains from 10 transplant patients were identified. All strains were extensively drug-resistant but sensitive to colistin and cefiderocol. WGS showed bla IMP-45 and bla VIM-1 on an IncP-2 megaplasmid. Phylogenetic analysis indicated high homology with plasmids carrying bla IMP-45. Further analysis of the genetic environment showed that the IncP-2 plasmid co-harboring bla VIM-1 and bla IMP-45 was formed by the insertion of a Tn3-family transposon carrying bla VIM-1 into the IncP-2 plasmid carrying bla IMP-45. In addition aztreonam-resistant strains (14/15) had a PBP3 (P527S) mutation, with molecular docking studies suggesting reduced aztreonam binding.<br><br>CONCLUSIONS: This study reports a clonal outbreak of ST313 P. aeruginosa strains co-producing IMP-45 and VIM-1 carbapenemases in a tertiary hospital. The evolutionary path of the IncP-2 plasmid co-harboring bla IMP-45 and bla VIM-1 was elucidated.},
}
@article {pmid40609725,
year = {2025},
author = {Chen, M and Song, L and Ye, C and Grossart, HP and Yang, Y and Li, S and Liao, H and Gong, Y and Che, R and Zhang, Q},
title = {Dynamic relationships of antibiotic resistomes and greenhouse gas-functioning microbes across diverse habitats.},
journal = {Environmental research},
volume = {284},
number = {},
pages = {122272},
doi = {10.1016/j.envres.2025.122272},
pmid = {40609725},
issn = {1096-0953},
abstract = {Reservoir ecosystems with diverse habitats form critical interfaces where antibiotic resistance genes (ARGs) and greenhouse gas (GHG) emissions converge. Despite their distribution and ecological implications of ARGs across diverse habitats remain greatly unknown. There is a critical gap in dissecting the interlinkages between antibiotic resistomes and GHG-functioning microbes. Thus, we aimed to investigate the relationship between antibiotic resistomes and GHG-functioning microbes in various habitats of the Three Gorges reservoir, encompassing water, sediment, and riparian top- and sub-soil. We provide a comprehensive assessment of ARG abundance and diversity across four habitats. Significant differences in ARG, with riparian zones exhibiting more than twice the ARG abundance of water. Horizontal gene transfer of ARGs was more frequent in water, suggesting a pivotal role in aquatic ARG dissemination. The GHG-functioning microbes displayed habitat-specific composition and diversity, with key genera like Neisseria and Azoarcus in riparian subsoil, contrasting with Streptomyces in other habitats. The dynamic relationship of antibiotic resistomes and GHG-functioning microbes ranges from synergistic to competitive in varied habitats, reflecting antibiotic resistomes can influence ecological function stability. This study emphasizes the importance of considering resistomes in the context of global change, advancing our understanding of environmental management and conservation strategies in these critical ecosystems.},
}
@article {pmid40607640,
year = {2025},
author = {Jia, X and Zhang, X and Chen, X and Fernie, AR and Wen, W},
title = {The horizontally transferred gene, CsMTAN, rewired purine traffic to build caffeine factories in tea leaves.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.13957},
pmid = {40607640},
issn = {1744-7909},
support = {32161133017//National Natural Science Foundation of China/ ; 32494781//National Natural Science Foundation of China/ ; },
abstract = {Purine-related metabolites are central to primary metabolic pathways in plants and serve as precursors for purine alkaloid biosynthesis in caffeinated species such as tea plants (Camellia sinensis). In this study, metabolite profiling of two tissues (young and mature leaves) was performed across 183 genetically diverse tea accessions, identifying and quantifying 10 purine alkaloid-related metabolites. Metabolite genome-wide association studies revealed 17 significant loci associated with these metabolites, including both known loci such as caffeine synthase and 16 novel loci (P < 1.05 × 10[-5]). Through functional annotation and in vitro enzymatic assay, we characterized 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (CsMTAN) as the causal gene underlying natural variation in adenosine and adenine content. CsMTAN can catalyze the degradation of both 5'-methylthioadenosine and S-adenosylhomocysteine to release adenine. The T → A nucleotide substitution at SNP55151898, which leads to a phenylalanine → tyrosine substitution at residue 179 (F179Y), resulted in a significant alteration of enzyme activity in vitro, as evidenced by an approximately 50% reduction in adenine abundance (P < 0.05). Transient overexpression of CsMTAN-A and CsMTAN-T in Nicotiana benthamiana both significantly increased adenine content and dramatically decreased adenosine content, providing direct evidence for the functional involvement of CsMTAN in plant purine metabolism. CsMTAN-T overexpression resulted in significantly lower adenosine level than CsMTAN-A (P < 0.05). Phylogenetic analysis across 115 species and protein structural modeling revealed a distinct evolutionary divergence between plant MTAN evolution and species phylogeny, strongly suggesting the occurrence of horizontal gene transfer events in the evolutionary history of plant MTANs. This study thus furthered our understanding of the genetics and molecular mechanisms regulating purine metabolism and purine alkaloid biosynthesis in tea plants and provided novel targets for molecular breeding and synthetic biology applications.},
}
@article {pmid40607638,
year = {2025},
author = {Hou, J and Liu, M and Yang, K and Liu, B and Liu, H and Liu, J},
title = {Genetic variation for adaptive evolution in response to changed environments in plants.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.13961},
pmid = {40607638},
issn = {1744-7909},
support = {No. 32030006//National Natural Science Foundation of China/ ; No. 32270302//National Natural Science Foundation of China/ ; 2024NSFSC0340//Natural Science Foundation of Sichuan Province/ ; },
abstract = {Plants adapt to their local environments through natural or artificial selection of optimal phenotypes. Recent advances in genomics and computational biology, which integrate phenotypic and multi-omics data, have facilitated the rapid identification of key genes and allelic variations that underlie these adaptive evolutionary processes. Understanding the underlying molecular mechanisms has significantly enhanced our knowledge of how plants respond to changed habitats, including various biotic and abiotic stresses. In this review, we highlight recent progress in elucidating the genetic basis of phenotypic variation in morphological traits and stress responses, as well as the emergence of new ecotypes, subspecies, and species during adaptive evolution across varied environments. This occurs through allelic divergences in both coding and non-coding regions in both model and non-model plants. Furthermore, the terrestrialization and early diversification of land plants involved the acquisition of additional genes, primarily through horizontal gene transfer and whole-genome duplication, which facilitated the development of complex molecular pathways to adapt to increasingly diverse environments. Finally, we discuss emerging trends and prospects for exploring and utilizing beneficial alleles for environmental adaptation, to guide crop breeding efforts in response to global climate change.},
}
@article {pmid40606176,
year = {2025},
author = {Du, H and Lu, C and Latif, MZ and Du, J and Liu, Y and Li, H and Ding, X},
title = {Thermophilic microbial agents promote the fermentation progression of spent mushroom compost and pig manure.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1575397},
pmid = {40606176},
issn = {1664-302X},
abstract = {Livestock and poultry manure, as a significant organic resource, had an enormous annual production but a utilization rate of less than 50%. Improperly managed manure had become the primary source of agricultural non-point pollution, posing severe challenges to the ecological environment. Achieving efficient resource utilization of livestock manure was a critical step in promoting green agricultural development. Existing research indicated that microbial activity significantly influences the transfer and dissemination of antibiotic resistance genes (ARGs) and the community dynamics of human pathogenic bacteria (HPB) during pig manure composting. However, the specific mechanisms remain unclear. This study innovatively introduced two thermophilic microbial agents (TMS1 and CTMS2) into a pig manure-spent mushroom compost (SMC) aerobic composting system to systematically investigate their regulatory effects on pollutant reduction. The results showed that persistent ARGs (ErmF, ErmQ, ErmX, blaR1, QnrA1, QnrA6, bla-F, QnrA2, QnrA5, Qnra4 and bla-VIM) primarily rely on vertical gene transfer (VGT) for dissemination, whereas easily removable ARGs (tetX, tetW, tetG, tetC, suI1 and suI2) were regulated by both horizontal gene transfer (HGT) and VGT. Notably, the co-addition of thermophilic microbial agents and SMC reduced persistent ARGs by lg0.45-3.73, significantly decreased the abundances of HPB such as Bacteroides and Treponema, and reduced the enrichment of related metabolic pathways, greatly improving compost quality. In stark contrast, the control group (with only SMC and no thermophilic microbial agents) exhibited ARG proliferation. Overall, the application of thermophilic microbial agents not only extended the high temperature phase of composting by over 30% and shortened the composting cycle by 50%, but more importantly, it achieved comprehensive improvement in compost quality by selectively enriching functional microbial communities such as Pseudomonas. This study provides a theoretical foundation and data support for the industrial application of CTMS2 in the safe production of organic fertilizers and the synergistic control of environmental risks.},
}
@article {pmid40606165,
year = {2025},
author = {Jers, C and Mišetić, H and Ravikumar, V and Garg, A and Franjević, D and Domazet-Lošo, T and Mijakovic, I},
title = {Gene age and genome organization in Escherichia coli and Bacillus subtilis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1512923},
pmid = {40606165},
issn = {1664-302X},
abstract = {Using genomic phylostratigraphy, we examined the organization of Escherichia coli and Bacillus subtilis genomes from the perspective of evolutionary age of their genes. Phylostratigraphy analysis classifies individual genes into age-related bins, called phylostrata. Based on this analysis, several common features emerged in the genomes of the two model bacteria. More recent genes tend to be shorter and are expressed less frequently, or only in specific conditions. In terms of genomic location, new genes are enriched in areas containing prophages, suggesting a link with horizontal gene transfer. Interestingly, while most bacterial transcription regulators belong to the oldest phylostrata, they regulate expression of both older and more recent genes alike. A large fraction of bacterial operons contains genes from different phylostrata. This suggests that newer genes are integrated in the existing framework for regulating gene expression, and that the establishment of new regulatory circuits typically do not accompany acquisition of new genes. One striking difference between E. coli and B. subtilis genomes was observed. About 87.0% of all E. coli genes belong to the evolutionary oldest physlostratum. In B. subtilis, this number is only 71.8%, indicating a more eventful evolutionary past in terms of acquisition of new genes, either by gene emergence or by horizontal transfer.},
}
@article {pmid40604389,
year = {2025},
author = {Yang, J and Wang, L and Liang, Q and Wang, Y and Yang, X and Wu, X and Pei, X},
title = {Microbiome, resistome, and potential transfer of antibiotic resistance genes in Chinese wet market under One Health sectors.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {406},
pmid = {40604389},
issn = {1471-2180},
support = {TB2024045//Special Funding for Postdoctoral Research Projects in Sichuan Province/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; },
}
@article {pmid40602897,
year = {2025},
author = {Liang, S and Zhang, W and Semaha, P and Rocher, D and Liu, L and Gao, Y},
title = {Microelectrolysis facilitated the plasmid-mediated horizontal transfer of antibiotic resistance genes at the microbial community level.},
journal = {Journal of environmental sciences (China)},
volume = {157},
number = {},
pages = {470-477},
doi = {10.1016/j.jes.2025.01.029},
pmid = {40602897},
issn = {1001-0742},
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents ; Wastewater/microbiology ; },
abstract = {The escalating global dissemination of plasmid-mediated antibiotic resistance poses a formidable threat to global health. Conjugation stands as a pivotal mechanism for horizontal gene transfer among bacterial populations, facilitating the spread of antibiotic resistance genes (ARGs). Microelectrolysis has garnered attention as an efficacious strategy for mitigating antibiotic concentrations in wastewater, yet its potential impact on ARG horizontal transfer remain largely unexplored. This comprehensive investigation unveils that microelectrolysis not only influences but significantly accelerates the conjugative transfer of ARG-harboring plasmids. Remarkably, this phenomenon is corroborated at the microbial community scale, underscoring its ecological relevance. Alarmingly, the study highlights the vulnerability of intestinal microorganisms to acquire antibiotic resistance under electrolytic stimulation, posing heightened risks to both animal and human health. Delving deeper, the study elucidates the underlying mechanisms responsible for this enhanced conjugative transfer. It reveals that microelectrolysis augments the abundance of mating-competent cells, triggers the generation of reactive oxygen species, inflicts modest membrane damage, and upregulates the expression of genes critical for conjugation. These findings collectively contribute to a more profound comprehension of the environmental dissemination dynamics and associated public health implications of ARGs in the context of wastewater treatment employing microelectrolytic technologies.},
}
@article {pmid40602895,
year = {2025},
author = {Li, S and Xi, Y and Wang, K and Wan, N and Liu, H and Ho, SH},
title = {Responses of antibiotic resistance genes and microbial community in the microalgae-bacteria system under sulfadiazine: Mechanisms and implications.},
journal = {Journal of environmental sciences (China)},
volume = {157},
number = {},
pages = {443-456},
doi = {10.1016/j.jes.2024.12.003},
pmid = {40602895},
issn = {1001-0742},
mesh = {*Microalgae/physiology ; *Sulfadiazine/toxicity ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects ; *Water Pollutants, Chemical/toxicity ; Waste Disposal, Fluid/methods ; *Microbiota/drug effects ; Anti-Bacterial Agents ; Genes, Bacterial ; Sewage/microbiology ; },
abstract = {Microalgae-bacteria system is an emerging alternative for sustainable wastewater treatment. Exploring the structure and diversity of microbial community in microalgae-bacteria system under sulfadiazine stress can contribute to the understanding of the sulfadiazine behavior in environments. Furthermore, as important carriers of antibiotic resistance genes (ARGs), microalgae can influence the profiles of ARGs either directly or indirectly through the secretion of metabolites. However, the effects of sulfadiazine on ARGs dissemination of microalgae-bacteria systems remain underreported. Herein, the impacts of sulfadiazine (1 mg/L) on the structural diversity and metabolic activity of microorganisms were examined in microalgae-bacteria systems. Results showed that microalgae-bacteria system could remove NH4[+]-N better (about 72.3 %) than activated sludge system, and hydrolysis was the first step in sulfadiazine degradation. A high level of intI1 (5.7 × 10[4] copies/mL) was detected in the initial media of the microalgae-bacteria system. Microalgae could hamper the rate of horizontal gene transfer activation. Compared with activated sludge system, the abundance of sul genes (sul1, sul2, sul3, and sulA) was significantly lowered after treating with microalgae-bacteria system. Additionally, the number of proteins and the sum of polysaccharides in the extracellular polymeric substances of the activated sludge system were lower than those of the microalgae-bacteria system. Microalgae can alter microbial communities. The genus Rozellomycota predominated all samples. Fungi with relatively high abundance increased in the microalgae-bacteria system, including Dipodascaceae, Rhodotorula, and Geotrichum. These results offer valuable insights into the application processes involving microalgae-bacteria system.},
}
@article {pmid40601807,
year = {2025},
author = {Wang, Y and Feng, Z and Wu, W and Zhan, Z and Huang, J and Guo, C and He, J},
title = {Emergence of highly virulent Aeromonas dhakensis in channel catfish aquaculture: Genomic insights into pathogenicity and antimicrobial resistance.},
journal = {Virulence},
volume = {16},
number = {1},
pages = {2525933},
doi = {10.1080/21505594.2025.2525933},
pmid = {40601807},
issn = {2150-5608},
mesh = {Animals ; *Fish Diseases/microbiology/pathology ; *Ictaluridae/microbiology ; *Gram-Negative Bacterial Infections/microbiology/veterinary/pathology ; Virulence ; *Aeromonas/pathogenicity/genetics/drug effects/isolation &amp; purification ; Aquaculture ; Virulence Factors/genetics ; Genome, Bacterial ; Whole Genome Sequencing ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Genomics ; *Drug Resistance, Bacterial ; },
abstract = {Aeromonas dhakensis has emerged as a significant pathogen in aquaculture, causing severe disease outbreaks and resulting in substantial economic losses. However, its pathogenic mechanism and virulence factors remain largely unexplored. In this study, we isolated a highly virulent strain of A. dhakensis, CWH5, from a severe disease outbreak in farmed channel catfish (Ictalurus punctatus). Through comprehensive whole-genome analysis, we elucidated its pathogenicity and the genetic basis for its high virulence and multi-antimicrobial resistance in channel catfish. Experimental infections showed that CWH5 exhibited exceptional virulence, with an LD50 of (5.37 ± 0.31) ×10[5] CFU/fish and causing 100% mortality within 24 h at a concentration of 10[7] CFU/fish. Histopathological examinations revealed severe multi-organ damage, including extensive hepatocellular necrosis, gill epithelial destruction, and fin tissue deterioration. Whole-genome sequencing revealed a 4.92 Mb circular chromosome encoding sophisticated virulence mechanisms, such as complete Type III, IV, and VI secretion systems, and a vast arsenal of 60 antibiotic resistance genes across 15 drug classes. Comparative genomic analysis positioned CWH5 within the A. dhakensis clade, sharing the highest sequence similarity with A. dhakensis CIP 107,500[T]. The co-localization of virulence and resistance determinants within mobile genetic elements suggests the potential for horizontal gene transfer. Our work underscored the importance of A. dhakensis CWH5 as an emerging pathogen in channel catfish aquaculture, providing crucial insights into the molecular mechanisms of its exceptional virulence and implying significant implications for disease management and antimicrobial resistance surveillance in aquaculture settings.},
}
@article {pmid40600175,
year = {2025},
author = {Etesami, H},
title = {The dual nature of plant growth-promoting bacteria: Benefits, risks, and pathways to sustainable deployment.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100421},
pmid = {40600175},
issn = {2666-5174},
abstract = {Plant growth-promoting bacteria (PGPB) are pivotal in sustainable agriculture, enhancing crop productivity and reducing reliance on chemical inputs. However, their dual role as beneficial agents and potential stressors remains underexplored. This review examines the paradoxical adverse effects of PGPB, challenging the predominantly optimistic narrative surrounding their use. At the plant level, unintended consequences include hormonal imbalances (e.g., auxin-induced root inhibition), phytotoxic metabolite production (e.g., hydrogen cyanide), and trade-offs between growth and defense mechanisms. At the soil level, risks encompass disrupted microbial diversity, altered nutrient cycling, and horizontal gene transfer that may foster pathogenicity. These outcomes are driven by environmental factors (soil pH and moisture), host-specific interactions, and application practices. Mitigation strategies emphasize rigorous strain selection, optimized dosing, and integrated soil management to balance efficacy with ecological safety. Advances in multi-omics technologies and synthetic consortia design offer predictive insights into strain behavior, while long-term ecological assessments are critical to address legacy impacts. The review underscores the necessity of a nuanced, evidence-based approach to PGPB deployment, harmonizing agricultural benefits with environmental stewardship. By addressing knowledge gaps in microbial ecology and risk assessment, this work supports strategies prioritizing both agricultural resilience and soil biodiversity to ensure PGPB contribute sustainably to global food security.},
}
@article {pmid40600145,
year = {2025},
author = {Piispa, M and Vainio, A and Halkilahti, J and Lyytikäinen, O and Räisänen, K},
title = {Detecting plasmid-mediated dissemination of bla KPC-3 and bla OXA-48-like genes in Enterobacterales across Finnish healthcare organizations using hybrid genome assembly.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1567913},
pmid = {40600145},
issn = {1664-302X},
abstract = {The spread of carbapenemase-producing Enterobacterales (CPE) is a global concern. While the majority of the CPE outbreaks are due to clonal spread, recent findings highlight the transmission of carbapenemase gene-carrying plasmids across various bacterial species, exacerbated by extensive antibiotic use in hospitals. This study aimed to identify plasmid-mediated horizontal transfer of carbapenemase genes among Enterobacterales isolated from patient samples and hospital environment samples in three healthcare organizations in Finland. Using a hybrid assembly of short and long reads, we could complete the genome assembly and compare the plasmids harboring the bla KPC-3 and bla OXA-48-like genes. Our findings reveal indications of interspecies and intraspecies plasmid-mediated gene transfer of bla KPC-3 and bla OXA-48-like, emphasizing the role of horizontal gene transfer (HGT) in outbreaks. The study underscores the need for comprehensive infection control and surveillance beyond specific species to prevent the spread of antimicrobial resistance genes. These results suggest that expanding outbreak investigations to an interspecies level could be beneficial.},
}
@article {pmid40600140,
year = {2025},
author = {Shahed, K and Islam, SI and Sangsawad, P and Jung, WK and Permpoonpattana, P and Linh, NV},
title = {Benchmarking pangenome dynamics and horizontal gene transfer in Mycobacterium marinum evolution.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1537826},
pmid = {40600140},
issn = {1664-302X},
abstract = {Horizontal gene transfer (HGT) is a key driver of microbial evolution, promoting genetic diversity and contributing to the emergence of antibiotic resistance. This study explores the pangenome dynamics and HGT in Mycobacterium marinum (M. marinum), a close relative of Mycobacterium tuberculosis. Multiple pangenome datasets were analyzed to quantify gene gain, loss, and pangenome openness, utilizing Panstripe and a Generalized Linear Model (GLM) framework to assess gene presence/absence across strains. Additionally, a comparative benchmarking analysis of gene ontology (GO) annotations were conducted using eggNOG and InterProScan to evaluate their functional annotation accuracy. Our findings demonstrated significant differences in gene gain and loss rates, suggesting variations in annotation accuracy and the presence of mobile genetic elements (MGE). Single nucleotide polymorphisms (SNPs) were also identified, highlighting the genetic variability that may impact strain-specific traits such as pathogenicity and antibiotic resistance. Pangenome of M. marinum was characterized as highly open, with substantial variability in gene content, reflecting ongoing genetic exchange and adaptability. Functional annotation benchmarking demonstrated that eggNOG and InterProScan provided complementary insights, with each tool excelling in distinct strengths of gene function identification. Overall, these findings highlight the complex interplay between HGT, pangenome evolution, and antibiotic resistance in M. marinum, and the analytical framework presented here provides a robust approach for future studies aiming to inform therapeutic interventions and vaccine development.},
}
@article {pmid40600027,
year = {2025},
author = {Lewicka, AJ and Lyczakowski, JJ and Pardyak, L and Dubniewicz, K and Latowski, D and Arent, Z},
title = {Beyond serology: saccharide profiling enables identification of antigenically similar Leptospira and prompts re-evaluation of bacterial lipopolysaccharide evolution.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1581587},
pmid = {40600027},
issn = {2296-889X},
abstract = {Leptospirosis is a zoonotic infectious disease of growing importance in both human and veterinary medicine. Gram-negative spirochetes of Leptospira are traditionally classified into serovars based on their antigenic identity, which must be ascertained to design effective treatment procedures for humans and appropriate vaccination strategies in pets and livestock. Unfortunately, identifying Leptospira serovars is challenging and currently requires access to a wide panel of reference strains, animal-derived antisera, or monoclonal antibodies. Here, we describe a new method for the identification of Leptospira serovars that is based on monosaccharide composition analysis of the polysaccharide part of bacterial lipopolysaccharide (LPS) structures. Our approach requires no animal sacrifice and can be implemented in any laboratory equipped for chromatographic analysis. An LPS sugar fingerprint that is specific to each bacterial isolate that we studied can be generated. Importantly, sugar profiling of LPS enables distinguishing Leptospira serovars that are antigenically very similar. Using our new approach, we discover that the LPS structures of two cattle pathogens belonging to two different species: Leptospira interrogans and Leptospira borgpetersenii, and to one serovar: Hardjo, can be distinguished despite sharing major similarities. Through extensive phylogenetic analysis, we reveal which specific glycosyltransferases of the LPS biosynthesis rfb locus likely drove the emergence of these similarities and identify a single glycosyltransferase that might have contributed to the formation of saccharide differences in the LPS structure. Our findings have implications for future work on the evolution of bacterial polysaccharide synthesis and highlight the importance of preventing horizontal gene transfer between pathogenic bacteria.},
}
@article {pmid40597104,
year = {2025},
author = {Blais, C and Colp, MJ and Sarre, LA and de Mendoza, A and Archibald, JM},
title = {Epigenetic silencing and genome dynamics determine the fate of giant virus endogenizations in Acanthamoeba.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {171},
pmid = {40597104},
issn = {1741-7007},
support = {GBMF5782//Gordon and Betty Moore Foundation/ ; GBMF5782//Gordon and Betty Moore Foundation/ ; GBMF5782//Gordon and Betty Moore Foundation/ ; RGPIN-2019-05058//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2019-05058//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2019-05058//Natural Sciences and Engineering Research Council of Canada/ ; ERC-StG 950230/ERC_/European Research Council/International ; ERC-StG 950230/ERC_/European Research Council/International ; },
mesh = {*Acanthamoeba/virology/genetics ; *Giant Viruses/genetics/physiology ; *Epigenesis, Genetic ; *Gene Silencing ; *Virus Integration/genetics ; *Genome, Protozoan ; *Genome, Viral ; Gene Transfer, Horizontal ; },
abstract = {BACKGROUND: Endogenized giant viruses are emerging as major contributors to the genome evolution of microbial eukaryotes, with both degraded and fully functional latent viruses being found integrated in diverse lineages. The mechanisms that determine the fate of viral integrants are poorly understood, however. Acanthamoeba is a unicellular eukaryote known for undergoing lateral gene transfer (LGT) with viruses. Here we have leveraged chromosome-scale assemblies of two strains of Acanthamoeba, Neff and C3, to investigate the genomic mechanisms that mediate the fate of viral integrations in eukaryotic genomes.<br><br>RESULTS: Viral integrations in the C3 and Neff genomes are largely non-overlapping and disproportionately found in sub-telomeric regions. Multiple partial copies of these insertions are found throughout the Neff genome, but they are not expressed, do not obviously encode functions associated with their own mobility, and are colonized by host mobile elements. Viral regions are hypermethylated and highly condensed, suggesting that the expression of recently acquired viral DNA is suppressed in heterochromatic regions.<br><br>CONCLUSIONS: We propose a model for the trajectory of viral sequences in Acanthamoeba: (i) integration of DNA from giant viruses, (ii) epigenetic suppression of the viral DNAs, allowing them to persist in the genome, and (iii) deterioration of viral genomes by point mutation, mobile element colonization, and intra- and inter-chromosomal recombination. Viral integrations in Acanthamoeba spp. are transient and may not have long-lasting effects on the fitness of the amoeba. Our work highlights the importance of host genome dynamics and epigenetic silencing for understanding the evolution of endogenized viral elements.},
}
@article {pmid40596330,
year = {2025},
author = {Puangseree, J and Hein, ST and Prathan, R and Srisanga, S and Chuanchuen, R},
title = {Genomic insights into multidrug - resistant Salmonella enterica isolates from pet dogs and cats.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22104},
pmid = {40596330},
issn = {2045-2322},
support = {N42A660897//National Research Council of Thailand/ ; HEAF67310045//Thailand Science Research and Innovation Fund Chulalongkorn University (Fundamental Fund) Fiscal year 2567/ ; },
mesh = {Animals ; Dogs ; Cats ; *Salmonella enterica/genetics/drug effects/isolation &amp; purification ; *Drug Resistance, Multiple, Bacterial/genetics ; *Pets/microbiology ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Plasmids/genetics ; *Salmonella Infections, Animal/microbiology ; *Dog Diseases/microbiology ; Microbial Sensitivity Tests ; *Cat Diseases/microbiology ; Genomics ; Genome, Bacterial ; },
abstract = {Companion animals are recognized as potential reservoirs and transmitters of antimicrobial resistance (AMR) within the One Health framework. However, in-depth knowledge on AMR in pet animals remains limited. This study aimed to characterize Salmonella from companion dogs and cats using Whole Genome Sequencing (WGS). A total of 25 Salmonella obtained from clinically healthy household dogs and cats were serotyped and had their antimicrobial susceptibility tested. A discrepancy between the serovars identified by traditional slide agglutination tests and those determined by WGS analysis was observed. The isolates exhibited multidrug resistance (MDR) (n = 18) and harbored several resistance genes either chromosomally encoded or plasmid associated. Tn3 and IS26 were commonly found flanking AMR genes and class 1 integrons, while an unusual qacL-IS256-sul3 arrangement was also frequently observed. Similar AMR genes and insertion sequences were found among dogs and cats from different provinces, suggesting clonal spread and horizontal gene transfer of AMR. The similarity between plasmids (i.e., IncX1 and IncI1 plasmid) carrying AMR genes (e.g., aadA1, qacL, sul3, blaTEM-1B, qnrS1, dfrA, tetA) in Salmonella from pets in this study and those from other sources (e.g., humans, food producing animals and environment) in different countries was revealed, suggesting that pet dogs and cats may play a significant role in the global spread of AMR. The finding underscores the role of household pets as silent reservoirs of MDR Salmonella and the need for a One Health approach to tackle the issue. Public health campaigns promoting hygiene practices among pet owners should be encouraged. Pet animals should be incorporated into AMR monitoring and surveillance programs as a component of One Health framework.},
}
@article {pmid40595289,
year = {2025},
author = {Kador, SM and Islam, KT and Rubaiyat, RN and Bhuiyan, MIU and Chakrovarty, T and Rahman, MS and Islam, OK and Islam, MT},
title = {Abundance and transmission of antibiotic resistance and virulence genes through mobile genetic elements in integrated chicken and fish farming system.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20953},
pmid = {40595289},
issn = {2045-2322},
support = {22-FoBST 05//Research Cell, Jashore University of Science and Technology/ ; SRG-221252//Special Research Grant, Ministry of Science and Technology, Bangladesh/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Interspersed Repetitive Sequences/genetics ; Aquaculture ; Fishes ; *Virulence Factors/genetics ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/pathogenicity/drug effects ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Virulence/genetics ; Bangladesh ; },
abstract = {Integrated chicken and fish farming systems, common in Bangladesh, present significant public health risks due to the spread of antimicrobial resistance genes (ARGs) and virulence factors (VFGs) through mobile genetic elements (MGEs). This study employs metagenomic sequencing to explore the diversity and abundance of ARGs, VFGs, and MGEs in various environmental samples from these farming systems. A total of 384 ARGs were detected, with tetracycline resistance genes such as tetM and tetX being the most abundant, alongside macrolide-lincosamide-streptogramin and aminoglycoside resistance genes. Droppings harbored the highest proportion of ARGs (62.2%), whereas sediment served as a reservoir for multi-metal resistance genes. Virulence factors associated with immune modulation, such as pvdL and tssH, and biofilm formation genes like algC were particularly prevalent in sediment and droppings. Among MGEs, plasmids and transposons like Tn6072 and Tn4001 were the most abundant, playing a critical role in horizontal gene transfer. Bacterial genera including Bacteroides, Clostridium, and Escherichia were strongly associated with MGEs, indicating their role in the dissemination of resistance and virulence traits. Statistical analyses revealed significant differences in the abundance of ARGs, VFGs, and MGEs across sample types, with sediment and droppings identified as hotspots for gene exchange. These findings underscore the urgent need for improved antibiotic stewardship and waste management practices to limit the spread of antimicrobial resistance and pathogenic bacteria within integrated farming environments.},
}
@article {pmid40595025,
year = {2025},
author = {Wedell, N},
title = {Harnessing lateral gene transfer and endosymbiosis for adaptation.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
pmid = {40595025},
issn = {1471-0064},
}
@article {pmid40594904,
year = {2025},
author = {Sayem, M and Rafi, MA and Mishu, ID and Mahmud, Z},
title = {Comprehensive genomic analysis reveals virulence and antibiotic resistance genes in a multidrug-resistant Bacillus cereus isolated from hospital wastewater in Bangladesh.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22915},
pmid = {40594904},
issn = {2045-2322},
mesh = {*Bacillus cereus/genetics/pathogenicity/isolation &amp; purification/drug effects ; *Wastewater/microbiology ; Bangladesh ; *Drug Resistance, Multiple, Bacterial/genetics ; Phylogeny ; Hospitals ; Virulence/genetics ; Genome, Bacterial ; Whole Genome Sequencing ; Genomics/methods ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Humans ; },
abstract = {Hospital wastewater represents a significant reservoir for antimicrobial-resistant bacteria, including multidrug-resistant (MDR) Bacillus cereus, a pathogen of growing concern due to its potential impact on public health and environmental safety. This study characterizes the genomic features, antimicrobial resistance (AMR) mechanisms, and virulence potential of Bacillus cereus MBC, isolated from hospital wastewater in Dhaka, Bangladesh. Using whole-genome sequencing (WGS) and advanced bioinformatics, we analyzed the isolate's taxonomy, phylogenetics, functional annotation, and biosynthetic potential. The genome, spanning 5.6 Mb with a GC content of 34.84%, contained 5,881 protein-coding sequences, including 1,424 hypothetical proteins, and 28 genes associated with AMR. Phylogenetic analysis revealed a close genetic relationship with Bacillus cereus ATCC 14579, sharing virulence factors such as hemolysin BL (HBL), non-hemolytic enterotoxin (NHE), and cytotoxin K (CytK), all contributing to its pathogenicity. The ability to form biofilms further enhances the strain's persistence and resistance in hospital environments. AMR profiling identified genes conferring resistance to beta-lactams (e.g., BcI, BcII, BcIII), tetracyclines (tetB(P)), glycopeptides (vanY), and fosfomycin, highlighting the bacterium's capacity to resist a wide array of antibiotics. Functional annotation revealed metabolic pathways involved in iron acquisition and the biosynthesis of siderophores such as petrobactin and bacillibactin, reinforcing the bacterium's adaptability in nutrient-limited environments. Mobile genetic elements, including prophages, CRISPR-Cas systems, and transposable elements, suggest significant horizontal gene transfer (HGT), enhancing genetic plasticity and resistance spread. Pangenomic analysis, involving 125 B. cereus strains, revealed a high degree of genetic diversity and close relationships with strains from clinical, food, and agricultural environments, emphasizing the overlap between clinical and environmental reservoirs of resistance. The strain's isolation from hospital wastewater underscores the complex interplay between environmental contaminants and bacterial evolution, which fosters MDR traits. Our findings underscore the urgent need for enhanced genomic surveillance and wastewater management strategies to mitigate the spread of MDR B. cereus and AMR genes in hospital environments.},
}
@article {pmid40592271,
year = {2025},
author = {Fan, Q and Bai, J and Jiao, T and Zhao, Z and Hou, F},
title = {Circular transmission network and reverse contribution pattern of antibiotic resistance genes in the Qinghai-Tibet Plateau ecosystem.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139054},
doi = {10.1016/j.jhazmat.2025.139054},
pmid = {40592271},
issn = {1873-3336},
abstract = {The dissemination of antibiotic resistance genes (ARGs) poses a major global public health challenge, yet transmission mechanisms within extreme ecosystems are poorly understood. Using metagenomics and metagenome-assembled genome (MAG) analysis, we investigated ARG composition, risk, and pathways across a complete Qinghai-Tibet Plateau food chain (soil, earthworm, herbage, yak, pika, snowfinch, herdsman). Contrary to conventional theory, ARG assemblages correlated negatively with microbial diversity. Our MAG-centric approach provided direct evidence that Horizontal Gene Transfer (HGT), including striking bacteria-archaea cross-domain transfer of 18 ARGs, predominates ARG dissemination, with specialized 'ARG reservoir' host phyla (e.g., Pseudomonadota) decoupling ARG functional diversity from overall microbial community structure. Earthworms function as 'ARG bioamplifiers', enriching 79.81 % of soil ARGs and contributing 49.43 % to herbage. Crucially, apex consumers (snowfinches, herdsmen) are not merely recipients; their feces drive a significant 'reverse contribution' of high-risk ARGs back into the ecosystem, establishing a complete circular ARG feedback network. Herdsman feces contained all Rank I-IV high-risk ARGs, while snowfinch feces held Rank II/IV, highlighting human activities' impact on escalating ARG risks in this extreme setting. These findings, particularly the novel HGT mechanisms and host specialization insights, challenge the traditional unidirectional transmission model, presenting a new paradigm for managing antibiotic resistance risks in extreme ecosystems within the One Health framework.},
}
@article {pmid40592212,
year = {2025},
author = {Byczkowska-Rostkowska, Z and Gajewska, J and Chajęcka-Wierzchowska, W},
title = {Whole genome analysis and antimicrobial resistance assessment of Staphylococcus epidermidis isolated from food sources.},
journal = {The Science of the total environment},
volume = {993},
number = {},
pages = {179999},
doi = {10.1016/j.scitotenv.2025.179999},
pmid = {40592212},
issn = {1879-1026},
abstract = {Coagulase-negative staphylococci (CoNS), including Staphylococcus epidermidis, are commonly occurrence in a variety of food products. Historically considered non-pathogenic, these microorganisms were excluded from routine food safety monitoring protocols. However, their increasing involvement in nosocomial infections underscores their pathogenic potential. Emerging evidence suggests that the food chain may serve as a reservoir and transmission route for antibiotic-resistant bacteria. In this study, 26 S. epidermidis isolates obtained from ready-to-eat food were subjected to whole-genome sequencing and comprehensive bioinformatics analyses. The antimicrobial susceptibility of the isolates was also evaluated against a broad spectrum of agents including aminoglycosides, β-lactams, fluoroquinolones, glycopeptides, lincosamides, macrolides, nitrofurantoins, oxalidinones, phenicols, steroids, sulphonamides and tetracyclines. Sequence typing revealed the presence of 17 distinct sequence types (STs), with ST329 being the most frequently identified (8/26, 30.77 %), followed by ST88 and ST152 (each 2/26; 7.69 %). Notably, one isolate harbored a novel multi-locus sequence type. Phenotypically resistance to erythromycin was most prevalent (21/26, 80.77 %), followed by resistance to clindamycin (19/26, 73.08 %). Genomic analysis confirmed the presence of multiple antimicrobial resistance genes including norA/C, vanT, mecA, dfrC and multidrug resistance genes. The carrying of mobile genetic elements was demonstrated by 25/26 (96.15 %) strains. These findings indicate that S. epidermidis strains isolated from ready-to-eat foods not only exhibit multidrug resistance but also carry a diverse array of antimicrobial resistance genes. The potential for horizontal gene transfer to commensal or pathogenic bacteria highlights the need for increased surveillance and risk assessment concerning CoNS in the food supply.},
}
@article {pmid40407375,
year = {2025},
author = {Lyra de Holanda Fonseca, D and Scheunemann, GS and Fortes, BN and Ishida, K and Galhardo, RS},
title = {Interaction of the SXT/R391 element ICEPmiJpn1 with its natural host Proteus mirabilis.},
journal = {Microbiology spectrum},
volume = {13},
number = {7},
pages = {e0033925},
pmid = {40407375},
issn = {2165-0497},
support = {2019/19435-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2020/00535-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2021/15170-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2021/10577-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2022/03986-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; finance code 01//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
mesh = {*Proteus mirabilis/genetics/pathogenicity/drug effects/physiology ; Conjugation, Genetic ; Gene Transfer, Horizontal ; Biofilms/growth &amp; development ; Escherichia coli/genetics ; *DNA Transposable Elements/genetics ; Proteus Infections/microbiology ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; *Interspersed Repetitive Sequences ; Bacterial Proteins/genetics ; },
abstract = {Integrative and conjugative elements (ICEs) of the SXT/R391 family are mobile genetic elements that integrate into the bacterial host chromosome and can be transferred horizontally, spreading antimicrobial resistance genes. Our study aimed to evaluate aspects of the relationship between ICEPmiJpn1, one of the most widespread SXT/R391 variants, with its natural host Proteus mirabilis. For this investigation, we used isogenic strains (containing or not the ICEPmiJpn1) that enabled us to evaluate the influence of this element on several physiological aspects of P. mirabilis as well as the effect of different P. mirabilis genetic backgrounds on the conjugative transmission of the element. ICEPmiJpn1 did not impact the fitness, self-recognition, swarming, pathogenicity, and persistence abilities of this bacterium but increased biofilm formation in one strain. Additionally, conjugative transfer of the element to Escherichia coli is widely variable when different P. mirabilis strains are used as donors in mating assays. Our results indicate that ICEPmiJpn1 has no adverse effects on the physiology or pathogenicity of P. mirabilis, reflecting a stable association between this element and its host. Furthermore, the findings support the notion that ICE transfer between bacteria is influenced not only by element-specific regulators but also by strain-specific factors.IMPORTANCEMobile genetic elements play a key role in the spread of antimicrobial resistance, raising concerns about multidrug-resistant bacteria, yet their interactions with bacterial hosts are not well characterized. This study explores the relationship between ICEPmiJpn1, a globally distributed SXT/R391 integrative and conjugative element (ICE), and its natural host Proteus mirabilis, revealing minimal effects on bacterial fitness and pathogenicity. Nevertheless, strain-specific factors significantly influence conjugative transfer. These findings highlight the need for further research on host-dependent regulatory mechanisms that drive the spread of these elements. Understanding these dynamics is essential for developing strategies to mitigate the dissemination of antibiotic resistance in clinically relevant bacterial populations.},
}
@article {pmid40590551,
year = {2025},
author = {Renno, AJ and Shields, RC and McLellan, LK},
title = {Bacterial evolution in the oral microbiome: the role of conjugative elements and horizontal gene transfer.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0006625},
doi = {10.1128/jb.00066-25},
pmid = {40590551},
issn = {1098-5530},
abstract = {As one of the most diverse bacterial populations within the human body, the oral microbiome encodes a wealth of genetic information. Horizontal gene transfer, driven by mobile genetic elements, takes advantage of this information to influence bacterial evolution and the spread of phenotypes (antibiotic resistances, virulence attributes, and metabolic capabilities) among oral microbes. Although widespread within microbial communities, fundamental aspects of the mobile elements that drive horizontal gene transfer within the oral cavity remain poorly understood. In this review, we explore what is known about the role of horizontal gene transfer in bacterial evolution within the oral microbiome and the elements that facilitate this transfer, with a specific focus on conjugative DNA transfer. Conjugative elements are found in virtually all bacterial phylogenetic clades, and some can mediate genetic exchange between distantly related organisms. This is of particular interest in the diverse microcosm of the oral cavity, specifically how it drives the evolution and virulence of dental pathogens. Finally, we highlight advances in our understanding of the unique biology within dental plaque and how these might influence our understanding of bacterial gene transfer, and thus human health and disease.},
}
@article {pmid40589066,
year = {2025},
author = {Collins, N and Levy, Y and Kolomeisky, AB},
title = {Theoretical Understanding of Target Search Dynamics in Horizontal Gene Transfer in Bacteria.},
journal = {The journal of physical chemistry. B},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jpcb.5c02436},
pmid = {40589066},
issn = {1520-5207},
abstract = {Horizontal gene transfer (HGT) is a fundamental process of increasing genetic diversity in microbial species. It allows bacterial cells to acquire new beneficial traits quickly by incorporating new genetic material into existing genomes. Despite the critical importance of HGT phenomena, the underlying molecular mechanisms are still poorly understood. Recent experiments investigated the dynamics of conjugation HGT processes in which DNA is transmitted directly from the donor to the recipient bacterial cell. It is accomplished by special mobile genetic particles known as integrative and conjugative elements (ICE). However, the molecular picture of how ICE can efficiently find the unique integration sites in a new genome is not yet clear. We present a novel theoretical model to explain the dynamic processes in HGT after ICE reaches the recipient cell. It is shown that the target search for integration sites can be viewed as a set of stochastic transitions between discrete states, allowing us to obtain an explicit description of the dynamic properties using analytical calculations supported by Monte Carlo computer simulations. Search times are found to depend on the location of integration sites, the size of the genome, the effective diffusion rate of mobile genetic elements, and the binding/unbinding transitions between ICE and DNA. Theoretical estimates for search times agree well with experimental observations for integration in Bacillus subtilis bacterial species. Physical-chemical arguments are presented to explain the dynamics of the ICE target search. This study clarifies some important mechanistic aspects of HGT phenomena.},
}
@article {pmid40588591,
year = {2025},
author = {Mancuso, CP and Baker, JS and Qu, EB and Tripp, AD and Balogun, IO and Lieberman, TD},
title = {Intraspecies warfare restricts strain coexistence in human skin microbiomes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40588591},
issn = {2058-5276},
support = {1DP2GM140922//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {Determining why only a fraction of encountered or applied strains engraft in a given person's microbiome is crucial for understanding and engineering these communities. Previous work has established that metabolic competition between bacteria can restrict colonization success in vivo, but other mechanisms may also prevent successful engraftment. Here we combine genomic analysis and high-throughput agar competition assays to demonstrate that intraspecies warfare presents a significant barrier to strain coexistence in the human skin microbiome by profiling 14,884 pairwise interactions between Staphylococcus epidermidis isolates cultured from 18 people from 6 families. We find that intraspecies antagonisms are abundant, mechanistically diverse, independent of strain relatedness and consistent with rapid evolution via horizontal gene transfer. Critically, these antagonisms are significantly depleted among strains residing on the same person relative to random assemblages, indicating a significant in vivo role. Wide variation in antimicrobial production and resistance suggests trade-offs between these factors and other fitness determinants. Together, our results emphasize that accounting for intraspecies warfare may be essential to the design of long-lasting probiotic therapeutics.},
}
@article {pmid40587929,
year = {2025},
author = {Chen, J and Guo, Y and Lin, Y and Zhang, Y and Qian, Q and Zhang, X and Lin, P and Chen, C and Xie, S},
title = {Fate, mobility and pathogenicity of antibiotic resistome in a full-scale drinking water treatment plant: Highlighting the chlorination risks.},
journal = {Journal of environmental management},
volume = {390},
number = {},
pages = {126425},
doi = {10.1016/j.jenvman.2025.126425},
pmid = {40587929},
issn = {1095-8630},
abstract = {Drinking water treatment plants (DWTPs) serve as the last barrier in preventing the spread of antibiotic resistance genes (ARGs) into tap water, yet the distribution and dissemination mechanisms of ARGs in DWTPs remain unclear. In this study, the antibiotic resistome of a full-scale DWTP using Nansi Lake (an important node of the South-to-North Water Diversion Project's eastern route, China) as water source was investigated based on metagenomic analysis. The results showed that coagulation and chlorination were the two crucial processes increasing the relative abundance of ARGs in the DWTP, and the former predominantly enhanced that of sulfonamide RGs, while the latter increased that of bacitracin, aminoglycoside and multidrug RGs. ARG hosts and mobile genetic elements (MGEs) both played significant roles in ARG compositions. The persistence of Sphingorhabdus during the conventional treatment stages and the dissemination potential of plasmids accounted for the relative abundance of sulfonamide RGs, while the chlorine and multidrug resistance of Acinetobacter, Acidovorax, and Pseudomonas, along with the coexistence of various MGEs, suggested the persistence and transmission risk of ARGs after chlorination. Ozonation and activated carbon filtration could eliminate some human-pathogenic bacteria (HPB), but the chlorination process significantly increased the relative abundance of HPB. The multidrug-resistant HPB such as Acinetobacter calcoaceticus and Acinetobacter haemolyticus were the key targets for risk control in the DWTP. Our findings provide new insights into the fate, mobility, and pathogenicity of ARGs in a typical DWTP, offering beneficial guidance for decision-making in the risk control of ARGs in DWTPs.},
}
@article {pmid40585299,
year = {2025},
author = {Chai, Z and Guo, Z and Chen, X and Yang, Z and Wang, X and Zhang, F and Kang, F and Liu, W and Liang, S and Ren, H and Yue, J and Jin, Y},
title = {Comprehensive profiling of integrative conjugative elements (ICEs) in Mollicutes: distinct catalysts of gene flow and genome shaping.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {2},
pages = {lqaf083},
pmid = {40585299},
issn = {2631-9268},
mesh = {*Genome, Bacterial ; Gene Transfer, Horizontal ; *Conjugation, Genetic ; *Gene Flow ; *Tenericutes/genetics ; Evolution, Molecular ; Phylogeny ; },
abstract = {Mollicutes, known as the simplest bacteria with streamlined genomes, were traditionally thought to evolve mainly through gene loss. Recent studies have highlighted their rapid evolutionary capabilities and genetic exchange within individual genomes; however, their evolutionary trajectory remains elusive. By comprehensive screening 1433 available Mollicutes genomes, we revealed widespread horizontal gene transfer (HGT) in 83.9% of investigated species. These genes involve type IV secretion systems and DNA integration, inferring the unique role of integrative conjugative elements (ICEs) or integrative and mobilizable elements (IMEs) as self-transmissible genetic elements. We systematically identified 263 ICEs/IMEs across most Mollicutes genera, being intact or fragmented, showing a strong correlation with HGT frequency (cor 0.573, P = .002). Their transfer tendency was highlighted across species sharing ecological niches, notably in livestock-associated mycoplasmas and insect-vectored spiroplasmas. ICEs/IMEs not only act as gene shuttles ferrying various phenotypic genes, but also promote increased large-scale chromosomal transfer events, shaping the host genomes profoundly. Additionally, we provided novel evidence that Ureaplasma ICE facilitates genetic exchange and the spread of antibiotic resistance gene tet(M) among other pathogens. These findings suggest that, despite the gene-loss pressure associated with the compact genomes of Mollicutes, ICEs/IMEs play a crucial role by introducing substantial genetic resources, providing essential opportunities for evolutionary adaptation.},
}
@article {pmid40584034,
year = {2025},
author = {Alhejaili, AY and Zhou, G and Halawa, H and Huang, J and Fallatah, O and Hirayban, R and Iftikhar, S and AlAsmari, A and Milner, M and Banzhaf, M and Alzaidi, AA and Rajeh, AA and Al-Otaiby, MA and Alabbad, SS and Bukhari, D and Aljurayyan, AN and Aljasham, AT and Alzeyadi, ZA and Alajel, SM and Alanazi, RH and Alghoribi, M and Almutairi, MM and Pain, A and Senok, A and Moradigaravand, D and Al Salem, W},
title = {Methicillin-resistant Staphylococcus aureus in Saudi Arabia: genomic evidence of recent clonal expansion and plasmid-driven resistance dissemination.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1602985},
pmid = {40584034},
issn = {1664-302X},
abstract = {OBJECTIVES: Staphylococcus aureus is a leading cause of hospital-acquired infections worldwide. Over recent decades, methicillin-resistant Staphylococcus aureus (MRSA), which is resistant to multiple antimicrobials, has emerged as a significant pathogenic strain in both hospital and community settings. The rapid emergence and dissemination of MRSA clones are driven by a dynamic and evolving population, spreading swiftly across regions on epidemiological time scales. Despite the vast geographical expanse and diverse demographics of the Kingdom of Saudi Arabia and the broader West Asia region, the population diversity of MRSA in hospitals in these areas remains underexplored.<br><br>METHODS: We conducted a large-scale genomic analysis of a systematic Staphylococcus aureus collection obtained from 34 hospitals across all provinces of KSA, from diverse body sites between 2022 and 2024. The dataset comprised 581 MRSA and 31 methicillin-susceptible Staphylococcus aureus (MSSA) isolates, all subjected to whole-genome sequencing. A combination of phylogenetic and population genomics approaches was utilized to analyze the genomic data. Hybrid sequencing approach was employed to retrieve the complete plasmid content.<br><br>RESULTS: The population displayed remarkable diversity, comprising 48 distinct sequence types (STs), with the majority harboring community-associated SCCmec loci (types IVa, V/VII, and VI). Virulence factors associated with community-acquired MRSA (CA-MRSA), including Panton-Valentine Leukocidin (PVL) genes, were identified in 12 distinct STs. Dominant clones, including ST8-t008 (USA300), ST88-t690, ST672-t3841, ST6-t304, and ST5-t311, were associated with infections at various body sites and were widely disseminated across the country. Linezolid and vancomycin resistance were mediated by cfr-carrying plasmids and mutations in the vraR gene (involved in cell-wall stress response) and the murF gene (involved in peptidoglycan biosynthesis) in five isolates, respectively. Phylodynamic analysis revealed rapid expansion of the dominant clones, with their emergence estimated to have occurred 10-20 years ago. Plasmidome analysis uncovered a diverse repertoire of blaZ-containing plasmids and the sharing of erm(C)-encoding plasmids among major clades. The acquisition of plasmids coincided with clonal expansion.<br><br>CONCLUSIONS: Our results highlight the recent concurrent expansion and geographical dissemination of CA-MRSA clones across hospitals. These findings also underscore the interplay between clonal spread and horizontal gene transfer in shaping the resistance landscape of MRSA.},
}
@article {pmid40582582,
year = {2025},
author = {Munshi, ID and Mathuria, A and Sharma, H and Acharya, M and Chaudhary, A and Jain, K and Ragini, and Dahiya, S and Arora, R and Singh, V and Saini, A and Mani, I},
title = {Emerging concept of genomic islands in bacterial adaptation and pathogenicity.},
journal = {Research in microbiology},
volume = {},
number = {},
pages = {104303},
doi = {10.1016/j.resmic.2025.104303},
pmid = {40582582},
issn = {1769-7123},
abstract = {Genomic Islands (GEIs) are distinct DNA segments acquired through horizontal gene transfer (HGT), driving bacterial evolution and adaptation. These include Pathogenicity Islands (PAIs), Symbiosis Islands, Antibiotic Resistance Islands, Xenobiotic-Degradation Islands, and Nitrogen Fixation Islands. GEIs contribute to genetic diversity, enhancing bacterial pathogenicity, symbiosis, antibiotic resistance, and xenobiotic degradation. Characterized by variations in GC content, codon bias, and integration sites, they distinguish themselves from the core genome. Advances in genome sequencing and bioinformatics have deepened our understanding of GEIs in bacteria like Salmonella, Vibrio, E. coli, and many more, offering insights into microbial evolution, pathogenicity, and antibiotic resistance mechanisms.},
}
@article {pmid40581000,
year = {2025},
author = {Fraikin, N and Samuel, B and Burstein, D and Lesterlin, C},
title = {Strategies for zygotic gene expression during plasmid establishment.},
journal = {Plasmid},
volume = {},
number = {},
pages = {102754},
doi = {10.1016/j.plasmid.2025.102754},
pmid = {40581000},
issn = {1095-9890},
abstract = {Conjugative plasmids are key drivers of horizontal gene transfer and the spread of antimicrobial resistance. Their successful establishment in new hosts requires overcoming diverse bacterial defence mechanisms, such as restriction-modification systems, CRISPR-Cas systems, and the SOS response. Plasmids achieve this through a leading region-encoded zygotic program of anti-defence genes expressed early in conjugation. This program employs diverse strategies, including single-stranded promoters, repressed double-stranded promoters, and protein translocation. This review explores the diversity of these zygotic programs, the mechanisms underlying their timely regulation, and the array of anti-defence functions they encode. Further investigation of leading region genes is crucial for discovering novel counter-defence strategies and understanding their tailored regulation across diverse plasmid and bacterial species, ultimately enabling us to better understand and potentially manipulate plasmid transfer.},
}
@article {pmid40580037,
year = {2025},
author = {},
title = {Correction to 'GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome'.},
journal = {Nucleic acids research},
volume = {53},
number = {12},
pages = {},
doi = {10.1093/nar/gkaf654},
pmid = {40580037},
issn = {1362-4962},
}
@article {pmid40579721,
year = {2025},
author = {O'Donnell, S and Rezende, G and Vernadet, JP and Snirc, A and Ropars, J},
title = {Harbouring Starships: The accumulation of large Horizontal Gene Transfers in Domesticated and Pathogenic Fungi.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf125},
pmid = {40579721},
issn = {1759-6653},
abstract = {Human-related environments, including food and clinical settings, present microorganisms with atypical and challenging conditions that necessitate adaptation. Several cases of novel horizontally acquired genetic material associated with adaptive traits have been recently described, contained within giant transposons named Starships. While a handful of Starships have been identified in domesticated species, their abundance has not yet been systematically explored in human-associated fungi. Here, we investigated whether Starships have shaped the genomes of two major genera of fungi occurring in food and clinical environments, Aspergillus and Penicillium, providing a unique opportunity to study several independent events of adaptation to similar niches. We found in all cases that the domesticated strains or species exhibited significantly greater Starship content compared with close relatives from non-human-related environments, containing an enrichment in genes involved in adaptation to food. We found a similar pattern in clinical contexts. Our findings have clear implications for agriculture, human health and the food industry as we implicate Starships as a widely recurrent mechanism of gene transfer aiding the rapid adaptation of fungi to novel environments.},
}
@article {pmid40578739,
year = {2025},
author = {Yang, Y and Tang, X and Zhang, P and Mo, C and Huang, F and Wen, Z},
title = {Effect of microplastics on antibiotic resistome risk in composting.},
journal = {Environmental research},
volume = {284},
number = {},
pages = {122241},
doi = {10.1016/j.envres.2025.122241},
pmid = {40578739},
issn = {1096-0953},
abstract = {Microplastics are a growing concern worldwide because of their impact on the environment and human health. Composting is an effective method for managing antibiotic resistome risk in organic waste, yet the effects of microplastics on antibiotic resistome risk in composting are not well understood. In this study of laying hen manure, the microplastic polypropylene increased the temperature of the compost but did not significantly affect the total composition, abundance and risk score of antibiotic resistance genes (ARGs) during composting. The dominant phyla on microplastics and manure were Actinobacteria, Firmicutes and Proteobacteria. Escherichia (bin.70), Oceanobacillus (bin.85) and Mycobacterium (bin.79) were the main ARG hosts. Among them, the abundance of the ARG host Mycobacterium (bin.79) was significantly higher in microplastics than in manure. Furthermore, ARG transfer occurred between the ARG host Mycobacterium (bin.79) and other microorganisms on microplastics and manure. These findings indicate that while microplastics may not strongly affect the overall antibiotic resistome risk during composting, they increase the likelihood of horizontal gene transfer in specific ARG hosts. This underscores the critical need to control both microplastic and resistance contamination.},
}
@article {pmid40434128,
year = {2025},
author = {Zhao, R and Nawrocki, A and Møller-Jensen, J and Liu, G and Olsen, JE and Thomsen, LE},
title = {Mechanistic divergence between SOS response activation and antibiotic-induced plasmid conjugation in Escherichia coli.},
journal = {Microbiology spectrum},
volume = {13},
number = {7},
pages = {e0009025},
doi = {10.1128/spectrum.00090-25},
pmid = {40434128},
issn = {2165-0497},
support = {//China Scholarship Council/ ; },
mesh = {*SOS Response, Genetics/drug effects ; *Escherichia coli/genetics/drug effects/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Plasmids/genetics/metabolism ; *Conjugation, Genetic/drug effects ; Escherichia coli Proteins/genetics/metabolism ; Cefotaxime/pharmacology ; Ciprofloxacin/pharmacology ; Gene Expression Regulation, Bacterial/drug effects ; Mitomycin/pharmacology ; Gene Transfer, Horizontal ; },
abstract = {The SOS response is a critical DNA damage repair mechanism in bacteria, designed to counteract genotoxic stress and ensure survival. This system can be activated by different classes of antimicrobial agents, each inducing the SOS response through different mechanisms. Moreover, it has been observed that certain antibiotics can enhance conjugative plasmid transfer frequencies. However, while previous studies have suggested that the SOS response contributes to horizontal transfer of certain genes, its role in plasmid conjugation remains unclear. In this study, we investigated the relationship between the SOS response and conjugation of IncI1 and IncFII plasmids harboring various blaCTX-M resistance genes. Results showed that cefotaxime and mitomycin C induced both the SOS response and conjugation, while ciprofloxacin induced the SOS response without affecting conjugation frequencies. Further analysis of SOS mutants, ranging from constitutively inactive to hyper-induced states, revealed no correlation between SOS levels and conjugation frequencies, despite upregulation of tra gene expression in a SOS hyper-induced strain. Proteomic analysis revealed that cefotaxime-induced conjugation was associated with increased transfer and pilus protein expression. In contrast, the SOS hyper-induced strain displayed limited upregulation of plasmid-encoded proteins, suggesting post-transcriptional regulation. Additionally, putative LexA binding sites on the IncI1 plasmid revealed potential SOS-mediated regulation of plasmid genes, highlighting the interaction between the SOS response and plasmid, although it did not significantly affect conjugation.IMPORTANCEPlasmids play a critical role in the dissemination of antibiotic resistance through conjugation. Recent research suggests that the use of antibiotics not only selects for already resistant variants but further increases the rate of plasmid-encoded conjugative transmission by increasing expression of the conjugative system. At the same time, these antibiotics are known to induce the stress-related SOS response in bacteria. To be able to counteract an antibiotic-induced increase in conjugative transfer of resistance plasmid, there is a need for a fundamental understanding of the regulation of transmission, including whether this happens through activation of the SOS response. In this research, we show that antibiotic-induced conjugation and induction of the SOS response happen through different mechanisms, and thus that future strategies to control the spread of antibiotics cannot interfere with the SOS response as its target.},
}
@article {pmid40408992,
year = {2025},
author = {Zhang, S and Li, J and Lai, J and Zhang, Q and Zhao, Z and Li, B},
title = {Transfer dynamics of intracellular and extracellular last-resort antibiotic resistome in hospital wastewater.},
journal = {Water research},
volume = {283},
number = {},
pages = {123833},
doi = {10.1016/j.watres.2025.123833},
pmid = {40408992},
issn = {1879-2448},
mesh = {*Wastewater/microbiology ; Hospitals ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; },
abstract = {The increasing prevalence of last-resort antibiotic resistance genes (LARGs) has posed severe public health hazards. Previous studies focused primarily on the profiles of intracellular LARGs (iLARGs) in hospital wastewater (HWW), while largely neglecting the expression patterns of iLARGs and the presence of extracellular LARGs (eLARGs). Currently, wastewater resistomes and transfer dynamics of LARGs are still poorly characterized. This study integrates Nanopore-metagenomic and metatranscriptomic sequencing to conduct the comprehensive longitudinal analysis of both iLARGs and eLARGs in HWW. Our study firstly revealed the distinct seasonal patterns of iLARGs and eLARGs. Specifically, iLARGs showed higher abundance during colder seasons, whereas eLARGs showed higher abundance in warm seasons. Both clinical pathogens and functional bacteria of wastewater treatments were identified as important hosts of LARGs, while clinical pathogens played predominant roles in the high expression levels of LARGs. Acinetobacter spp. was identified as major host of blaNDM-1 in HWW, which is unrestricted by plasmid host range compatibility. However, HWW treatments could not remove LARGs effectively and instead facilitated their transmission by enhancing the expression and horizontal transfer of mobile genetic element (MGE)-derived LARGs. Our study provides comprehensive insights for the atlas and transfer dynamics of LARGs in HWW for the development of control strategies under worldwide spread of antibiotic resistance.},
}
@article {pmid40578617,
year = {2025},
author = {Villarroel, CA and Gonzalez-Gonzalez, A and Chamorro, M and Villarreal, P and Cubillos, FA and Ramírez, CC},
title = {Discovery of the first aphid-infecting nudiviruses reveal bidirectional host-virus gene transfer.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108393},
doi = {10.1016/j.jip.2025.108393},
pmid = {40578617},
issn = {1096-0805},
abstract = {Nudiviruses are double-stranded DNA viruses that infect invertebrate species, ranging from aquatic arthropods to insects from diverse orders. Remnants of nudiviral infections have been found as introgressions in the genome of several insect hosts, such as aphids pest species (Hemiptera: Aphididae). However, a nudivirus infecting aphids has yet to be reported. Here, we describe the complete genome sequences of two nudiviruses found in the aphid Neuquenaphis staryi, a species that branched out early in the Aphididae family and is endemic to southern beech forests in South America. These nudiviruses (NsNV-1 and NsNV-2) share 98% of nucleotide identity between them and belong to the Alphanudivirus genus. Notably, we found that the prevalence of NsNV-1 was 16 times higher than NsNV-2 in natural N. staryi populations, and co-infections were not observed. Furthermore, we show that horizontal gene transfer between aphids and nudiviruses has been bidirectional, providing evidence of their dynamic co-evolutionary relationship. This study provides the first documentation of nudivirus infections in aphids and expands our understanding of the evolutionary interactions between nudiviruses and their insect hosts.},
}
@article {pmid40578104,
year = {2025},
author = {Li, X and Wang, H and Abdelrahman, HA and Kelly, AM and Roy, LA and Soto, E and Wang, L},
title = {Resistome and microbiome shifts in catfish rearing water: the influence of temperature and antibiotic treatments.},
journal = {Water research},
volume = {285},
number = {},
pages = {124074},
doi = {10.1016/j.watres.2025.124074},
pmid = {40578104},
issn = {1879-2448},
abstract = {The increasing reliance on aquaculture for sustainable protein production highlights the need for responsible antibiotic use to manage bacterial infections, particularly in intensive farming systems. This study investigated the effects of three FDA-approved antibiotics (Aquaflor®, Romet®, Terramycin®) at common fish bacterial disease outbreak temperatures (20 °C, 25 °C, and 30 °C) on the microbiome and resistome of aquaculture water using a catfish model system. Metagenomic analyses evaluated the abundance, diversity, and mobility of antimicrobial resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). The impact of temperature on Aquaflor- and Romet-induced changes in ARG abundance, richness, and resistome composition followed a U-shaped trend, with the least effect observed at 25 °C. Of the three antibiotics tested, Terramycin exerted the most significant influence on the water microbiome and resistome, enriching tetracycline resistance genes and co-selecting for floR, sul, and dfrA genes. Temperature also induced notable shifts in the ARB population, with Mantel tests revealing strong correlations between ARG profiles and changes in the overall bacterial community and ARB populations. While certain ARG classes consistently remained associated with specific host phyla, others shifted, highlighting the potential for horizontal gene transfer (HGT) as a critical mechanism for disseminating resistance genes like tet(C), particularly after antibiotic treatment. This is further supported by the observed reduction in plasmid numbers following treatment, which coincided with increased HGT events. Our findings highlight the pivotal role of temperature in influencing resistome dynamics, emphasizing the importance of accounting for environmental factors when applying antibiotics to effectively mitigate antimicrobial resistance in aquaculture systems.},
}
@article {pmid40576355,
year = {2025},
author = {López, L and Jumbo, M and Mosquera, P and Donoso, G and Graham, J and Trueba, G},
title = {Oral and parenteral treatment with a third-generation cephalosporin promotes the proliferation of diverse ESBL-producing Escherichia coli in the chicken intestinal tract.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0022725},
doi = {10.1128/msphere.00227-25},
pmid = {40576355},
issn = {2379-5042},
abstract = {The global rise of antimicrobial resistance is a major public health threat, with Escherichia coli facilitating the spread of extended-spectrum beta-lactamase (ESBL) genes like blaCTX-M, which confer resistance to third-generation cephalosporins (3GCs). This study examines the impact of 3GC treatment on resistant E. coli clones and horizontal gene transfer (HGT) of ESBL genes in broiler chickens in Quito, Ecuador. Fifteen-day-old Ross broilers were divided into three groups: oral ceftriaxone (100 mg/kg), parenteral ceftriaxone (100 mg/kg intramuscular), and control (no treatment). The study included three phases: baseline, antimicrobial administration (5 days), and recovery (15 days). Fecal cultures on McConkey agar, with and without ceftriaxone (2 µg/mL), measured the ratio of 3GC-resistant lactose fermenters. Regardless of the administration route, ceftriaxone significantly increased resistant coliforms (>80%). Five E. coli colonies per animal and time point were analyzed using single-gene typing, with clonal candidates subjected to whole-genome sequencing. Clonal analysis revealed high genetic diversity, averaging three distinct clones per animal. A unique lineage (H34) emerged exclusively during treatment, and new clones appeared post-treatment. The blaCTX-M-55 variant was the most abundant ESBL gene, persisting despite fluctuations in other blaCTX-M variants. Comparative plasmid analysis suggested blaCTX-M-55 HGT, as plasmids were identified in two genetically distinct E. coli isolates from the same host. Most plasmids belonged to IncFII, with IncX1 and IncN also present. These findings highlight how 3GC treatments rapidly impact ESBL-producing E. coli diversity in the intestine.IMPORTANCEThe global rise of antimicrobial resistance (AMR) poses a critical public health challenge, with Escherichia coli playing a central role in the spread of extended-spectrum beta-lactamase (ESBL) genes like blaCTX-M, which confer resistance to third-generation cephalosporins (3GCs). This study highlights the significant impact of 3GC treatment on the frequency and diversity of 3GC-resistant E. coli clones and horizontal gene transfer of ESBL genes in the intestinal microbiota of broiler chickens. Understanding how antimicrobial treatments drive resistance dynamics in animal populations is crucial for developing strategies to mitigate AMR in both human and veterinary settings.},
}
@article {pmid40573425,
year = {2025},
author = {Lewandowska, N and Bloch, S and Łukasiak, A and Wesołowski, W and Węgrzyn, G and Nejman-Faleńczyk, B},
title = {The Role of Bacteriophage-Derived Small RNA Molecules in Bacterial and Phage Interactions.},
journal = {Viruses},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/v17060834},
pmid = {40573425},
issn = {1999-4915},
support = {2018/29/B/NZ1/00549//National Science Center/ ; 2018/30/E/NZ1/00400//National Science Center/ ; },
mesh = {*Bacteriophages/genetics/physiology ; *Bacteria/virology/genetics ; *RNA, Small Untranslated/genetics/metabolism ; *RNA, Viral/genetics/metabolism ; Gene Expression Regulation, Bacterial ; *Host Microbial Interactions ; RNA, Bacterial/genetics ; Host-Pathogen Interactions ; Gene Transfer, Horizontal ; },
abstract = {Small regulatory RNAs (sRNAs) play a critical role in bacterial gene expression, modulating various cellular processes, including stress responses, metabolism, virulence, and many others. While well-characterized in bacterial systems, an emerging class of phage-derived sRNAs has been identified, suggesting an underexplored regulatory network at phage-host interactions. These sRNAs, encoded within phage genomes, influence both bacterial and viral life cycles by modulating transcriptional and post-transcriptional gene expression processes. The interplay between phage-derived sRNAs and the host genome reveals a complex network of gene regulation, with an impact on bacterial fitness, pathogenesis, and horizontal gene transfer. This review explores the diverse functions of phage-encoded sRNAs, highlighting recent discoveries and their impact on bacterial physiology and phage-host interactions.},
}
@article {pmid40572258,
year = {2025},
author = {Gonzalez Moreno, PJ and Nishiguchi, MK},
title = {The Competitive Edge: T6SS-Mediated Interference Competition by Vibrionaceae Across Marine Ecological Niches.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572258},
issn = {2076-2607},
support = {NSF DBI-2214028//U.S. National Science Foundation/ ; EXO 80NSSC18K1053/NASA/NASA/United States ; School of Natural Sciences//University of California, Merced/ ; },
abstract = {Interference competition, wherein bacteria actively antagonize and damage their microbial neighbors, is a key ecological strategy governing microbial community structure and composition. To gain a competitive edge, bacteria can deploy a diverse array of antimicrobial weapons-ranging from diffusible toxins to contact-mediated systems in order to eliminate their bacterial rivals. Among Gram-negative bacteria, the type VI secretion system (T6SS) has emerged as a potent and sophisticated contact-dependent mechanism that enables the delivery of toxic cargo into neighboring cells, thereby promoting the colonization and dominance of a bacterial taxon within an ecological niche. In this review, we examine the ecological significance of T6SS-mediated interference competition by members of the Vibrionaceae family across a range of marine habitats that include free-living microbial communities and host-associated niches such as coral and squid symbioses. Additionally, we explore the ecological impact of T6SS-mediated competition in modulating biofilm community structure and promoting horizontal gene transfer within those complex microbial populations. Together, these insights underscore the ecological versatility of the T6SS and emphasize its role in driving antagonistic bacterial interactions and shaping microbial community dynamics within marine ecosystems.},
}
@article {pmid40572209,
year = {2025},
author = {Antequera-Zambrano, L and Parra-Sánchez, &#xc1; and González-Paz, L and Fernandez, E and Martinez-Navarrete, G},
title = {Distribution of Genetic Determinants Associated with CRISPR-Cas Systems and Resistance to Antibiotics in the Genomes of Archaea and Bacteria.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572209},
issn = {2076-2607},
abstract = {The CRISPR-Cas system represents an adaptive immune mechanism found across diverse Archaea and Bacteria, allowing them to defend against invading genetic elements such as viruses and plasmids. Despite its broad distribution, the prevalence and complexity of CRISPR-Cas systems differ significantly between these domains. This study aimed to characterize and compare the genomic distribution, structural features, and functional implications of CRISPR-Cas systems and associated antibiotic resistance genes in 30 archaeal and 30 bacterial genomes. Through bioinformatic analyses of CRISPR arrays, cas gene architectures, direct repeats (DRs), and thermodynamic properties, we observed that Archaea exhibit a higher number and greater complexity of CRISPR loci, with more diverse cas gene subtypes exclusively of Class 1. Bacteria, in contrast, showed fewer CRISPR loci, comprising a mix of Class 1 and Class 2 systems, with Class 1 representing the majority (~75%) of the detected systems. Notably, Bacteria lacking CRISPR-Cas systems displayed a higher prevalence of antibiotic resistance genes, suggesting a possible inverse correlation between the presence of these immune systems and the acquisition of such genes. Phylogenetic and thermodynamic analyses further highlighted domain-specific adaptations and conservation patterns. These findings support the hypothesis that CRISPR-Cas systems play a dual role: first, as a defense mechanism preventing the integration of foreign genetic material-reflected in the higher complexity and diversity of CRISPR loci in Archaea-and second, as a regulator of horizontal gene transfer, evidenced by the lower frequency of antibiotic resistance genes in organisms with active CRISPR-Cas systems. Together, these results underscore the evolutionary and functional diversification of CRISPR-Cas systems in response to environmental and selective pressures.},
}
@article {pmid40572139,
year = {2025},
author = {Balata, D and Rosado, T and Pina-Martins, F and Manageiro, V and Menezes, C and Ferreira, E and Paulo, OS and Caniça, M and Dias, E},
title = {Prediction of Antibiotic Resistance Genes in Cyanobacterial Strains by Whole Genome Sequencing.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572139},
issn = {2076-2607},
support = {PTDC/BIA-BMA/31451/2017; UIDB/00211/2020//Portuguese Foundation for Science and Technology/ ; },
abstract = {Cyanobacteria are ubiquitous in freshwater environments, but their role in aquatic resistome remains unclear. In this work, we performed whole genome sequencing on 43 cyanobacterial strains isolated from Portuguese fresh/wastewaters. From 43 available non-axenic unicyanoabacterial cultures (containing only one cyanobacterial strain and their co-occurring bacteria), it was possible to recover 41 cyanobacterial genomes from the genomic assemblies using a genome binning software, 26 of which were classified as high-quality based on completeness, contamination, N50 and contig number thresholds. By using the comprehensive antibiotic resistance database (CARD) on the assembled samples, we detected four antibiotic resistance gene (ARG) variants, conferring resistance in pathogenic bacteria to tetracyclines, fluoroquinolones (adeF-type) and macrolides (ermF-type, mefC-type and mphG-type). Among these, adeF-type was the most prevalent gene, found across 11 cyanobacterial genomes from the Nostocales order. Planktothrix presented the highest variety of close ARG matches, with hits for the macrolide resistance genes ermF-type, mefC-type and mphG-type. An analysis of the genomic assemblies also revealed an additional 12 ARGs in bacteria from the phyla Firmicutes, Proteobacteria and Bacteroidetes, present in the cyanobacterial cultures, foreseeing the horizontal gene transfer of ARGs with cyanobacteria. Additionally, more than 200 partial ARGs were detected on each recovered cyanobacterial genome, allowing for future studies of antibiotic resistance genotype/phenotype in cyanobacteria. These findings highlight the importance of further efforts to understand the role of cyanobacteria on the aquatic resistome from a One Health perspective.},
}
@article {pmid40572111,
year = {2025},
author = {Lucero, J and Nishiguchi, MK},
title = {Host-Associated Biofilms: Vibrio fischeri and Other Symbiotic Bacteria Within the Vibrionaceae.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572111},
issn = {2076-2607},
support = {1T32GM141862-24S3/NH/NIH HHS/United States ; DBI 2214038//National Science Foundation/ ; },
abstract = {Biofilm formation is important for microbial survival, adaptation, and persistence within mutualistic and pathogenic systems in the Vibironaceae. Biofilms offer protection against environmental stressors, immune responses, and antimicrobial treatments by increasing host colonization and resilience. This review examines the mechanisms of biofilm formation in Vibrio species, focusing on quorum sensing, cyclic-di-GMP signaling, and host-specific adaptations that influence biofilm structure and function. We discuss how biofilms differ between mutualistic and pathogenic species based on environmental and host signals. Recent advances in omics technologies such as transcriptomics and metabolomics have enhanced research in biofilm regulation under different conditions. Horizontal gene transfer and phase variation promote the greater fitness of bacterial biofilms due to the diversity of environmental isolates that utilize biofilms to colonize host species. Despite progress, questions remain regarding the long-term effects of biofilm formation and persistence on host physiology and biofilm community dynamics. Research integrating multidisciplinary approaches will help advance our understanding of biofilms and their implications for influencing microbial adaptation, symbiosis, and disease. These findings have applications in biotechnology and medicine, where the genetic manipulation of biofilm regulation can enhance or disrupt microbiome stability and pathogen resistance, eventually leading to targeted therapeutic strategies.},
}
@article {pmid40571945,
year = {2025},
author = {Elmahdy, MH and Azmy, AF and Dishisha, T and El-Gendy, AO and Sebak, M},
title = {Fundamental changes in the antimicrobial resistance profile of Klebsiella quasipneumoniae ATCC 700603 in response to meropenem stress.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {369},
pmid = {40571945},
issn = {1471-2180},
mesh = {*Meropenem/pharmacology ; *Klebsiella/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Bacterial Proteins/genetics/metabolism ; beta-Lactamases/genetics/metabolism ; *Drug Resistance, Bacterial/genetics ; Stress, Physiological ; Gene Transfer, Horizontal ; Gene Expression Regulation, Bacterial/drug effects ; },
abstract = {BACKGROUND: Klebsiella is one of the most challenging superbugs having a high tendency to acquire rapid resistance to many antibiotics, even the ones recognized as the last resort. In several hospitals and environmental niches, Klebsiella is continuously exposed to residual amounts of antibiotics at sub-inhibitory concentrations forming an environmental stress motivating them to adapt and evolve antimicrobial resistance. In the present study, meropenem (MEM) resistance was induced experimentally in a MEM-sensitive strain of K. quasipneumoniae ATCC 700603 through sequential sub-culturing in presence of sub-inhibitory concentrations of MEM over a period of 20 days. To uncover the possible mechanisms standing behind the evolution of antimicrobial resistance upon successive exposure to stress of MEM rather than horizontal gene transfer (HGT) of antibiotic resistance genes.<br><br>RESULTS: Fully adapted cells of the 20th generation (G20) showed MEM-resistance with elevated minimum inhibitory concentration (MIC) by 256-fold compared to the parent cells (G0). The main mechanism of resistance was the production of carbapenemases, which was assured by different tests including nitrocefin, modified-Hodge test (MHT), and modified carbapenem inactivation method (mCIM). The degradation of MEM reached 65.93% by the produced carbapenemases of G20 as determined by the HPLC analysis. Transcriptomics analysis of the class D carbapenemase encoding gene, blaOXA-2, revealed that it was significantly over-expressed by a 3.12-fold (p&#x2009;<&#x2009;0.05) in G20 compared to G0.<br><br>CONCLUSION: The evolved MEM resistance aroused mainly from MEM degradation by carbapenemases, neither increased efflux nor decreased influx of MEM. The rational use of antibiotics is essential to reduce bacterial exposure to the environmental basal levels of antibiotics and decreasing the evolution of antimicrobial resistance.},
}
@article {pmid40570498,
year = {2025},
author = {Zhang, X and Jiao, P and Li, B and Zhang, XX and Ma, L},
title = {Phage lysis-mediated reduction of antibiotic-resistant bacteria alleviates micro/nanoplastic-driven antimicrobial resistance dissemination in anaerobic digestion.},
journal = {Water research},
volume = {285},
number = {},
pages = {124046},
doi = {10.1016/j.watres.2025.124046},
pmid = {40570498},
issn = {1879-2448},
abstract = {Micro/nanoplastics (MPs/NPs) prevalent in anaerobic digestion (AD) have posed escalating threats to antimicrobial resistance (AMR) dissemination, yet mechanistic insights remain insufficient. Here we investigated polypropylene (PP)-MPs (200 μm) and PP-NPs (100 nm) at environmentally relevant concentrations (10, 50, and 100 mg/g TS) on antibiotic resistance gene (ARG) dynamics and transfer mechanisms using metagenomics and bioinformatic modeling. PP-MPs/NPs significantly elevated (6.4-17.8 %, p < 0.05) ARG abundance through selective enrichment of aminoglycoside, mupirocin, multidrug, polymyxin, sulfonamide, tetracycline, and novobiocin ARGs. Metagenomic assembly revealed the particle-induced ecological niche specialization of antibiotic-resistant bacteria (ARB), notably the multi-resistant ESKAPE pathogen Enterobacter hormaechei (53.4-69.4 % enrichment, p < 0.05), which harbored mobile aadA, qacEdelta1, and sul1 via conjugative plasmids. Mechanistically, MPs/NPs facilitated horizontal gene transfer (HGT) through synergism of plasmids and phages. The enhanced abundance of conjugation elements, enriched plasmid-borne ARGs, and extensive HGT events promoted plasmid-conjugative transfer, while the strongly correlated ARG-carrying lysogenic phage-host pairs highlighted phage-mediated transfer under MPs/NPs. The significant increase of phage-to-host-ratio (1.0-1.2 folds) revealed the underestimated role of phages lysing ARB under MPs/NPs stress, thereby contributing to ARG load reduction. A novel risk assessment framework prioritizing prevalence, enrichment, mobility, and host pathogenicity identified dfrA3, mefB, OXA-347, and tet44 as high-risk biomarkers and quantified 1.5-9.9 % increased health risks in digestate-exposed scenarios. These findings reveal the neglected role of phage lysis driving ARG reduction, providing actionable targets for mitigating plastic-driven resistance in AD.},
}
@article {pmid40452436,
year = {2025},
author = {Tannier, E and Tricou, T and Benali, S and de Vienne, DM},
title = {HGTs are not SPRs: In the Presence of Ghost Lineages, Series of Horizontal Gene Transfers do not Result in Series of Subtree Pruning and Regrafting.},
journal = {Molecular biology and evolution},
volume = {42},
number = {6},
pages = {},
doi = {10.1093/molbev/msaf128},
pmid = {40452436},
issn = {1537-1719},
support = {ANR-19-CE45-0010//Agence Nationale de la Recherche/ ; },
mesh = {*Gene Transfer, Horizontal ; *Phylogeny ; *Models, Genetic ; Evolution, Molecular ; Computer Simulation ; },
abstract = {When a gene is horizontally transferred (HGT), under the "replacement" model where the transferred gene replaces its homolog in the recipient genome, the corresponding gene phylogeny departs from the species phylogeny by a Subtree Prune and Regraft (SPR) operation: the "recipient branch" is moved from its initial position to attach to the "donor branch". Based on this observation, various methods have used SPRs to infer HGTs. We examine this apparent equivalence in the light of ghost lineages, i.e. related species absent from the phylogeny because they are extinct, unknown, or have not been sampled. In this case, an SPR is not directly interpretable by an HGT from the donor branch, because HGTs can have ghost lineages as donors. A possible and frequent interpretation-that we call "induced HGT"-is that the transferred gene leaves the sampled phylogeny for a ghost lineage at the donor branch and is transferred back from a ghost lineage at the recipient branch. We show by simulations that this interpretation is misleading in a significant number of cases. For instance, if the studied phylogeny represents 1% of all the species susceptible to exchange genetic material with the 100 sampled species, and 11 transfers occurred, then SPRs do not correspond to induced HGTs in around 50% of the cases. This leaves the question of a coherent interpretation of SPR in the presence of ghosts open and applies to a certain extent to other phylogenetic simulation or inference methods of HGT, like reconciliation, or phylogenetic networks.},
}
@article {pmid40568145,
year = {2025},
author = {Brezner, S and Garushyants, SK and Wolf, YI and Koonin, EV and Snir, S},
title = {Evolution of gene order in prokaryotes is driven primarily by gene gain and loss.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.04.03.647019},
pmid = {40568145},
issn = {2692-8205},
abstract = {UNLABELLED: Evolution of bacterial and archaeal genomes is highly dynamic including extensive gene gain via horizontal gene transfer and gene loss as well as different types of genome rearrangements, such as inversions and translocations, so that gene order is not highly conserved even among closely related organisms. We sought to quantify the contributions of different genome dynamics processes to the evolution of the gene order relying on the recently developed "jump" model of gene translocation. The jump model has been completely solved analytically and provides the exact distribution of syntenic gene block lengths (SBL) in compared genomes based on gene translocations alone. Comparing the SBL distribution predicted by the jump model with the distributions empirically observed for multiple groups of closely related bacterial and archaeal genomes, we obtained robust estimates of the genome rearrangement to gene flux (gain and loss) ratio. In most groups of bacteria and archaea, this ratio was found to be on the order of 0.1 indicating that the loss of synteny in the evolution of bacteria and archaea is driven primarily by gene gain and loss rather than by gene translocation.<br><br>SIGNIFICANCE: Evolution of bacterial and archaeal genomes is a highly dynamic process that includes extensive gene gain via horizontal gene transfer and gene loss as well as different types of genome rearrangements, so that gene order is not highly conserved even among closely related organisms. We developed a theoretical framework to quantify the contributions of different genome dynamics processes to the evolution of the gene order and found that in most groups of bacteria and archaea, the genome rearrangement to gene flux (combined gain and loss) is on the order of 0.1. Thus, the loss of genomic synteny in the evolution of bacteria and archaea appears to be driven primarily by gene gain and loss rather than by gene translocation.},
}
@article {pmid40565594,
year = {2025},
author = {Saccone, S and Brancato, D and Bruno, F and Coniglio, E and Sturiale, V and Federico, C},
title = {Origin and Evolution of Genes in Eukaryotes: Mechanisms, Dynamics, and Functional Implications.},
journal = {Genes},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/genes16060702},
pmid = {40565594},
issn = {2073-4425},
mesh = {Humans ; *Evolution, Molecular ; Animals ; *Eukaryota/genetics ; Gene Duplication ; Gene Transfer, Horizontal ; Selection, Genetic ; },
abstract = {The origin and evolution of genes are central themes in evolutionary biology and genomics, shedding light on how molecular innovations shape biological complexity and adaptation. This review explores the principal mechanisms underlying gene emergence in eukaryotes, including gene duplication, de novo gene birth, horizontal gene transfer, viral gene domestication, and exon shuffling. We examine the population dynamics that govern the fixation of new genes, their functional integration, and the selective forces acting upon them-from purifying selection to adaptive innovation. Examples such as NOTCH2NL and SRGAP2C, which originated through recent segmental duplications followed by neofunctionalization, illustrate how duplicate-derived de novo genes can play a key role in human brain development. In addition, we highlight the emerging relevance of nuclear architecture in determining the evolutionary fate of new genes, offering a spatial dimension to gene innovation. We also discuss methodological approaches for detecting new genes and inferring selection, and finally, we highlight the emerging role of the human pangenome in revealing hidden gene diversity and its implications for evolutionary and biomedical research. Understanding gene innovation not only enhances our grasp of evolutionary processes but also informs clinical studies on disease susceptibility and human uniqueness.},
}
@article {pmid40565227,
year = {2025},
author = {Fu, W and Wang, Y and Ge, Y and Gao, H and Sun, X and Deng, Z and Wang, L and Chen, S and He, X and Wu, G},
title = {Molecular Insight into the Recognition of DNA by the DndCDE Complex in DNA Phosphorothioation.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125765},
pmid = {40565227},
issn = {1422-0067},
support = {32170030//National Natural Science Foundation of China/ ; 2020YFA0907300//National Key R&amp;D Program of China/ ; 2022YFA0912200//National Key R&amp;D Program of China/ ; },
mesh = {Escherichia coli/metabolism/genetics ; *Escherichia coli Proteins/metabolism/chemistry/genetics ; Protein Binding ; *DNA, Bacterial/metabolism/chemistry ; *DNA/metabolism/chemistry ; Streptomyces lividans/metabolism/genetics ; *Bacterial Proteins/metabolism/chemistry ; Models, Molecular ; },
abstract = {In a vast variety of prokaryotes such as Escherichia coli and Streptomyces lividans, the DNA degradation (Dnd) CDE protein complex (consisting of DndC, DndD, and DndE), together with the DndA/IscS protein and the DndFGH complex, function as a defense barrier to prevent the invasion of non-self-DNA. The DndCDE complex introduces phosphorothioation (PT) modifications into DNA, and the DndFGH complex specifically cleaves non-PT DNA and, thus, restricts horizontal gene transfer and phage invasion. Despite the central importance of the DndCDE complex in DNA PT modification, which catalyzes the oxygen-sulfur swap on DNA, our understanding of this key complex remains poor. Here, we employed protein structure prediction to provide a reasonably reliable prediction of the structure of the DndCDE complex and a 23 bp DNA-DndCDE complex. We found that among the three proteins in the DndCDE complex, DndC, especially its "specificity loop", plays a key role in recognizing the consensus PT modification sequence. In addition, the DndD protein is found to possess a highly conserved structural surface on its globular domain, presumably mediating the dimerization of DndD as well as the DndCDE complex. Furthermore, our normal mode analysis showed that there exists a dynamic transition between a closed and an open state for the DndCDE complex, facilitating its association and release of DNA. Our conclusions were corroborated by biochemical assays using purified proteins. On the whole, we provide molecular insights into the assembly and DNA-recognition mechanism of a central protein complex involved in DNA phosphorothioation.},
}
@article {pmid40560800,
year = {2025},
author = {Ruf, A and Blumenkamp, P and Ludwig, C and Lippegaus, A and Brachmann, A and Klingl, A and Goesmann, A and Brinkrolf, K and Papenfort, K and Robatzek, S},
title = {Extracellular Vesicles From Xylella fastidiosa Carry sRNAs and Genomic Islands, Suggesting Roles in Recipient Cells.},
journal = {Journal of extracellular vesicles},
volume = {14},
number = {6},
pages = {e70102},
pmid = {40560800},
issn = {2001-3078},
support = {EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; INST 95/1435-1 FUGG//Deutsche Forschungsgemeinschaft/ ; RO 3550/16-1//Deutsche Forschungsgemeinschaft/ ; RO 3550/17-1//Deutsche Forschungsgemeinschaft/ ; RO 3550/18-1//Deutsche Forschungsgemeinschaft/ ; SPP2389 - Project-ID 503931087//Deutsche Forschungsgemeinschaft/ ; ERC Adv Grant 884235//H2020 European Research Council/ ; },
mesh = {*Extracellular Vesicles/metabolism/genetics ; *Genomic Islands/genetics ; *Xylella/genetics/pathogenicity/metabolism ; *RNA, Small Untranslated/genetics/metabolism ; Plant Diseases/microbiology ; Gene Transfer, Horizontal ; RNA, Bacterial/genetics/metabolism ; Bacterial Proteins/metabolism/genetics ; Virulence ; RNA-Binding Proteins/metabolism ; },
abstract = {Xylella fastidiosa (Xf) is a Gram-negative bacterial plant pathogen responsible for severe diseases in a variety of economically important crops. A critical aspect of its virulence is the production of extracellular vesicles (EVs). In this study, we discovered that DNA-binding proteins and nonribosomal RNA-binding proteins are abundant in the corona of Xf-EVs. DNA-seq revealed enrichment of three genomic islands (GIs) in EVs, which carry molecular signatures indicative of horizontal gene transfer (HGT). The most abundant GI encodes five homologous small RNAs designated sXFs. RNA sequencing revealed a distinct pattern of noncoding RNAs enriched in EVs, including four island-encoded sXFs. One of the sXF's stem-loops contains motifs for binding the RNA chaperone Hfq, which is also abundant in EVs. Predicted target analysis suggests that sXFs play a role in regulation of natural competence in bacteria. Additionally, sXF plant target prediction identifies a coiled-coil nucleotide-binding domain leucine-rich repeat receptor (CNL) immune gene that is downregulated following Xf infection and Xf-EV treatment. We propose a model where Xf releases nucleic acid carrying EVs with two functions: one to deliver RNA-related cargo that regulates gene expression in both bacterial and plant cells, and another to deliver DNA-related cargo for the genetic transfer of genomic islands. We highlight island-encoded sXFs as potential virulence factors and vesiduction as a mechanism of HGT of sXFs in Xf. Taken together, our data on Xf-EV cargoes provide a molecular framework for understanding the virulence of Xf.},
}
@article {pmid40559614,
year = {2025},
author = {Martz, K and Alomar, D and Karim, M and Knezevic, S and D'Costa, VM},
title = {Characterization of the Diversity in Host Range of an Extensively Drug-Resistant (XDR) Type IV Secretion System-Encoding Plasmid in Acinetobacter.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
pmid = {40559614},
issn = {2076-0817},
support = {PJ4-175369/CAPMC/CIHR/Canada ; PJT-178191/CAPMC/CIHR/Canada ; },
mesh = {*Plasmids/genetics ; *Acinetobacter baumannii/genetics/drug effects/pathogenicity ; *Drug Resistance, Multiple, Bacterial/genetics ; Humans ; *Type IV Secretion Systems/genetics ; Acinetobacter Infections/microbiology ; *Host Specificity ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The World Health Organization (WHO) cites antimicrobial resistance as among the greatest threats to human health. The multidrug-resistant pathogen Acinetobacter baumannii, recognized as a priority pathogen for healthcare and research, is responsible for a diverse array of infections including respiratory tract, soft tissue and wound, and bloodstream infections. Despite this importance, the mechanisms of its pathogenesis remain poorly understood. Conjugation represents a central mechanism for bacterial adaptation and evolution and is responsible for the spread of genes that promote pathogen survival, antibiotic resistance, virulence, and biofilm formation. Our laboratory recently characterized a large group of almost 120 Type IV Secretion System (T4SS)-encoding plasmids in Acinetobacter, distributed globally across 20 countries spanning four continents, and demonstrated that an XDR A. baumannii plasmid from this family was transmissible to another A. baumannii strain. This research investigated the potential diversity of host strains for this representative member plasmid. Using the GC1 lineage strain A. baumannii AB5075-UW harbouring the XDR plasmid p1AB5075 and a series of previously characterized clinical and environmental Acinetobacter strains, conjugative analyses demonstrated transfer of the XDR plasmid to both A. baumannii strains of more genetically divergent sequence types and to non-baumannii Acinetobacter species both inside and outside the Acinetobacter calcoaceticus-baumannii (ACB) complex. Successful recipients included diverse strains of both clinical and environmental origin within the Acinetobacter genus. Collectively, this research could provide insights into an important genetic element for future surveillance.},
}
@article {pmid40559557,
year = {2025},
author = {Enciso-Martínez, Y and Barrios-Villa, E and Ballesteros-Monrreal, MG and Navarro-Ocaña, A and Valencia, D and González-Aguilar, GA and Martínez-Téllez, MA and Palomares-Navarro, JJ and Ayala-Zavala, F},
title = {Virulence and Antibiotic Resistance of aEPEC/STEC Escherichia coli Pathotypes with Serotype Links to Shigella boydii 16 Isolated from Irrigation Water.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/pathogens14060549},
pmid = {40559557},
issn = {2076-0817},
mesh = {Humans ; Virulence ; Serogroup ; *Shigella boydii/genetics/isolation &amp; purification/drug effects/pathogenicity/classification ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; *Water Microbiology ; *Drug Resistance, Bacterial ; HeLa Cells ; *Shiga-Toxigenic Escherichia coli/genetics/drug effects/isolation &amp; purification/pathogenicity/classification ; Agricultural Irrigation ; Virulence Factors/genetics ; Microbial Sensitivity Tests ; },
abstract = {Irrigation water can serve as a reservoir and transmission route for pathogenic Escherichia coli, posing a threat to food safety and public health. This study builds upon a previous survey conducted in Hermosillo, Sonora (Mexico), where 445 samples were collected from a local Honeydew melon farm and associated packing facilities. Among the 32 E. coli strains recovered, two strains, A34 and A51, were isolated from irrigation water and selected for further molecular characterization by PCR, due to their high pathogenic potential. Both strains were identified as hybrid aEPEC/STEC pathotypes carrying bfpA and stx1 virulence genes. Adhesion assays in HeLa cells revealed aggregative and diffuse patterns, suggesting enhanced colonization capacity. Phylogenetic analysis classified A34 within group B2 as associated with extraintestinal pathogenicity and antimicrobial resistance, while A51 was unassigned to any known phylogroup. Serotyping revealed somatic antigens shared with Shigella boydii 16, suggesting possible horizontal gene transfer or antigenic convergence. Antibiotic susceptibility testing showed resistance to multiple β-lactam antibiotics, including cephalosporins, linked to the presence of blaCTX-M-151 and blaCTX-M-9. Although no plasmid-mediated quinolone resistance genes were detected, resistance may involve efflux pumps or mutations in gyrA and parC. These findings are consistent with previous reports of E. coli adaptability in agricultural environments, suggesting potential genetic adaptability. While our data support the presence of virulence and resistance markers, further studies would be required to demonstrate mechanisms such as horizontal gene transfer or adaptive evolution.},
}
@article {pmid40558211,
year = {2025},
author = {Enshaie, E and Nigam, S and Patel, S and Rai, V},
title = {Livestock Antibiotics Use and Antimicrobial Resistance.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antibiotics14060621},
pmid = {40558211},
issn = {2079-6382},
abstract = {Background/Objectives: Antibiotic resistance or antimicrobial resistance (AMR) in livestock is a growing global concern that threatens both human and animal health. The overuse and misuse of antibiotics in livestock production have led to an increased propensity for the development of AMR bacterial strains in animals, which can be spread to humans through the consumption of contaminated animal products, direct contact, or environmental exposure. This review aims to summarize the development and transmission of AMR in livestock, explore its underlying mechanisms and impact on human and animal health, and discuss current practices and potential strategies for mitigation and prevention. Methods: For this narrative review, we searched articles on PubMed and Google Scholar using the terms antibiotic resistance, livestock, and environment, alone or in combination. Results: The history of antibiotic use in livestock and its link to increased AMR, along with the involved mechanisms, including the enzymatic breakdown of antibiotics, alterations in bacterial targets, horizontal gene transfer, and efflux pumps, are important. Antibiotics in livestock are used for growth promotion, disease prevention and control, and metaphylactic use. The role of livestock and the environment as reservoirs for resistant pathogens, their impact on human health, chronic infections, allergic reactions, toxicity, and the development of untreatable diseases is important to understand AMR. Conclusions: Given the widespread use of antibiotics and the potential consequences of AMR, collaborative global efforts, increased public awareness, coordinated regulations, and advancements in biological technology are required to mitigate the threat AMR poses to human and animal health. Regulatory solutions and the development of new therapeutic alternatives like antimicrobial peptides and bacteriophage therapy, and preventive measures such as DNA and mRNA vaccines, are future perspectives.},
}
@article {pmid40558188,
year = {2025},
author = {Mohammed, EAH and Kovács, B and Kuunya, R and Mustafa, EOA and Abbo, ASH and Pál, K},
title = {Antibiotic Resistance in Aquaculture: Challenges, Trends Analysis, and Alternative Approaches.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antibiotics14060598},
pmid = {40558188},
issn = {2079-6382},
support = {TKP2021-NKTA-32//National Research, Development, and Innovation Fund of Hungary/ ; },
abstract = {Antibiotic resistance in aquaculture has emerged as a global crisis, representing a serious threat to the health of aquatic animals, environment, and human. The extensive use of antibiotics in aquaculture has led to rapid development of resistant bacterial strains, resulting in environmental contamination and the dissemination of resistant genes. Understanding of the research trends, key contributors, and thematic evolution of this field is essential for guiding future studies and policy interventions. The study aimed to conduct a bibliometric analysis of research on antibiotic resistance development in aquaculture, identifying key areas of research, leading contributors, emerging challenges, and alternative solutions. Data were extracted from the Web of Science (WoS) database covering the period from 2000 to 2025. A systematic search strategy was employed, utilizing terms including "antibiotic resistance" AND "bacteria," AND "aquaculture". Relevant publications were extracted from the WoS using these keywords. R-tool was then used to analyze the obtained metadata including keywords, citation patterns, and co-authored country. The analysis revealed a remarkable increase in publications over the past 25 years, with key contributions from China, India, and the USA. The most significant articles focused on the presence of multidrug resistant bacteria in the aquatic environments and, antibiotic-resistant genes, and horizontal gene transfer. Probiotics are the alternative solution to overcome the antibiotic resistance and enhance aquaculture sustainability. Future research should focus on the interdisciplinary collaboration, novel antimicrobial alternatives, and global monitoring approaches.},
}
@article {pmid40558133,
year = {2025},
author = {Ye, Z and Li, M and Jing, Y and Liu, K and Wu, Y and Peng, Z},
title = {What Are the Drivers Triggering Antimicrobial Resistance Emergence and Spread? Outlook from a One Health Perspective.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antibiotics14060543},
pmid = {40558133},
issn = {2079-6382},
support = {2022YFF1103100//National Key Research and Development Program of China/ ; 32172314//National Natural Science Foundation of China/ ; 22193064//National Natural Science Foundation of China/ ; },
abstract = {Antimicrobial resistance (AMR) has emerged as a critical global public health threat, exacerbating healthcare burdens and imposing substantial economic costs. Currently, AMR contributes to nearly five million deaths annually worldwide, surpassing mortality rates of any single infectious disease. The economic burden associated with AMR-related disease management is estimated at approximately $730 billion per year. This review synthesizes current research on the mechanisms and multifaceted drivers of AMR development and dissemination through the lens of the One Health framework, which integrates human, animal, and environmental health perspectives. Intrinsic factors, including antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs), enable bacteria to evolve adaptive resistance mechanisms such as enzymatic inactivation, efflux pumps, and biofilm formation. Extrinsic drivers span environmental stressors (e.g., antimicrobials, heavy metals, disinfectants), socioeconomic practices, healthcare policies, and climate change, collectively accelerating AMR proliferation. Horizontal gene transfer and ecological pressures further facilitate the spread of antimicrobial-resistant bacteria across ecosystems. The cascading impacts of AMR threaten human health and agricultural productivity, elevate foodborne infection risks, and impose substantial economic burdens, particularly in low- and middle-income countries. To address this complex issue, the review advocates for interdisciplinary collaboration, robust policy implementation (e.g., antimicrobial stewardship), and innovative technologies (e.g., genomic surveillance, predictive modeling) under the One Health paradigm. Such integrated strategies are essential to mitigate AMR transmission, safeguard global health, and ensure sustainable development.},
}
@article {pmid40558095,
year = {2025},
author = {Milhomem Pilati Rodrigues, B and Janssen, L and da Silva, LA and Acacio, SSVG and Magalhães, MT and Ribeiro, BM},
title = {Experimental and evolutionary evidence for horizontal transfer of an envelope fusion protein gene between thogotoviruses and baculoviruses.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0214824},
doi = {10.1128/jvi.02148-24},
pmid = {40558095},
issn = {1098-5514},
abstract = {Baculoviruses are insect-specific viruses with large, double-stranded DNA genomes classified into four genera. Alphabaculoviruses, which infect lepidoptera, are further divided into group I (G1-α) and group II (G2-α). The GP64 protein, essential for cell attachment and viral entry in G1-α baculoviruses, is thought to have originated through horizontal gene transfer (HGT) from thogotoviruses (family Orthomyxoviridae). This study investigates the functional substitution of GP64 by thogotovirus fusion proteins. Through RNA-seq data mining, we identified a novel thogotovirus, Melitaea didyma thogotovirus 1 (MediTHOV-1), in lepidopteran hosts. Phylodynamic analysis of G1-α baculovirus and thogotovirus glycoproteins suggests that the HGT event occurred during the Mesozoic era. To test functional substitution, we constructed recombinant Autographa californica multiple nucleopolyhedrovirus (AcMNPV) carrying either the envelope fusion protein (EFP) genes from MediTHOV-1 or Apis thogotovirus 1 (ATHOV-1), while deleted for its native gp64 gene. Our results show that, while the MediTHOV-1 glycoprotein failed to rescue AcMNPV infectivity, the ATHOV-1 fusion protein (EFP) partially restored infectivity, albeit with reduced efficiency. Cryo-electron microscopy revealed lower incorporation of ATHOV-1 EFP into viral envelopes compared to GP64. The recombinant AcMNPV carrying ATHOV-1 EFP (Ac-ATHOVGPgp64Δ) displayed delayed replication kinetics and lower viral titers. Interestingly, ATHOV-1 EFP significantly enhanced baculovirus entry and gene transduction in mosquito cells. These findings provide experimental support for the HGT hypothesis, demonstrating the functional incorporation of a thogotovirus glycoprotein into a baculovirus. This study sheds light on the evolutionary relationship between baculovirus GP64 and glycoproteins, offering insights into viral evolution and potential biotechnological applications in gene delivery and protein expression.IMPORTANCEBaculoviruses are widely utilized for the biological control of insect pests and as versatile biotechnological tools, with their effectiveness largely dependent on the activity of their envelope fusion proteins (EFPs). Thogotoviruses, in contrast, are emerging vector-borne pathogens of significant concern. In this study, we present the first successful functional substitution of the baculovirus GP64 protein with a thogotovirus EFP, alongside the identification of what appears to be a lepidopteran-associated thogotovirus, Melitaea didyma thogothovirus 1. Our work provides functional and phylogenetic insights into the evolutionary relationship between these distantly related viral groups, particularly the hypothesized horizontal gene transfer event that gave rise to baculoviral gp64 gene. These findings offer a deeper understanding of the determinants underlying the adaptation of baculoviral glycoproteins to novel hosts. Furthermore, the discovery of novel viral genes highlights promising opportunities for biotechnological advancements, including the development of enhanced baculovirus-based gene delivery systems and tools for protein expression.},
}
@article {pmid40556893,
year = {2025},
author = {Di Marcantonio, L and Chiatamone Ranieri, S and Toro, M and Marchegiano, A and Cito, F and Sulli, N and Del Matto, I and Di Lollo, V and Alessiani, A and Foschi, G and Platone, I and Paoletti, M and D'Alterio, N and Garofolo, G and Janowicz, A},
title = {Comprehensive regional study of ESBL Escherichia coli: genomic insights into antimicrobial resistance and inter-source dissemination of ESBL genes.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1595652},
pmid = {40556893},
issn = {1664-302X},
abstract = {INTRODUCTION: The global dissemination of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) poses a significant public health challenge, particularly in regions with high antimicrobial resistance (AMR) occurrence. This study investigated the occurrence, genomic characteristics, and dissemination dynamics of ESBL-producing E. coli in Abruzzo, Italy, by analyzing 956 isolates from humans, livestock, wildlife, and food products.<br><br>METHODS: Phenotypic and genomic analyses were performed on the isolates to assess ESBL-E. coli occurrence and characteristics. Multilocus sequence typing (MLST) was used to identify sequence types (STs), and plasmid profiling alongside synteny analysis was conducted to investigate horizontal gene transfer and resistance gene integration. Spatial analysis was also carried out to identify hotspots of ESBL-positive isolates.<br><br>RESULTS: An overall ESBL-E. coli occurrence of 14.1% (135/956 samples) was found, with significant variation across hosts: companion animals exhibited the highest occurrence (16.2%), followed by livestock and food matrices (14.6%), and wildlife (7.0%). Spatial analysis identified a hotspot in northeastern Abruzzo, where ESBL-positive isolates were 5.34 times more likely to occur (p&#x202f;<&#x202f;0.001). MLST identified 58 sequence types (STs), with ST131 dominating human isolates (12/19). In cattle, predominant sequence types were ST16565 (5 isolates) and ST540 (4 isolates); in poultry, ST43 (5 isolates), ST10 (4 isolates), and ST6215 (3 isolates) were most common; ST206 (8 isolates) was predominant in swine; and in dogs, ST10 (4 isolates) and ST3580 (3 isolates) were most prevalent. Genomic analysis revealed host-specific distributions of ESBL genes: bla CTX-M-15 predominated in humans and dogs, while bla CTX-M-1 was most common in pigs. Plasmid profiling revealed IncF and IncI plasmids as key vectors for horizontal gene transfer. Synteny analysis showed identical flanking regions of bla CTX-M-1 and bla CTX-M-15 across phylogenetically distant strains, suggesting chromosomal integration and stable maintenance of resistance genes.<br><br>DISCUSSION: These findings underscore the interconnectedness of human, animal, and environmental reservoirs in AMR dissemination. The high genetic diversity observed within farms and the detection of shared clusters across hosts emphasize the need for integrated One Health interventions, including reduced antibiotic use in livestock and enhanced surveillance of high-risk environments. This study provides critical insights into local AMR dynamics, offering a model for regional mitigation strategies.},
}
@article {pmid40556891,
year = {2025},
author = {Chekole, WS and Potgieter, L and Adamu, H and Sternberg-Lewerin, S and Tessema, TS and Magnusson, U},
title = {Genomic insights into antimicrobial resistance and virulence of E. coli in central Ethiopia: a one health approach.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1597580},
pmid = {40556891},
issn = {1664-302X},
abstract = {Antimicrobial resistance is a global threat causing millions of deaths annually. The study aimed to identify antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence genes (VGs) and track their dissemination among E. coli isolates. Seventy-seven isolates from calves, environments, and human sources were studied. The study involved WGS sequencing, bacterial strains characterized; pan genome, multi-locus sequence typing, and serotyping using O-, and H-typing. The ARGs, VGs, and MGEs were identified using ABRicate against selected respective databases. A maximum likelihood SNP (single nucleotide polymorphism) tree was constructed and visualized with an interactive tree of life (IToL). Descriptive statistics were used to analyze the data. Seventy-seven of the isolates were identified as E. coli, later grouped into 5 clades and four known phylogroups. ST10 and O16:H48 were most prevalent in 12 and 42 isolates, respectively. There were about 106 unique ARGs detected between 1.3% and 91.9%, with 57 detected in 40% of isolates. In terms of ARGs, the most common were bla-ampH (90.9%), bla-AmpC1 (89.6%), tet(A) (84.4%), mdf(A) (81.8%), aph(3")-Ib (79%), sul2 (79%), aph(6)-Id (75%), and bla-PBP (70%). It was found that 95 percent (96/106) of ARGs came from at least two sources. The majority of detected ARGs exhibited high concordance between phenotypic resistance and ARGs profiles (JSI ≥ 0.5). In eight isolates, mutations in the gyrA (3) and par-C/E (5) genes led to ciprofloxacin and nalidixic acid resistance. The most common co-occurrences of ARG and MGE were Tn3 with bla-TEM-105 (34), Int1 with sul1 (13), and dhfr7 (11). Meanwhile, the most frequently detected VGs (n ≥ 71 isolates) included elfA-G, fimB-I, hcpA-C, espL, ibeC, entA, fepA-C, ompA, ecpA-E, fepD, fes, and ibeB. Nearly, 88.3% (128/1450) VGs were shared in isolates from at least two sources. ETEC (53.2%), EAEC (22.1%), and STEC (14.3%) were the three most frequently predicted pathotypes. Despite significant ST diversity, ARGs and VGs showed an extensive distribution among the study groups. These findings suggest limited clonal transmission of isolates. In comparison, the wide distribution of ARGs and VGs may be attributed to horizontal gene transfer driven by similar antibiotic selection pressures in the study area.},
}
@article {pmid40556499,
year = {2025},
author = {Yang, Y and Jin, X and Zhao, Z},
title = {Distribution and Evolutionary Trajectories of β-Lactamases in Vibrio: Genomic Insights from CARB-Type Enzymes in the Harveyi and Cholerae Clades.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf128},
pmid = {40556499},
issn = {1759-6653},
abstract = {Antibiotic resistance mediated by β-lactamases (BLs), encoded by bla genes, is a significant global health threat, necessitating systematic studies of their diversity and evolution, particularly among pathogenic bacteria lineages. Leveraging over 6,000 quality-filtered Vibrio genomes alongside six newly sequenced marine symbiotic strains representing 128 nominal and 57 unclassified Vibrio species, our study extends taxonomic breadth and resolution for investigating BL diversity. We identified 4,431 BLs across 41 species, encompassing all four Ambler Classes (A∼D). Among these, CARBenicillin-hydrolyzing Class A BLs (CARBs encoded by blaCARB family) were the most prevalent (60.7%) and exhibited a clade-centric distribution particularly in Harveyi clade and V. cholerae, underscoring influence of specific ecological and evolutionary pressures. We refined CARB classification into two subfamilies: CARB-17-like (blaCARB-17-like) confined to Harveyi clade, and CARB-1-like (blaCARB-1-like) found exclusively outside Harveyi clade, based on phylogenetic placement, sequence similarity, and inheritance patterns, providing a clearer framework for delineating their functional and phylogenetic nuances. Notably, blaCARB-17-like genes in non-pathogenic Harveyi Subclade II showed significantly relaxed selection, accompanied by unusual mutations within key conserved motifs especially catalytic serine residues, suggesting evolutionary drift that may compromise canonical enzymatic activity. Furthermore, blaCARB-17-like genes, present as a single copy, emerged as a core gene in Harveyi clade, showing promise as a diagnostic marker for clinically significant Harveyi clade species, despite limited yet significant interspecies genetic exchanges mediated by recombination or mobile genetic elements. Our study advances the understanding of BL evolution and genomic distribution in Vibrio, with broad implications for diagnostic applications and resistance management strategies.},
}
@article {pmid40556036,
year = {2025},
author = {Li, Y and Liu, X and Yang, J and Li, R and Wang, M and Kuang, S},
title = {Characteristics of intracellular/extracellular antibiotic resistance genes and microbial community in sludge compost under sulfadiazine stress.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/09593330.2025.2522480},
pmid = {40556036},
issn = {1479-487X},
abstract = {The accumulation of emerging antibiotics in sewage sludge, which serves as a repository for antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), is raising growing concern. To accurately assess the environmental risks, it is essential to separately investigate intracellular and extracellular ARGs (iARGs and eARGs) due to their distinct roles in resistance persistence and horizontal gene transfer. However, the impact of sulfadiazine (SDZ) on iARGs and eARGs, and the mechanisms involved in the composting process remain under further investigation. In this study, composts with SDZ concentrations of 5 and 50 mg/kg were constructed, and ARGs, microbial community composition and functional pathways were analyzed. The results showed that the abundance of iARGs varied significantly under SDZ selective pressure, while eARGs showed no significant differences. Specifically, i-erm decreased in the 50SDZ group, likely due to competition for ecological niches. The abundance of ermA, ermB and ermF decreased by approximately 97%, 85%, and 84%, respectively. i-sul increased by 127% to 156% in SDZ-added groups but not dose-dependently. Bacillus, Paracoccus, Pseudomonas, and Caproiciproducens were predominant in the SDZ-added groups. The abundance of potential ARG hosts, such as Bacillus and Paracoccus, increased significantly, with Paracoccus showing 2.3-fold and 1.8-fold higher abundance in the 50SDZ and 5SDZ treatments, respectively, compared to the CK. Functional genes related to the ABC-2 type transport system, signal transduction, and genome maintenance decreased with SDZ application. These findings suggested that the dynamics of ARGs should be continuously monitored during sludge composting and land application of compost products to reduce their environmental risks.},
}
@article {pmid40555322,
year = {2025},
author = {Ying, S and Zhang, Z and Xiang, R},
title = {Metagenomic and Whole-Genome Characterization of Carbapenem-Resistant Acinetobacter baumannii Carrying blaOXA-23 Gene within the Tn2006 Transposon Among ICU Patients.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.06.009},
pmid = {40555322},
issn = {2213-7173},
abstract = {PURPOSE: To characterize carbapenem-resistant Acinetobacter baumannii carrying blaOXA-23 genes within the Tn2006 transposon using metagenomic and whole-genome sequencing, focusing on their genetic features, antimicrobial resistance, and potential for clonal spread and horizontal gene transfer among ICU patients.<br><br>METHODS: Bronchoalveolar lavage fluid samples from 28 ICU patients were analyzed using mNGS to detect pathogens and resistance genes. A. baumannii isolates underwent whole-genome sequencing for genetic diversity assessment. Antimicrobial susceptibility testing and comparative genomic analysis were performed.<br><br>RESULTS: mNGS revealed mixed infections in 71.4% of patients, identifying multiple bacteria, viruses, fungi, and mycoplasma species. A. baumannii was detected in 25 samples, often alongside other pathogens. All isolates harbored blaOXA-23 within Tn2006 on the chromosome and belonged to sequence type ST2, indicating clonal dissemination despite significant genetic diversity (up to 2,969 SNP differences). The isolates were highly resistant to multiple antibiotics but remained susceptible to tigecycline and colistin. Comparative genomic analysis with 238 global CRAB genomes confirmed the prevalence of the Tn2006 transposon carrying blaOXA-23 in ST2 strains, emphasizing the potential for rapid spread of this resistance mechanism.<br><br>CONCLUSION: The widespread presence of multidrug-resistant A. baumannii carrying blaOXA-23 within Tn2006 among ICU patients poses a significant public health concern. The high rate of mixed infections and the potential for horizontal gene transfer complicate infection management in critically ill patients. Enhanced infection control measures, continuous surveillance, and targeted interventions are urgently needed to prevent further dissemination of these resistant strains in hospital settings.},
}
@article {pmid40459279,
year = {2025},
author = {Parras-Moltó, M and Lund, D and Ebmeyer, S and Larsson, DGJ and Johnning, A and Kristiansson, E},
title = {The transfer of antibiotic resistance genes between evolutionarily distant bacteria.},
journal = {mSphere},
volume = {10},
number = {6},
pages = {e0011425},
doi = {10.1128/msphere.00114-25},
pmid = {40459279},
issn = {2379-5042},
mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects/classification ; Phylogeny ; *Drug Resistance, Bacterial/genetics ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Evolution, Molecular ; *Genes, Bacterial ; Humans ; },
abstract = {UNLABELLED: Infections from antibiotic-resistant bacteria threaten human health globally. Resistance is often caused by mobile antibiotic resistance genes (ARGs) shared horizontally between bacterial genomes. Many ARGs originate from environmental and commensal bacteria and are transferred between divergent bacterial hosts before they reach pathogens. This process remains, however, poorly understood, which complicates the development of countermeasures that reduce the spread of ARGs. In this study, we aimed to systematically analyze the ARGs transferred between the most evolutionarily distant bacteria, defined here based on their phylum. We implemented an algorithm that identified inter-phylum transfers (IPTs) by combining ARG-specific phylogenetic trees with the taxonomy of the bacterial hosts. From the analysis of almost 1 million ARGs identified in >400,000 bacterial genomes, we identified 661 IPTs, which included transfers between all major bacterial phyla. The frequency of IPTs varies substantially between ARG classes and was highest for the aminoglycoside resistance gene AAC(3), while the levels for beta-lactamases were generally lower. ARGs involved in IPTs also differed between phyla, where, for example, tetracycline ARGs were commonly transferred between Firmicutes and Proteobacteria, but rarely between Actinobacteria and Proteobacteria. The results, furthermore, show that conjugative systems are seldom shared between bacterial phyla, suggesting that other mechanisms drive the dissemination of ARGs between divergent hosts. We also show that bacterial genomes involved in IPTs of ARGs are either over- or underrepresented in specific environments. These IPTs were also found to be more recent compared to transfers associated with bacteria isolated from water, soil, and sediment. While macrolide and tetracycline ARGs involved in IPTs almost always were >95% identical between phyla, corresponding β-lactamases showed a median identity of <60%. We conclude that inter-phylum transfer is recurrent, and our results offer new insights into how ARGs are disseminated between evolutionarily distant bacteria.<br><br>IMPORTANCE: Antibiotic-resistant infections pose a growing threat to global health. This study reveals how genes conferring antibiotic resistance can move between bacteria that belong to different phyla lineages previously thought to be too evolutionarily distant for frequent gene exchange. By analyzing nearly 1 million resistance genes from over 400,000 bacterial genomes, the researchers uncovered hundreds of inter-phylum transfer events, exposing surprising patterns in how different classes of resistance genes spread. The findings highlight that conjugative systems are less common than expected in cross-phyla transfers and suggest that alternative mechanisms may play key roles. This new understanding of how resistance genes leap between vastly different bacterial groups can inform strategies to slow the emergence of drug-resistant infections, aiding in the development of more effective public health interventions.},
}
@article {pmid40298963,
year = {2025},
author = {Karki, S and Barth, ZK and Aylward, FO},
title = {Ancient Host-Virus Gene Transfer Hints at a Diverse Pre-LECA Virosphere.},
journal = {Journal of molecular evolution},
volume = {93},
number = {3},
pages = {295-305},
pmid = {40298963},
issn = {1432-1432},
support = {2141862//National Science Foundation/ ; },
mesh = {Phylogeny ; *DNA Viruses/genetics ; Evolution, Molecular ; *Eukaryota/genetics/virology ; *Gene Transfer, Horizontal ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed RNA Polymerases/genetics ; },
abstract = {The details surrounding the early evolution of eukaryotes and their viruses are largely unknown. Several key enzymes involved in DNA synthesis and transcription are shared between eukaryotes and large DNA viruses in the phylum Nucleocytoviricota, but the evolutionary relationships between these genes remain unclear. In particular, previous studies of eukaryotic DNA and RNA polymerases often show deep-branching clades of eukaryotes and viruses indicative of ancient gene exchange. Here, we performed updated phylogenetic analysis of eukaryotic and viral family B DNA polymerases, multimeric RNA polymerases, and mRNA-capping enzymes to explore their evolutionary relationships. Our results show that viral enzymes form clades that are typically adjacent to eukaryotes, suggesting that they originate prior to the emergence of the Last Eukaryotic Common Ancestor (LECA). The machinery for viral DNA replication, transcription, and mRNA capping are all key processes needed for the maintenance of virus factories, which are complex structures formed by many nucleocytoviruses during infection, indicating that viruses capable of making these structures are ancient. These findings hint at a diverse and complex pre-LECA virosphere and indicate that large DNA viruses may encode proteins that are relics of extinct proto-eukaryotic lineages.},
}
@article {pmid40197024,
year = {2025},
author = {Gillett, DL and Selinidis, M and Seamons, T and George, D and Igwe, AN and Del Valle, I and Egbert, RG and Hofmockel, KS and Johnson, AL and Matthews, KRW and Masiello, CA and Stadler, LB and Chappell, J and Silberg, JJ},
title = {A roadmap to understanding and anticipating microbial gene transfer in soil communities.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {89},
number = {2},
pages = {e0022524},
doi = {10.1128/mmbr.00225-24},
pmid = {40197024},
issn = {1098-5557},
mesh = {*Soil Microbiology ; *Microbiota/genetics ; *Gene Transfer, Horizontal ; Soil/chemistry ; Bacteria/genetics ; Synthetic Biology ; Biotechnology ; },
abstract = {SUMMARYEngineered microbes are being programmed using synthetic DNA for applications in soil to overcome global challenges related to climate change, energy, food security, and pollution. However, we cannot yet predict gene transfer processes in soil to assess the frequency of unintentional transfer of engineered DNA to environmental microbes when applying synthetic biology technologies at scale. This challenge exists because of the complex and heterogeneous characteristics of soils, which contribute to the fitness and transport of cells and the exchange of genetic material within communities. Here, we describe knowledge gaps about gene transfer across soil microbiomes. We propose strategies to improve our understanding of gene transfer across soil communities, highlight the need to benchmark the performance of biocontainment measures in situ, and discuss responsibly engaging community stakeholders. We highlight opportunities to address knowledge gaps, such as creating a set of soil standards for studying gene transfer across diverse soil types and measuring gene transfer host range across microbiomes using emerging technologies. By comparing gene transfer rates, host range, and persistence of engineered microbes across different soils, we posit that community-scale, environment-specific models can be built that anticipate biotechnology risks. Such studies will enable the design of safer biotechnologies that allow us to realize the benefits of synthetic biology and mitigate risks associated with the release of such technologies.},
}
@article {pmid40553200,
year = {2025},
author = {Xie, X and Ren, Z and Wang, R and Tian, K and Huang, X and Lyu, Y and Cao, G and Fu, J},
title = {Mobile Genomic Island GEI-FN1A in Aeromonas salmonicida FN1 Contributes to the Spread of Antibiotic-Resistance Genes.},
journal = {Current microbiology},
volume = {82},
number = {8},
pages = {345},
pmid = {40553200},
issn = {1432-0991},
support = {ZR2022MH107//Shandong Provincial Natural Science Foundation/ ; M-2023040//TCM science and technology project of Shandong Province/ ; },
mesh = {*Genomic Islands ; Anti-Bacterial Agents/pharmacology ; Animals ; Gene Transfer, Horizontal ; *Aeromonas salmonicida/genetics/drug effects/isolation &amp; purification ; *Drug Resistance, Multiple, Bacterial/genetics ; Chickens ; Whole Genome Sequencing ; Genome, Bacterial ; Feces/microbiology ; Soil Microbiology ; Genes, Bacterial ; Bacterial Proteins/genetics ; Microbial Sensitivity Tests ; },
abstract = {Antibiotics are used to treat severe bacterial infections. However, owing to excessive antibiotic use, bacteria under high selective pressure for antibiotics develop resistance through spontaneous mutation or by acquiring antibiotic-resistance genes (ARGs) through horizontal gene transfer (HGT). Horizontal transfer of ARGs among bacteria in the environment can lead to the emergence of multidrug-resistant (MDR) bacteria that infect animals and humans, thus causing disease outbreaks. In this study, MDR strain FN1 was isolated from a feces-contaminated soil sample from a chicken farm under pressure from the antibiotic florfenicol (16 mg/L) and identified as Aeromonas salmonicida. Whole-genome sequencing and analysis revealed the 86.8-kb antibiotic-resistant genomic island, GEI-FN1A, in the FN1 genome. Genome annotation revealed that GEI-FN1A carried several ARGs, including two tetracycline-resistance genes [tetR and tet(A)], three aminoglycoside-resistance genes [aph(6), aph(3"), and aac(3)], one trimethoprim-resistance gene (dfrB4), two chloramphenicol/florfenicol-resistance genes (catB3 and floR), three macrolide-resistance genes [mphR(A), mrx(A), and mph(A)] and two sul1 genes. GEI-FN1A also contained genes encoding integrase, transposase, and recombinase, which mediate the horizontal transfer of MDR genes. These findings suggest that GEI-FN1A in A. salmonicida FN1 can potentially spread ARGs among environmental bacteria.},
}
@article {pmid40553195,
year = {2025},
author = {Sonkar, V and Devtalla, H and Kumar, S},
title = {Pesticide-driven antimicrobial resistance in water bodies: insights on environmental concerns, health implications and mitigation strategies.},
journal = {Environmental geochemistry and health},
volume = {47},
number = {7},
pages = {282},
pmid = {40553195},
issn = {1573-2983},
mesh = {*Pesticides/toxicity/analysis ; *Water Pollutants, Chemical/toxicity/analysis ; *Drug Resistance, Microbial/drug effects ; Humans ; India ; Agriculture ; Water Microbiology ; },
abstract = {Pesticide contamination in water bodies is an emerging driver of antimicrobial resistance (AMR), posing severe environmental and public health risks. Due to excessive agricultural use, pesticides routinely end up in water bodies due to leaching, improper disposal, and agricultural runoff. Pesticides act as selective pressures, promoting resistant microbial strains by providing evolutionary pressure for the strains to thrive. Pesticides facilitate the dissemination of resistance genes through several mechanisms; horizontal gene transfer, bio-film formation, and co-selection with heavy metals. Pathogens carrying antibiotic resistance genes, are emerging as a threat to global populations exposed to contaminated water, as they are increasingly more challenging to treat with traditional antibiotics. Moreover, these issues escalate due to the overlap in disposal of agricultural runoffs and untreated hospital waste into water bodies leading to co-selection pressure facilitating multi drug resistance. Current review examines the critical role of pesticides contamination in driving AMR in Indian aquatic ecosystems, a novel intersection threatening global health and deteriorating aquatic life. However, existing policies are insufficient, necessitating stricter regulations to control the problem. There also needs to be stronger laws in place to limit and monitor pollution in the water bodies. The increasing incidences of health issues linked to resistant strains in Indian population, need to be tackled more comprehensively. Mitigation requires stringent agricultural regulations, improved waste management, and interdisciplinary strategies to curb this growing threat.},
}
@article {pmid40552317,
year = {2025},
author = {Jafari, E and Azizian, R and Tabasi, M and Banakar, M and Bagheri Lankarani, K},
title = {Human Gut Bacteriophageome: Insights Into Drug Resistance Mechanisms in Tuberculosis.},
journal = {Interdisciplinary perspectives on infectious diseases},
volume = {2025},
number = {},
pages = {8811027},
pmid = {40552317},
issn = {1687-708X},
abstract = {Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a major global health burden. The emergence of drug-resistant strains presents a critical challenge in TB management. The recent research has explored the interaction between TB and the human gut bacteriophage community (phageome). The gut phageome plays a crucial role in regulating microbial diversity and functionality, and its composition and function have been linked to various health conditions. Examining the gut phageome through metagenomic analysis provides insights into its composition, role in health, and interactions with the host immune system. Exploring the interaction between the gut phageome and M. tuberculosis may reveal how phages affect the bacterium's pathogenicity, survival, and mechanisms of drug resistance. Understanding the gut phageome's impact on TB drug resistance could inform novel therapeutic strategies, such as phage therapy, and highlight the importance of microbiome-based interventions in combating drug-resistant TB strains. This review explores the role of the gut phageome in influencing drug resistance in TB, focusing on interaction mechanisms and potential therapeutic implications, synthesizing current research findings, and identifying knowledge gaps in this emerging field. This review also synthesizes the current evidence on the gut phageome's role in TB drug resistance, focusing on phage-mediated horizontal gene transfer (e.g., rpoB, katG), immune modulation, and preclinical efficacy of mycobacteriophage therapies. Key findings highlight phage cocktails (e.g., DS6A, D29 LysB) as promising adjuncts to antibiotics, reducing M. tuberculosis burden in murine models. These insights advocate for phage therapy as a complementary strategy against drug-resistant TB, urging clinical validation to bridge the existing knowledge gaps.},
}
@article {pmid40551445,
year = {2025},
author = {Deshamukhya, C and Das, BJ and Dhar, D and Bhattacharjee, A},
title = {Influence of AHL and Imipenem on blaNDM Conjugation and sRNA Rydb Expression in Escherichia coli.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70074},
doi = {10.1002/jobm.70074},
pmid = {40551445},
issn = {1521-4028},
abstract = {The rise of carbapenem resistance in Escherichia coli is mainly due to the rapid spread of carbapenemase-encoding genes through horizontal gene transfer, particularly via bacterial conjugation. Recent research has highlighted the role of a small RNA molecule known as RydB in bacterial conjugation, specifically through its interaction with the protein SdiA. This study investigated the effects of sub-inhibitory concentrations of imipenem and N-acyl homoserine lactones (AHLs) on the expression of rydB in E. coli strains that overexpress sdiA. Additionally, we examined how AHLs influence the bacterial conjugation of plasmids that contain carbapenem resistance genes. We selected a carbapenem-resistant isolate of E. coli harbouring the blaNDM gene and its corresponding plasmid-cured derivative, based on the overexpression of the sdiA gene in response to AHLs. Conjugation experiments were conducted, both without AHL treatment and with AHL treatments, to assess the transferability of the blaNDM plasmid. The transcriptional response of rydB gene was evaluated in the plasmid-cured derivative, the native type, the transconjugant, and E. coli J53. Our findings indicated that AHLs and imipenem inhibit the expression of the rydB gene. Interestingly, while RydB does not seem to impact bacterial conjugation when suppressed by these agents, the combination of AHLs enhances the conjugation of plasmid that carry the blaNDM gene. This study enhances our understanding of the regulatory roles that quorum sensing signal molecules, including C4 AHL and C12AHL, as well as imipenem, play in bacterial conjugation and sRNA expression.},
}
@article {pmid40548977,
year = {2025},
author = {Bhadra, S and Das, C and Bawali, S and Bhattacharya, A},
title = {Evolutionary analysis of the Leishmania major orthologues for the newly identified cyclic AMP response proteins.},
journal = {Archives of microbiology},
volume = {207},
number = {8},
pages = {184},
pmid = {40548977},
issn = {1432-072X},
mesh = {*Leishmania major/genetics/metabolism ; Phylogeny ; *Evolution, Molecular ; *Protozoan Proteins/genetics/metabolism/chemistry ; *Cyclic AMP/metabolism ; Gene Transfer, Horizontal ; },
abstract = {Cyclic AMP (cAMP) signalling is largely noncanonical in kinetoplastids. With virtual absence of canonical cAMP effectors including cyclic nucleotide sensitive protein kinase A regulatory subunits. Through a number of RNAi screens, a group of novel cAMP-responsive effectors were identified from Trypanosoma with 11 members, assigned as cAMP Response Proteins (CARPs, CARP1 to 11). Four of the CARPs were reported earlier, recently the remaining seven were identified. Except for CARP3 and CARP11, the orthologues for other CARPs can be identified from Leishmania. An intricate evolutionary analysis performed earlier indicated CARP1 and CARP4 from Leishmania major comprise features of horizontally transferred genes. Aiming for comprehensive understanding of the evolution of CARPs, the study further extends the evolutionary analysis to newly annotated CARP orthologues from L. major. The study reveals the phylogenetic relation among kinetoplastid CARP orthologues and functional divergence. A systemic codon adaptation profiling suggested horizontal transfer for some of the CARPs. Alongside, structural analysis highlighted heterogeneity among the T. brucei and L. major orthologues.},
}
@article {pmid40548945,
year = {2025},
author = {},
title = {Correction to 'Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome'.},
journal = {Nucleic acids research},
volume = {53},
number = {12},
pages = {},
doi = {10.1093/nar/gkaf631},
pmid = {40548945},
issn = {1362-4962},
}
@article {pmid40548717,
year = {2025},
author = {Xu, C and Li, X and Zhang, Y and Li, Y and Li, Y and Zhang, R and Dong, N},
title = {Interorder horizontal gene transfer of tet(X3) between Acinetobacter spp. and Enterobacteriaceae.},
journal = {Antimicrobial agents and chemotherapy},
volume = {},
number = {},
pages = {e0194524},
doi = {10.1128/aac.01945-24},
pmid = {40548717},
issn = {1098-6596},
}
@article {pmid40544776,
year = {2025},
author = {Huang, W and Wang, F and Su, Y and Huang, H and Luo, J},
title = {Underestimated roles of phages in biological wastewater treatment systems: Recent advances and challenges.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139007},
doi = {10.1016/j.jhazmat.2025.139007},
pmid = {40544776},
issn = {1873-3336},
abstract = {Bacteriophages (phages) are vital components in biological wastewater ecosystems, whose concentrations are far exceeding those bacteria. Despite their importance, they are often overlooked and regarded as the "dark matter" in biological treatment processes. Phages play a pivotal role in shaping the dynamic evolution of host microbial communities within wastewater treatment plants (WWTPs), driving their functional evolution through interactions with host microorganisms. Phages are crucial in driving microbial ecological dynamics and regulating metabolic functions. At the macroscopic scale, the organic matters released through viral shunting demonstrate enhanced bioavailability and facilitated organic element cycling based on viral shuttle-mediated bio-pump. Additionally, at the micro-scale, gene transfer mediated by phages can assist functional microorganisms in enhancing metabolic efficiency and adapting to environmental stress. However, this process also introduces environmental risks, particularly the dissemination of antibiotic resistance genes through horizontal gene transfer and plasmids. Phages offer distinct advantages over conventional chemical and physical methods, including superior efficiency and environmental sustainability. Nonetheless, the development of phage-based biocontrol strategies is constrained by phage specificity and the complexity of biological treatment systems. Recent advances in artificial intelligence and genetic technologies provide promising avenues for optimizing phage applications. Further research into phage ecology is essential to lay a theoretical foundation for enhancing operational stability, treatment efficiency, and targeted biocontrol strategies.},
}
@article {pmid40544537,
year = {2025},
author = {Sinha, S and Upadhyay, LSB},
title = {Understanding antimicrobial resistance (AMR) mechanisms and advancements in AMR diagnostics.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {2},
pages = {116949},
doi = {10.1016/j.diagmicrobio.2025.116949},
pmid = {40544537},
issn = {1879-0070},
abstract = {The overuse and abuse of antibiotics, which results in the evolution of resistant microorganisms, is the primary cause of the global health catastrophe known as antimicrobial resistance (AMR). The enzymatic breakdown of antibiotics, target site modification, efflux pump overexpression, and the formation of biofilm are some of the mechanisms responsible for acquiring antimicrobial resistance (AMR). These mechanisms enable bacteria to evade or neutralize the effects of antimicrobial agents, complicating treatment options and increasing mortality rates. The rapid dissemination of resistance genes via horizontal gene transfer further exacerbates the problem, necessitating urgent intervention. Advanced AMR diagnostics are transforming the fight against antimicrobial resistance. Biosensors enable rapid, point-of-care detection; Cluster regularly interspaced short palindromic repeat (CRISPR) technologies offer precise identification of resistance genes; and mass spectrometry provides fast, accurate profiling. Automated systems streamline workflows and boost throughput, while flow cytometry delivers real-time, single-cell analysis of phenotypic resistance. Together, these innovations accelerate detection and support targeted antimicrobial stewardship, essential for combating the global AMR threat. This review covers the mechanisms underlying antimicrobial resistance (AMR) and recent advancements in AMR diagnostic technologies.},
}
@article {pmid40542629,
year = {2025},
author = {Aristova, EO and Volkhin, IA and Denisova, AA and Nikitin, PA and Petrukhin, ER},
title = {[De Novo Gene Birth].},
journal = {Molekuliarnaia biologiia},
volume = {59},
number = {1},
pages = {22-31},
pmid = {40542629},
issn = {0026-8984},
mesh = {*Evolution, Molecular ; Humans ; *Gene Duplication ; *Gene Transfer, Horizontal ; Animals ; },
abstract = {According to classic ideas, new genes emerge from old genes by duplication or horizontal transfer. Analyses of a large number of genomes in recent decades have shown that some genes have no visible homologs and have presumably emerged de novo from previously noncoding sequences. The review considers possible mechanisms of de novo gene formation, the properties of protein sequences encoded by such genes, and features of their expression and selection. The problem of identification of de novo arising gene is discussed separately.},
}
@article {pmid40540566,
year = {2025},
author = {Woods, PH and Speth, DR and Laso-Pérez, R and Utter, DR and Ruff, SE and Orphan, VJ},
title = {Identification of key steps in the evolution of anaerobic methanotrophy in Candidatus Methanovorans (ANME-3) archaea.},
journal = {Science advances},
volume = {11},
number = {25},
pages = {eadq5232},
pmid = {40540566},
issn = {2375-2548},
mesh = {*Methane/metabolism ; Anaerobiosis ; Phylogeny ; *Evolution, Molecular ; Genome, Archaeal ; *Archaea/genetics/metabolism ; Metagenomics ; Gene Transfer, Horizontal ; },
abstract = {Despite their large environmental impact and multiple independent emergences, the processes leading to the evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics of a recently evolved but understudied ANME group, "Candidatus Methanovorans" (ANME-3), to identify evolutionary processes and innovations at work in ANME, which may be obscured in earlier evolved lineages. We identified horizontal transfer of hdrA homologs and convergent evolution in carbon and energy metabolic genes as potential early steps in Methanovorans evolution. We also identified the erosion of genes required for methylotrophic methanogenesis along with horizontal acquisition of multiheme cytochromes and other loci uniquely associated with ANME. The assembly and comparative analysis of multiple Methanovorans genomes offers important functional context for understanding the niche-defining metabolic differences between methane-oxidizing ANME and their methanogen relatives. Furthermore, this work illustrates the multiple evolutionary modes at play in the transition to a globally important metabolic niche.},
}
@article {pmid40379877,
year = {2025},
author = {Gonzalez-Duran, E and Kroop, X and Schadach, A and Bock, R},
title = {Suppression of plastid-to-nucleus gene transfer by DNA double-strand break repair.},
journal = {Nature plants},
volume = {11},
number = {6},
pages = {1154-1164},
pmid = {40379877},
issn = {2055-0278},
mesh = {*DNA Breaks, Double-Stranded ; *Plastids/genetics ; *DNA Repair ; *Nicotiana/genetics ; *Cell Nucleus/genetics ; *Gene Transfer, Horizontal ; Symbiosis/genetics ; },
abstract = {Plant nuclear genomes contain thousands of genes of mitochondrial and plastid origin as the result of endosymbiotic gene transfer (EGT). EGT is a still-ongoing process, but the molecular mechanisms determining its frequency remain largely unknown. Here we demonstrate that nuclear double-strand break (DSB) repair is a strong suppressor of EGT. Through large-scale genetic screens in tobacco plants, we found that EGT from plastids to the nucleus occurs more frequently in somatic cells when individual DSB repair pathways are inactive. This effect is explained by the expected increase in the number and residence time of DSBs available as integration sites for organellar DNA. We also show that impaired DSB repair causes EGT to increase 5- to 20-fold in the male gametophyte. Together, our data (1) uncover DSB levels as a key determinant of EGT frequency, (2) reveal the strong mutagenic potential of organellar DNA and (3) suggest that changes in DNA repair capacity can impact EGT across evolutionary timescales.},
}
@article {pmid40544427,
year = {2025},
author = {Lamberte, LE and Darby, EM and Kiu, R and Moran, RA and Acuna-Gonzalez, A and Sim, K and Shaw, AG and Kroll, JS and Belteki, G and Clarke, P and Felgate, H and Webber, MA and Rowe, W and Hall, LJ and Van Schaik, W},
title = {Staphylococcus haemolyticus is a reservoir of antibiotic resistance genes in the preterm infant gut.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2519700},
doi = {10.1080/19490976.2025.2519700},
pmid = {40544427},
issn = {1949-0984},
abstract = {Staphylococcus haemolyticus is an important cause of sepsis in preterm infants, with gut colonization being recognized as a risk factor for infection. To better understand the diversity of S. haemolyticus among preterm infants, we generated genome sequences of S. haemolyticus strains (n = 140) from 44 stool samples of 22 preterm infants from four hospitals in England. Core genome phylogenetic analyses, incorporating 126 publicly available S. haemolyticus genome sequences, showed that 85/140 (60.1%) of the isolates, from three different hospitals, formed a clonal group with 78/85 (91.7%) strains having Multi-Locus Sequence Type (ST) 49. Antibiotic resistance genes were prevalent in the genomes. There was a strong association between the presence of mecA and phenotypic resistance to oxacillin, and the aacA-aphD gene and phenotypic resistance to gentamicin. While mecA was near-ubiquitous, none of the strains from the preterm infant cohort had a complete Staphylococcal Cassette Chromosome mec (SCCmec) element. The aacA-aphD gene was associated with the transposon Tn4001 in multiple chromosomal and plasmid contexts. Our data suggest the existence of a distinct sub-population of S. haemolyticus that has adapted to colonize the gut of preterm infants, and widespread horizontal gene transfer and recombination among this frequent colonizer of the preterm infant gut.},
}
@article {pmid40544087,
year = {2025},
author = {Bhattacharya, D and Van Etten, J and Panayotakis, G and McDermott, T and Stephens, TG},
title = {Gene transfer drives community cooperation in geothermal habitats.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.06.004},
pmid = {40544087},
issn = {1878-4380},
abstract = {Cyanidiophyceae red algae dominate many geothermal habitats and provide important tools for investigating the evolution of extremophilic eukaryotes and associated microbial communities. We propose that resource sharing drove genome reduction in Cyanidiophyceae and enabled the neofunctionalization of genes in multi-enzyme pathways. Utilizing arsenic detoxification as a model, we discuss how the sharing of gene functions by other members of the microbial assemblage weakened selection on homologs in the Cyanidiophyceae, allowing long-term gene persistence via the putative gain of novel functions. This hypothesis, referred to as the Integrated Horizontal Gene Transfer (HGT) Model (IHM), attempts more generally to explain how extremophilic eukaryotes may have transitioned from 'hot start' milieus by functional innovations driven by the duplication and divergence of HGT-derived genes.},
}
@article {pmid40543345,
year = {2025},
author = {Li, S and Jiang, Y and Wang, J and Bartlam, M and Wang, Y},
title = {Chiral naproxen enhances horizontal transfer of antibiotic resistance genes in biofilms: Molecular docking reveals stereoselective mechanisms.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138980},
doi = {10.1016/j.jhazmat.2025.138980},
pmid = {40543345},
issn = {1873-3336},
abstract = {The dissemination of antibiotic resistance genes (ARGs) is a growing global health concern. This study investigates how the chiral enantiomers of the non-antibiotic drug naproxen (NAP) influence ARG dissemination in biofilms. Metagenomic sequencing and binning analyses revealed that NAP enantiomers selectively enriched ARGs and their bacterial hosts, enhancing resistance to specific antibiotics. Notably, the stereoselective effects of NAP enantiomers not only shaped microbial community composition but also affected the potential for ARG spread. Mechanistically, exposure to R-NAP, in comparison to S-NAP, resulted in a 1.53-fold increase in reactive oxygen species (ROS) production, an 18.20 % enhancement in cell membrane permeability, and a 1.93-fold rise in the abundance of genes associated with the type IV secretion system (T4SS). These physiological and genetic changes promoted microbial aggregation and DNA conjugation, particularly enhancing the transfer of the sul1 gene within the Aquabacter genus through the coordinated action of T4SS, two-component systems (TCS), and quorum sensing (QS). Molecular docking and qRT-PCR analyses further revealed that the stereoselectivity of NAP enantiomers stemmed from their distinct binding interactions with proteins involved in horizontal gene transfer, shedding light on the molecular mechanisms underlying ARG dissemination under chiral NAP exposure.},
}
@article {pmid40541684,
year = {2025},
author = {Sies, AN and Nowlan, JP and Schnell, LJ and Lumsden, JS and Russell, S and Cameron, ADS},
title = {Discovery and assembly of plasmids in the fish pathogen Tenacibaculum.},
journal = {Plasmid},
volume = {},
number = {},
pages = {102753},
doi = {10.1016/j.plasmid.2025.102753},
pmid = {40541684},
issn = {1095-9890},
abstract = {Members of the marine bacterial genus Tenacibaculum cause disease in finfish and outbreaks result in significant animal harm and losses in aquaculture around the globe. Plasmids have not been previously identified in Tenacibaculum, but long-read DNA sequencing of genomes from disease-associated Tenacibaculum isolates collected between 2017 and 2020 in British Columbia, Canada, revealed circular putative plasmids in three Tenacibaculum species. In addition to high-quality circular assembly, the putative plasmids contained genes encoding plasmid replication, mobility, and partitioning proteins. Genes for type B conjugation machinery and type 6iii secretion system components were also identified on each of the two largest plasmid sequences. Several protocols were tested to visualize and enrich Tenacibaculum plasmid DNA. Rolling-circle replication with Phi29 DNA polymerase amplified putative plasmids smaller than 100 kb. Alkaline lysis extraction provided weak enrichment of putative plasmid DNA, and plasmids could not be confidently resolved by Eckhardt extraction and electrophoresis in agarose gels. The newly assembled plasmids matched previously sequenced Tenacibaculum contigs, highlighting that publicly available Tenacibaculum genomes contain unrecognized plasmids. The discovery of putative plasmids in Tenacibaculum is significant because plasmids often confer important functions to host cells and serve as vehicles for horizontal gene transfer within and beyond the host species.},
}
@article {pmid40539803,
year = {2025},
author = {Mapiki, P and Laiser, E and Mufungwe, J and Shawa, M and Siamujompa, M and Johnson, T and Namukonde, N and Mwaanga, P and Hang'ombe, BM},
title = {Bacteriological quality of fresh and processed black soldier fly Hermetia illucens larvae reared on chicken manure in Kitwe, Zambia.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0057024},
doi = {10.1128/spectrum.00570-24},
pmid = {40539803},
issn = {2165-0497},
abstract = {UNLABELLED: Black soldier fly larvae (BSFL) have high nutrient content and are rapidly becoming an alternative protein source for animal feed. However, microbial contamination is a potential risk due to the environment in which they are reared. This study assessed the bacteriological quality of fresh and processed BSFL by comparing the processed BSFL using two traditional methods (oven-dried and sun-dried), on their effectiveness at reducing the bacterial load and further elucidated bacterial composition. PCR was used to identify extended-spectrum β-lactamase (ESBL) and mecA genes in Escherichia coli and Staphylococcus spp., respectively. A total of 51 fresh BSFL samples were collected from a commercial poultry farm in Kitwe, Zambia. The results showed various bacterial genera, with a higher diversity among gram-positive isolates. The comparison of the effectiveness of two traditional processing methods for BSFL, sun-drying and oven-drying, showed that both methods significantly reduced the bacterial load, with oven-drying causing a larger reduction. While various genera were identified, we focused on E. coli and Staphylococcus spp. This is because some E. coli harbor ESBLs that hydrolyze β-lactam antibiotics like cephalosporins and penicillin, leading to resistance. Similarly, the genus Staphylococcus was selected since some strains are potentially pathogenic and contain the mecA gene that encodes resistance to β-lactam antibiotics. Molecular characterization of the isolated strains revealed blaCTX-M and blaTEM genes among E. coli, but the mecA gene was not detected among Staphylococcus. This study revealed that BSFL harbor bacteria of zoonotic significance, emphasizing the need for good processing methods to eliminate potential risks.<br><br>IMPORTANCE: Isolation and identification of Escherichia coli and Staphylococcus spp. in processed black soldier fly larvae (BSFL) samples meant for animal feed indicate insufficient processing methods and pose a public health risk. For instance, some E. coli harbor extended-spectrum &#x3b2;-lactamases (ESBLs) that hydrolyze &#x3b2;-lactam antibiotics like cephalosporins and penicillin, leading to resistance. In addition, some E. coli commensals can transfer antimicrobial resistance genes to pathogenic bacteria through horizontal gene transfer using various mobile genetic elements, leading to resistance. Similarly, for Staphylococcus spp., some strains of the genus Staphylococcus are potentially pathogenic and contain the mecA gene that encodes resistance to &#x3b2;-lactam antibiotics. In this study, we used PCR to screen E. coli isolates for the two commonly reported ESBL genes in Zambia, blaCTX-M and blaTEM, and Sanger sequencing was used to reveal blaCTX-M gene alleles. Our results highlight the importance of using adequate processing methods for BSFL to eliminate potential health risks to animal feed.},
}
@article {pmid40535478,
year = {2025},
author = {Zhang, Y and Su, Z and Qiu, X and Liu, H and Wen, D and Chen, L},
title = {Distinct ARG profiles associated with class 1 integrons in municipal and industrial wastewater treatment plants.},
journal = {Environmental science and ecotechnology},
volume = {26},
number = {},
pages = {100586},
pmid = {40535478},
issn = {2666-4984},
abstract = {Class 1 integrons facilitate horizontal gene transfer, significantly influencing antibiotic resistance gene (ARG) dissemination within microbial communities. Wastewater treatment plants (WWTPs) are critical reservoirs of ARGs and integrons, yet the integron-mediated dynamics of ARG transfer across different WWTP types remain poorly understood. Here we show distinct ARG profiles associated with class 1 integrons in municipal and industrial WWTPs using a novel approach combining nested-like high-throughput qPCR and PacBio sequencing. Although industrial WWTPs contained higher absolute integron abundances, their relative ARG content was lower (1.27 × 10[7]-9.59 × 10[7] copies/ng integron) compared to municipal WWTPs (3.72 × 10[7]-1.98 × 10[8] copies/ng integron). Of the 132,084 coding sequences detected from integrons, 56.8 % encoded antibiotic resistance, with industrial plants showing lower ARG proportions, reduced ARG array diversity, and greater incorporation of non-ARG sequences. These findings suggest industrial WWTP integrons integrate a broader array of exogenous genes, reflecting adaptation to complex wastewater compositions. This work enhances our understanding of integron-driven ARG dynamics in wastewater and offers a robust strategy for environmental integron analysis.},
}
@article {pmid40533044,
year = {2025},
author = {Tian, Y and Li, J and Meng, J and Li, J},
title = {Deciphering antibiotic resistance gene transfer in activated sludge systems for piggery wastewater: behaviors, hosts and drivers.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122166},
doi = {10.1016/j.envres.2025.122166},
pmid = {40533044},
issn = {1096-0953},
abstract = {Understanding the transfer and driving mechanisms of antibiotic resistance genes (ARGs) in activated sludge is essential for mitigating environmental risks, particularly during real wastewater treatment where these processes remain poorly characterized. This study investigated the prevalence of ARGs in a sequencing batch reactor (SBR) - up-flow microaerobic sludge reactor (UMSR) system treating high-risk piggery wastewater and revealed critical pathways for resistance propagation. Ten prevalent ARG subtypes, categorized into three types, were selected as target genes, exhibiting a total relative abundance of 0.52 copies per 16S rRNA in raw wastewater. The SBR-UMSR system reduced total ARGs by 0.04 log in wastewater, with half of subtypes decreasing 0.14-1.30 log, despite 0.23-0.58 log enrichment in sludge. By integrating correlation analysis with partial least-squares path modeling, this study identified Burkholderiaceae as the primary potential host of ARGs and pinpointed other high-risk hosts. It further revealed two crucial mechanisms: (1) conjugation-mediated horizontal gene transfer dominated ARG propagation, and (2) bacterial community succession served as the main driving force for ARG transfer. This study advances mechanistic understanding of ARG transmission in real wastewater systems, providing critical insights for optimizing sludge management to mitigate antibiotic resistance risks.},
}
@article {pmid40530826,
year = {2025},
author = {Carolak, E and Czajkowska, J and Stypułkowska, A and Waszczuk, W and Dutkiewicz, A and Grzymajlo, K},
title = {Being a better version of yourself: genetically engineered probiotic bacteria as host defense enhancers in the control of intestinal pathogens.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2519696},
doi = {10.1080/19490976.2025.2519696},
pmid = {40530826},
issn = {1949-0984},
mesh = {*Probiotics ; Humans ; *Gastrointestinal Microbiome ; Genetic Engineering ; Animals ; *Microorganisms, Genetically-Modified/genetics ; *Bacteria/genetics ; },
abstract = {Intestinal pathogens pose a significant global health burden, and traditional antibiotic treatments often disrupt the beneficial gut microbiota that plays a crucial role in maintaining host health through pathogen prevention and immune regulation. Although probiotics have emerged as promising therapeutic agents, their efficacy is limited by strain-dependent variations, survival challenges in the gastrointestinal tract, and inconsistent immune responses. Recent advances in genetic engineering, particularly CRISPR-Cas systems and their combinations with complementary technologies, such as Cre-lox and RecE/T, have enabled the precise modification of probiotic strains to enhance their therapeutic potential. These enhanced probiotics demonstrate improved functionality through multiple mechanisms, including increased adhesion via the expression of specific proteins (InlA, FnBPA, and LAP), targeted antimicrobial activity through engineered sensing systems (Lactococcus lactis detecting Vibrio cholerae CAI-1), and enhanced immunomodulation through cytokine production. Results have demonstrated the potential of genetically modified probiotics in preventing and treating gastrointestinal infections through mechanisms that include competitive exclusion, bacteriocin production, intestinal barrier reinforcement, and immune modulation. However, challenges remain in ensuring genetic stability and preventing horizontal gene transfer. Future research should focus on optimizing probiotic strains for targeted applications while addressing biosafety concerns. By understanding the complex interplay between probiotics, pathogens, and host immunity, innovative strategies can be developed to harness the full therapeutic potential of probiotic interventions in maintaining gut health.},
}
@article {pmid40529306,
year = {2025},
author = {Xu, J and Zhang, M and Yan, Y and Li, Z and Lu, X},
title = {Intestinal flora metabolites indole-3-butyric acid and disodium succinate promote IncI2 mcr-1-carrying plasmid transfer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1564810},
pmid = {40529306},
issn = {2235-2988},
mesh = {*Plasmids/genetics ; Reactive Oxygen Species/metabolism ; *Indoles/metabolism/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Escherichia coli/genetics/drug effects ; *Gene Transfer, Horizontal/drug effects ; Conjugation, Genetic/drug effects ; *Succinic Acid/metabolism ; Cell Membrane Permeability/drug effects ; Drug Resistance, Bacterial/genetics ; },
abstract = {INTRODUCTION: Plasmid-driven horizontal transfer of resistance genes in bacterial communities is a major factor in the spread of resistance worldwide. The gut microbiome, teeming with billions of microorganisms, serves as a reservoir for resistance genes. The metabolites of gut microorganisms strongly influence the physiology of their microbial community, but the role of the metabolites in the transfer of resistance genes remains unclear.<br><br>METHODS: A dual-fluorescence conjugation model was established. We assessed the effects of different concentrations of indole-3-butyric acid (IBA) and disodium succinate (DS) on plasmid transfer using conjugation assays. The growth of bacteria (donors, recipients, and transconjugants), the reactive oxygen species (ROS) levels and membrane permeability were measured under IBA and DS exposure. The plasmid copy number, and transcriptional levels of conjugation-related genes (including the related genes of the regulation of ROS production, the SOS response, cell membrane permeability, pilus generation, ATP synthesis, and the type IV secretion system (T4SS)) were evaluated by qPCR.<br><br>RESULTS: In this study, we demonstrated that IBA and DS at low concentrations, which can also be ingested through diet, enhance the interspecies transfer ratio of IncI2 mcr-1-carrying plasmid in Escherichia coli. At 20 mg/L, the transfer ratios in the presence of IBA or DS increased by 2.5- and 2.7-fold compared to that of the control, respectively. Exposure to this concentration of IBA or DS increased the production of reactive oxygen species (ROS), the SOS response, cell membrane permeability, and plasmid copy number. The transcription of genes of the related pathways and of pilus, ATP, and the T4SS was upregulated.<br><br>DISCUSSION: Our findings revealed that low-dose gut microbiota metabolites-particularly those with dietary origins-promote plasmid-mediated resistance gene dissemination through multifaceted mechanisms involving oxidative stress, SOS activation, and conjugation machinery enhancement. This highlights potential public health risks associated with microbiota metabolites, especially those utilized in food production.},
}
@article {pmid40528005,
year = {2025},
author = {Baker, BA and McCarthy, CGP and López-García, P and Leroy, RB and Susko, E and Roger, AJ and Eme, L and Moreira, D},
title = {Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40528005},
issn = {2058-5276},
support = {787904//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 101141745//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 803151//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 101141745//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 803151//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 812811//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 812811//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; },
abstract = {The episymbiotic DPANN archaea are thought to be one of the four major archaeal clades. However, the monophyly and placement of DPANN within the archaeal tree remain debated, and their fast-evolving reduced genomes render phylogenetic reconstructions challenging. Here we used 126 highly conserved protein markers, extensive taxon sampling representing the 11 known DPANN phyla and in-depth phylogenomic analyses to reassess DPANN monophyly and their relationships to other archaea. Our analyses robustly support the monophyly and placement within Euryarchaeota, and we identify the probably free-living Altiarchaeota as the earliest diverging DPANN branch. Our phylogenies suggest DPANN probably acquired several hallmark proteins through ancient horizontal gene transfer events from different bacterial donors, notably Patescibacteria and Omnitrophota, two bacterial phyla that also exhibit episymbiotic lifestyles. Overall, the monophyletic DPANN archaea probably evolved from a free-living, euryarchaeal-like ancestor, with proteins of bacterial origin playing a role in the emergence of their episymbiotic lifestyle.},
}
@article {pmid40527192,
year = {2025},
author = {Yin, Y and Xiao, K and Wang, YF and Cao, JM and Dong, JP and Zhu, D and Zhu, YG},
title = {Nanoplastics released from textile washing enrich antibiotic resistance and virulence genes in sewage sludge microbiomes.},
journal = {Environment international},
volume = {202},
number = {},
pages = {109611},
doi = {10.1016/j.envint.2025.109611},
pmid = {40527192},
issn = {1873-6750},
abstract = {The washing of synthetic textiles is a major source of microplastic pollution, contributing to the widespread presence of nanoplastics (NPs) in wastewater treatment plants (WWTPs). However, the role of laundry-released NPs in shaping microbial communities and facilitating the spread of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in sludge remains unclear. Here, we quantified the concentration and size distribution of NPs released during the washing of polyamide (PA), polypropylene (PP), and polyethylene terephthalate (PET) textiles using nanoparticle tracking analysis. Substantial NP release was observed, with concentrations ranging from 3.4 × 10[7] to 1.7 × 10[8] particles mL[-1], and sizes between 130 and 240 nm. We then evaluated their impact on ARG and VFG profiles, as well as bacterial communities in anaerobic sludge through metagenomic and 16S rRNA gene sequencing. Laundry-released NPs significantly increased the abundance of ARGs, VFGs, and mobile genetic elements (MGEs) in sludge, with D8A-2 and Halomonas identified as potential ARG and VFG hosts. Notably, the mechanisms driving ARG enrichment varied by NP type. PA-released NPs elevated reactive oxygen species levels in bacterial communities, facilitating horizontal gene transfer via MGEs, while PP- and PET-released NPs enhanced ARG enrichment through both horizontal gene transfer and shifts in bacterial community composition. These findings highlight the risks posed by laundry-released NPs accumulating in WWTPs, emphasizing the urgent need for improved wastewater management strategies to mitigate their environmental and public health impacts.},
}
@article {pmid40520376,
year = {2025},
author = {Cao, H and Shen, Y and Ma, K and Zheng, D and Xu, Y and Qiao, X},
title = {Molecular characterization of clinical non-typhoidal Salmonella isolates shows high antimicrobial resistance burden in Jiangsu, China.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1587421},
pmid = {40520376},
issn = {1664-302X},
abstract = {Non-typhoidal Salmonella (NTS) poses a significant global health burden due to its association with gastroenteritis and rising antimicrobial resistance (AMR). This study conducted a genomic analysis of 62 Salmonella isolates from outpatient cases in Jiangsu, China, to monitor the epidemiological characteristics of NTS, including genetic diversity, AMR profiles, and resistance transmission mechanisms 18 serovars and 21 sequence types (STs) were identified by whole genome sequencing, with S. enteritidis (27.42%) and S. typhimurium (19.35%) predominating. 61 resistance genes from ten different antimicrobial categories were found by genotypic AMR screening. 90.32% of isolates had β-lactam resistance genes, indicating a high frequency of extended-spectrum β-lactamases (ESBL). Serovar-dependent resistance patterns were highlighted by the most varied AMR profile (40/61 genes) found in S. typhimurium. The co-occurrence of genes for aminoglycoside resistance, sul2, and blaTEM indicated clustering driven by mobile genetic elements. A plasmid in a S. Stanley isolate harbored 12 AMR genes, which showed structural changes suggestive of horizontal gene transfer and active recombination. These findings underscore the role of plasmids in disseminating MDR and the urgent need for enhanced antimicrobial stewardship, food safety protocols, and One Health interventions to mitigate the spread of resistant Salmonella clones.},
}
@article {pmid40517254,
year = {2025},
author = {Gozashti, L and Corbett-Detig, R},
title = {Double-stranded DNA viruses may serve as vectors for horizontal transfer of intron-generating transposons.},
journal = {Mobile DNA},
volume = {16},
number = {1},
pages = {25},
pmid = {40517254},
issn = {1759-8753},
support = {R35GM128932/GM/NIGMS NIH HHS/United States ; },
abstract = {Specialized transposable elements capable of generating introns, termed introners, are one of the major drivers of intron gain in eukaryotes. Horizontal transfer of transposable elements (HTT) is thought to play an important role in shaping introner distributions. Viruses could function as vehicles of introner HTT since they often integrate into host genomes and have been implicated in widespread HTT in eukaryotes. We annotated integrated viral elements in diverse dinoflagellate genomes with active introners and queried viral elements for introner sequences. We find that 25% of viral elements contain introners. The vast majority of viral elements represent maverick-polinton-like double-stranded DNA (dsDNA) viruses in the family eupolintoviridae as well as giant dsDNA viruses. By querying a previously annotated set of eupolintoviral proviruses, we show that introners populate full-length elements with machinery required for transposition as well as viral infection. Introners in the vast majority of viral elements are younger than or similar in age to others in their host genome, suggesting that most viral elements acquired introners after integration. However, a subset of viral elements shows the opposite pattern wherein viral introners are significantly older than other introners, possibly consistent with virus-to-host horizontal transfer. Together, our results suggest that dsDNA viruses may serve as vectors for HTT of introners between individuals and species, resulting in the introduction of intron-generating transposons to new lineages.},
}
@article {pmid40069292,
year = {2025},
author = {Lang, AS and Buchan, A and Burrus, V},
title = {Interactions and evolutionary relationships among bacterial mobile genetic elements.},
journal = {Nature reviews. Microbiology},
volume = {23},
number = {7},
pages = {423-438},
pmid = {40069292},
issn = {1740-1534},
mesh = {*Interspersed Repetitive Sequences/genetics ; *Bacteria/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; },
abstract = {Mobile genetic elements (MGEs) have profound influence on the ecology and evolution of organisms, including bacteria. During the past two decades, a great number of new types of MGEs have been discovered that now seem to be prevalent in diverse bacterial lineages. With the rapid discovery of new categories of MGEs comes an array of new acronyms that present a challenge to grasp. Moreover, it is now clear that there are complex evolutionary connections and molecular interactions among MGEs, and that these entities are not discrete, independent genetic elements acting in isolation. Different types of MGEs share and exchange genes, and coresident MGEs interact with each other within cells, in both cooperative and antagonistic ways. This all greatly affects the end results that are felt by the host organism. In this Review, we strive to clarify emerging bacterial MGE terms and elements while also presenting a comprehensive overview of the current knowledge landscape regarding MGEs in bacteria, their evolutionary relationships and interactions with their host and with one another.},
}
@article {pmid40516885,
year = {2025},
author = {Cunha da Silva, G and Rossi, CC},
title = {Defense systems and mobile elements in Staphylococcus haemolyticus: a genomic view of resistance dissemination.},
journal = {Microbial pathogenesis},
volume = {206},
number = {},
pages = {107808},
doi = {10.1016/j.micpath.2025.107808},
pmid = {40516885},
issn = {1096-1208},
abstract = {Staphylococcus haemolyticus is a multidrug-resistant opportunistic pathogen and a major reservoir of antimicrobial resistance (AMR) genes within the Staphylococcaceae family. Its high genomic plasticity, frequent association with mobile genetic elements (MGEs), and prevalence in clinical settings underscore its relevance as both a threat and a conduit for resistance dissemination. In this study, we performed a comprehensive pan-genomic analysis of the S. haemolyticus defensome - including restriction-modification (RM), abortive infection (Abi), and CRISPR-Cas systems - across 692 high-quality genomes. Our results reveal a highly diverse and modular repertoire of immune systems, often organized in physical clusters and frequently associated with MGEs. We identified evidence of antagonistic interactions, with both defense and anti-defense elements encoded on plasmids and prophages. CRISPR spacer analysis showed a predominant targeting of phages, and genomes encoding CRISPR-Cas systems exhibited a lower abundance of MGEs and AMR genes, suggesting a trade-off between defense and gene acquisition. RNA-seq data from one reference strain indicate that only a fraction of the defensome is actively transcribed under standard conditions, hinting at environment-responsive regulation. Together, these findings provide new insights into the genomic strategies sustaining the persistence and adaptability of S. haemolyticus in clinical environments. The interplay between its immune systems and mobilome likely contributes not only to its evolutionary trajectory, but also to its role in the horizontal transfer of resistance determinants among pathogenic staphylococci. A deeper understanding of this immune-mobilome interface may help inform future strategies to limit the spread of resistance.},
}
@article {pmid40516407,
year = {2025},
author = {Fang, C and Liu, H and Chen, X and Lu, H and Ren, C and Hu, Z and Wang, Y and Zhang, J},
title = {Thioredoxin-mediated sulfur cycling and biogenic sulfur encapsulation synergistically enhance co-removal of nitrogen, sulfamethoxazole, and resistance genes in constructed wetlands.},
journal = {Water research},
volume = {284},
number = {},
pages = {123939},
doi = {10.1016/j.watres.2025.123939},
pmid = {40516407},
issn = {1879-2448},
abstract = {The interplay between sulfur-driven denitrification and antibiotic resistance genes (ARGs) proliferation remains unresolved in constructed wetlands (CWs), where sulfide accumulation and reactive oxygen species generation paradoxically enhance nitrogen removal while compromising microbial integrity. To resolve this conflict, this study engineered a FeS2@S° composite filler that synergized thioredoxin (Trx)-mediated sulfur cycling and biogenic sulfur (bio-S[0]) encapsulation. Upregulation of trxA/B genes (2.3-fold increase) enabled Trx to convert toxic sulfide into adhesive bio-S[0], exhibiting higher microbial adhesion that shielded functional denitrifiers like Thiomonas (84.03 % viability under SMX stress). Concurrently, sulfur vacancies (SVs) at FeS2 {210}
crystal facets generated hydroxyl radicals (•OH) and singlet oxygen ([1]O2) via vacancy-activated pathways, selectively degrading about 73.00 % of extracellular polymeric substance (EPS)-bound ARGs while suppressing horizontal gene transfer (tolC downregulation). The 6:4 FeS2@S[0] system achieved 68.66 % total nitrogen removal and 50.17 % sulfamethoxazole degradation, outperforming conventional substrates by 28.00-39.00 %, alongside a 61.24-67.31 % reduction in ARG abundance. A self-sustaining sulfur cycle recycled about 89.00 % of sulfides into bio-S[0] or FeS2, minimizing H2S emissions (0.045 mg·m[-2]·h[-1]) and maintaining electron flux. By bridging Trx-driven redox homeostasis and bio-S[0]'s physical protection, this work redefines CWs as robust systems capable of simultaneous nitrogen retention, antibiotic degradation, and ARGs suppression, establishing a transformative paradigm for sustainable wastewater treatment.},
}
@article {pmid40513520,
year = {2025},
author = {Wu, K and Yang, J and Zhang, T and Zuo, J and Lin, H and Wang, J and Zhang, A and Lei, C and Wang, H},
title = {Emergence and traceability of Salmonella enterica serotype Mbandaka harboring blaOXA-10 from chickens in China.},
journal = {Veterinary microbiology},
volume = {307},
number = {},
pages = {110593},
doi = {10.1016/j.vetmic.2025.110593},
pmid = {40513520},
issn = {1873-2542},
abstract = {Salmonella enterica serotype Mbandaka (S. Mbandaka), a multi-host adapted non-typhoidal Salmonella, has emerged as a significant public health concern in recent years. In this study, we isolated S. Mbandaka strains carrying a multidrug-resistant IncHI2A/IncHI2 plasmid from deceased chickens in China and performed whole-genome sequencing and comparative genomic analyses to investigate their global dissemination and evolutionary adaptation. The multidrug-resistant IncHI2A/IncHI2 plasmid in isolate YK35 harbored multiple antibiotic resistance genes (ARGs) including blaOXA-10, which was firstly observed in S. Mbandaka in China. It exhibited high sequence identity with IncHI2A/IncHI2 plasmids identified in other bacterial species, including S. Typhimurium, Klebsiella aerogenes, and E. coli, which suggested the cross-species dissemination of IncHI2A/IncHI2 plasmids and ARGs. Global genomic epidemiology classified S. Mbandaka strains into seven distinct clades, with the majority originating from the USA and the UK. The pan-genomic analysis indicated an open pan-genome structure, with continuous expansion of accessory genes, particularly those associated with replication, recombination, repair, and defense mechanisms, underscoring the evolutionary adaptation of S. Mbandaka to external environments. Evolutionary analysis further traced the international transmission routes of S. Mbandaka, revealing potential cross-regional spread, particularly from the USA and the UK to other countries, including China. The findings emphasize the global spread and evolutionary adaptation of S. Mbandaka, likely driven by international trade and horizontal gene transfer, including the acquisition of ARGs, which have contributed to its increasing public health risks. This study underscores the urgent need for enhanced surveillance and control measures to mitigate the spread of S. Mbandaka and its antibiotic resistance, particularly in the context of global food supply chains and international trade.},
}
@article {pmid40506592,
year = {2025},
author = {Singh, H and Pandya, S and Jasani, S and Patel, M and Kaur, T and Rustagi, S and Shreaz, S and Yadav, AN},
title = {Integrons: the hidden architects of bacterial adaptation, evolution, and the challenges of antimicrobial resistance.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {7},
pages = {90},
pmid = {40506592},
issn = {1572-9699},
mesh = {*Integrons/genetics ; *Bacteria/genetics/drug effects ; *Evolution, Molecular ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; *Adaptation, Physiological ; },
abstract = {Integrons, a diverse group of genetic elements, have emerged as key players in bacterial adaptation and evolution. These elements, commonly found in both environmental as well as clinical settings, facilitate the acquisition, exchange, and expression of integron cassettes, allowing bacteria to rapidly adapt to changing environments and acquire antibiotic resistance. This review provides an in-depth exploration of the various classes of clinical integrons, including class 1, 2, and 3, highlighting their origins, distribution, and associated mobile elements. We delve into the astonishing success of "class 1 integrons", emphasizing their ability to recognize diverse attachment sites known as "attC sites" and getting integrated within many different integron cassettes from diverse sources. Class 1 integrons are able to propagate widely among bacterial hosts due to their lack of host specificity, interaction with transposons, and broad host range plasmids. Moreover, we discuss the substantial impact of class 1 integrons in antimicrobial resistance, as they accumulate an array of resistance genes through strong positive selection. Additionally, we address the challenging issue regarding the evolution and function of integrons and integron cassettes, including the role of promoters, origins of integron cassettes, and the abundance of unknown proteins encoded within them. The future prospects of integron research are also explored, highlighting the need to understand cassette expression patterns, assess the contribution of chromosomal/superintegron arrays to host fitness, unravel the mechanisms of cassette generation, and investigate the connection between the SOS induction and horizontal gene transfer. Overall, this review underlines the significance of integrons as hidden architects driving bacterial adaptation and evolution, providing valuable insights into their ecological and evolutionary dynamics, and shaping the future direction of research in this field.},
}
@article {pmid40505955,
year = {2025},
author = {Kaneko, S and Fukushima, H and Nakahama, M and Tsuge, K and Ishii, J and Aizawa, Y and Itaya, M and Kondo, A},
title = {Versatile Methodology for Efficient Large-sized DNA Delivery between Microorganisms without in vitro purification.},
journal = {Journal of molecular biology},
volume = {},
number = {},
pages = {169289},
doi = {10.1016/j.jmb.2025.169289},
pmid = {40505955},
issn = {1089-8638},
abstract = {Purified DNA plasmids traditionally used for microbial transformation have been supplanted by extracellular plasmids released via host bacterial lysis, offering an alternative approach for DNA-plasmid delivery. Specifically, shuttle vector plasmids liberated from host Bacillus subtilis were directly employed for the transformation of chemically competent cells Escherichia coli, eliminating the need for biochemical purification. This unconventional DNA delivery technique, referred to as 'Cell Lysis Technology to provide Transformable Extra-cellular DNA; CELyTED', has been successfully adapted for the transformation of microorganism Saccharomyces cerevisiae as well. The protocol includes optimized conditions for efficient cell lysis of the donor host cells. Notably, ' CELyTED ' enables the introduction of large-sized DNA plasmids exceeding 50 kb into target microorganisms mitigating the potential adverse effects of physical shearing during the purification process. This simplicity in the delivery protocol makes it versatile for both prokaryotic and eukaryotic microorganisms, establishing a fundamental platform in the synthetic genome field. Our study demonstrates the feasibility of introducing large DNA plasmids into cells E. coli and S. cerevisiae using the lysate of donor host cells, showcasing the potential of 'CELyTED ' as a streamlined approach in genetic transformation methodologies.},
}
@article {pmid40505265,
year = {2025},
author = {Chen, M and Wang, G and Ma, B and Musat, N and Shen, P and Wei, Z and Wei, Y and Richnow, HH and Zhang, J},
title = {Deciphering the transfer of antimicrobial resistance genes in the urban water cycle from water source to reuse: a review.},
journal = {Environment international},
volume = {201},
number = {},
pages = {109584},
doi = {10.1016/j.envint.2025.109584},
pmid = {40505265},
issn = {1873-6750},
abstract = {Antimicrobial resistance genes (ARGs) threaten ecosystems and human health, impacting United Nations Sustainable Development Goal 3 (Good Health and Well-being). This review examines ARG occurrence and transfer within the urban water cycle (UWC) from drinking water source to wastewater reuse, highlighting molecular mechanisms and research gaps. Quantitative and metagenomic data reveal that UWC amplifies ARG spread, with plasmid-mediated ARGs rising from ∼ 2.23 % to ∼ 49.51 % and high-risk ARGs increasing from ∼ 0.25 % to ∼ 5.07 %, enhancing horizontal gene transfer in receiving waters. The primary sources of ARGs in UWC are wastewater treatment plants and combined sewage overflows. Multidrug-resistant Pseudomonas aeruginosa in drinking water treatment plant and multidrug-resistant fecal coliforms in wastewater treatment plants should be emphasized. These pose significant risks to both the environment and human health and underscore the urgent need for targeted monitoring and mitigation strategies within the UWC to safeguard public health and aquatic ecosystems. Future research should: (1) map ARG dynamics across the entire UWC, (2) identify hosts of high-risk ARGs and key pathogens, (3) elucidate HGT mechanisms and risk transmission, and (4) develop targeted control technologies for high-risk ARGs at critical UWC points. These insights will inform strategies to ensure water security and curb ARG proliferation in aquatic environments.},
}
@article {pmid40503823,
year = {2025},
author = {Karlsson, PA and Zhang, T and Järhult, JD and Joffré, E and Wang, H},
title = {Heterogeneity and metabolic diversity among Enterococcus species during long-term colonization.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0316024},
doi = {10.1128/spectrum.03160-24},
pmid = {40503823},
issn = {2165-0497},
abstract = {Urinary tract infections (UTIs), traditionally dominated by Gram-negative pathogens, are increasingly complicated by antimicrobial-resistant Enterococcus spp. in hospital settings, particularly during the use of indwelling catheters. This study screened urine samples from 210 catheterized intensive care unit patients at Uppsala University Hospital (June 2020-September 2021), identifying 39 unique PhenePlate™-RF types across E. faecium, E. faecalis, and E. durans. E. faecium isolates showed considerable diversity, primarily within clonal complex 17 (CC17), known for its virulence and antibiotic resistance. We identified multiple lineages and sequence types (STs), such as in patient HWP143, who had isolates from both ST80 and ST22 (an ancestral CC17 lineage). Notably, metabolic adaptations, such as increased L-arabinose metabolism, and shifts in antibiotic resistance were observed. Variations and similarities in plasmid content between individual lineages suggest horizontal gene transfer. E. faecalis isolates exhibited less diversity, but still significant metabolic variability across patients and mixed infections, as seen in patient HWP051, colonized by both ST16 (CC58) and ST287. E. durans, though less common, shared important metabolic traits with E. faecium and displayed polyclonal characteristics, highlighting its potential role in UTIs and the complexity of enterococcal infections. E. durans was sometimes misidentified, underlining the need for accurate identification methods. This research underscores the importance of understanding genetic and metabolic diversity, plasmid variations, and horizontal gene transfer (HGT) in Enterococcus spp., which influence antibiotic resistance, virulence, and ultimately, treatment outcomes.IMPORTANCEOur study, performed in Uppsala University Hospital, Sweden, uncovers novel insights into the genetic and metabolic diversity of Enterococcus species, focusing on E. faecium, E. faecalis, and E. durans. Unlike prior studies, which often have focused on single lineages, we reveal multiple clones and lineages within individual catheterized intensive care unit patients, including clones from clonal complex 17 and the emerging sequence type (ST) 192, highlighting notable metabolic adaptations and shifts in antibiotic resistance. The detection of mixed colonization with varied ST types and E. durans misidentification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry further emphasizes the challenges in Enterococcus species identification. Our findings have significant implications for understanding the complexity of Enterococcus infections, stressing the need to consider genetic and metabolic diversity to improve disease management and treatment outcomes.},
}
@article {pmid40501780,
year = {2025},
author = {Dubinkina, V and Smith, B and Zhao, C and Pino, C and Pollard, KS},
title = {Linkage of nucleotide and functional diversity varies across gut bacteria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.06.658399},
pmid = {40501780},
issn = {2692-8205},
abstract = {Understanding the forces shaping genomic diversity within bacterial species is essential for interpreting microbiome evolution, ecology, and host associations. Here, we analyze over one hundred prevalent gut bacterial species using the Unified Human Gut Genome (UHGG) collection to characterize patterns of intra-specific genomic variability. Gene content divergence scales predictably with divergence in core genome single nucleotide polymorphisms (SNPs), though there is substantial variability in evolutionary dynamics across species. Overall, accessory genes exhibit consistently faster linkage decay compared to core SNPs, highlighting the fluidity of functional repertoires within species boundaries. This signal is strongest for mobile genetic elements, which show minimal linkage to core genome SNPs. Together, our findings reveal species-specific recombination regimes in the gut microbiome, underscoring the importance of accounting for horizontal gene transfer and genome plasticity in microbiome-wide association studies and evolutionary models.},
}
@article {pmid40501577,
year = {2025},
author = {Babajanyan, SG and Garushyants, SK and Wolf, YI and Koonin, EV},
title = {Evolution of antivirus defense in prokaryotes depending on the environmental virus prevalence and virome dynamics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.27.656525},
pmid = {40501577},
issn = {2692-8205},
abstract = {UNLABELLED: Prokaryotes can acquire antivirus immunity via two fundamentally distinct types of processes: direct interaction with the virus as in CRISPR-Cas adaptive immunity systems and horizontal gene transfer (HGT) which is the main route of transmission of innate immunity systems. These routes of defense evolution are not mutually exclusive and can operate simultaneously, but empirical observations suggest that at least in some bacterial and archaeal species, one or the other route dominates the defense landscape. We hypothesized that the observed dichotomy stems from different life-history tradeoffs characteristic of these organisms. To test this hypothesis, we analyzed a mathematical model of a well-mixed prokaryote population under a stochastically changing viral prevalence. Optimization of the long-term population growth rate reveals two contrasting modes of defense evolution. In stable, predictable and fluctuating, unpredictable environments with a moderate viral prevalence, direct interaction with the virus and horizontal transfer of defense genes become the optimal routes of immunity acquisition, respectively. In the HGT-dominant mode, we observed a universal distribution of the fraction of microbes with different immune repertoires. Under very low virus prevalence, the cost of immunity exceeds the benefits such that the optimal state of a prokaryote is complete defense systems. By contrast, under very high virus prevalence, horizontal spread of defense systems dominates regardless of the stability of the virome. These findings might explain consistent but enigmatic patterns in the spread of antivirus defense systems among prokaryotes such as the ubiquity of adaptive immunity in hyperthermophiles contrasting their patchy distribution among mesophiles.<br><br>IMPORTANCE: The virus-host arms race is a major component of the evolutionary process in all organisms that drove the evolution of a broad variety of immune mechanisms. In the last few years, over 200 distinct antivirus defense systems have been discovered in prokaryotes. There are two major modes of immunity acquisition: innate immune systems spread through microbial populations via horizontal gene transfer (HGT) whereas adaptive-type immune systems acquire immunity via direct interaction with the virus. We developed a mathematical model to explore the short term evolution of prokaryotic immunity and show that in stable environments with predictable viral repertoires, adaptive-type immunity is the optimal defense strategy whereas in fluctuating environments with unpredictable virus composition, HGT dominates the immune landscape.},
}
@article {pmid40500700,
year = {2025},
author = {Salem, S and Osama, D and Abdelsalam, NA and Shata, AH and Mouftah, SF and Elhadidy, M},
title = {Comparative genomics of Acinetobacter baumannii from Egyptian healthcare settings reveals high-risk clones and resistance gene mobilization.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {803},
pmid = {40500700},
issn = {1471-2334},
mesh = {*Acinetobacter baumannii/genetics/drug effects/isolation &amp; purification/classification ; Egypt/epidemiology ; Humans ; *Acinetobacter Infections/microbiology/epidemiology ; Anti-Bacterial Agents/pharmacology ; Pilot Projects ; Microbial Sensitivity Tests ; *Drug Resistance, Multiple, Bacterial/genetics ; Genomics ; Whole Genome Sequencing ; Virulence Factors/genetics ; Genome, Bacterial ; Gene Transfer, Horizontal ; Multilocus Sequence Typing ; beta-Lactamases/genetics ; Health Facilities ; Bacterial Proteins/genetics ; },
abstract = {BACKGROUND: Acinetobacter baumannii (A. baumannii) has emerged as a major public health threat in low- and middle-income countries (LMICs), particularly in Egypt, due to its remarkable ability to acquire and transfer resistance genes, as highlighted in the WHO bacterial Priority Pathogens List 2024 classification. This pilot study aimed to characterize 18 A. baumannii isolates from Egyptian healthcare settings, focusing on clonal lineages, antibiotic resistance determinants, horizontal gene transfer potential, and the presence of virulence factors and chromosomal mutations.<br><br>METHODS: Antimicrobial susceptibility testing was performed to determine resistance profiles using minimum inhibitory concentrations. Whole-genome sequencing was used to identify &#x3b2;-lactamase, carbapenemase, and other antibiotic resistance genes (ARGs), as well as mobile genetic elements (MGEs). Clonal relationships among isolates were assessed via core genome multilocus sequence typing (cgMLST).<br><br>RESULTS: Phenotypic analysis revealed that 72% of the isolates were extensively drug-resistant (XDR), exhibiting resistance to all tested antibiotics except colistin. Clonal diversity analysis identified 11 Oxford sequence types (STs), including two novel STs (ST3309[OXF] and ST3321[OXF]), and six international clonal (IC) groups, with IC2 being the most prevalent. Additionally, eight Pasteur STs were detected, with ST570[PAS] being the most frequent. The cgMLST analysis showed that two Egyptian ST570[PAS] isolates clustered with a strain from Saudi Arabia, suggesting potential regional transmission. Genomic analysis revealed the widespread dissemination of ARGs via MGEs, particularly rep plasmids and insertion sequence elements, which contributed significantly to genomic diversity and antibiotic resistance.<br><br>CONCLUSIONS: This pilot study highlights the clonal diversity of A. baumannii in Egypt and underscores the critical role of MGEs in the spread of resistance genes. Targeted genomic surveillance and infection control are essential to curb the spread of high-risk resistant A. baumannii clones in Egyptian clinical settings.},
}
@article {pmid40500303,
year = {2025},
author = {Shang, KM and Ma, H and Elsheikha, HM and Wei, YJ and Zhao, JX and Qin, Y and Li, JM and Zhao, ZY and Zhang, XX},
title = {Comprehensive genome catalog analysis of the resistome, virulome and mobilome in the wild rodent gut microbiota.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {101},
pmid = {40500303},
issn = {2055-5008},
support = {No.32170538//the National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Genome, Bacterial ; Virulence Factors/genetics ; *Rodentia/microbiology ; *Bacteria/genetics/drug effects/classification/pathogenicity/isolation &amp; purification ; Interspersed Repetitive Sequences ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Animals, Wild/microbiology ; },
abstract = {Wild rodent's gut microbiota serves as a crucial reservoir of antibiotic resistance genes (ARGs), where antimicrobial-resistant bacteria interact with mobile genetic elements (MGEs) to facilitate horizontal gene transfer. This study analyzed 12,255 gut-derived bacterial genomes from wild rodents to characterize the distribution of ARGs and virulence factor genes (VFGs), and to identify their bacterial hosts. A total of 8119 ARGs and 7626 VFGs were identified. The most prevalent ARGs conferred resistance to elfamycin, followed by those associated with multi-class antibiotic resistance. Enterobacteriaceae, particularly Escherichia coli, harbored the highest numbers of ARGs and VFGs. A strong correlation between the presence of MGEs, ARGs, and VFGs was observed, highlighting the potential for co-selection and mobilization of resistance and virulence traits. These findings underscore the importance of expanded surveillance to monitor and mitigate the risk of transmission of resistant and potentially pathogenic bacteria from wild rodents to human and animal populations.},
}
@article {pmid40499773,
year = {2025},
author = {Ma, Y and Dong, X and Sun, Y and Li, B and Ma, H and Li, H and Zhao, X and Ran, S and Zhang, J and Ye, Y and Li, J},
title = {Diversity and Functional Roles of Viral Communities in Gene Transfer and Antibiotic Resistance in Aquaculture Waters and Microplastic Biofilms.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126636},
doi = {10.1016/j.envpol.2025.126636},
pmid = {40499773},
issn = {1873-6424},
abstract = {This study presents a comprehensive metagenomic analysis of viral communities in seawater and microplastic biofilms, uncovering their diversity, functional roles, and ecological significance. We identified 4,999 DNA and 22 RNA viral operational taxonomic units. Seawater samples exhibited greater viral diversity, while microplastic biofilms harbored specialized viral assemblages with enriched metabolic functions, particularly in carbohydrate and amino acid metabolism. Auxiliary metabolic genes were detected, suggesting viral involvement in microbial metabolism and nutrient cycling. The dominance of lytic viruses (98 and 100%) indicates a significant role in microbial regulation. Moreover, antibiotic resistance genes and virulence factors were found, highlighting microplastic biofilms as potential re2servoirs for gene transfer, raising concerns about antibiotic resistance dissemination. The detection of Klebsiella pneumoniae OmpK37 in viruses further underscores the risk of horizontal gene transfer. These findings emphasize the ecological implications of virus-host interactions in marine environments and the urgent need for continued monitoring of viral dynamics in anthropogenically influenced ecosystems.},
}
@article {pmid40498454,
year = {2025},
author = {Brezner, S and Garushyants, SK and Wolf, YI and Koonin, EV and Snir, S},
title = {Evolution of gene order in prokaryotes is driven primarily by gene gain and loss.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {24},
pages = {e2502752122},
doi = {10.1073/pnas.2502752122},
pmid = {40498454},
issn = {1091-6490},
support = {Intramural Research Program//HHS | NIH (NIH)/ ; 2021139.//US-Israel Binational Science Foundation/ ; },
mesh = {*Evolution, Molecular ; *Archaea/genetics ; *Gene Order ; Genome, Archaeal ; Genome, Bacterial ; Models, Genetic ; *Bacteria/genetics ; *Prokaryotic Cells/metabolism ; Gene Transfer, Horizontal ; *Gene Deletion ; },
abstract = {Evolution of bacterial and archaeal genomes is highly dynamic, including extensive gene gain via horizontal gene transfer (HGT) and gene loss as well as different types of genome rearrangements, such as inversions and translocations, so that gene order is not highly conserved even among closely related organisms. We sought to quantify the contributions of different genome dynamics processes to the evolution of the gene order in prokaryote genomes, relying on the recently developed, simple, stochastic model of genome rearrangement through single gene translocations ("jump" model). The jump model was completely solved analytically in our previous work and provides the exact distribution of syntenic gene block lengths (SBL) in compared genomes based on gene translocations alone. Comparing the SBL distribution predicted by the jump model with the distributions empirically observed for multiple groups of closely related bacterial and archaeal genomes, we obtained robust estimates of the genome rearrangement to gene flux (gain and loss) ratio. In most groups of bacteria and archaea, this ratio was found to be on the order of 0.1 indicating that the loss of synteny in the evolution of bacteria and archaea is driven primarily by gene gain and loss rather than by gene translocation.},
}
@article {pmid40497057,
year = {2025},
author = {Mediouni, M and Diallo, AB and Makarenkov, V},
title = {Quantifying antimicrobial resistance in food-producing animals in North America.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1542472},
pmid = {40497057},
issn = {1664-302X},
abstract = {The global misuse of antimicrobial medication has further exacerbated the problem of antimicrobial resistance (AMR), enriching the pool of genetic mechanisms previously adopted by bacteria to evade antimicrobial drugs. AMR can be either intrinsic or acquired. It can be acquired either by selective genetic modification or by horizontal gene transfer that allows microorganisms to incorporate novel genes from other organisms or environments into their genomes. To avoid an eventual antimicrobial mistreatment, the use of antimicrobials in farm animal has been recently reconsidered in many countries. We present a systematic review of the literature discussing the cases of AMR and the related restrictions applied in North American countries (including Canada, Mexico, and the USA). The Google Scholar, PubMed, Embase, Web of Science, and Cochrane databases were searched to find plausible information on antimicrobial use and resistance in food-producing animals, covering the time period from 2015 to 2024. A total of 580 articles addressing the issue of antibiotic resistance in food-producing animals in North America met our inclusion criteria. Different AMR rates, depending on the bacterium being observed, the antibiotic class being used, and the farm animal being considered, have been identified. We determined that the highest average AMR rates have been observed for pigs (60.63% on average), the medium for cattle (48.94% on average), and the lowest for poultry (28.43% on average). We also found that Cephalosporines, Penicillins, and Tetracyclines are the antibiotic classes with the highest average AMR rates (65.86%, 61.32%, and 58.82%, respectively), whereas the use of Sulfonamides and Quinolones leads to the lowest average AMR (21.59% and 28.07%, respectively). Moreover, our analysis of antibiotic-resistant bacteria shows that Streptococcus suis (S. suis) and S. auerus provide the highest average AMR rates (71.81% and 69.48%, respectively), whereas Campylobacter spp. provides the lowest one (29.75%). The highest average AMR percentage, 57.46%, was observed in Mexico, followed by Canada at 45.22%, and the USA at 42.25%, which is most probably due to the presence of various AMR control strategies, such as stewardship programs and AMR surveillance bodies, existing in Canada and the USA. Our review highlights the need for better strategies and regulations to control the spread of AMR in North America.},
}
@article {pmid40495475,
year = {2025},
author = {Wang, JY and Dunon, V and Ardevol, VN and Béguet, J and Jechalke, S and Pauwelyn, E and Lavigne, R and Smalla, K and Martin-Laurent, F and Springael, D},
title = {Dynamics of IS1071 and Its Accessory Gene Functions During Start-Up of an On-Farm Biopurification System.},
journal = {Environmental microbiology},
volume = {27},
number = {6},
pages = {e70120},
doi = {10.1111/1462-2920.70120},
pmid = {40495475},
issn = {1462-2920},
support = {222625//European Union's 7th Framework Programme (FP7) for Research and Technological Development/ ; RUN/19/001//KU Leuven/ ; C14/20/063//KU Leuven/ ; G0E8122N//the Research Foundation - Flanders (FWO) and the National Natural Science Foundation of China (NSFC)/ ; 202107650033//China Scholarship Council Fellowship/ ; },
mesh = {*DNA Transposable Elements/genetics ; *Microbiota/genetics ; *Pesticides/metabolism ; *Bacteria/genetics/metabolism/classification ; Wastewater/microbiology ; Farms ; Biodegradation, Environmental ; Betaproteobacteria/genetics/metabolism ; },
abstract = {Insertion sequences (IS) are drivers of bacterial diversification by facilitating recruitment and horizontal transfer of adaptive genes involving composite transposon structures, but their evolutionary role at the community level is rarely addressed. This study explores the dynamics of IS1071 and the cargo of IS1071-associated putative composite transposons in the establishment of a pesticide-degrading microbiome in an on-farm biopurification system (BPS)-which treats pesticide-contaminated wastewater and is considered a hotspot of microbial evolution-during the crucial start-up phase. Pesticide mineralisation assays and quantitative PCR targeting pesticide catabolic genes showed that the microbial community, upon feeding on the pesticide-contaminated wastewater, rapidly evolved into a pesticide-degrading microbiome. Concomitantly, an increase in the relative abundances of several mobile genetic elements, including IS1071, was observed, as well as a striking enrichment of xenobiotic catabolic genes in the cargo of putative IS1071-flanked composite transposons. The IS1071 cargo catabolic genes diversified over time and were mainly of Betaproteobacterial origin. Clear changes in community composition were observed both in the total bacterial community and the Betaproteobacterial community. We conclude that IS1071 supports the rapid establishment of pesticide catabolism in the BPS microbiome, highlighting the contribution of IS elements to microbial community adaptation to environmental changes.},
}
@article {pmid40494306,
year = {2025},
author = {Slot, J and Hoffmeister, D},
title = {Psychedelic fungi.},
journal = {Current biology : CB},
volume = {35},
number = {11},
pages = {R513-R518},
doi = {10.1016/j.cub.2025.02.026},
pmid = {40494306},
issn = {1879-0445},
mesh = {*Hallucinogens/metabolism ; *Fungi/metabolism/genetics ; Humans ; Psilocybin/metabolism ; Animals ; },
abstract = {Several species of fungi, collectively known as 'psychedelic fungi', produce a range of psychoactive substances, such as psilocybin, ibotenic acid, muscimol and lysergic acid amides. These substances interact with neurotransmitter receptors in the human brain to induce profound psychological effects. These substances are found across multiple fungal phyla, in the mushroom-forming genera Psilocybe, Amanita, and others, and also the ergot-producing Claviceps and insect-pathogenic Massospora. The ecological roles of these psychedelics may include deterring predators or facilitating spore dispersal. Enzymes for psychedelic compound biosynthesis are encoded in metabolic gene clusters that are sometimes dispersed by horizontal gene transfer, resulting in a patchy distribution of psychedelics among species. The (re-)emerging science of these strange substances creates new opportunities and challenges for science and humanity at large.},
}
@article {pmid40493666,
year = {2025},
author = {Gumustop, I and Genel, I and Kurt, IC and Ortakci, F},
title = {Comparative genomics of Lentilactobacillus buchneri reveals strain-level hyperdiversity and broad-spectrum CRISPR immunity against human and livestock gut phages.},
journal = {PloS one},
volume = {20},
number = {6},
pages = {e0325832},
pmid = {40493666},
issn = {1932-6203},
mesh = {Animals ; Humans ; *Bacteriophages/genetics/immunology ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Genomics ; Livestock/microbiology/virology ; Cattle ; Genome, Bacterial ; Plasmids/genetics ; Prophages/genetics ; },
abstract = {This study conducted a comparative genomic investigation of 40 strains of Lentilactobacillus buchneri isolated from various environments-including fermented foods, silage, cattle rumen, and the nasopharynx-to identify species-level diversity and assess their CRISPR immunity. An average genome size of 2.55 ± 0.07 Mb, a GC content of 44.18 ± 0.15%, and 2444 ± 83 coding sequences were identified. Prophages were found in all strains except for two, while 17 strains contained plasmids. No genes associated with bacteriocins were identified. CRISPR analysis revealed the presence of 42 Type II-A and 45 Type I-E systems, with each strain having at least one Type II-A system (~ 2 systems per strain). Among the 33 tested strains, 29 encoded complete LbCas9 proteins, consisting of 1371 amino acids. In-silico analysis of PAM in Type II-A systems revealed a 5'-DNAWDHV-3' motif, with a noted preference for 5'-AAAA-3' at positions 3-6. The spacers found in CRISPR arrays targeted proteins involved in plasmid mobilization as well as components of phage tails, indicating their roles in inhibiting horizontal gene transfer and providing defense against phages. Remarkably, 27 spacers from 24 strains were found to match phages associated with human gut microbiomes, with several showing the ability to cross-target phages from livestock, kefir, and wastewater. This research expands the genomic understanding of L. buchneri from 10 to 40 genomes, uncovering the dynamics of CRISPR-phage co-evolution. The defined PAM preferences of the identified CRISPR systems, together with the broad predicted target range of their spacers, highlight their potential for biotechnological applications-most notably targeted CRISPRization of L. buchneri strains and in-silico-guided phage control during fermentation. These findings deepen our understanding of the ecological adaptability of L. buchneri and provide a foundation for future industrial exploitation of its native CRISPR immunity.},
}
@article {pmid40353659,
year = {2025},
author = {Sobkowiak, A and Schwierzeck, V and van Almsick, V and Scherff, N and Schuler, F and Bessonov, K and Robertson, J and Harmsen, D and Mellmann, A},
title = {The dark matter of bacterial genomic surveillance-antimicrobial resistance plasmid transmissions in the hospital setting.},
journal = {Journal of clinical microbiology},
volume = {63},
number = {6},
pages = {e0012125},
doi = {10.1128/jcm.00121-25},
pmid = {40353659},
issn = {1098-660X},
support = {SEED 019/23//Interdisciplinary Center of Clinical Research, University Muenster/ ; NUM 2.0 Grant No. 01KX2121 Project: Collateral Effects of Pandemics - CollPan//German Federal Ministry of Education and Research (BMBF) Network of University Medicine 2.0/ ; },
mesh = {*Plasmids/genetics ; Humans ; Multilocus Sequence Typing ; *Drug Resistance, Multiple, Bacterial/genetics ; Whole Genome Sequencing ; Tertiary Care Centers ; Anti-Bacterial Agents/pharmacology ; *Cross Infection/microbiology/epidemiology/transmission ; *Gram-Negative Bacteria/genetics/drug effects/isolation &amp; purification ; Genome, Bacterial ; *Gram-Negative Bacterial Infections/microbiology/epidemiology/transmission ; Gene Transfer, Horizontal ; Hospitals ; Molecular Epidemiology ; Microbial Sensitivity Tests ; },
abstract = {UNLABELLED: Dissemination of antimicrobial resistance (AMR) is a growing global public health burden. The aim of this study was to characterize AMR plasmid transmissions within a tertiary care hospital and identify relevant AMR plasmid transmission pathways. During an 18-month observation period, 540 clinical gram-negative multidrug-resistant bacterial (MDRB) isolates were collected during routine hospital surveillance and subjected to Pacific Biosciences long-read whole genome sequencing. Potential clonal transmissions were determined based on core genome multilocus sequence typing (cgMLST), and plasmid transmissions were detected using a novel real-time applicable tool for plasmid transmission detection. Potential transmissions were validated using epidemiological data. Among the 471 eligible MDRB isolates, we detected 1,539 plasmids; 84.41% of these were circularized. We identified 38 potential clonal transmissions in 24 clusters based on cgMLST and 121 potential plasmid transmissions in 24 clusters containing genetically related AMR plasmids. Among the latter clusters, 10 contained different multilocus sequence types (involving 2-38 isolates, median: 3 isolates), and nine contained multiple species (2-18 isolates, median: 4). Epidemiological data confirmed 19 clonal transmissions (in seven clusters) and an additional 12 plasmid transmissions (within eight plasmid clusters). Among these, we identified seven cases of intra-host and five patient-to-patient plasmid transmissions. We demonstrate that intra-host and patient-to-patient transmissions of AMR plasmids can be identified by combining long-read sequencing with real-time applicable tools during routine molecular surveillance. In addition, our study highlights that more than a decade of bacterial genomic surveillance missed at least one-third of all AMR transmission events due to plasmids.<br><br>IMPORTANCE: Antimicrobial resistance (AMR) poses a significant threat to human health. Most AMR determinants are encoded extra-chromosomally on plasmids. Although current infection control strategies primarily focus on clonal transmission of multidrug-resistant bacteria, until today, AMR plasmid transmission routes are neither understood nor analyzed in the hospital setting. In our study, we simultaneously determined both clonal, that is, based on chromosomes, and AMR plasmid transmissions during routine molecular surveillance by combining long-read sequencing with a novel real-time applicable software tool and validated all potential transmission events with epidemiological data. Our analysis determined not only the yet unknown plasmid transmissions within healthcare facilities or within the community but also resulted, in addition to the clonal transmissions, in at least a third more transmissions due to AMR plasmids.},
}
@article {pmid40315481,
year = {2025},
author = {Ottenbrite, M and Yilmaz, G and Chan, M and Devenish, J and Kang, M and Dan, H and Lau, C and Capitani, S and Carrillo, C and Bessonov, K and Nash, J and Topp, E and Guan, J},
title = {Food-borne microbes influence conjugative transfer of antimicrobial resistance plasmids in pre-disturbed gut microbiome.},
journal = {Canadian journal of microbiology},
volume = {71},
number = {},
pages = {1-11},
doi = {10.1139/cjm-2024-0168},
pmid = {40315481},
issn = {1480-3275},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; Mice ; *Conjugation, Genetic ; *Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Salmonella typhimurium/genetics/drug effects ; *Gene Transfer, Horizontal ; Feces/microbiology ; Bacteria/genetics/drug effects ; Female ; Food Microbiology ; Streptomycin/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Drug Resistance, Bacterial ; },
abstract = {Ingestion of antibiotic-resistant bacteria following antibiotic treatments may lead to the transfer of antimicrobial resistance genes (ARGs) within a disturbed gut microbiota. However, it remains unclear whether and how microbes present in food matrices influence ARG transfer. Thus, a previously established mouse model, which demonstrated the conjugative transfer of a multi-drug resistance plasmid (pIncA/C) from Salmonella Heidelberg (donor) to Salmonella Typhimurium (recipient), was used to assess the effects of food-borne microbes derived from fresh carrots on pIncA/C transfer. Mice were pre-treated with ampicillin, streptomycin, sulfamethazine, or left untreated as a control to facilitate bacterial colonization. Contrary to previous findings where high-density colonization of the donor and recipient bacteria occurred in the absence of food-borne microbes, the presence of these microbes resulted in a low abundance of S. Typhimurium and no detection of S. Typhimurium transconjugants in the fecal samples from any of the mice. However, in mice pre-treated with streptomycin, a significant reduction in microbial species richness allowed for the significant enrichment of Enterobacteriaceae and pIncA/C transfer to bacteria from the genera Escherichia, Enterobacter, Citrobacter, and Proteus. These findings suggest that food-borne microbes may enhance ARG dissemination by influencing the population dynamics of bacterial hosts within a pre-disturbed gut microbiome.},
}
@article {pmid40492734,
year = {2025},
author = {Samadi, ZF and Hodroj, ZR and Jabbour, ZC and Hussein, HM and Kurdi, A and Shoukair, D and Bitar, RF and Chebaro, HH and Al Semaani, JMJ and Al Hajjar, MT and Zeaiter, HH and Hamadeh, L and Mahfouz, R and Noueihed, LH and Hachem, JH and Khalil, MI and El Hajj, R and Matar, GM and Abou Fayad, AG},
title = {Nationwide surveillance of carbapenem-resistant Gram-negative pathogens in the Lebanese environment.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0193224},
doi = {10.1128/aem.01932-24},
pmid = {40492734},
issn = {1098-5336},
abstract = {UNLABELLED: Gram-negative ESKAPE pathogens with carbapenem resistance pose a significant health threat. Despite extensive research on the spread of these pathogens within Lebanese hospital settings, their emergence in environmental settings remains understudied. This study aimed to explore the environmental spread of carbapenem resistance among Gram-negative bacteria isolated from environmental samples in nine districts across Lebanon. A total of 250 samples were collected from wild animals, sewage, water, and soil between June 2022 and September 2023. Samples were streaked on MacConkey agar plates supplemented with 2 mg/L meropenem. Bacterial species were identified primarily using API20E. Antimicrobial susceptibility profiles were determined by the disk diffusion method and the Vitek 2 compact system. Meropenem-resistant Gram-negative bacteria were further characterized by whole-genome sequencing, and each of the bacterial species, sequence types, resistance genes, and plasmids was detected by sequence data analysis. We successfully isolated 130 carbapenem-resistant isolates from various samples, 67 of which belonged to the ESKAPE pathogens list and showed a multidrug-resistant (MDR) profile. The distribution of the latter was as follows: Escherichia coli (65.67%), Acinetobacter baumannii (16.42%), Pseudomonas aeruginosa (11.94%), and Klebsiella pneumoniae (5.97%). Several carbapenem resistance genes were detected, with a prevalence of blaNDM-5 in Escherichia coli and Klebsiella pneumoniae, blaIMP-1 and mexAB-OprM efflux pumps in Pseudomonas aeruginosa, and blaOXA-23 in Acinetobacter baumannii. Our findings revealed a widespread distribution of carbapenem-resistant ESKAPE bacteria in Lebanon, underscoring the significant public health risk posed by these pathogens. This highlights the urgent need to address the dissemination of antibiotic resistance in Lebanese environmental settings.<br><br>IMPORTANCE: The emergence of antimicrobial resistance (AMR) extremely burdens public health and increases morbid and mortal threats in Lebanon. While the majority of the studies in our country target antimicrobial resistance in clinical settings, fewer studies focus on antimicrobial resistance dissemination in the environment. The significance of our research is that it sheds light on the environment as a less explored yet equally crucial sector in the spread of AMR. Here, we isolated carbapenemase-producing bacteria (Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii) that were categorized as multidrug resistant (MDR) from diverse environmental sources in multiple provinces across Lebanon. The finding of carbapenem-resistant bacteria carrying plasmids represents a potential risk due to the possible spread of resistance genes via horizontal gene transfer across the environment and hospital settings. This highly recommends the implementation of regular surveillance to monitor the spread of antimicrobial resistance among environmental bacteria, which consequently leads to its spread within communities and thus poses a great threat to human health.},
}
@article {pmid40492084,
year = {2025},
author = {Vezina, B and Morampalli, BR and Nguyen, HA and Gomez-Simmonds, A and Peleg, AY and Macesic, N},
title = {The rise and global spread of IMP carbapenemases (1996-2023): a genomic epidemiology study.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.25.25328332},
pmid = {40492084},
abstract = {BACKGROUND: IMP carbapenemases confer extensive drug resistance and are increasingly noted worldwide. Despite this, little is known regarding the global epidemiology of IMP carbapenemases.<br><br>METHODS: We comprehensively identified bla IMP genes in all publicly available bacterial genomes, then systematically analysed the distribution of variants across species, lineages, plasmids and mobile elements, examining patterns over time, across geographic regions and by source. Structural analysis of IMP variants was performed.<br><br>FINDINGS: 4,556 bla IMP -containing genomes were identified from 1996-2023, including 52 bla IMP variants across 93 bacterial species. Key variants (bla IMP-1 , bla IMP-4 , bla IMP-7 , bla IMP-8 and bla IMP-13) achieved global endemicity, while bla IMP-26 and bla IMP-27 were regionally endemic in Southeast Asia and North America, respectively. bla IMP dissemination was driven by horizontal gene transfer, facilitating inter-species spread. Proliferation of multidrug-resistant Enterobacter hormaechei , Pseudomonas aeruginosa and Klebsiella pneumoniae lineages led to local outbreaks. Dereplication removed 3,175/4,556 (69.9%) genomes, indicating that most bla IMP -containing genomes were highly related. bla IMP variants were associated with mobile genetic element combinations including class 1 integrons and insertion sequences (99.7%), aiding mobilisation into &#x2265;52 plasmid clusters, predominantly IncHI2A, IncN, IncL/M and IncC. Genomes of environmental and animal origin accounted for 10.0% and 1.1% of the dataset, respectively. Evidence of cross-source transmission was limited, with most spillover occurring between genomes of human and environmental origin. Structural analysis revealed a conserved carbapenemase structure (mean lDDT 0.977), with convergent missense mutations at seven catalytically relevant sites.<br><br>INTERPRETATION: Global analysis enabled us to historically reconstruct the emergence and variant-specific epidemiologies of bla IMP carbapenemase genes. Intersecting mobile elements enabled bla IMP genes to spread across multiple plasmids and bacterial genera, facilitating global and multi-source spread within a One Health framework. Additionally, convergent evolutionary patterns indicate that IMP variants may continue evolving, potentially evading novel beta-lactam antimicrobial agents.<br><br>FUNDING: NHMRC EL1 (APP1176324) to N.M.; NHMRC PF (APP1117940) to A.Y.P.; NIH/NIAID R01AI175414 to A.G-S.<br><br>RESEARCH IN CONTEXT PANEL: Evidence before this study: Despite being a major cause of carbapenem resistance in Gram negative infections, little is known about the global epidemiology of IMP carbapenemases. IMP carbapenemases are metallo-beta-lactamases that were first identified in 1991 and have evolved into 96 different IMP variants. On May 21 2025, we searched all published reports available in PubMed using the terms "'IMP' and 'carbapenemase' genomics NOT (Review[Publication Type]) NOT (Case Reports[Publication Type]) NOT PCR" with no language restrictions and no publication date restrictions. We identified 223 articles, 62 and 121 of which reported single species or a single study centre/country, respectively. Only 6 articles employed genomics to examine multi-species and multi-geographical isolates, though this was in the context of carbapenem resistance more broadly rather than IMP carbapenemases specifically. The most relevant study included 38 globally distributed genomes across four species and tracked seven blaIMP variants across mobile genetic elements.Added value of this study: To our knowledge, this global characterisation provides the most comprehensive account of bla IMP carbapenemase gene epidemiology. To analyse the global distribution and diversity of bla IMP genes, we compiled all available public genome data resulting in a dataset of 4,646 genomes. This has allowed us to identify local, regional and international spread of bla IMP variants and determine the contributions of clonal expansion, plasmid proliferation and co-localised mobile genetic elements. We demonstrated that key bla IMP variants display global (IMP-1, IMP-4, IMP-7, IMP-8 and IMP-13) and regional (IMP-26 within Southeast Asia and IMP-27 within North America) endemicity and that these patterns have been previously unacknowledged, reframing the previous understanding that IMP carbapenemases were largely confined to the Asia-Pacific region. Our observation of convergent evolutionary patterns raise concern that IMP variants may continue to evolve, potentially evading new &#x3b2;-lactam antimicrobials. This analysis has revealed the under-recognised contribution IMP carbapenemases make to global carbapenem resistance. Implications of all the available evidence: These findings provide the first comprehensive atlas of bla IMP carbapenemase gene dissemination and underscore the silent global spread of IMP carbapenemases. We note the critical need for enhanced surveillance systems, particularly in low- and middle-income countries, that can detect complex plasmid-mediated and mobile genetic element-associated spread, as we noted with bla IMP carbapenemase genes. Moreover, our analyses show that systematic sampling across human, animal, and environmental reservoirs is crucial to address the One Health dimensions of emerging antimicrobial resistance threats. The study provides a framework for future interventions aimed at tracking and stopping the spread of IMP carbapenemases and calls for co-ordinated, real-time public health responses to this growing challenge.},
}
@article {pmid40490413,
year = {2025},
author = {Gang, D and Li, Z and Yu, H and Hu, C and Qu, J},
title = {PFAS Stress on Functional Expression of Periphyton Communities and Trade-off Strategies for Horizontal/Vertical Transfer of Resistance Genes.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c02692},
pmid = {40490413},
issn = {1520-5851},
abstract = {The dissemination of antibiotic resistance genes (ARGs) induced by perfluoroalkyl and polyfluoroalkyl substances (PFAS) and their ecological impacts have gained significant attention. Periphyton communities on sediments play crucial hydroecological roles and serve as bioindicators of PFAS contamination. However, research on their microbial structure and ARG dissemination in response to PFAS remains limited. This study explored how PFAS stress influences periphyton communities' ecological functions and ARGs dynamics. PFAS varying exposure inhibited communities' formation by decreasing biomass (3.0-26.2%) and significantly reducing protein and polysaccharides (p < 0.05) of periphyton communities. Methanogenic archaea abundance increased by 4.79-159290 times, while Variovorax and Nitrospira decreased by 1266.1-2303.5 and 36.1-140.4 times, respectively. Notably, PFAS enhanced ARGs families (multidrug, aminoglycoside, and glycopeptide) and subtypes (macB, evgS, tetA58, and bcrA), strengthening correlations between the mobile genetic elements (MGEs) and antibiotic efflux (R[2] = 0.941) or target alteration (R[2] = 0.961). Horizontal gene transfer (HGT) mediated by MGEs played a dominant role in ARGs dissemination compared to vertical gene transfer in periphyton communities. Mechanistic insights revealed that PFAS-induced reactive oxygen species elevation, increased membrane permeability, enhanced energy provision, and overexpression of adherent molecular genes collectively facilitated HGT-driven ARGs spread. This study provides new insights into the complex interactions between PFAS and ARGs and its potential risks in microbial habitats.},
}
@article {pmid40488491,
year = {2025},
author = {Franco, MEE and Nickerson, MN and Bowen, BP and Louie, K and Northen, TR and U'Ren, JM},
title = {Hyperdiverse, bioactive, and interaction-specific metabolites produced only in co-culture suggest diverse competitors may fuel secondary metabolism of xylarialean fungi.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0046825},
doi = {10.1128/msystems.00468-25},
pmid = {40488491},
issn = {2379-5077},
abstract = {Xylariales is one of the largest and most ecologically diverse fungal orders that is well-known for its chemical diversity. Enhanced secondary metabolism of Xylariales taxa is associated with increased gene duplication and horizontal gene transfer (HGT) of biosynthetic gene clusters (BGCs), especially in generalist taxa with both greater saprotrophic abilities and broader host ranges as foliar endophytic symbionts. Thus, one hypothesis for BGC diversification among more generalist fungi is that diverse competitive interactions-in both their free-living and symbiotic life stages with many hosts-may exert selective pressure for HGT and a diverse metabolic repertoire. Here, we used untargeted metabolomics to examine how competition (pairwise co-cultures) between seven xylarialean fungi influenced their metabolite production. Of the >9,000 total features detected, 6,115 and 2,071 were over-represented in co-cultures vs monocultures, respectively. For each strain, each additional co-culture interaction resulted in an 11- to 14-fold increase in metabolite richness compared to monocultures, reflecting the limited amount of metabolite overlap among different co-culture combinations. Phylogenetic relatedness and BGC content did not impact the diversity of metabolites produced in co-culture; however, co-cultures between more ecologically distinct fungi elicited the strongest metabolic response. Overall, the diversity, specificity, and putative bioactivity of metabolites over-represented in co-culture support the role of widespread and diverse competitive fungal interactions to drive xylarialean metabolic diversification. Additionally, as fungal-produced plant hormones were only detected in co-culture, our results reveal the potential for in planta interactions among fungal endophytes to influence the host plant.IMPORTANCESaprotrophic and endophytic xylarialean fungi are among the most prolific producers of bioactive secondary metabolites, with numerous industrial uses as antibiotics, pharmaceuticals, and insecticidal toxins. Fungal secondary metabolites are typically encoded in biosynthetic gene clusters (sets of physically clustered genes), but the products of most clusters are unknown as the genes are not active in typical culture conditions. Co-cultures can help to "turn on" fungal secondary metabolite production, yet factors that can influence co-culture outcomes are largely unknown. Here, we used untargeted metabolomics to assess how differences in genomic content, ecology, and phylogenetic relatedness among seven diverse xylarialean fungal strains impact metabolic production in co-culture. As expected, co-culturing significantly increased metabolite diversity, as well as the abundance of putatively bioactive metabolites. Each new pairwise combination produced different metabolites, indicative of strain-specific responses to competitors. This new information will enable further characterization of the immense biotechnological potential of xylarialean fungi.},
}
@article {pmid40485081,
year = {2025},
author = {Tran, V and Langschied, F and Muelbaier, H and Dosch, J and Arthen, F and Balint, M and Ebersberger, I},
title = {Feature architecture-aware ortholog search with fDOG reveals the distribution of plant cell wall-degrading enzymes across life.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf120},
pmid = {40485081},
issn = {1537-1719},
abstract = {The decomposition of plant material is a key driver of the global carbon cycle, traditionally attributed to fungi and bacteria. However, some invertebrates also possess orthologs to bacterial or fungal cellulolytic enzymes, likely acquired via horizontal gene transfer. This reticulated mode of evolution necessitates ortholog searches in large taxon sets to comprehensively map the repertoire of plant cell wall degrading enzymes (PCDs) across the tree of life, a task surpassing capacities of current software. Here, we use fDOG, a novel profile-based ortholog search tool to trace 235 potential PCDs across more than 18,000 taxa. fDOG allows to start the ortholog search from a single protein sequence as a seed, it performs on par with state-of-the-art software that require the comparison of entire proteomes, and it is unique in routinely scoring protein feature architecture differences between the seed protein and its orthologs. Visualizing the presence-absence patterns of PCD orthologs using a UMAP highlights taxa where recent changes in the enzyme repertoire indicate a change in lifestyle. Three invertebrates have a particularly rich set of PCD orthologs encoded in their genome. Only few of the orthologs show differing protein feature architectures relative to the seed that suggest functional modifications. Thus, the corresponding species represent lineages within the invertebrates that may contribute to the global carbon cycle. This study shows how fDOG can be used to create a multi-scale view on the taxonomic distribution of a metabolic capacity that ranges from tree of life-wide surveys to individual feature architecture changes within a species.},
}
@article {pmid40473141,
year = {2025},
author = {Luo, Y and Liao, H and Wu, L and Wu, M and Luo, Y and Yao, Y and Ji, W and Gao, L and Xia, X},
title = {Temperature adaptability drives functional diversity and horizontal gene transfer within microbial communities in Daqu solid-state fermentation.},
journal = {Bioresource technology},
volume = {433},
number = {},
pages = {132770},
doi = {10.1016/j.biortech.2025.132770},
pmid = {40473141},
issn = {1873-2976},
abstract = {The spontaneous solid-state fermentation of high-temperature Daqu (HTD) is a temperature-dependent stacking bioprocessing for enriching microbiota and enzymes to guarantee efficient substrate utilization and fermentation. However, there is a lack of clarity regarding how temperature adaptability affects HTD microbial assembly, domestication direction, and metabolic profile. Here, the flavor substances, microbial assembly, metabolic network, and horizontal gene transfer (HGT) events of three HTDs from Renshu (RS), Jiushang (JS), and Maoyuan (MY) were analyzed. 125 volatile compounds were identified, tetramethylpyrazine, 3-methyl-butanoic acid, phenylethyl alcohol, and trimethylpyrazine were clarified as the typical flavor substances. Bacillus and Kroppenstedtia were the shared dominant bacterial genera. Paecilomyces, Aspergillus, Rasamsonia, and Lichtheimia were dominant fungal genera. Differences in flavor metabolism, microbial structure, and key enzyme metabolism are strongly correlated with sample distance. As proximity decreases, the microbial structural and functional metabolic traits tend to exhibit greater similarity. The frequency of HGT events was analyzed using MetaCHIP, 49, 9 and 69 groups of HGT events occurred in RS, JS, and MY, respectively. HGT events occurred most abundantly in Bacillaceae, and the microbial taxa with a closer phylogenetic relationship possessed the highest incidence of HGT. Specifically, the occurrence of HGT was mainly associated with high-temperature adaptability. It was also linked to characteristic flavor metabolism. Our results revealed the effects of temperature stress on microbial regulation of HTD and adaptive transfer of relevant genes in stacked fermented HTDs. This work provides important insights into HTD quality classification and regulation of solid-state fermentation quality and efficiency through microbial domestication.},
}
@article {pmid40473138,
year = {2025},
author = {Wang, F and Li, Y and Zhang, L and Su, Y and Zhang, Y and Hong, S and Zhan, M and Xie, B},
title = {Biochar alleviates adverse effects of polystyrene microplastics on anaerobic digestion performance of food waste and antibiotic resistance gene propagation.},
journal = {Bioresource technology},
volume = {434},
number = {},
pages = {132771},
doi = {10.1016/j.biortech.2025.132771},
pmid = {40473138},
issn = {1873-2976},
abstract = {This study systematically evaluated the efficacy of feedstock-derived biochars (maize straw, rice husk, bamboo) in mitigating polystyrene microplastic (PSMP)-induced inhibition of food waste anaerobic digestion performance and antibiotic resistance gene (ARG) dissemination. Biochar addition increased cumulative methane production by 4.3%-8.3% and reduced total ARG absolute abundance by 35.5%-72.1%. Maize straw-derived biochar demonstrated superior mitigation capacity, attributed to its elevated specific surface area, functional group density, and electrical conductivity compared to other biochar. Mechanistically, biochar alleviated PSMP-induced inhibition of organic conversion and acid accumulation through metabolic pathway enhancement. Biochar enhanced methanogenesis by facilitating direct interspecies electron transfer and enriching diverse methanogenic archaea, thereby promoting metabolic pathway diversification. Additionally, biochar reduced ARG abundance through direct adsorption, reactive oxygen species suppression, selective inhibition of potential host bacteria, and horizontal gene transfer interference. This study confirmed that biochar addition simultaneously mitigates PSMP-induced suppression of methanogenesis and ARG propagation while elucidating the underlying mechanisms.},
}
@article {pmid40472788,
year = {2025},
author = {Lunde, TM and Tansirichaiya, S and Xue, Y and Al-Haroni, M},
title = {Evolutionary dynamics of Tn916 in Streptococcus oralis: Fitness cost and persistent metabolic shifts post-acquisition.},
journal = {Archives of oral biology},
volume = {177},
number = {},
pages = {106317},
doi = {10.1016/j.archoralbio.2025.106317},
pmid = {40472788},
issn = {1879-1506},
abstract = {OBJECTIVES: The acquisition and transfer of mobile genetic elements (MGEs) are major drivers of antibiotic resistance in bacterial populations. Despite the fitness cost associated with the acquisition of MGEs, the mechanisms underlying their persistence remain poorly understood. This study investigates the evolutionary dynamics of the integrative conjugative element (ICE) Tn916 in a naïve Streptococcus oralis host, focusing on growth rates and metabolic activity.<br><br>METHODS: We tracked the evolutionary trajectory of Tn916 in S. oralis by monitoring changes in growth rates and maximum metabolic activities over 1000 generations. Comparative analyses were conducted between Tn916-free and Tn916-carrying populations to assess fitness cost and evolutionary adaptations.<br><br>RESULTS: Following Tn916 integration, the S. oralis host exhibited a significant initial fitness cost, characterized by reduced growth rates and maximum metabolic activity. However, within 500 generations, the fitness cost was mitigated, and by 1000 generations, evolved Tn916- transconjugant populations outcompeted their unevolved counterparts. Despite the restoration of growth rates, a persistent reduction in maximum metabolic rate was observed, suggesting resource reallocation favoring growth and ICE maintenance.<br><br>CONCLUSION: The acquisition of Tn916 imposes initial fitness cost on S. oralis, but the cost is rapidly mitigated through evolution, leading to competitive advantages in the long term. However, the persistence of lower maximum metabolic rate indicates that Tn916 acquisition affects cellular functions beyond growth, underscoring the need to monitor metabolic activity to fully understand the impact of horizontal gene transfer, MGEs, and ICEs on bacterial populations.},
}
@article {pmid40471191,
year = {2025},
author = {Ramirez, P and Martinez Montoya, H and Aramayo, R and Mateos, M},
title = {Diverse toxin repertoire but limited metabolic capacities inferred from the draft genome assemblies of three Spiroplasma (Citri clade) strains associated with Drosophila.},
journal = {Microbial genomics},
volume = {11},
number = {6},
pages = {},
doi = {10.1099/mgen.0.001408},
pmid = {40471191},
issn = {2057-5858},
mesh = {Animals ; *Drosophila/microbiology ; Phylogeny ; *Spiroplasma/genetics/metabolism/classification ; *Genome, Bacterial ; *Bacterial Toxins/genetics/metabolism ; Symbiosis ; },
abstract = {Spiroplasma (class Mollicutes) is a diverse wall-less bacterial genus whose members are strictly dependent on eukaryotic hosts (mostly arthropods and plants), with which they engage in pathogenic to mutualistic interactions. Spiroplasma are generally fastidious to culture in vitro, especially those that are vertically transmitted by their hosts, which include flies in the genus Drosophila. Drosophila has been invaded by at least three independent clades of Spiroplasma: Poulsonii (the best studied, contains reproductive manipulators and defensive mutualists associated with two major clades of Drosophila and has amongst the highest substitution rates within bacteria), Citri (restricted to the repleta group of Drosophila) and Ixodetis. We report the first genome drafts of Drosophila-associated Citri clade Spiroplasma: strain sMoj from Drosophila mojavensis, strain sAld-Tx from Drosophila aldrichi from Texas (newly discovered; also associated with Drosophila mulleri) and strain sHy2 from Drosophila hydei (the only Drosophila species known to naturally also harbour a Poulsonii clade strain, thereby providing an arena for horizontal gene transfer). Compared to their Poulsonii clade counterparts, we infer that the three Citri clade strains have the following: (1) equal or worse DNA repair abilities; (b) more limited metabolic capacities, which may underlie their comparatively lower titres and transmission efficiency; and (c) similar content of toxin domains, including at least one ribosome-inactivating protein, which is implicated in the Poulsonii-conferred defence against natural enemies. As a byproduct of our phylogenomic analyses and exhaustive search for certain toxin domains in public databases, we document the toxin repertoire in close relatives of Drosophila-associated Spiroplasma, and in a very divergent newly discovered lineage (i.e. 'clade X'). Phylogenies of toxin-encoding genes or domains imply substantial exchanges between closely and distantly related strains. Surprisingly, despite encoding several toxin genes and achieving relatively high prevalences in certain natural populations (sAld-Tx in this study; sMoj in prior work), fitness assays of sMoj (this study) and sAld-Tx (prior work) in the context of wasp parasitism fail to detect a beneficial effect to their hosts. Thus, how Citri clade strains persist in their Drosophila host populations remains elusive.},
}
@article {pmid40471045,
year = {2025},
author = {Hayward, C and Whiley, H and Ashbolt, NJ},
title = {The plumbing problem: rising antimicrobial resistance in building water systems.},
journal = {Current opinion in infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1097/QCO.0000000000001119},
pmid = {40471045},
issn = {1473-6527},
abstract = {PURPOSE OF REVIEW: This review examines the interplay between biological and anthropogenic factors in the development and persistence of antimicrobial resistance (AMR) within building plumbing systems, which is of particular concern in high risk setting such as healthcare facilities. The review highlights the role of biofilms and amoeba as reservoirs for AMR and explores how engineering and design decisions, governance structures, and cleaning protocols influence microbial resistance dynamics.<br><br>RECENT FINDINGS: Biofilms provide a protective environment that facilitates horizontal gene transfer and enhances bacterial resistance to disinfection. Amoeba-hosted bacteria can evade standard cleaning practices, further promoting AMR persistence. Emerging technologies, such as digital twin modelling, offer new opportunities to optimize risk mitigation strategies. However, more consideration is needed to be given to design or management decision that may have unintended consequences, such as unintended design outcomes, such as increased biofilm growth from tap mixers and low-flow fixtures, and ineffective cleaning protocols, which can inadvertently worsen AMR.<br><br>SUMMARY: Effectively managing AMR in plumbing systems requires a multidisciplinary approach that integrates microbiology, engineering, and policy. Data driven risk assessments can identify high-risk areas that may require design changes but also can enable targeted cleaning strategies, reducing reliance on widespread disinfection that may drive resistance. Future policies must consider system-wide implications to prevent unintended consequences. By addressing both biological and anthropogenic drivers, we can develop sustainable solutions to mitigate AMR risks in healthcare and beyond.},
}
@article {pmid40468151,
year = {2025},
author = {Pourrostami Niavol, K and Bordoloi, A and McKelvey, S and Suri, RPS},
title = {How does food waste to municipal sludge ratio affect anaerobic digestion: performance evaluation and fate of antibiotic resistance genes.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {40468151},
issn = {1614-7499},
abstract = {Anaerobic co-digestion of food waste (FW) and sewage sludge (SS) has shown superior performance over anaerobic mono-digestion. However, the fate of antibiotic resistance genes (ARGs) under various co-digestion ratios has been rarely reported to date. Thus, this study investigates the effects of FW:SS ratios on the digester's performance and the fate of ARGs at different FW:SS ratios. The results demonstrated that at a 50:50 FW:SS ratio, 738 mL.g[-1] VS of biogas and 393 mL.g[-1] VS of methane were produced in the system on day 18. Response surface methodology (RSM) was also used for optimization, showing 42.5% FW is the optimal FW content for maximum biogas and minimum H2S production. The distribution of select ARGs (qnrS, tetA, emrB, blaTEM, ampR) was tracked in the liquid and solid fraction of the digestate. Results illustrated a decrease (83-99% reduction) in the overall abundance of the ARGs in the solid fraction after AD. A similar trend was observed for the ARGs in the liquid fractions (65-99% reduction), except for ermB which became 1.74-10.6-fold higher in the final digestate. Also, at 50% FW, the abundance of intl1 increased in the liquid and solid fraction of digestate, indicating increased potential of ARG dissemination via horizontal gene transfer.},
}
@article {pmid40467884,
year = {2025},
author = {Jung, G and Zin, H and Son, B and Shin, H and Kim, J},
title = {Characterization of a plasmid dependent DNA phage targeting Escherichia coli harboring a conjugative plasmid and its impact on gut microbiota.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19701},
pmid = {40467884},
issn = {2045-2322},
support = {2022R1A6A1A03055869//National Research Foundation of Korea/ ; R2024057//National Institute of Fisheries Science/ ; },
mesh = {*Escherichia coli/virology/genetics ; *Plasmids/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Phylogeny ; *Bacteriophages/genetics ; Conjugation, Genetic ; Feces/microbiology ; Gene Transfer, Horizontal ; },
abstract = {The emergence and spread of antimicrobial resistance in bacteria pose a significant global threat to public health. One of the main drivers of this spread is the horizontal transfer of antimicrobial resistance genes via conjugative plasmids. In this study, we isolated a novel phage, PDP46, which specifically targets Escherichia coli strains carrying a conjugative plasmid that encodes antibiotic resistance genes. PDP46 requires a conjugative IncF plasmid for infection, enabling it to selectively target bacterial strains capable of plasmid-mediated gene transfer. Phylogenetic analysis based on the major capsid protein revealed that PDP46 clusters with several phages that use O-antigen as a receptor. However, the tail fiber of PDP46 differs from those of the clustered phages, suggesting that the tail fiber structure of PDP46 may play a key role in its plasmid-dependent infectivity. Furthermore, to explore its therapeutic potential, we evaluated PDP46's effects on the gut microbiota using an in vitro human fecal incubation model. Our findings suggest that phage PDP46 could inhibit the growth of target bacteria harboring conjugative plasmids without disrupting overall microbial diversity. By inhibiting the growth of donor cells carrying antibiotic resistance-associated plasmids, PDP46 may serve as a targeted gut microbiota modulator.},
}
@article {pmid40467487,
year = {2025},
author = {Nakayama, T and Harada, R and Yabuki, A and Nomura, M and Shiba, K and Inaba, K and Inagaki, Y},
title = {Marked Genome Reduction Driven by a Parasitic Lifestyle: Two Complete Genomes of Endosymbiotic Bacteria Possibly Hosted by a Dinoflagellate.},
journal = {Microbes and environments},
volume = {40},
number = {2},
pages = {},
doi = {10.1264/jsme2.ME25005},
pmid = {40467487},
issn = {1347-4405},
mesh = {*Symbiosis ; Phylogeny ; *Genome, Bacterial ; *Dinoflagellida/microbiology/physiology ; *Gammaproteobacteria/genetics/classification/isolation &amp; purification/physiology ; Base Composition ; Gene Transfer, Horizontal ; Genome Size ; },
abstract = {Bacteria with endosymbiotic lifestyles often show marked genome reduction. While the shrinkage of genomes in intracellular symbionts of animals, including parasitic bacteria, has been extensively exami-ned, less is known about symbiotic bacteria associated with single-celled eukaryotes. We herein report the genomes of two novel gammaproteobacterial lineages, RS3 and XS4, identified as putative parasitic endosymbionts of the dinoflagellate Citharistes regius. Phylogenetic ana-lyses suggest that RS3 and XS4 belong to the family Fastidiosibacteraceae within the order Beggiatoales, forming independent lineages therein. The genomes of RS3 and XS4 are 529 and 436‍ ‍kbp in size, respectively, revealing marked reductions from related bacterial genomes. XS4, which has a very reduced genome with a low GC content, uses a different genetic code, in which UGA assigned tryptophan. The small genomes of RS3 and XS4 encode a limited number of proteins, retaining only approximately 20% of the predicted ancestral proteome. Metabolic reconstruction suggests that RS3 and XS4 are parasitic symbionts that are heavily dependent on their host for essential metabolites. Furthermore, we found that the ancestor of both genomes likely acquired an ADP:ATP antiporter gene via horizontal gene transfer, an event that may have enabled their evolution as energy parasites by facilitating the acquisition of ATP from their host. These results on novel bacteria with highly reduced genomes expand our understanding of the phylogenetic and genomic diversities of endosymbiotic bacteria in protists.},
}
@article {pmid40158282,
year = {2025},
author = {Feng, Y and Li, T and Zhao, S and Li, X and Zhai, Y and Yuan, L and Liu, J and Hu, G and He, D and Pan, Y},
title = {Genetic characterization and transmission of the multidrug resistance gene cfr in fecal and environmental pathways on a chicken farm in China.},
journal = {Poultry science},
volume = {104},
number = {6},
pages = {105079},
pmid = {40158282},
issn = {1525-3171},
mesh = {Animals ; China ; *Chickens ; *Drug Resistance, Multiple, Bacterial/genetics ; *Escherichia coli/genetics/drug effects ; Feces/microbiology ; Plasmids ; *Klebsiella pneumoniae/genetics/drug effects ; *Poultry Diseases/microbiology/transmission/epidemiology ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; *Bacterial Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; },
abstract = {The emergence and spread of the multidrug-resistant gene cfr have raised significant public health concerns worldwide. To investigate its prevalence and dissemination dynamics, 18 cfr-positive strains were isolated in 2021 from fecal and environmental samples. Antimicrobial susceptibility testing showed that all strains were 100 % multidrug-resistant. Conjugation experiments demonstrated that a cfr- carrying IncFII(K)-IncR-IncFIB multi-replicon plasmid could transfer to E. coli J53. S1-nuclease digestion and Southern blotting identified cfr on plasmids of varying sizes, while whole-genome sequencing confirmed its presence on multiple plasmid types: IncX4, IncN, IncFII(K)-IncR-IncFIB, IncFIB-IncFII-IncR-IncHI2-IncHI2A multi-replicon plasmids, and two plasmids of unknown types. Genetic environment analysis revealed that cfr is categorized into five distinct structures (Types I-V). Reverse PCR results showed that Types I, II, and IV can form three circular intermediates of varying lengths (cfr-IS26). Network analysis further indicated strong association between cfr, tet(M), and dfrA14 mediated by IS26. Phylogenetic analysis revealed that the four ST1140 E. coli strains and all nine K. pneumoniae strains showed minimal genetic divergence. These findings suggest both clonal and horizontal transmission of cfr within the poultry farm. Continuous monitoring of cfr in animal-related environments is essential to mitigate its potential transfer to humans.},
}
@article {pmid40466317,
year = {2025},
author = {Li, W and Zeng, J and Zheng, N and Ge, C and Li, Y and An, X and Yao, H},
title = {Astragalus polysaccharide slows the dissemination of antibiotic resistance genes and reduces the prevalence of opportunistic pathogens in the fish gut.},
journal = {Journal of environmental management},
volume = {389},
number = {},
pages = {126058},
doi = {10.1016/j.jenvman.2025.126058},
pmid = {40466317},
issn = {1095-8630},
abstract = {There is irrefutable evidence that the overuse of antibiotics in aquaculture contributes to the propagation and dissemination of antibiotic resistance genes (ARGs). In recent years, traditional Chinese medicines such as astragalus polysaccharide (APS) have been widely used as feed additives in aquaculture because of their ability to promote growth and enhance immunity and disease resistance. However, few studies have assessed whether APS exacerbates the ecological and health risk of ARG transmission. In this study, microcosm experiments were conducted with different concentrations of APS to assess the effects on the gut resistome and microbial community of a fish (Cyprinus carpio) using amplicon sequencing technology and high-throughput quantitative PCR. The results indicated that APS significantly reduced the total abundance of ARGs and mobile genetic elements (MGEs) in the gut (26.67 %-38.24 %). APS exposure led to a decrease in the abundance of Chlamydiae and opportunistic pathogens of the genus Aeromonas (41.54 %-87.86 %) in the gut. Network analysis revealed that Aeromonas is a potential host for most ARGs and MGEs, which exhibited similar trends in abundance changes. Functional analysis via PICRUSt2 indicated that APS markedly downregulated pathway activity related to drug resistance: antimicrobial, infectious diseases: bacterial and biofilm formation. The structural equation model based on partial least-squares path model indicated that the bacterial community, MGEs, and functional modules collectively determined the composition and distribution of gut ARGs under APS exposure. In summary, our study evaluated the health risks of the use of APS as a feed supplement, ensuring its appropriate use and sustainable aquaculture practices.},
}
@article {pmid40465274,
year = {2025},
author = {Hassen, B and Hammami, S},
title = {Environmental Phages: Ecosystem Dynamics, Biotechnological Applications and their limits, and Future Directions.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf136},
pmid = {40465274},
issn = {1365-2672},
abstract = {Phages, the most abundant biological entities on Earth, play a crucial role in various microbial ecosystems, significantly impacting biogeochemical cycles and bacterial evolution. They inhabit diverse environments, including soil, water, and extreme conditions, where they contribute to the contribute to regulating microbial populations, facilitate genetic exchange and aid in nutrient cycling. Recent research has highlighted their potential in addressing antibiotic resistance, enhancing wastewater treatment, promoting agricultural sustainability, and tackling environmental issues. However, their ability to disseminate antibiotic resistance genes through horizontal gene transfer raises important concerns, warranting a thorough assessment of their ecological and biotechnological applications. This review synthesizes current knowledge on the diversity, ecological roles, and practical uses of environmental phages, emphasizing both their benefits and limitations. By analyzing recent findings and real-world applications, it provides insights into the challenges encountered and future directions for leveraging phages in environmental management, biotechnology, and healthcare.},
}
@article {pmid40462285,
year = {2025},
author = {Ding, P and Lu, J and Lei, T and Guo, Y and Zhu, B and Zhao, Y and Wang, Y and Engelstädter, J and Schembri, MA and Guo, J},
title = {Antidepressant drugs promote the spread of broad-host-range plasmid in mouse and human gut microbiota.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2514138},
doi = {10.1080/19490976.2025.2514138},
pmid = {40462285},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; Humans ; Mice ; *Plasmids/genetics ; *Antidepressive Agents/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Gene Transfer, Horizontal/drug effects ; RNA, Ribosomal, 16S/genetics ; Duloxetine Hydrochloride/pharmacology ; Drug Resistance, Bacterial/genetics ; Male ; Mice, Inbred C57BL ; },
abstract = {Antibiotic resistance is a global public health challenge. The gut microbiota serves as a reservoir for antibiotic resistance genes (ARGs), facilitating their transfer between bacteria. With the rising incidence of major depressive disorders (MDD), antidepressant prescriptions have surged. Previous pure-culture studies suggest that antidepressants exhibit antibiotic-like side effects, but their impact on gene transfer in microbial communities remains unclear. Here, we report that clinically relevant doses of antidepressants duloxetine and sertraline enhance the transfer of a broad-host range conjugative plasmid across bacterial phyla from mice gut microbiota. Tests in human gut simulators confirmed that duloxetine facilitates plasmid transfer in human gut microbiota. Mechanistic analyses revealed that antidepressants increase reactive oxygen species levels and alter bacterial cell membrane permeability. Using fluorescence-activated cell sorting and 16S rRNA gene sequencing, we discovered that antidepressants alter plasmid transfer patterns at both phylum and genus levels, driving ARG exchange among opportunistic pathogens. Our findings suggest that antidepressant use may promote the spread of antibiotic resistance between commensal and pathogenic bacteria, raising important public health concerns.},
}
@article {pmid40458482,
year = {2025},
author = {Islam, MS and Polash, MA and Haque, MH},
title = {First Molecular Characterization and Antibiogram of Bacteria Isolated From Dairy Farm Wastewater in Bangladesh.},
journal = {Veterinary medicine international},
volume = {2025},
number = {},
pages = {7253393},
pmid = {40458482},
issn = {2090-8113},
abstract = {This pioneering study in Bangladesh combines phenotypic and genotypic approaches to characterize antibiotic-resistant bacteria in dairy farm wastewater, addressing a critical gap in regional antimicrobial resistance (AMR) research. Dairy farming is integral to global food production, yet the wastewater generated by these operations is a significant source of environmental and public health concerns, particularly in the context of antibiotic resistance. This study aimed to isolate and identify antibiotic-resistant bacteria from dairy farm wastewater and evaluate their antibiogram profiles to inform effective management strategies. A total of 60 wastewater samples were collected and subjected to conventional bacterial characterization, followed by molecular detection via PCR and 16S rRNA gene sequencing. The study identified Pseudomonas aeruginosa (35%), Escherichia coli (30%), Bacillus subtilis (16.67%), and Acinetobacter junii (8.33%) as the predominant bacterial species. Sequencing results demonstrated high compatibility with reference sequences, confirming the identities of the isolates. Antibiogram analysis revealed significant resistance patterns: P. aeruginosa exhibited the highest resistance to penicillin (85.71%) and amoxicillin (76.19%), while demonstrating greater sensitivity to ciprofloxacin and cotrimoxazole. E. coli showed notable resistance to penicillin (88.89%), amoxicillin, and ceftriaxone, while B. subtilis and A. junii also demonstrated high levels of resistance to multiple antibiotics. Notably, a substantial proportion of the isolates exhibited multidrug resistance (MDR), with MAR indices ranging from 0.37 to 0.75. Moreover, several antibiotic resistance genes (ARGs) including penA, bla TEM , bla CTX-M , tetA, tetB, tetC, and ermB were detected across the bacterial species, with high prevalence rates in P. aeruginosa and A. junii, suggesting the potential for horizontal gene transfer and further spread of resistance. These findings underscore the critical need for a One Health approach to mitigate the risks posed by antibiotic-resistant bacteria in dairy farm wastewater, emphasizing the critical importance of responsible antibiotic use and sustainable farming practices to protect public health and environmental integrity.},
}
@article {pmid40457174,
year = {2025},
author = {Okuno, M and Yamamoto, T and Ogura, Y},
title = {Blastn2dotplots: multiple dot-plot visualizer for genome comparisons.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {146},
pmid = {40457174},
issn = {1471-2105},
support = {24K10210//Japan Society for the Promotion of Science/ ; },
mesh = {*Software ; *Genomics/methods ; *Sequence Alignment/methods ; *Genome ; Computer Graphics ; },
abstract = {BACKGROUND: Dot-plots, along with linear comparisons, are fundamental visualization methods in genome comparisons, widely used for analyzing structural variations, repeat regions, and sequence similarities. However, existing tools often have limitations in visualization flexibility, particularly requiring the concatenation of multiple sequences into a single continuous axis. This constraint can make it difficult to apply highlights or user-defined grid lines effectively, reducing interpretability in comparative genomic analyses.<br><br>RESULTS: We developed blastn2dotplots, a Python 3-based tool that utilizes the Matplotlib library to generate customizable dot-plots from local blastn results. Unlike traditional approaches, blastn2dotplots treats each alignment as a separate subplot, allowing for independent axis labeling, adjustable spacing between plots, and enhanced visualization flexibility. Users can highlight specific regions of interest, apply custom grid lines, and tailor the display to suit different genomic analyses. This tool is particularly useful for chromosomal structure analyses, detection of horizontal gene transfer events, and visualization of repetitive elements, offering an intuitive and adaptable framework for sequence comparison.<br><br>CONCLUSIONS: By addressing key limitations of existing dot-plot visualization tools, blastn2dotplots enhances the clarity and flexibility of comparative genomic analyses. Its ability to handle multiple alignments separately while preserving independent axis control and customization options makes it a valuable resource for a wide range of genomic studies. This tool provides a novel and effective solution for researchers needing precise and adaptable visualization of sequence alignments, thereby maximizing the potential of dot-plots in bioinformatics.},
}
@article {pmid40455052,
year = {2025},
author = {Zhang, YQ and Cheng, LC and Zhao, FJ and Chen, MM and Wang, P},
title = {Chiral Pesticides Selectively Influence the Dissemination of Antibiotic Resistance Genes: An Overlooked Environmental Risk.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c13010},
pmid = {40455052},
issn = {1520-5851},
abstract = {The global spread of antibiotic resistance genes (ARGs) poses a critical threat to public health and environmental safety. Among environmental factors, the widespread use of chiral pesticides has raised ecological concerns, yet their enantioselective impacts on ARG propagation remain largely unexplored. Here, we investigate how chiral pesticides influence microbial ARG dissemination at the enantiomeric level. Using flurtamone as a model, we successfully separated and quantitatively analyzed its enantiomers (R-flurtamone and S-flurtamone) and evaluated their effects at environmentally relevant concentrations (0-80 μg/L). Remarkably, R-flurtamone significantly enhanced the horizontal transfer of ARGs, surpassing the effects of Rac-flurtamone, whereas S-flurtamone exerted a negligible influence. Mechanistic insights revealed that R-flurtamone is more easily recognized by bacterial cells and induces more cellular stress responses. Additionally, R-flurtamone induced an increase in cell membrane permeability, excessive reactive oxygen species (ROS) production, SOS responses, and boosted ATP levels, further accelerating ARG propagation. By integrating experimental findings with molecular simulations, we elucidated the enantioselective mechanisms underpinning ARG transfer. This study highlights the overlooked risks associated with racemic chiral pesticides at the enantiomeric level and provides a foundation for mitigating ARG dissemination in agricultural and environmental systems.},
}
@article {pmid40453648,
year = {2025},
author = {},
title = {Correction to 'Current state and future prospects of Horizontal Gene Transfer detection'.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {2},
pages = {lqaf078},
doi = {10.1093/nargab/lqaf078},
pmid = {40453648},
issn = {2631-9268},
mesh = {*Gene Transfer, Horizontal ; Humans ; },
abstract = {[This corrects the article DOI: 10.1093/nar/lqaf005.].},
}
@article {pmid40451789,
year = {2025},
author = {Yue, X and Yang, J and Qi, J and Gao, S and Huo, Q and Guo, X and Guo, H and Luo, J and Wang, Y and Zhao, Y and Liu, R and Wang, H and Yi, S and Fu, Y and Ji, X and Wei, Y and He, W and Guo, B},
title = {Loss of Pathogenicity and Evidence of Horizontal Gene Transfer in Colletotrichum gloeosporioides From a Medicinal Plant.},
journal = {Molecular plant pathology},
volume = {26},
number = {6},
pages = {e70098},
doi = {10.1111/mpp.70098},
pmid = {40451789},
issn = {1364-3703},
support = {GX2346//Xi'an Beilin District Science and Technology Plan Project/ ; 2018ZDXM-SF-016//Key Research and Development Plan Project of Shaanxi Province/ ; 23JHQ056//Shaanxi Institute of Basic Sciences Project/ ; 2023-JC-YB-165//Natural Science Basis Research Plan in Shaanxi Province of China/ ; },
mesh = {*Colletotrichum/pathogenicity/genetics ; *Gene Transfer, Horizontal/genetics ; *Plants, Medicinal/microbiology ; Phylogeny ; *Huperzia/microbiology ; Virulence/genetics ; },
abstract = {Colletotrichum gloeosporioides is a major agricultural pathogen of crops that has also been identified as an endophyte of the medicinal plant Huperzia serrata. Both H. serrata and C. gloeosporioides produce huperzine A, a potential treatment for Alzheimer's disease. In this study, a nonpathogenic C. gloeosporioides strain (NWUHS001) was isolated and its genome sequenced. Gene structure prediction identified 15,413 protein-coding genes and 879 noncoding RNAs. Through PHI-base database prediction, we found that NWUHS001 lacks two key pathogenicity genes CgDN3 and cap20, which may be the cause of its nonpathogenicity. Comparative genomic analysis showed that the number of genes encoding pectin lyase B (pelB), pectin lyase (pnl) and polygalacturonase (pg) in NWUHS001 was significantly lower than that in pathogenic strains during the expansion of mycelium into host tissues. This caused slow growth and incapability to penetrate host cells. In contrast, in NWUHS001, genes involved in carbon acquisition such as ribose and amino sugar metabolic pathways were enriched, indicating active metabolite exchange with the host. In addition, by comparing the genome of NWUHS001 with that of the host H. serrata, we found that polyketosynthetase (pksIII), a key gene in the host huperzine A biosynthetic pathway, may possibly have been acquired from the fungus by horizontal gene transfer (HGT). This study explained the possible genetic evolution mechanism of C. gloeosporioides from pathogenicity to nonpathogenicity, which is of value for studying the interaction between microorganisms and plants. It also provided clues to the genetic evolution of the biosynthetic pathway of huperzine A.},
}
@article {pmid40451201,
year = {2025},
author = {Spirin, S and Grishin, A and Rusinov, I and Alexeevski, A and Karyagina, A},
title = {Restriction-Modification Systems Specific toward GGATC, GATGC, and GATGG. Part 2. Functionality and Structure.},
journal = {Biochemistry. Biokhimiia},
volume = {90},
number = {4},
pages = {513-521},
doi = {10.1134/S0006297925600152},
pmid = {40451201},
issn = {1608-3040},
mesh = {*DNA Restriction-Modification Enzymes/metabolism/chemistry ; DNA Modification Methylases/metabolism/chemistry ; Substrate Specificity ; },
abstract = {The structural and functional basics of protein functionality of restriction-modification systems recognizing GGATC/GATCC, GATGC/GCATC, and GATGG/CCATC sites have been studied using bioinformatics methods. Such systems include a single restriction endonuclease and either two separate DNA methyltransferases or a single fusion DNA methyltransferase with two catalytic domains. It is known that some of these systems methylate both adenines in the recognition sites to 6-methyladenine, but the role of each of the two DNA methyltransferases remained unknown. In this work, we proved the functionality of most known systems. Based on the analysis of structures of related DNA methyltransferases, we hypothesized which of the adenines within the recognition site is modified by each of the DNA methyltransferases and suggested a possible molecular mechanism of changes in the DNA methyltransferase specificity from GATGG to GATGC during horizontal transfer of its gene.},
}
@article {pmid40451200,
year = {2025},
author = {Spirin, S and Rusinov, I and Makarikova, O and Alexeevski, A and Karyagina, A},
title = {Restriction-Modification Systems Specific toward GGATC, GATGC, and GATGG. Part 1. Evolution and Ecology.},
journal = {Biochemistry. Biokhimiia},
volume = {90},
number = {4},
pages = {502-512},
doi = {10.1134/S0006297925600115},
pmid = {40451200},
issn = {1608-3040},
mesh = {*Evolution, Molecular ; *DNA Restriction-Modification Enzymes/metabolism/genetics/chemistry ; *DNA Restriction Enzymes/metabolism/genetics/chemistry ; Phylogeny ; },
abstract = {The article presents the results of studies on the evolution of proteins from restriction-modification systems consisting of restriction endonucleases with the REase_AlwI family domain and either two DNA methyltransferases, each with the MethyltransfD12 family domain, or a single DNA methyltransferase with two domains of this family. It was found that all such systems recognized one of the three DNA sequences, namely GGATC, GATGC or GATGG. Based on the sequence similarity, restriction endonucleases of these systems could be attributed to three clades that unambiguously corresponded to the RM system specificity. The DNA methyltransferase domains of these systems were classified into two groups based on sequence similarity, with the two domains of each system belonging to different groups. Within each group, the domains were attributed to three clades according to their specificity. An evidence of multiple interspecific horizontal transfer of entire restriction-modification systems has been found, as well as the transfer of individual genes between the systems (including the transfer of one of DNA methyltransferases accompanied by changes in its specificity). Evolutionary relationships of DNA methyltransferases from the studied systems with other DNA methyltransferases, including orphan DNA methyltransferases, have been revealed.},
}
@article {pmid40445756,
year = {2025},
author = {Holt, JD and Peng, Y and Dalia, TN and Dalia, AB and Nadell, CD},
title = {Environmental DNA adsorption to chitin can promote horizontal gene transfer by natural transformation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {22},
pages = {e2420708122},
doi = {10.1073/pnas.2420708122},
pmid = {40445756},
issn = {1091-6490},
support = {826672//Simons Foundation (SF)/ ; R35GM151158//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35GM128674//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*Chitin/metabolism/chemistry ; *Gene Transfer, Horizontal ; *Vibrio cholerae/genetics/metabolism ; *DNA, Environmental/genetics/chemistry ; Adsorption ; Fimbriae, Bacterial/metabolism/genetics ; *Transformation, Bacterial ; },
abstract = {Horizontal gene transfer by natural transformation (NT) is induced in Vibrio cholerae upon attachment to chitin surfaces in the aquatic environment. Here, we show that free environmental DNA adsorbs to chitin surfaces under physiologically realistic conditions. Using live-cell imaging and a fluorescent NT reporter, we demonstrate with cellular resolution microscopy that V. cholerae utilizes chitin-bound DNA as a reservoir for genetic exchange. Additionally, we demonstrate that uptake of DNA from this chitin-bound reservoir requires the forceful retraction of competence type IV pili. These findings uncover a role for retraction force in driving pilus-dependent NT and suggest that chitin particle surfaces can act as hotspots for horizontal gene transfer.},
}
@article {pmid40444634,
year = {2025},
author = {Ellison, TJ and Ellison, CK},
title = {Improved DNA binding to a type IV minor pilin increases natural transformation.},
journal = {Nucleic acids research},
volume = {53},
number = {10},
pages = {},
pmid = {40444634},
issn = {1362-4962},
support = {R35GM150916/NH/NIH HHS/United States ; DFS6023/DRCRF/Damon Runyon Cancer Research Foundation/United States ; },
mesh = {*Acinetobacter/genetics/metabolism ; *Fimbriae Proteins/metabolism/genetics/chemistry ; Gene Transfer, Horizontal ; *Transformation, Bacterial ; *DNA, Bacterial/metabolism ; Protein Binding ; Fimbriae, Bacterial/metabolism/genetics ; DNA-Binding Proteins/metabolism ; },
abstract = {Bacteria take up environmental DNA using dynamic appendages called type IV pili (T4P) to elicit horizontal gene transfer in a process called natural transformation. Natural transformation is widespread amongst bacteria yet the parameters that enhance or limit this process across species are poorly understood. We show that the most naturally transformable species known, Acinetobacter baylyi, owes this property to uniquely high levels of DNA binding by its orphan minor pilin, FimT. Expression of A. baylyi FimT in a closely related Acinetobacter pathogen substantially improves its capacity for natural transformation, showing that the acquisition of a single gene is sufficient to increase rates of horizontal gene transfer. We show that, compared with its homologs, A. baylyi FimT contains multiple regions of positively charged residues that additively promote DNA binding efficiency. These results demonstrate the importance of T4P-DNA binding in establishing natural transformation rates and provide a basis for improving or limiting this mechanism of horizontal gene transfer in different species.},
}
@article {pmid40443099,
year = {2025},
author = {Chen, H and Qin, X and Chen, Y and Zhang, H and Feng, Y and Tan, J and Chen, X and Hu, L and Xie, J and Xie, J and Yang, Z},
title = {Chromosome-level genome assembly of Pinus massoniana provides insights into conifer adaptive evolution.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf056},
pmid = {40443099},
issn = {2047-217X},
support = {Guike AD19254004//Guangxi Science and Technology Base and Talent/ ; 2024YFD2201301-1//National Key R&amp;D Program of China/ ; No.2022YFD2201600//National Key R&amp;D Program of China/ ; 2022YFD2200602//National Key R&amp;D Program of China/ ; 2019A26//Bagui Scholar/ ; 2019AQ17//Bagui Young Scholar/ ; 32371906//National Natural Science Foundation of China/ ; 32022057//National Natural Science Foundation of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent/ ; QNTD202305//Fundamental Research Funds for the Central Universities/ ; BFUKF202413//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Pinus/genetics/metabolism ; *Genome, Plant ; *Evolution, Molecular ; *Chromosomes, Plant/genetics ; *Adaptation, Physiological/genetics ; Genomics/methods ; Phylogeny ; },
abstract = {Pinus massoniana, a conifer of significant economic and ecological value in China, is renowned for its wide adaptability and oleoresin production. We sequenced and assembled the chromosomal-level P. massoniana genome, revealing 80,366 protein-coding genes and significant gene family expansions associated with stress response and plant-pathogen interactions. Long-intron genes, which are predominantly presented in low-copy gene families, are strongly linked to the recent long terminal repeat burst in the Pinus genome. By reanalyzing population transcriptomic data, we identified genetic markers linked to oleoresin synthesis, including those within the CYP450 and TPS gene families. The results suggest that the genes of the resin terpene biosynthesis pathway can be activated in several cell types, and the oleoresin yield may depend on the rate-limiting enzymes. Using a multiomics algorithm, we identified several regulatory factors, including PmMYB4 and PmbZIP2, that interact with TPS and CYP450 genes, potentially playing a role in oleoresin production. This was further validated through molecular genetics analyses. We observed signatures of adaptive evolution in dispersed duplicates and horizontal gene transfer events that have contributed to the species adaptation. This study provides insights for further research into the evolutionary biology of conifers and lays the groundwork for genomic-assisted breeding and sustainable management of Masson pine.},
}
@article {pmid40440992,
year = {2025},
author = {Zhao, H and Zhao, HM and Wu, F and Liu, BL and Li, H and Li, YW and Cai, QY and Xiang, L and Mo, CH and Li, QX},
title = {Perfluorooctane sulfonate (PFOS) promotes transformational transfer of antibiotic resistance genes and cross-resistance between antibiotics and PFOS.},
journal = {Water research},
volume = {284},
number = {},
pages = {123868},
doi = {10.1016/j.watres.2025.123868},
pmid = {40440992},
issn = {1879-2448},
abstract = {Both per- and polyfluoroalkyl substances (PFASs) pollution and antibiotic resistance genes (ARGs) dissemination pose significant threats to global public health. PFASs and ARGs coexist in the environment, but little research was done on associations between PFASs and ARGs dissemination. This study demonstrated that perfluorooctane sulfonate (PFOS) increased ARGs transformation by 1.5-1.7-fold in Escherichia coli DH5α carrying pBR322 plasmid as a model. Moreover, pre-exposure of DH5α to PFOS increased ARGs transformation up to 7-fold. PFOS triggered up-regulation of the gene of outer membrane protein A (OmpA), enhancing cell membrane permeability and thus increasing ARGs transformation. Interestingly, the presence of ARGs decreased ompA gene expression and consequently lowered the accumulation and toxicity response of transformants to PFOS, which established cross-resistance between antibiotics and PFOS. This cross-resistance is attributed to the multifunctional role of the OmpA that acted as a major channel for ARGs entry into cells and facilitated cellular accumulation of PFOS. The OmpA-mediated cellular accumulation was also observed in structurally analogous PFASs (perfluorohexylsulfonic acid and pentadecafluorooctanoic acid), indicating a potential universality in the cross-resistance between antibiotics and PFASs. The United States, Canada and China are likely being confronted with high risks of PFOS-induced ARGs dissemination based on the global risk assessments. These findings demonstrate the overlooked eco-environmental risks associated with the interactions among PFASs, ARGs, and microorganisms, highlighting adaptability of organisms to chemical stress.},
}
@article {pmid40440354,
year = {2025},
author = {Marcarian, HQ and Sivakoses, A and Arias, AM and Ihedioha, OC and Lee, BR and Bishop, MC and Bothwell, ALM},
title = {Renal cancer cells acquire immune surface protein through trogocytosis and horizontal gene transfer.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0325043},
pmid = {40440354},
issn = {1932-6203},
mesh = {Humans ; *Kidney Neoplasms/genetics/immunology/pathology/metabolism ; *Carcinoma, Renal Cell/genetics/immunology/pathology/metabolism ; *Gene Transfer, Horizontal ; Gene Expression Regulation, Neoplastic ; Carbonic Anhydrase IX ; Tumor Microenvironment/immunology ; Leukocyte Common Antigens/metabolism/genetics ; Cell Line, Tumor ; *Membrane Proteins/metabolism/genetics ; Biomarkers, Tumor/metabolism ; },
abstract = {Trogocytosis is an underappreciated phenomenon that shapes the immune microenvironment surrounding many types of solid tumors. The consequences of membrane-bound proteins being deposited from a donor immune cell to a recipient cancer cell via trogocytosis are still unclear. Here, we report that human clear cell renal carcinoma tumors stably express the lymphoid markers CD45, CD56, CD14, and CD16. Flow cytometry performed on fresh kidney tumors revealed consistent CD45 expression on tumor cells, as well as varying levels of the other markers mentioned previously. These results were consistent with our immunofluorescent analysis, which also revealed colocalization of lymphoid markers with carbonic anhydrase 9, a standard kidney tumor marker. RNA analysis showed a significant upregulation of genes typically associated with immune cells by tumor cells. Finally, we show evidence of chromosomal DNA being transferred from immune cells to tumor cells through physical contact. This horizontal gene transfer has transcriptional consequences in the recipient tumor cell, resulting in a fusion phenotype that expresses both immune and cancer specific proteins. This work demonstrates a novel mechanism by which tumor cell protein expression is altered through the acquisition of surface membrane fragments and genomic DNA from infiltrating lymphocytes. These results alter the way in which we understand tumor-immune cell interactions and may reveal new insights into the mechanisms by which tumors develop. Additionally, further studies into trogocytosis and other mechanisms of contact-mediated cellular transfer will help push the field towards the next generation of immunotherapies and biomarkers for treating renal cell carcinoma and other cancers.},
}
@article {pmid40438350,
year = {2025},
author = {Peng, H and Fu, J},
title = {Unveiling horizontal gene transfer in the gut microbiome: bioinformatic strategies and challenges in metagenomics analysis.},
journal = {National science review},
volume = {12},
number = {6},
pages = {nwaf128},
pmid = {40438350},
issn = {2053-714X},
}
@article {pmid40436596,
year = {2025},
author = {Tan, G and Lin, K and Hu, M and Wang, Y and Li, X and Li, X and Chen, S and Zhang, Q and Zheng, Z},
title = {Uncovering the resistome and mobilome across different types of ready-to-eat fermented foods.},
journal = {Food research international (Ottawa, Ont.)},
volume = {213},
number = {},
pages = {116577},
doi = {10.1016/j.foodres.2025.116577},
pmid = {40436596},
issn = {1873-7145},
mesh = {*Fermented Foods/microbiology ; *Food Microbiology ; *Fast Foods/microbiology ; Interspersed Repetitive Sequences ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; Dairy Products/microbiology ; Vegetables/microbiology ; },
abstract = {Antimicrobial resistance in food poses a significant threat to public health, and the persistence of antibiotic resistance genes (ARGs) in ready-to-eat fermented foods (RTE-FFs) is a growing concern. However, information on the diversity, origins, and transferability of ARGs in RTE-FFs is limited. This study investigated the distribution of ARGs and mobile genetic elements (MGEs) in four types of RTE-FFs: soybean, dairy, meat, and vegetable products. Using whole metagenomic sequencing, we identified significant variations in the bacterial diversity, ARG profiles, and MGE profiles among these food types. Bean-based RTE-FFs exhibited the highest diversity of ARGs and MGEs, while dairy products showed the lowest diversity (p < 0.05). Eight types of ARGs were significantly more prevalent in bean-based foods than in the other food categories (p < 0.05). Several ARGs were highly abundant in the RTE-FFs, including aphA2, blaTEM-116, PBP1a, PBP1b, OqxA, OqxBgb, lsa(A), tet(34), and tet(58). Plasmids carried the highest number of ARGs among all MGEs, particularly those associated with beta-lactam, macrolide-lincosamide-streptogramin, tetracycline, and aminoglycoside resistance, suggesting a higher risk with plasmid-mediated transfer, especially in bean-based RTE-FFs. Metagenomic binning analysis recovered 76 high-quality metagenome-assembled genomes (MAGs), including four novel species. A total of 13 types of ARGs, encompassing 95 subtypes, were identified across the MAGs; Bacillus paranthracis, Enterococcus casseliflavus, and Enterococcus gallinarum had the most ARGs (16, 12, and 14, respectively). Dairy RTE-FFs (yogurt and cheese) contained a high abundance of Streptococcus thermophilus resistant to beta-lactams (PBP1b) and tetracycline (tetB(60)), raising concerns about ARG transfer in these food products. Bean RTE-FFs (sufu) harbored two pathogenic Acinetobacter species carrying carbapenem resistance genes (blaOXA-180, blaOXA-211, and blaOXA-230). No ARGs were found in the MGEs (prophages, insertion sequences, or transposons) within the MAGs. Overall, our results provide valuable insights into the antibiotic resistome and mobilome of various RTE-FFs to inform food production and management practices.},
}
@article {pmid40436163,
year = {2025},
author = {Gagneja, S and Capalash, N and Sharma, P},
title = {Whole genome sequence analysis of an environmental isolate Bacillus subtilis K3C: Genome plasticity and acquisition of hyaluronic acid capsule traits through horizontal multigene transfer.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {144696},
doi = {10.1016/j.ijbiomac.2025.144696},
pmid = {40436163},
issn = {1879-0003},
abstract = {B. subtilis K3C was isolated from an environmental sample. Genomic analysis revealed that the GRAS strain harbors a circular chromosome of 4,120,051 bp composed of 4361 protein coding sequences with a GC content of 43.4 %, 80 tRNA, and 3 rRNA genes. Two regions containing complete assembly of prophages encoded by 83 prophage genes were present suggesting the role of bacteriophage infection in evolutionary accumulation of strain-specific genes contributing towards strain diversification. Strong recombination, repair, transfer and competence systems were identified, suggesting their role in strain fitness and evolutionary process. Pan-genomic analysis revealed 3824 protein homologs as the bacterial core genome shared among different strains and 390 singletons in the pan-genome orthologous groups. The hyaluronic acid capsule trait in the isolate seems to be acquired through selective pressure to adapt in environmentally stressed niches. Phyloproteomic analysis showed that the acquired genes responsible for HA production were phylogenetically closer to Streptococcal clade, evidencing the role of horizontal gene transfer. The bacterial genome showed the presence of multiple HA genes translating HasB and HasC proteins suggesting gene dosage in the strain. However, no gene rearrangement events seem to have taken course as the HA genes were integrated in different contigs of the genome.},
}
@article {pmid40433443,
year = {2025},
author = {Dahal, U and Bansal, A},
title = {Unravelling Prokaryotic Codon Usage: Insights from Phylogeny, Influencing Factors and Pathogenicity.},
journal = {Current genomics},
volume = {26},
number = {2},
pages = {81-94},
pmid = {40433443},
issn = {1389-2029},
abstract = {Analyzing prokaryotic codon usage trends has become a crucial topic of study with significant ramifications for comprehending microbial genetics, classification, evolution, and the control of gene expression. This review study explores the numerous facets of prokaryotic codon usage patterns, looking at different parameters like habitat and lifestyle across broad groups of prokaryotes by emphasizing the role of codon reprogramming in adaptive strategies and its integration into systems biology. We also explored the numerous variables driving codon usage bias, including natural selection, mutation, horizontal gene transfer, codon-anticodon interaction, and genomic composition in prokaryotes through a thorough study of current literature. Furthermore, a special session on codon usage on pathogenic prokaryotes and the role of codon usage in the phylogeny of prokaryotes has been discussed. We also looked at the various software and indices that have been recently applied to prokaryotic genomes. The promising directions that lay ahead to map the future of codon usage research on prokaryotes have been emphasized. Codon usage variations across prokaryotic communities could be better understood by combining environmental, metagenomic, and system biology approaches.},
}
@article {pmid40431712,
year = {2025},
author = {Nikulina, AN and Nikulin, NA and Suzina, NE and Zimin, AA},
title = {Treatment of E. coli Infections with T4-Related Bacteriophages Belonging to Class Caudoviricetes: Selecting Phage on the Basis of Their Generalized Transduction Capability.},
journal = {Viruses},
volume = {17},
number = {5},
pages = {},
doi = {10.3390/v17050701},
pmid = {40431712},
issn = {1999-4915},
support = {&#x2116;24-64-00017//Russian Science Foundation/ ; },
mesh = {*Phage Therapy/methods ; *Escherichia coli/virology ; *Escherichia coli Infections/therapy ; *Bacteriophage T4/genetics/physiology ; *Transduction, Genetic ; Humans ; Gene Transfer, Horizontal ; *Coliphages/genetics/physiology ; Animals ; },
abstract = {The problem of the multidrug resistance of pathogenic bacteria is a serious concern, one which only becomes more pressing with every year that passes, motivating scientists to look for new therapeutic agents. In this situation, phage therapy, i.e., the use of phages to combat bacterial infections, is back in the spotlight of research interest. Bacterial viruses are highly strain-specific towards their hosts, which makes them particularly valuable for targeting pathogenic variants amidst non-pathogenic microflora, represented by such commensals of animals and humans as E. coli, S. aureus, etc. However, selecting phages for the treatment of bacterial infections is a complex task. The prospective candidates should meet a number of criteria; in particular, the selected phage must not contain potentially dangerous genes (e.g., antibiotic resistance genes, genes of toxins and virulence factors etc.)-or be capable of transferring them from their hosts. This work introduces a new approach to selecting T4-related coliphages; it allows one to identify strains which may be safer in terms of involvement in the horizontal gene transfer. The approach is based on the search for genes that reduce the frequency of genetic transduction.},
}
@article {pmid40431550,
year = {2025},
author = {Elbir, H},
title = {No Genomic Signatures Were Found in Escherichia coli Isolates from Camels With or Without Clinical Endometritis.},
journal = {Veterinary sciences},
volume = {12},
number = {5},
pages = {},
doi = {10.3390/vetsci12050457},
pmid = {40431550},
issn = {2306-7381},
abstract = {Clinical endometritis is a leading cause of infertility in she-camels. We commonly isolate E. coli from camel uteri with and without endometritis during our routine diagnosis of conception failure. From an epidemiological standpoint, it is critical to know if certain E. coli genotypes and virulence factors are specifically associated with endometritis. Thus, we aimed to compare the abundance of virulence elements and genotypes in uterine E. coli from camels with and without endometritis and understand their evolution. For this investigation, we retrieved data from the genomes of 28 E. coli isolates from humans, cats, dogs, horses, cows, and birds and 14 sequenced genomes of camel uterine E. coli isolates. We found no specific E. coli genotype or virulence factor associated with endometritis. Instead, multiple genotypes and high genomic diversity were observed. Moreover, horizontal gene transfer driven by genomic islands and plasmids contributed to the genetic diversity of the isolates, resulting in the acquisition of virulence genes, metabolic characteristics, and antibiotic resistance determinants to trimethoprim, sulfonamide, streptomycin, and tetracycline. Additionally, the phylogenetic position of the E. coli isolates from camel uteri suggests that they originated from intestinal strains. In conclusion, there was no evidence of E. coli specialization, and E. coli alone may not be able to develop endometritis, as other factors are required. Also, we elucidated the mechanism behind the diversity of the gene repertoire of E. coli isolated from camel uteri. These findings provide insight into the evolutionary origins of E. coli isolates from camel uteri.},
}
@article {pmid40431301,
year = {2025},
author = {Wang, K and Zhang, C and Munang'andu, HM and Xu, C and Cai, W and Yan, X and Tao, Z},
title = {Comparative Genomic Analysis of Two Vibrio harveyi Strains from Larimichthys crocea with Divergent Virulence Profiles.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051129},
pmid = {40431301},
issn = {2076-2607},
support = {42376108//National Natural Science Foundation of China/ ; },
abstract = {Vibrio harveyi is a significant pathogen in marine aquaculture, causing vibriosis in various marine species. This study presents a comparative genomic analysis of two V. harveyi strains, N8T11 and 45T2, which exhibit differing virulence profiles. Virulence assays revealed that N8T11 caused 92% mortality in infected fish, while 45T2 resulted in 0% mortality. Whole-genome sequencing revealed that strain N8T11 harbors five plasmids (pN8T11a, pN8T11b, pN8T11c, pN8T11d and pN8T11e) absent in 45T2, encoding genes potentially linked to virulence, such as siderophore-mediated iron acquisition and stress response mechanisms. Pan-genome analysis highlighted substantial genomic plasticity within V. harveyi, with mobile genetic elements, including plasmids and prophages, contributing to horizontal gene transfer. Conjugation experiments demonstrated that all five N8T11 plasmids can transfer to 45T2 with efficiencies up to 87%, with pN8T11b remaining stable across multiple subcultures, enabling the dissemination of virulence-associated genes. These findings suggest that plasmid-mediated gene transfer plays a role in the virulence variability observed between V. harveyi strains. This study contributes to understanding the genomic factors underlying pathogenicity in V. harveyi and provides insights for future research aimed at controlling vibriosis in aquaculture.},
}
@article {pmid40431267,
year = {2025},
author = {Duarte, MLO and Rodrigues, DLN and de Lima, GBV and Ariute, JC and Gouveia, GV and de Simoni Gouveia, JJ and Azevedo, V and Brenig, B and Guédon, E and Tavares, GC and da Costa, MM and Pereira, UP and Aburjaile, FF},
title = {In Silico Characterization of Resistance and Virulence Genes in Aeromonas jandaei Strains Isolated from Oreochromis niloticus in Brazil.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051094},
pmid = {40431267},
issn = {2076-2607},
support = {408898/2022-4//CNPq/MCTI/CT-Sa&#xfa;de n&#xba; 52/2022/ ; },
abstract = {Understanding the genetic characteristics of Aeromonas jandaei in Brazilian aquaculture is crucial for developing effective control strategies against this fish pathogen. The present study conducted a genomic analysis of Brazilian A. jandaei strains with the objective of investigating their virulence potential and resistance profiles. Four Brazilian isolates were subjected to sequencing, and comparative genomic analyses were conducted in conjunction with 48 publicly available A. jandaei genomes. The methods employed included quality assessment, de novo assembly, annotation, and analyses of antimicrobial resistance and virulence factors. The results demonstrated the presence of fluoroquinolone resistance genes within the core genome. Notably, these antibiotics are not authorized for use in aquaculture in Brazil, suggesting that their resistance determinants may originate from other selective pressures or horizontal gene transfer unrelated to aquaculture practices. The analysis identified significant virulence mechanisms, including T2SS, T3SS, and notably T6SS (vgrG3 gene), which was more prevalent in Brazilian isolates. Additionally, genes associated with motility, adhesion, and heavy metal resistance were identified. These findings highlight the enhanced adaptability of Brazilian A. jandaei strains and raise concerns about antimicrobial resistance in aquaculture, emphasizing the need for improved regulatory oversight and control strategies.},
}
@article {pmid40428151,
year = {2025},
author = {Müller, GA},
title = {The Transformation Experiment of Frederick Griffith II: Inclusion of Cellular Heredity for the Creation of Novel Microorganisms.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {12},
number = {5},
pages = {},
doi = {10.3390/bioengineering12050532},
pmid = {40428151},
issn = {2306-5354},
abstract = {So far, synthetic biology approaches for the construction of artificial microorganisms have fostered the transformation of acceptor cells with genomes from donor cells. However, this strategy seems to be limited to closely related bacterial species only, due to the need for a "fit" between donor and acceptor proteomes and structures. "Fitting" of cellular regulation of metabolite fluxes and turnover between donor and acceptor cells, i.e. cybernetic heredity, may be even more difficult to achieve. The bacterial transformation experiment design 1.0, as introduced by Frederick Griffith almost one century ago, may support integration of DNA, macromolecular, topological, cybernetic and cellular heredity: (i) attenuation of donor Pneumococci of (S) serotype fosters release of DNA, and hypothetically of non-DNA structures compatible with subsequent transfer to and transformation of acceptor Pneumococci from (R) to (S) serotype; (ii) use of intact donor cells rather than of subcellular or purified fractions may guarantee maximal diversity of the structural and cybernetic matter and information transferred; (iii) "Blending" or mixing and fusion of donor and acceptor Pneumococci may occur under accompanying transfer of metabolites and regulatory circuits. A Griffith transformation experiment design 2.0 is suggested, which may enable efficient exchange of DNA as well as non-DNA structural and cybernetic matter and information, leading to unicellular hybrid microorganisms with large morphological/metabolic phenotypic differences and major features compared to predeceding cells. The prerequisites of horizontal gene and somatic cell nuclear transfer, the molecular mechanism of transformation, the machineries for the biogenesis of bacterial cytoskeleton, micelle-like complexes and membrane landscapes are briefly reviewed on the basis of underlying conceptions, ranging from Darwin's "gemmules" to "stirps", cytoplasmic and "plasmon" inheritance, "rhizene agency", "communicology", "transdisciplinary membranology" to up to Kirschner's "facilitated variation".},
}
@article {pmid40426537,
year = {2025},
author = {Touaitia, R and Mairi, A and Ibrahim, NA and Basher, NS and Idres, T and Touati, A},
title = {Staphylococcus aureus: A Review of the Pathogenesis and Virulence Mechanisms.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/antibiotics14050470},
pmid = {40426537},
issn = {2079-6382},
support = {grant number IMSIU-DDRSP2501//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; },
abstract = {Staphylococcus aureus is a formidable human pathogen responsible for infections ranging from superficial skin lesions to life-threatening systemic diseases. This review synthesizes current knowledge on its pathogenesis, emphasizing colonization dynamics, virulence mechanisms, biofilm formation, and antibiotic resistance. By analyzing studies from PubMed, Scopus, and Web of Science, we highlight the pathogen's adaptability, driven by surface adhesins (e.g., ClfB, SasG), secreted toxins (e.g., PVL, TSST-1), and metabolic flexibility in iron acquisition and amino acid utilization. Nasal, skin, and oropharyngeal colonization are reservoirs for invasive infections, with biofilm persistence and horizontal gene transfer exacerbating antimicrobial resistance, particularly in methicillin-resistant S. aureus (MRSA). The review underscores the clinical challenges of multidrug-resistant strains, including vancomycin resistance and decolonization strategies' failure to target single anatomical sites. Key discussions address host-microbiome interactions, immune evasion tactics, and the limitations of current therapies. Future directions advocate for novel anti-virulence therapies, multi-epitope vaccines, and AI-driven diagnostics to combat evolving resistance. Strengthening global surveillance and interdisciplinary collaboration is critical to mitigating the public health burden of S. aureus.},
}
@article {pmid40426515,
year = {2025},
author = {Olanrewaju, TO and Dooley, JSG and Coleman, HM and McGonigle, C and Arnscheidt, J},
title = {Bacterivorous Ciliate Tetrahymena pyriformis Facilitates vanA Antibiotic Resistance Gene Transfer in Enterococcus faecalis.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/antibiotics14050448},
pmid = {40426515},
issn = {2079-6382},
abstract = {Background: Wastewater treatment plants (WWTPs) are hotspots for the emergence and spread of antibiotic resistance genes (ARGs). In activated sludge treatment systems, bacterivorous protozoa play a crucial role in biological processes, yet their impact on the horizontal gene transfer in Gram-positive enteric bacteria remains largely unexplored. This study investigated whether the ciliate Tetrahymena pyriformis facilitates the transfer of antibiotic resistance genes between Enterococcus faecalis strains. Methods: Conjugation assays were conducted under laboratory conditions using a vanA-carrying donor and a rifampicin-resistant recipient at an initial bacterial concentration of 10[9] CFU/mL and ciliate density of 10[5] N/mL. Results: Transconjugant numbers peaked at 2 h when experiments started with recipient bacteria harvested in the exponential growth phase, and at 24 h when bacteria were in the stationary phase. In both cases, vanA gene transfer frequency was highest at 24 h (10[-4]-10[-5] CFU/mL), and the presence of energy sources increased gene transfer frequency by one order of magnitude. Conclusions: These findings suggest that ciliate grazing may contribute to vanA gene transfer in WWTP effluents, potentially facilitating its dissemination among permissive bacteria. Given the ecological and public health risks associated with vanA gene persistence in wastewater systems, understanding protozoan-mediated gene transfer is crucial for mitigating the spread of antibiotic resistance in aquatic environments.},
}
@article {pmid40425158,
year = {2025},
author = {Chrismas, N and Bird, K and Laundon, D and Lieng, C and Hesketh-Best, P and Cunliffe, M},
title = {Adaptive traits for chitin utilization in the saprotrophic aquatic chytrid fungus Rhizoclosmatium globosum.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2047},
pages = {20250337},
doi = {10.1098/rspb.2025.0337},
pmid = {40425158},
issn = {1471-2954},
support = {//HORIZON EUROPE European Research Council/ ; //Natural Environment Research Council/ ; },
mesh = {*Chitin/metabolism ; Chitinases/metabolism/genetics ; *Chytridiomycota/genetics/physiology/metabolism/enzymology ; Genome, Fungal ; Phylogeny ; Fungal Proteins/metabolism/genetics ; },
abstract = {The Chytridiomycota (chytrids) are early diverging fungi, many of which function in ecosystems as saprotrophs; however, associated adaptive traits are poorly understood. We focused on chitin degradation, a common ecosystem function of aquatic chytrids, using the model chitinophilic Rhizoclosmatium globosum and comparison of other chytrid genomes. Zoospores are chemotactic to the chitin monomer N-acetylglucosamine and accelerate development when grown with chitin. The R. globosum secretome is dominated by different glycoside hydrolase (GH) family GH18 chitinases, with abundance matching reciprocal transcriptome mRNA sequences. Models of the secreted chitinases indicate a range of sizes and domain configurations. Along with R. globosum, the genomes of other chitinophilic chytrids also have expanded inventories of GH-encoding genes responsible for chitin processing. Several R. globosum GH18 chitinases have bacteria-like chitin-binding module domains, also present in the genomes of other chitinophilic chytrids yet absent in non-chitinophilic chytrids. Chemotaxis, increased abundance and diversity of secreted chitinases, complemented with the acquisition of novel chitin-binding capability, are probably adaptive traits that facilitate chitin saprotrophy. Our study reveals the underpinning mechanisms that have supported the niche expansion of some chytrids to utilize lucrative chitin-rich particles in aquatic ecosystems and is a demonstration of the adaptive ability of this successful fungal group.},
}
@article {pmid40422289,
year = {2025},
author = {Derriche, M and Nouvel, LX and Gaudino, M and Sagné, E and Simon, E and Robert, H and Pot, G and Meyer, G and de la Fe, C and Arfi, Y and Maillard, R and Citti, C and Baranowski, E},
title = {Bacterial conjugation in the ruminant pathogen Mycoplasma agalactiae is influenced by eukaryotic host factors.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0086825},
doi = {10.1128/aem.00868-25},
pmid = {40422289},
issn = {1098-5336},
abstract = {Horizontal gene transfer (HGT) plays a pivotal role in the evolution and adaptation of genome-reduced mycoplasmas. The conjugative properties of these organisms are key in this phenomenon but are largely understudied, particularly in vivo. In the present study, the ruminant pathogen Mycoplasma agalactiae was used as a model organism to document mycoplasma conjugation in environments of increasing complexity, from axenic to cell and organotypic culture conditions. Compared to axenic mating conditions, mycoplasma co-cultivation with goat epithelial cells or bovine precision-cut lung slices resulted in enhanced mating frequencies with high rates of M. agalactiae integrative and conjugative element (ICEA) self-dissemination. These results were conditioned by the presence of eukaryotic cells in the culture and influenced by competition between mating partners but were not limited to M. agalactiae, as similar results were observed with Mycoplasma bovis. Mycoplasma conjugation ex vivo was further characterized by analyzing mycoplasma chromosomal transfer (MCT), a newly discovered mechanism of horizontal exchange of chromosomal DNA that generates mosaic genomes. Compared to ICEA transfer, MCT was detected at lower rates under cell and organotypic culture conditions, suggesting a negative impact of these cellular environments on MCT or its progeny. Finally, mating experiments under nutrient-deprived conditions identified nucleotide stress as a potential factor influencing the modulation of mycoplasma conjugation by eukaryotic host cells. In conclusion, these results suggest that HGT in vivo is likely underestimated and provide valuable models to further study mycoplasma conjugation ex vivo.IMPORTANCEConjugation is an evolutionary shortcut that bacteria use to exchange genetic information with their neighbors. Despite the fast evolution rate of the genome-reduced mycoplasmas, their conjugative properties remain largely understudied, particularly in vivo. Here we used the ruminant pathogen Mycoplasma agalactiae to study how mycoplasmas conjugate in co-culture with host-derived cells and tissues. Interestingly, conjugation was stimulated when mycoplasmas were co-cultured with eukaryotic cells. This was documented by monitoring the self-propagation of a mobile genetic element known as integrative and conjugative element (ICE) and the exchange of chromosomal DNA leading to the formation of mosaic genomes. While ICE transfer was observed at high frequency, only a few mosaic genomes were detected in the presence of eukaryotic cells. Further data point toward nucleotide stress as a possible factor modulating mycoplasma conjugation in cellular environments. These results suggest that mycoplasma-host interactions may stimulate conjugation in vivo.},
}
@article {pmid40419976,
year = {2025},
author = {Vidal-Quist, JC and Ortego, F and Lambrecht, BN and Rombauts, S and Hernández-Crespo, P},
title = {Stage-specific transcriptomic analysis reveals insights into the development, reproduction and biological function of allergens in the European house dust mite Dermatophagoides pteronyssinus.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {527},
pmid = {40419976},
issn = {1471-2164},
support = {01M01521//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Animals ; Female ; Male ; *Allergens/genetics/metabolism ; *Gene Expression Profiling ; *Dermatophagoides pteronyssinus/genetics/growth &amp; development/physiology ; Reproduction/genetics ; *Transcriptome ; Gene Expression Regulation, Developmental ; },
abstract = {BACKGROUND: House dust mites (HDMs) such as Dermatophagoides pteronyssinus are major allergy elicitors worldwide, yet their gene expression across developmental stages remains underexplored. Herein, we report a comprehensive RNAseq analysis of larvae, nymphs, and adult males and females, mapped to a recently published high-quality genome with extended functional annotations.<br><br>RESULTS: Analysis of differentially expressed genes (DEG) revealed that female-biased expression was the most prevalent profile (16% of genes), while males exhibited the highest fold-change differences. DEG data, combined with network clustering and functional enrichment analysis, highlighted distinct genes and biological processes for each stage and sex: females showed upregulation of genes related to cell division and oogenesis, with vitellogenins among the most abundant transcripts; males exhibited increased expression of genes encoding putative seminal fluid proteins (e.g. endopeptidases, serpins, antimicrobial peptides), and those involved in reproductive regulation (e.g. testis-specific serine kinases); while juveniles displayed enhanced expression of genes related to energy metabolism and growth. Further analysis of endocrine pathways revealed non-canonic mechanisms compared to insect models, particularly in ecdysteroid and sesquiterpenoid biosynthesis and regulation. Expression patterns in genes involved in cuticle formation were also identified, reflecting their role in developmental transitions and sexual differentiation. Allergen and allergen-related gene expression showed an overall increase in feeding juveniles, as well as sex-biased expression, with Der p 27 upregulated in females. These findings provide insight into the physiological roles of allergens in digestion, immunity, and muscle formation, among other functions. Additionally, seven new horizontally transferred genes, including a DNA-repair photolyase linked to females, and novel multigene families (e.g. 119 male-specific beta-propeller proteins, 70 hypothetical cuticular proteins, 23 tetraspanin-like proteins, 5 female-associated putative odorant-binding proteins) were identified.<br><br>CONCLUSIONS: This study provides the first genome-wide transcriptomic analysis of a HDM across life stages and sexes, expanding our understanding of the molecular mechanisms underlying mite development, sexual reproduction, and allergen expression. The generated data, fully available via supplementary spreadsheet and the ORCAE online platform, provide a valuable foundation for future allergy research and the development of new mite control strategies.},
}
@article {pmid40305681,
year = {2025},
author = {Bennett, BD and Meier, DAO and Lanclos, VC and Asrari, H and Coates, JD and Thrash, JC},
title = {Polyhydroxybutyrate production by freshwater SAR11 (LD12).},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf087},
pmid = {40305681},
issn = {1751-7370},
mesh = {Phylogeny ; *Fresh Water/microbiology ; *Hydroxybutyrates/metabolism ; *Polyhydroxyalkanoates/metabolism/biosynthesis ; Escherichia coli/genetics/metabolism ; *Alphaproteobacteria/metabolism/genetics/classification ; Bacterial Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Polyhydroxybutyrates ; },
abstract = {SAR11 bacteria (order Pelagibacterales) are oligotrophs and often the most abundant bacterioplankton in aquatic environments. A subset of sequenced SAR11 genomes, predominantly in the brackish and freshwater SAR11 subclades, contain homologs of pha genes, which in other organisms confer the ability to store carbon and energy via polyhydroxyalkanoate (PHA) polymers. Here, we investigated the relevance of PHA production to SAR11 biology. Phylogenetics showed that Pha proteins occurred on a long branch and provided evidence for origin at the common ancestor of the brackish IIIa and freshwater LD12 subclades, followed by horizontal transfer within SAR11. Using the LD12 representative "Candidatus Fonsibacter ubiquis" strain LSUCC0530, we found that many LSUCC0530 cells contained a single Nile red-staining granule, confirmed that the cells produced polyhydroxybutyrate, a common form of PHA, and estimated the total polyhydroxybutyrate content in the cells. We heterologously expressed the LSUCC0530 phaCAB locus in Escherichia coli, finding it to be functional and the likely origin of the polyhydroxybutyrate. We also determined that, irrespective of changes to carbon, nitrogen, and phosphorus concentrations, a similar fraction of LSUCC0530 cells generated polyhydroxybutyrate granules and expression of the phaCAB locus remained constant. We suggest that polyhydroxybutyrate synthesis in LSUCC0530 may be constitutively active due to the slow growth dynamics and minimal regulation that characterize SAR11 bacteria. This work characterizes polymer storage in SAR11, providing new insights into the likely fitness advantage for cells harboring this metabolism.},
}
@article {pmid40417658,
year = {2025},
author = {Bhuvaragavan, S and Sruthi, K and Nivetha, R and Keerthana, CB and Marieshwari, BN and Janarthanan, S},
title = {PacBio-based de novo transcriptomics of the coconut rhinoceros beetle Oryctes rhinoceros identifies physiologically important full-length genes and sheds insights into the molecular relationship (chitin synthase) between Scarabaeidae (Coleoptera) and Hymenoptera.},
journal = {3 Biotech},
volume = {15},
number = {6},
pages = {182},
pmid = {40417658},
issn = {2190-572X},
abstract = {UNLABELLED: The sparser molecular data in non-model insects such as Oryctes rhinoceros prompted us to investigate and identify its physiologically important genes using the novel PacBio Iso-Seq Sequel II platform with single-molecule real-time (SMRT) technology. SMRT library was prepared from various tissues and sequenced. In total, 16,916,297 subreads clustered into 17,547 contigs which collapsed to form 8708 full-length sequences out of which 4352 functionally annotated transcripts were identified. Genes involved in innate immunity, growth and development, hormonal regulation, cellular process, peritrophic membrane, melanogenesis, integument, circulation, cuticle formation, glycan metabolism, etc., were identified. The transcripts' orthologues were identified predominantly in Coleoptera and Hymenoptera in which chitin synthase (CHS), toll, haemocytin, serine protease/limulus clotting factor c, vitellogenin and trehalose transporter exhibited significant molecular relationships between these two insect orders. Chitin synthase 8 (CHS-8) found in ant has been identified for the first time in the order Coleoptera. (O. rhinoceros) at the translational level and projected a potential to explore evolution (horizontal gene transfer) of CHS in insects. The findings will bridge the molecular data between the genome and transcriptome of O. rhinoceros, thus helping develop molecular targets for its control and management.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04348-9.},
}
@article {pmid40409398,
year = {2025},
author = {Zhang, Y and Zou, D and Ji, Y and Liu, S and Jiang, Y and Fan, F and Zou, C},
title = {The combined effect of microplastics and tetracycline on soil microbial communities and ARGs.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126482},
doi = {10.1016/j.envpol.2025.126482},
pmid = {40409398},
issn = {1873-6424},
abstract = {Microplastics (MPs), due to their difficult degradation and adsorption characteristics, are highly prone to form compound contamination with antibiotic residues in the soil environment, thereby disrupting the soil ecosystem. To address this issue of compound contamination, this study investigated the effects of compound contamination composed of three common MPs-polyethylene (PE), polyamide (PA), and polyvinyl chloride (PVC)-combined with tetracycline(TC), on the structure of soil microbial communities and resistance genes. The results showed that the effects of composite pollution on soil physicochemical properties, enzyme activities, bacterial communities, and antibiotic resistance genes (ARGs) were more significant compared to single-contaminant pollution. Among the composite contaminants, TC combined with PVC and PE significantly increased the absolute abundance of the tetC gene, while the composite contamination of TC with PA had the greatest effect on bacterial diversity. This also increased the relative abundance of the phylum Actinobacteria and significantly affected the relative abundance of the phylum Ascomycetes. In addition, significant correlations were found between soil physicochemical properties, enzyme activities, microbial communities, and ARGs. A positive correlation between the intl1 integrator gene and all target genes suggests that horizontal gene transfer contributes to the enrichment of ARGs. Furthermore, the bacterial genera correlated with ARGs-Ascomycetes, Acidobacteria, Actinobacteria, and Anaplasma-are the major bacterial hosts for ARGs in soil samples. This study provides data to support the investigation of combined microplastic and antibiotic contamination in soil.},
}
@article {pmid40408144,
year = {2025},
author = {Quiñonero-Coronel, MDM and Cabello-Yeves, PJ and Haro-Moreno, JM and Rodriguez-Valera, F and Garcillán-Barcia, MP},
title = {The type IV secretion system of Patescibacteria is homologous to the bacterial monoderm conjugation machinery.},
journal = {Microbial genomics},
volume = {11},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001409},
pmid = {40408144},
issn = {2057-5858},
mesh = {Phylogeny ; *Type IV Secretion Systems/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; *Conjugation, Genetic ; Computational Biology ; },
abstract = {The Candidate Phyla Radiation, also known as Patescibacteria, represents a vast and diverse division of bacteria that has come to light via culture-independent 'omics' technologies. Their limited biosynthetic capacity, along with evidence of their growth as obligate epibionts on other bacteria, suggests a broad reliance on host organisms for their survival. Nevertheless, our understanding of the molecular mechanisms governing their metabolism and lifestyle remains limited. The type IV secretion system (T4SS) represents a superfamily of translocation systems with a wide range of functional roles. T4SS genes have been identified in the Patescibacteria class Saccharimonadia as essential for their epibiotic growth. In this study, we used a comprehensive bioinformatics approach to investigate the diversity and distribution of T4SS within Patescibacteria. The phylogenetic analysis of the T4SS signature protein VirB4 suggests that most of these proteins cluster into a distinct monophyletic group with a shared ancestry to the MPFFATA class of T4SS. This class is found in the conjugative elements of Firmicutes, Actinobacteria, Tenericutes and Archaea, indicating a possible horizontal gene transfer from these monoderm micro-organisms to Patescibacteria. We identified additional T4SS components near virB4, particularly those associated with the MPFFATA class, as well as homologues of other T4SS classes, such as VirB2-like pilins, and observed their varied arrangements across different Patescibacteria classes. The absence of a relaxase in most of these T4SS clusters suggests that the system has been co-opted for other functions in Patescibacteria. The proximity of T4SS components to the origin of replication (gene dnaA) in some Patescibacteria suggests a potential mechanism for increased expression. The broad ubiquity of a phylogenetically distinct T4SS, combined with its chromosomal location, underscores the significance of T4SS in the biology of Patescibacteria.},
}
@article {pmid40407872,
year = {2025},
author = {Suhajda, &#xc1; and Al-Nussairawi, M and Amara, I and Sörös, C and Tömösközi-Farkas, R and Kriszt, B and Farkas, M and Cserháti, M},
title = {Co-Occurrence of Beauvericin and Fumonisin Producing Ability of Fusarium Strains Isolated from Crop Plants in Hungary.},
journal = {Current microbiology},
volume = {82},
number = {7},
pages = {302},
pmid = {40407872},
issn = {1432-0991},
support = {TKP2021-NVA-22//"The feasibility of the circular economy during national defense activities" of 2021 Thematic Excellence Programme of the National Research Development and Innovation Office/ ; TKP2021-NVA-22//"The feasibility of the circular economy during national defense activities" of 2021 Thematic Excellence Programme of the National Research Development and Innovation Office/ ; TKP2021-NVA-22//"The feasibility of the circular economy during national defense activities" of 2021 Thematic Excellence Programme of the National Research Development and Innovation Office/ ; TKP2021-NVA-22//"The feasibility of the circular economy during national defense activities" of 2021 Thematic Excellence Programme of the National Research Development and Innovation Office/ ; TKP2021-NVA-22//"The feasibility of the circular economy during national defense activities" of 2021 Thematic Excellence Programme of the National Research Development and Innovation Office/ ; },
mesh = {*Depsipeptides/metabolism ; *Fusarium/metabolism/isolation &amp; purification/genetics/classification ; *Fumonisins/metabolism/analysis ; *Zea mays/microbiology ; Hungary ; Mycotoxins/metabolism ; Fungal Proteins/genetics/metabolism ; *Crops, Agricultural/microbiology ; Peptide Synthases/genetics ; },
abstract = {Beauvericin (BEA) is an emerging mycotoxin with wide-ranging bioactivity (antimicrobial and insecticide), making it a potential target for drug and pesticide development. BEA primarily produced by Beauveria, Isaria, and Fusarium species. The BEA-producing abilities of a collection of 100 Fusarium strains isolated from maize were tested using a gene-specific primer (Beas_1, Beas_2) by PCR. Among all, 23 were found to have the beauvericin synthetase (BEAS) gene sequence, which is responsible for the production of BEA. Fusarium proliferatum (6) and F. verticillioides (14) strains were producing the highest BEA concentrations. The toxin-producing ability of the strains was investigated in small bioreactors. Parallel with BEA, the most frequent Fusarium toxins such as deoxynivalenol (DON), T2, HT-2, zearalenone (ZEA), fumonisin B1 (FB1), and fumonisin B2 (FB2) were also measured. Only FB1 and FB2 were observed above the detection limit, the coexistence of the FBs and BEA was measured in high concentration. In all BEA-producing strains, the FBs production could be detected. The highest BEA concentration was 3131 mg/kg, and the highest FB1 and FB2 concentrations were 4393 mg/kg and 1390 mg/kg, respectively. In the present study, the gene sequences responsible for the production of BEA in F. verticilloides isolates have not only been detected but also demonstrated with UHPLC-ESI-MS/MS to be capable of biosynthesis. From the phylogenic analysis of the BEAS gene sequences, the assumption could be made that the ability to produce BEA was conferred via horizontal gene transfer.},
}
@article {pmid40407325,
year = {2025},
author = {Mom, J and Valette, O and Pieulle, L and Pelicic, V},
title = {Unraveling the molecular mechanisms of DNA capture by the Com pilus in naturally transformable monoderm bacteria.},
journal = {mBio},
volume = {},
number = {},
pages = {e0085125},
doi = {10.1128/mbio.00851-25},
pmid = {40407325},
issn = {2150-7511},
abstract = {UNLABELLED: Transformation is a mechanism of horizontal gene transfer widespread in bacteria. The first step in transformation-capture of exogenous DNA-is mediated by surface-exposed filaments belonging to the type 4 filament (T4F) superfamily. How these protein polymers, composed of major and minor pilin subunits, interact with DNA remains poorly understood. Here, we address this question for the Com pilus, a widespread T4F mediating DNA capture in competent monoderm species. Our functional analysis, performed in Streptococcus sanguinis, was guided by a complete structural model of the Com pilus. We show that the major pilin ComGC does not bind DNA. In contrast, a systematic mutational analysis of electropositive residues exposed at the filament surface in the four minor pilins (ComGD, ComGE, ComGF, and ComGG) reveals that the interface between ComGD and ComGF is important for DNA capture. Sequential mutations in these two interacting subunits lead to complete abolition of transformation, without affecting piliation. We further demonstrate the physical interaction between ComGD and ComGF using disulfide crosslinking, upon mutagenesis of two strategically positioned residues into cysteines. A structural model of the Com pilus tip interacting with DNA recapitulates all these findings and highlights a novel mode of DNA-binding, conserved in hundreds of monoderm species.<br><br>IMPORTANCE: Bacteria are capable of evolving and diversifying very rapidly by acquiring new genetic material via horizontal gene transfer (HGT). Transformation is a widespread mechanism of HGT, which results from the capture of extracellular DNA by surface-exposed pili belonging to the type 4 filament (T4F) superfamily. How T4F-composed of major and minor pilins-interact with DNA remains poorly understood, especially in monoderm species that use a unique T4F for DNA capture, known as Com pilus or T4dP. The significance of this work is in characterizing a novel mode of DNA-binding by showing that the interface between two minor pilins, part of a tip-located complex of four pilins-found in different T4F-has been functionalized in monoderms to capture DNA. This is an evolutionary mechanism promoting the exceptional functional versatility of T4F.},
}
@article {pmid40403929,
year = {2025},
author = {Shin, JI and Park, SH and Park, C and Jung, SH and Lee, DG},
title = {Genomic investigation of NDM-1 producing Enterobacterales transmission in a South Korean hospital.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.05.010},
pmid = {40403929},
issn = {2213-7173},
abstract = {OBJECTIVES: Prolonged detection of multispecies New Delhi metallo-β-lactamase (NDM)-1-producing Enterobacterales was observed previously in clinical and environmental samples collected from a South Korean hospital. This study aimed to investigate the transmission mechanisms of blaNDM-1 and assess the role of environmental reservoirs in its persistence.<br><br>METHODS: Epidemiological data were collected, and antibiotic susceptibility testing, carbapenemases detection, and whole-genome sequencing were performed on 42 clinical and 13 environmental isolates collected between November 2018 and February 2021, during the pre-outbreak, outbreak (July-September 2019), and post-outbreak periods. Long-read complete-genome sequencing was performed on four clinical and four environmental isolates to characterize plasmids carrying blaNDM-1 and associated mobile genetic elements (MGEs). Phylogenetic analyses were also performed.<br><br>RESULTS: blaNDM-1 was detected in 15 different species across clinical and environmental isolates. During the 2019 outbreak, clonal spread of Klebsiella pneumoniae and Klebsiella quasipneumoniae in the hospital was the primary mechanism of dissemination. During the post-outbreak period, horizontal gene transfer (HGT), mediated by the IncX3 plasmid carrying blaNDM-1, was the dominant transmission mechanism. This plasmid, detected in both clinical and environmental isolates, showed high genetic conservation with IncX3 plasmids reported worldwide. These plasmids contained conserved MGEs, including the IS26-dsbD-trpF-ble-blaNDM-1 structure.<br><br>CONCLUSION: This study highlights the dual roles of clonal spread and plasmid-mediated HGT in the dissemination of blaNDM-1 in hospital settings. The persistence of highly conserved IncX3 plasmids in environmental isolates underscores the complexity of carbapenem resistance control. Comprehensive infection control strategies targeting patient-to-patient transmission and environmental reservoirs are crucial for mitigating the spread of NDM-producing Enterobacterales.},
}
@article {pmid40402828,
year = {2025},
author = {Bremer, N and Martin, WF and Steel, M},
title = {Surprising effects of differential loss in genome evolution: the last-one-out.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf051},
pmid = {40402828},
issn = {1574-6968},
abstract = {Gene loss is an important process in genome evolution, though its power is often underestimated. If a gene is present at the root of a phylogenetic tree and can be lost in one lineage across the tree, it can potentially be lost in all, leading to gene extinction. Just before gene extinction, there will be one lineage that still retains the gene, generating a 'last-one-out' distribution. Such an isolated gene presence will emulate the result of recent lateral gene acquisition, even though its distribution was generated by loss. How probable is it to observe 'last-one-out' distributions in real data? Here we mathematically derive this probability and find that it is surprisingly high, depending upon the tree and the gene loss rate. Examples from real data show that loss can readily account for observed frequencies of last-one-out gene distributions that might otherwise be attributed to lateral gene transfer.},
}
@article {pmid40402243,
year = {2025},
author = {Gozashti, L and Nakamoto, A and Russell, S and Corbett-Detig, R},
title = {Horizontal transmission of functionally diverse transposons is a major source of new introns.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {21},
pages = {e2414761122},
doi = {10.1073/pnas.2414761122},
pmid = {40402243},
issn = {1091-6490},
support = {R35GM128932//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R00GM135583//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; GRFP//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; },
mesh = {*Introns/genetics ; *DNA Transposable Elements/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; Genome ; Retroelements/genetics ; Eukaryota/genetics ; Animals ; Humans ; },
abstract = {Since the discovery of spliceosomal introns in eukaryotic genomes, the proximate molecular and evolutionary processes that generate new introns have remained a critical mystery. Specialized transposable elements (TEs), introners, are thought to be one of the major drivers of intron gain in diverse eukaryotes. However, the molecular mechanism(s) and evolutionary processes driving introner propagation within and between lineages remain elusive. Here, we analyze 8,716 genomes, revealing 1,093 introner families in 201 species spanning 1.7 billion years of evolution. Introners are derived from functionally diverse TEs including families of terminal-inverted-repeat DNA TEs, retrotransposons, cryptons, and helitrons as well as mobile elements with unknown molecular mechanisms. We identify eight cases where introners recently transferred between divergent host species and show that giant viruses that integrate into genomes may facilitate introner transfer across lineages. We propose that ongoing intron gain is primarily a consequence of TE activity in eukaryotes, thereby resolving a key mystery of genome structure evolution.},
}
@article {pmid40401976,
year = {2025},
author = {Qamar, MU and Sierra, R and Jabeen, K and Rizwan, M and Rashid, A and Dar, YF and Andrey, DO},
title = {Genomic characterization of plasmids harboring blaNDM-1, blaNDM-5, and blaNDM-7 carbapenemase alleles in clinical Klebsiella pneumoniae in Pakistan.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0235924},
doi = {10.1128/spectrum.02359-24},
pmid = {40401976},
issn = {2165-0497},
abstract = {UNLABELLED: Klebsiella pneumoniae is notorious for causing healthcare-associated infections, which become more complicated by the acquisition of blaNDM genes via mobile genetic elements. Although Pakistan is a well-established hot spot of blaNDM-positive K. pneumoniae, detailed molecular descriptions of blaNDM-carrying plasmids are scarce. Seven K. pneumoniae isolates harboring blaNDM were recovered from clinical sample sources during a 6 month period and tested for antimicrobial susceptibility. A long-read approach was used for whole-genome sequencing to obtain circularized plasmids and chromosomes for typing, annotation, and comparative analysis. The isolates were susceptible to colistin and tigecycline only among the tested antibiotics. We identified five sequence types (STs): ST11, ST16, ST716, ST464, and ST2856. Notably, three strains possessed the hypervirulent capsule KL2, while five were classified as O locus type O2a. Evidence of genetic diversity was further highlighted by the presence of four IncC plasmids harboring blaNDM-1, two IncX3 plasmids harboring blaNDM-5, and a single hybrid IncFIB/IncHI1B plasmid harboring blaNDM-7. These plasmids also carried additional antimicrobial resistance (AMR) genes conferring resistance to aminoglycosides, cephalosporins, and fluoroquinolones. We identified the plasmidome of the K. pneumoniae isolates and characterized the New Delhi metallo-beta-lactamase (NDM)-carrying plasmids. Genetic analysis confirmed the presence of blaNDM-1 and blaNDM-5 on broad host range plasmids and blaNDM-7 in a previously unreported hybrid plasmid backbone. We emphasized the critical role of plasmids in spreading blaNDM in the clinical setting in Pakistan. Hence, we stressed the urgent need for enhanced surveillance, not least in low-middle income countries, infection control measures, and adherence to the "Access," "Watch," and "Reserve" guidelines in antibiotics use.<br><br>IMPORTANCE: Infections caused by NDM-producing Klebsiella pneumoniae are a significant challenge to treat and represent a crucial health burden in low- and middle-income countries (LMICs). Most of the blaNDM are located on plasmids that promote horizontal gene transfer. However, there is a lack of comprehensive information on the genetic context of the NDM-carrying plasmids in Pakistan. This study presents a detailed analysis of seven NDM-plasmids in clinical K. pneumoniae isolates, shedding light on their high-risk sequence types and multiple resistance determinants. We also describe the plasmid-bearing NDM alleles (blaNDM-1, blaNDM-5, and blaNDM-7). Notably, we are the first to report blaNDM-7 on the hybrid IncFIB/IncHI1B backbone in Pakistan, a plasmid that has rarely been reported previously globally. Understanding the plasmid genomic landscape is paramount to comprehensively understanding the AMR scenario in this LMIC.},
}
@article {pmid40400687,
year = {2025},
author = {Guerrero-Flores, S and Contreras-Peruyero, H and Ibarra-Rodríguez, JM and Lovaco-Flores, JA and Nieto-de la Rosa, FS and Fontove-Herrera, F and Sélem-Mojica, N},
title = {Topological data analysis captures horizontal gene transfer in antimicrobial resistance gene families among clinically relevant bacteria.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1461293},
pmid = {40400687},
issn = {1664-302X},
abstract = {Antibiotic resistance, projected to cause 10 million deaths annually by 2050, remains a critical health threat. Hospitals drive multidrug resistance via horizontal gene transfer. The 2023 Critical Assessment of Massive Data Analysis challenge presents resistance markers from 146 Johns Hopkins bacterial isolates, aiming to analyze resistomes without metadata or genomic sequences. Persistent homology, a topological data analysis method, effectively captures processes beyond vertical inheritance. A 1-hole is a topological feature representing a loop or gap in the data, where relationships form a circular structure rather than a linear one. Unlike vertical inheritance, which lacks topological 1-holes, horizontal gene transfer generates distinct patterns. Since antimicrobial resistance genes often spread via horizontal gene transfer, we simulated vertical and horizontal inheritance in bacterial resistomes. The number of 1-holes from simulations and a documented horizontal gene transfer case was analyzed using persistence barcodes. In a simulated population of binary sequences, we observed that, on average, two 1-holes form for every three genomes undergoing horizontal gene transfer. Using a presence-absence gene table, we confirmed the existence of 1-holes in a documented case of horizontal gene transfer between two bacterial genera in a Pittsburgh hospital. Notably, the Critical Assessment of Massive Data Analysis resistomes of Klebsiella and Escherichia exhibit 1-holes, while Enterobacter shows none. Lastly, we provide a mathematical example of a non-tree-like space that contains no 1-holes. Persistent homology provides a framework for uncovering complex clinical patterns, offering an alternative to understanding resistance mobility using presence-absence data, which could be obtained through methods beyond genomic sequencing.},
}
@article {pmid40400517,
year = {2025},
author = {Ohata, Y and Sugimoto, TN and Wybouw, N and Tagami, Y},
title = {Suppression of cytoplasmic incompatibility in the leaf-mining fly Liriomyza sativae with a nuclear Wolbachia insert.},
journal = {Royal Society open science},
volume = {12},
number = {5},
pages = {242137},
pmid = {40400517},
issn = {2054-5703},
abstract = {Cytoplasmic incompatibility (CI) drives maternally transmitted endosymbionts such as Wolbachia through insect populations by inducing embryonic mortality when infected males fertilize uninfected females. CI is controlled by Wolbachia cif operons that are categorized into multiple phylogenetic types. CI strength is further shaped by poorly understood host factors, including development and genetic background. To study the strength of CI across different host species, we genotyped a Japanese field population of Liriomyza sativae. By uncovering paternal transmission of Wolbachia genic elements, we collected strong evidence of horizontal genome transfer, including Type I and Type V cif operons, from Wolbachia into the nuclear genome of L. sativae. We established a transinfection of wLtri in L. sativae, a Wolbachia variant that induces strong CI in Liriomyza trifolii. No CI was observed in both intraspecific and interspecific reciprocal crosses with L. trifolii, suggesting that both uninfected females and infected males of L. sativae completely suppress wLtri-mediated CI. Our results raise the appealing hypothesis that host suppression of Wolbachia-induced CI might evolve owing to horizontal transfer of cif operons into the host nuclear genome.},
}
@article {pmid40398027,
year = {2025},
author = {Zhang, J and Li, B and Shen, Z and Zhang, Z and Feng, J and Wong, JWC},
title = {Antibiotic resistance patterns and cross-family ARG transfer in families Burkholderiaceae and Sphingomonadaceae: A large-scale genome-wide analysis of over 10 K genomes.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138642},
doi = {10.1016/j.jhazmat.2025.138642},
pmid = {40398027},
issn = {1873-3336},
abstract = {Members of Burkholderiaceae and Sphingomonadaceae play an active role in pollutant degradation, yet their antibiotic resistance risks are frequently overlooked. This study analyzed 9406 Burkholderiaceae and 2343 Sphingomonadaceae genomes to investigate the distribution, horizontal gene transfer (HGT), and co-occurrence patterns of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs). ARGs were prevalent in Burkholderiaceae (93.2 % of genomes), dominated by bacitracin (89.0 %), multidrug (88.1 %), and beta-lactam (40.5 %) resistance, while Sphingomonadaceae exhibited lower ARG prevalence (11.6 %). Notably, Burkholderia and Caballeronia displayed high multidrug resistance (10.1 ARGs per genome) and frequent ARG-MRG co-occurrence (84.4 %). Strong ARG-MRG-MGE correlations were observed in Burkholderiaceae, suggesting MGEs play a key role in resistance dissemination. Additionally, ARGs correlated with metabolic genes, linking metabolic versatility to resistance. Genes like capO (chloramphenicol oxidase) and blaTEM-116 (beta-lactamase) were shared among distantly related genera, while mcr-5.1 (MCR phosphoethanolamine transferase) co-occurred with MRGs across Cupriavidus species, highlighting HGT and co-selection risks. ARG transfer between Burkholderiaceae, Sphingomonadaceae and clinical pathogens was frequent (114-1306 events/10,000 genome pairs), with sulfonamide resistance dominating (51.3 % of HGT). These findings highlight Burkholderiaceae and Sphingomonadaceae as critical reservoirs of resistance genes and emphasize the need for enhanced surveillance and mitigation strategies to curb the spread of multidrug resistance.},
}
@article {pmid40298401,
year = {2025},
author = {Pan, T and Li, Q},
title = {Mobile genetic elements in Klebsiella pneumoniae.},
journal = {Journal of bacteriology},
volume = {207},
number = {5},
pages = {e0001225},
doi = {10.1128/jb.00012-25},
pmid = {40298401},
issn = {1098-5530},
mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/drug effects ; *Interspersed Repetitive Sequences ; Humans ; Virulence/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Plasmids/genetics ; Klebsiella Infections/microbiology ; Genome, Bacterial ; DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial ; },
abstract = {Klebsiella pneumoniae is a clinically important pathogenic bacteria that poses a serious threat to human health. In particular, the emergence of hypervirulent and multidrug-resistant K. pneumoniae has posed great challenges in clinical anti-infective therapy. In the K. pneumoniae genome, mobile genetic elements (MGEs), such as plasmids, prophages, transposons, and insertion sequences, enhance bacterial viability and adaptation by mediating the horizontal transfer of virulence genes, antibiotic resistance genes, and other adaptive genes. This paper reviews the types and characteristics of the main MGEs in K. pneumoniae, focusing on their effects on bacterial virulence and antibiotic resistance, with the aim of providing clues for developing infection control measures and new antibacterial drugs.},
}
@article {pmid40397871,
year = {2025},
author = {Granato, ET and Palmer, JD and Kirk, C and Sharp, C and Shillcock, G and Foster, KR},
title = {Horizontal gene transfer of molecular weapons can reshape bacterial competition.},
journal = {PLoS biology},
volume = {23},
number = {5},
pages = {e3003095},
doi = {10.1371/journal.pbio.3003095},
pmid = {40397871},
issn = {1545-7885},
mesh = {*Gene Transfer, Horizontal ; *Escherichia coli/genetics ; Plasmids/genetics ; Colicins/genetics ; *Bacteria/genetics ; },
abstract = {Bacteria commonly use molecular weaponry to kill or inhibit competitors. Genes encoding many weapons and their associated immunity mechanisms can be transmitted horizontally. These transfer events are striking because they appear to undermine bacterial weapons when given to competing strains. Here, we develop an ecological model of bacterial warfare to understand the impacts of horizontal gene transfer. Our model predicts that weapon gene transfer from an attacker to a target strain is possible, but will typically occur at a low rate such that transfer has a negligible impact on competition outcomes. We tested the model empirically using a transmissible plasmid encoding colicin E2, a potent antibacterial toxin produced by Escherichia coli. As predicted by the model, we find that toxin plasmid transfer is feasible during warfare, but the resulting transconjugants remain rare. However, exploring the model further reveals realistic conditions where transfer is predicted to have major impacts. Specifically, the model predicts that whenever competing strains have access to unique nutrients, transconjugants can proliferate and reach high abundances. In support of these predictions, short- and long-term experiments show that transconjugants can thrive when nutrient competition is relaxed. Our work shows how horizontal gene transfer can reshape bacterial warfare in a way that benefits a weapon gene and strains that receive it. Interestingly, we also find that there is little cost to a strain that transfers a weapon gene, which is expected to further enable the horizontal gene transfer of molecular weapons.},
}
@article {pmid40396743,
year = {2025},
author = {Zhang, T and Han, Y and Peng, Y and Deng, Z and Shi, W and Xu, X and Wu, Y and Dong, X},
title = {The risk of pathogenicity and antibiotic resistance in deep-sea cold seep microorganisms.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0157124},
doi = {10.1128/msystems.01571-24},
pmid = {40396743},
issn = {2379-5077},
abstract = {UNLABELLED: Deep-sea cold seeps host high microbial biomass and biodiversity that thrive on hydrocarbon and inorganic compound seepage, exhibiting diverse ecological functions and unique genetic resources. However, potential health risks from pathogenic or antibiotic-resistant microorganisms in these environments remain largely overlooked, especially during resource exploitation and laboratory research. Here, we analyzed 165 metagenomes and 33 metatranscriptomes from 16 global cold seep sites to investigate the diversity and distribution of virulence factors (VFs), antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs). A total of 2,353 VFs are retrieved in 689 metagenome-assembled genomes (MAGs), primarily associated with indirect pathogenesis like adherence. In addition, cold seeps harbor nearly 100,000 ARGs, as important reservoirs, with high-risk ARGs (11.22%) presenting at low abundance. Compared to other environments, microorganisms in cold seeps exhibit substantial differences in VF and ARG counts, with potential horizontal gene transfer facilitating their spread. These virulome and resistome profiles provide valuable insights into the evolutionary and ecological implications of pathogenicity and antibiotic resistance in extreme deep-sea ecosystems. Collectively, these results indicate that cold seep sediments pose minimal public health risks, shedding light on environmental safety in deep-sea resource exploitation and research.<br><br>IMPORTANCE: In the "One Health" era, understanding pathogenicity and antibiotic resistance in vast and largely unexplored regions like deep-sea cold seeps is critical for assessing public health risks. These environments serve as critical reservoirs where resistant and virulent bacteria can persist, adapt, and undergo genetic evolution. The increasing scope of human activities, such as deep-sea mining, is disrupting these previously isolated ecosystems, heightening the potential for microbial exchange between deep-sea communities and human or animal populations. This interaction poses a significant risk for the dissemination of resistance and virulence genes, with potential consequences for global public health and ecosystem stability. This study offers the first comprehensive analysis of virulome, resistome, and mobilome profiles in cold seep microbial communities. While cold seeps act as reservoirs for diverse ARGs, high-risk ARGs are rare, and most VFs were low risk that contribute to ecological functions. These results provide a reference for monitoring the spread of pathogenicity and resistance in extreme ecosystems, informing environmental safety assessments during deep-sea resource exploitation.},
}
@article {pmid40390443,
year = {2025},
author = {Xu, M and Gao, P and Chen, HQ and Gao, Y and Xiong, SJ and Wang, XH},
title = {[Effects of Typical Microplastics on Methanogenesis and Antibiotic Resistance Genes in Anaerobic Digestion of Sludge].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {5},
pages = {3189-3199},
doi = {10.13227/j.hjkx.202405273},
pmid = {40390443},
issn = {0250-3301},
mesh = {*Sewage/microbiology/chemistry ; *Methane/metabolism/biosynthesis ; *Drug Resistance, Microbial/genetics ; Anaerobiosis ; *Microplastics ; *Waste Disposal, Fluid/methods ; Bioreactors/microbiology ; Bacteria/genetics ; },
abstract = {Waste sludge is an important carrier of antibiotic resistance genes （ARGs） and an important place for the enrichment of microplastics （MPs）. To explore the impacts of typical MPs on sludge recycling and harmless disposal, the effects of polyamide （PA）, polyethylene （PE）, and polypropylene （PP） MPs on the methanogenesis efficiency of anaerobic digestion were investigated. Meanwhile, based on metagenomic sequencing, the effects of MPs on ARGs, mobile genetic elements （MGEs）, microbial community structure, and host bacteria during anaerobic digestion were analyzed. The results showed that PA-MPs, PE-MPs, and PP-MPs increased the distribution of methane production by 2.2%, 22.3%, and 28.8%, respectively. MPs promoted methanation by improving the dissolution and hydrolysis efficiency of organic matter, and the enrichment of hydrogenotrophic methanogens by PP-MPs further improved the methanogenic efficiency. PA-MPs contributed to the removal of ARGs, while PE-MPs and PP-MPs had adverse effects on the reduction of ARGs. Horizontal gene transfer mediated by integron and insertion sequences was an important factor in the spread of ARGs. Proteobacteria was the key host leading to the diffusion of ARGs. The removal of pathogens from Bacteroidetes by anaerobic digestion contributed to the reduction of ARGs. The selective enrichment or inhibition of Arenimonas, Acinetobacter, Actinobacillus, Nitrospira, and other important host bacteria by MPs was the major cause for the difference in the removal effect of ARGs.},
}
@article {pmid40382874,
year = {2025},
author = {Miao, S and Zhang, Y and Wu, L and Wang, Y and Zuo, J},
title = {Resistance induction potency assessment of antibiotic production wastewater and associated resistome shaping mechanisms.},
journal = {Water research},
volume = {283},
number = {},
pages = {123811},
doi = {10.1016/j.watres.2025.123811},
pmid = {40382874},
issn = {1879-2448},
abstract = {Antibiotic production wastewater (APW) contains multiple substances known to select for and facilitate horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs); however, whether these substances can induce the evolution of antibiotic resistance in real wastewater environments and the fate of such resistance induction potency during the treatment process are poorly understood, nor are its relationship with wastewater quality parameters and function in shaping the antibiotic resistome. In this study, the impacts of filter-sterilized APW and municipal wastewater on the resistance selection of Escherichia coli and the transfer dynamics of conjugative RP4 plasmid-borne ARGs across indigenous sludge communities were evaluated. The resistance development and transfer processes were accelerated in APW owing to enhanced growth inhibition, oxidative stress, and membrane permeability, with antibiotic concentrations much lower than their minimum inhibition concentrations. The effects were reduced simultaneously with the removal of COD and NH3N, but APW effluents still exhibited significant resistance induction potency with wastewater quality parameters meeting discharge standards. In contrast, municipal wastewater did not result in any detectable changes. Based on the metagenomic assembly and binning, stronger resistance induction potency in the antibiotic production wastewater treatment plant endowed indigenous sludge and effluent with greater accumulation, genetic mobility, and pathogenic accessibility of ARGs than in the municipal wastewater treatment plant. Antibiotic resistome assembly was determined primarily by deterministic processes, driven jointly by resistance induction potency, mobilome variance, and microbiome shifts. These results provide novel insights into the application of bioassays to comprehensively evaluate the antibiotic resistance induction effects of APW and their relationships with the resistome to manage risks during the treatment process.},
}
@article {pmid39988053,
year = {2025},
author = {Monesi, N and Fernandes, GM and Valer, FB and Uliana, JVC and Trinca, V and Azzolini, AECS and Gorab, E and Alberici, LC},
title = {Identification and characterization of a laterally transferred alternative oxidase (AOX) in a terrestrial insect, the dipteran Pseudolycoriella hygida.},
journal = {Biochimie},
volume = {233},
number = {},
pages = {60-74},
doi = {10.1016/j.biochi.2025.02.007},
pmid = {39988053},
issn = {1638-6183},
mesh = {Animals ; *Mitochondrial Proteins/genetics/metabolism/antagonists &amp; inhibitors ; *Oxidoreductases/genetics/metabolism/antagonists &amp; inhibitors ; *Plant Proteins/genetics/metabolism ; *Diptera/enzymology/genetics ; Mitochondria/enzymology/metabolism ; *Gene Transfer, Horizontal ; *Insect Proteins/genetics/metabolism ; Phylogeny ; Salicylamides ; },
abstract = {Alternative oxidase (AOX) (EC 1.10.3.11) is a terminal oxidase in the mitochondrial inner membrane that branches the canonical electron transport system (ETS). AOX is ubiquitous in plants, frequently found in fungi and protists and presents a more sporadic distribution in metazoans. More recently, AOX has gained attention due to its potential application in gene therapy for treatment of mitochondrial diseases. Here we characterized the AOX in the basal Dipteran, Pseudolycoriella hygida using a combination of genomic analyses, molecular, functional and in vivo survival assays. AOX is a single copy gene that encodes three developmental stage specific protein isoforms. AOX localizes to the mitochondria in adult thoracic muscles, which present cyanide-resistant respiration that is sensitive to the AOX inhibitor salicylhydroxamic acid (SHAM). Both the cyanide-resistant respiration and AOX levels gradually increase during aging, but are not influenced by thermal stress. Thoracic mitochondria respire using substrates derived from several metabolic routes, such as pyruvate, proline, acylcarnitine, NADH and glycerol-3P, and present values of oxidative phosphorylation capacity ((P-L)/E = 0.70) and coupling (P/L = 4.35; L/E = 0.21). Adult flies exhibit a high survival resistance for SHAM-sensitive complex III inhibition. Together, our results demonstrate the presence of a functional AOX in a terrestrial arthropod and provide insights regarding AOX function in animals and evolution of respiratory systems in metazoans. Psl. hygida emerges as a natural and valuable model for comprehensive AOX research at the whole-organism level which complements models expressing the heterologous enzyme.},
}
@article {pmid40381794,
year = {2025},
author = {Yaikhan, T and Singkhamanan, K and Dechathai, T and Chukamnerd, A and Chusri, S and Pomwised, R and Wonglapsuwan, M and Surachat, K},
title = {Genome-based alert on a clinical Plesiomonas shigelloides PSU59 from Thailand: Resistance and virulence features.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105764},
doi = {10.1016/j.meegid.2025.105764},
pmid = {40381794},
issn = {1567-7257},
abstract = {Plesiomonas shigelloides, an aquatic Gram-negative bacterium, is increasingly recognized as an emerging pathogen with antimicrobial resistance (AMR) potential. This study provides a genome-based alert on P. shigelloides PSU59, isolated from a patient in Thailand. Whole-genome sequencing (WGS) revealed a 3.6 Mb draft genome (38 contigs, 51.9 % GC) encoding 3265 coding sequences and 129 RNA genes. Thirteen AMR genes were identified, including efflux pumps (adeF, tet(A)), target modifiers (dfrA1, sul2), and aminoglycoside-inactivating enzymes. Mobile genetic elements (MGEs) flanking resistance genes suggest horizontal gene transfer (HGT). Virulence analysis revealed 48 factors, notably flagellar genes (fliM, fliN, flhA) linked to motility. Phylogenetic comparison placed PSU59 in Clade 3, closely related to a food-derived strain. These results highlight the pathogenic and drug-resistant potential of P. shigelloides PSU59 and underscore the importance of genomic surveillance in tracking emerging threats among under-recognized pathogens.},
}
@article {pmid40381353,
year = {2025},
author = {Xin, Y and Zhang, J and Tang, Q and Wei, M and Zhu, L and Zhao, Y and Cui, Y and Sun, T and Wei, Y and Richnow, HH},
title = {Virus-host interactions driving the transfer of antibiotic resistance genes in a river-reservoir system under heavy rainfall.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138605},
doi = {10.1016/j.jhazmat.2025.138605},
pmid = {40381353},
issn = {1873-3336},
abstract = {Global river systems are grappling with severe pollution from antibiotic resistance genes (ARGs), with river-reservoir (R-R) systems being a common feature in urban waterways. The intensified extreme rainfall events triggered by global climate change exacerbate the spread of ARGs posed by non-point source pollution and combined sewage overflows. This study employs a metagenomics approach to decipher the profile of ARGs and virus-host interactions driving their transfer under heavy rainfall in North Canal, Beijing, with extensive R-R systems. Results indicated that R-R systems contributed to ARGs reduction despite continuous discharge of treated wastewater into the North Canal. The ARGs assembly is predominantly governed by stochastic process, and heavy rainfall enhances the dispersal capability. Nonetheless, the deterministic process determined the assembly of both microbial and viral community. Heavy rainfall not only significantly increased the abundance and diversity of ARGs within the rivers with minimal change in the reservoir, but also promotes the horizontal gene transfer of ARGs with higher conjugative mobility. Although the species accumulation curves approached saturation, no viruses carrying ARGs were detected among the 23,835 non-redundant viral operational taxonomic units (vOTUs), and lytic phage-ARB interactions drove the ARGs reduction with higher VHRs, highlighting its contribution to the reduction of ARGs in R-R system after heavy rainfall.},
}
@article {pmid40379875,
year = {2025},
author = {Guédon, G and Charron-Bourgoin, F and Lacroix, T and Hamadouche, T and Soler, N and Douzi, B and Chiapello, H and Leblond-Bourget, N},
title = {Massive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gut.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {17013},
pmid = {40379875},
issn = {2045-2322},
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Genome, Bacterial ; *Faecalibacterium/genetics/physiology ; *Conjugation, Genetic ; *Adaptation, Physiological/genetics ; Feces/microbiology ; Phylogeny ; },
abstract = {Faecalibacterium is one of the most abundant bacteria of the human gut microbiota of healthy adults and is recognized to have positive effects on health. Here, we precisely and comprehensively analyzed the conjugative mobilome of four complete Faecalibacterium genomes. Despite lacking any plasmid, these bacteria harbor a vast arsenal of 130 elements, including 17 integrative and conjugative elements (ICEs) and 83 integrative and mobilizable elements (IMEs), collectively comprising 14-23% of the genome. Genome comparison of two strains isolated from the same fecal sample (Faecalibacterium and Roseburia strains) revealed almost identical elements indicating that transfer of ICEs and IMEs shape gut microbiome. ICEs and IMEs from Faecalibacterium encode many and diverse predicted functions such as defense and stress response (phages, multidrug, antibiotics, oxidative stress, biliar salts, antimicrobial peptides), nutrient import and metabolisms (Fe[3+], carbohydrates) and riboflavin synthesis. This hints at their important role in the survival and adaptation of Faecalibacterium strains to the gut ecosystem. A rapid survey of 29 additional Faecalibacterium genomes uncovered many putative ICEs and IMEs, reinforcing their role in the rapid and massive evolution of Faecalibacterium genomes.},
}
@article {pmid40378740,
year = {2025},
author = {Ding, Y and Dong, S and Ding, D and Chen, X and Xu, F and Niu, H and Xu, J and Fan, Y and Chen, R and Xia, Y and Qiu, X and Feng, H},
title = {Overlooked risk of dissemination and mobility of antibiotic resistance genes in freshwater aquaculture of the Micropterus salmoides in Zhejiang, China.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138604},
doi = {10.1016/j.jhazmat.2025.138604},
pmid = {40378740},
issn = {1873-3336},
abstract = {Residual antibiotics in aquaculture ecosystems can exert selective pressures on bacterial communities, driving bacteria to acquire antibiotic resistance genes (ARGs) through gene mutations or horizontal gene transfer (HGT). This study investigated the antibiotic resistance risk in freshwater aquaculture ecosystems of Micropterus salmoides in Zhejiang Province. The results revealed that oxytetracycline, ciprofloxacin and florfenicol were up to 300 ng/L, and the proportion of multidrug-resistant genes varied from 32.20 % to 50.70 % in the surveyed aquaculture water. Additionally, approximately 9.80 % of all annotated ARGs were identified as possessing plasmid-mediated horizontal transfer risks. The ARGs host prediction revealed that Actinobacteria carried the highest abundance of ARGs, up to 159.38 (coverage, ×/Gb). Furthermore, the abundance of Paer_emrE, ksgA, ompR and golS were positively correlated with Chlorophyll a concentration (p < 0.05), suggesting that algal blooms might facilitate the evolution and transfer of ARGs. Correlations between ARG abundances and total phosphorus, total nitrogen, pH, electrical conductivity indicated that modulating water quality parameters may serve as a viable strategy to mitigate the eco-environmental risk of ARGs in aquaculture water. This study identified antibiotic resistance characteristics in freshwater aquaculture ecosystems of Micropterus salmoides in Zhejiang Province, establishing a foundation on managing antibiotic resistance risks in such aquaculture environments.},
}
@article {pmid40378350,
year = {2025},
author = {Bean, EL and Smith, JL and Grossman, AD},
title = {Identification of insertion sites for the integrative and conjugative element Tn916 in the Bacillus subtilis chromosome.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0318964},
pmid = {40378350},
issn = {1932-6203},
mesh = {*Bacillus subtilis/genetics ; *Chromosomes, Bacterial/genetics ; *DNA Transposable Elements/genetics ; *Conjugation, Genetic ; Base Sequence ; Bacterial Proteins/metabolism/genetics ; Gene Transfer, Horizontal ; },
abstract = {Integrative and conjugative elements (ICEs) are found in many bacterial species and are mediators of horizontal gene transfer. Tn916 is an ICE found in several Gram-positive genera, including Enterococcus, Staphylococcus, Streptococcus, and Clostridioides (previously Clostridium). In contrast to the many ICEs that preferentially integrate into a single site, Tn916 can integrate into many sites in the host chromosome. The consensus integration motif for Tn916, based on analyses of approximately 200 independent insertions, is an approximately 16 bp AT-rich sequence. Here, we describe the identification and mapping of approximately 105 independent Tn916 insertions in the Bacillus subtilis chromosome. The insertions were distributed between 1,554 chromosomal sites, and approximately 99% of the insertions were in 303 sites and 65% were in only ten sites. One region, between ykuC and ykyB (kre), was a 'hotspot' for integration with ~22% of the insertions in that single location. In almost all of the top 99% of sites, Tn916 was found with similar frequencies in both orientations relative to the chromosome and relative to the direction of transcription, with a few notable exceptions. Using the sequences of all insertion regions, we determined a consensus motif which is similar to that previously identified for C. difficile. The insertion sites are largely AT-rich, and some sites overlap with regions bound by the nucleoid-associated protein Rok, a functional analog of H-NS of Gram-negative bacteria. Rok functions as a negative regulator of at least some horizontally acquired genes. We found that the presence or absence of Rok had little or no effect on insertion site specificity of Tn916.},
}
@article {pmid40378191,
year = {2025},
author = {Policarpo, M and Salzburger, W and Maumus, F and Gilbert, C},
title = {Multiple horizontal transfers of immune genes between distantly related teleost fishes.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf107},
pmid = {40378191},
issn = {1537-1719},
abstract = {Horizontal gene transfer (HGT) is less frequent in eukaryotes than in prokaryotes, yet can have strong functional implications and was proposed as causal factor for major adaptations in several eukaryotic lineages. Most cases of eukaryote HGT reported to date are inter-domain transfers and few studies have investigated eukaryote-to-eukaryote HGTs. Here, we performed a large-scale survey of HGT among 242 species of ray-finned fishes. We found multiple lines of evidence supporting 19 teleost-to-teleost HGT events that involve 17 different genes in 11 teleost fish orders. The genes involved in these transfers show lower synonymous divergence than expected under vertical transmission, their phylogeny is inconsistent with that of teleost fishes, and they occur at non syntenic positions in donor and recipient lineages. The distribution of HGT events in the teleost tree is heterogenous, with eight of the 19 transfers occurring between the same two orders (Osmeriformes and Clupeiformes). Though we favor a scenario involving multiple HGT events, future work should evaluate whether hybridization between species belonging to different teleost orders may generate HGT-like patterns. Besides the previously reported transfer of an antifreeze protein, most transferred genes play roles in immunity or are pore forming proteins, suggesting that such genes may be more likely than others to confer strong selective advantage to the recipient species. Overall, our work shows that teleost-to-teleost HGT has occurred on multiple occasions, and it will be worth further quantifying these transfers and evaluating their impact on teleost evolution as more genomes are sequenced.},
}
@article {pmid40374465,
year = {2025},
author = {Toribio-Celestino, L and San Millan, A},
title = {Plasmid-bacteria associations in the clinical context.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.04.011},
pmid = {40374465},
issn = {1878-4380},
abstract = {Antimicrobial resistance (AMR) is one of the most pressing global health problems, with plasmids playing a central role in its evolution and dissemination. Over the past decades, many studies have investigated the ecoevolutionary dynamics between plasmids and their bacterial hosts. However, what drives the epidemiological success of certain plasmid-bacterium associations remains unclear. In this opinion article, we review which factors influence these associations and underline that studying plasmid-host interactions of clinical relevance is critical for understanding the evolution and spread of AMR. We also highlight the increasing importance of integrating experimental research with bioinformatics and machine learning tools to study plasmid-bacteria dynamics. This combined approach will assist researchers to dissect the molecular mechanisms underlying successful plasmid-host associations and to design strategies to prevent and predict future high-risk associations.},
}
@article {pmid40373943,
year = {2025},
author = {Bhuiya, S and Kaushik, S and Logheeswaran, J and Karthika, P and Prathiviraj, R and Selvin, J and Kiran, GS},
title = {Emergence of Recurrent Urinary Tract Infection: Dissecting the mechanism of Antimicrobial Resistance, Host-Pathogen Interaction, and Hormonal Imbalance.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107698},
doi = {10.1016/j.micpath.2025.107698},
pmid = {40373943},
issn = {1096-1208},
abstract = {Urinary tract infection is one of the most common infections worldwide, causing numerous deaths every year. The gut-bladder axis has been recently found to be a key factor in initiating UTI pathogenesis, along with the imbalance in the gut microbiome, which is associated with advanced susceptibility to rUTI. The patients who suffer from UTIs are, more often than not, the ones who have the lowest levels of butyrate-producing gut bacteria. Antibiotics cause dysbiosis in the gut and increase the growth of uropathogenic strains. Moreover, the gut-vagina and vagina-bladder axes are involved in UTIs by transferring microbial species, modulating the immune response, and developing intracellular bacterial reservoirs in the bladder. The rising usage of antibiotics has raised antimicrobial resistance (AMR) worldwide and recently worsened the treatment of UTIs. Resistance mechanisms include enzymatic hydrolysis of antibiotics, efflux systems, biofilm formation, horizontal gene transfer, and a weakened host's immune system, allowing bacteria to escape from the treatments. Besides, in pregnant women and adolescents, the alterations in sex hormone levels increase the risk of rUTIs. Knowledge of microbiota that harbor in the gut-vagina and vagina-bladder axes might lead to the invention of nonantibiotic preventive and therapeutic techniques in the future. In conclusion, this review emphasizes the need for a study to understand the host-microbe interactions, gut health, and AMR to effectively deal with and prevent recurrent UTIs. Also, the review explores a comprehensive analysis of the epigenetic network between host UTIs and marker genes in E. coli.},
}
@article {pmid40373395,
year = {2025},
author = {He, Y and Liu, C and Zhang, J and Wang, G and Liu, H and Peng, C and Liu, X and Wang, J},
title = {Invisible threat: Marine suspended particles mediate delayed decay of antibiotic resistome in coastal effluents.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138610},
doi = {10.1016/j.jhazmat.2025.138610},
pmid = {40373395},
issn = {1873-3336},
abstract = {Suspended particles are recognized as hotspots of antibiotic resistance genes (ARGs) in coastal waters. However, the dynamics of ARGs associated with suspended particles during sewage discharge into coastal environments remain poorly understood. This study simulated sewage influx into coastal waters using microcosms to investigate the decay dynamics of particle-associated (PA) and free-living (FL) ARGs. Results showed that four ARGs, including two sulfonamide resistance genes (sul1 and sul2) and two tetracycline resistance genes (tetB and tetG), exhibited significantly lower decay rates in the PA fraction than in the FL fraction. Specifically, bacterial decay (k = 0.96 day[-1]) and horizontal gene transfer decay (k = 0.62 day[-1]) were both slower in the PA fraction compared to the FL fraction (1.56 day[-1] and 1.98 day[-1], respectively). These results indicated that suspended particles slow down the decay of ARGs. Microbial community analysis revealed approximately 80 % similarity between sewage and seawater at day 0, but a marked increase in unique bacterial genera and unknown-source taxa was observed at day 15. These results suggest that sewage discharge rapidly alters the composition of native seawater communities. Furthermore, suspended particles harbored higher abundances of unknown-source bacteria and displayed stronger bacterial community interactions than the surrounding water. These findings advance our understanding of ARG persistence and microbial community dynamics, offering critical insights for understanding ARGs dissemination from wastewater discharge.},
}
@article {pmid40372033,
year = {2025},
author = {Kiiru, S and Kasiano, P and Maina, J and Mwaniki, JN and Songoro, E and Kariuki, S},
title = {Molecular characterization of multidrug-resistant E. coli recovered from diarrheagenic children under 5 years from Mukuru Informal Settlement, Nairobi, Kenya, based on whole-genome sequencing analysis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0142024},
doi = {10.1128/spectrum.01420-24},
pmid = {40372033},
issn = {2165-0497},
abstract = {UNLABELLED: High genomic plasticity within Escherichia coli enables it to acquire and accumulate genetic material through horizontal gene transfer. In this study, we sought to investigate the virulence genes, phylogroups, antibiotic resistance genes, plasmid replicons, multilocus sequence types (MLST), and core genome MLST of multidrug-resistant E. coli recovered from diarrheagenic children under 5 years from Mukuru Informal Settlement in Nairobi, Kenya. A total of 39 multidrug-resistant (MDR) strains had their DNA extracted, and whole-genome sequencing was done using the Illumina HiSeq 2000 platform. Twenty-six E. coli assemblies were analyzed using web-based bioinformatics tools available at the Centre for Genomic Epidemiology and EnteroBase. The isolates were categorized into four main phylogroups, where 10/26 (38.5%) belonged to the B2 phylogroup, 4/26 (15.4%) belonged to D, 3/26 (11.5%) belonged to A, 1/26 (3.8%) belonged to B1, while 8/26 (30.8%) were not determined. FimH30 was predominantly found in the most frequent phylogroup B2 and sequence type (ST) 131. The most common beta-lactam resistance genes were bla TEM-1B and blaCTXM 15, followed by three fluoroquinolone resistance genes [qnrS1 6/26 (23.1%), qnrB4 2/26 (7.7%), and aac(6')-Ib-cr, 8/26 (30.8%)]. Of 26 isolates, 15 had at least one amino acid substitution in the housekeeping genes gyrA (p.S83L), gyrA (p.D87N), parC (p.S80I), parC (p.E84V), parC (p.S57T), and parE (p.I529L), associated with resistance to fluoroquinolones. A total of 40 diverse virulence genes were detected among the isolates. Thirteen different STs were isolated from the E. coli genomes, which included ST 131, ST 3036, ST 38, ST 10, ST 12569, ST 15271, ST 2076, ST 311, ST 3572, ST 394, ST 453, ST 46, and ST 1722. Only two isolates (2/26, 7.7%) from the Municipal City Council clinic were genetically related. Additionally, the most abundant plasmid replicon identified belonged to the IncF family, IncFII(pRSB107), in particular, followed by the Col family. The study highlighted the first E. coli ST46 to harbor the bla NDM5 gene encoded in Col(BS512), IncFII(pRSB107), and IncFIB(AP001918) plasmid replicons in Kenya. We further demonstrated the diversity of MDR E. coli associated with diarrhea in an endemic setting in Kenya.<br><br>IMPORTANCE: This study investigated the molecular characterization of multidrug-resistant Escherichia coli isolated from diarrheagenic children under 5 years of age in Mukuru Informal Settlement in Nairobi, Kenya. This is an important addition to the genomic analysis data of multi-drug resistant diarrheal Escherichia coli in Kenya. The use of whole-genome sequencing to identify and characterize these isolates is valuable and provides valuable insights into the molecular epidemiology of E. coli in the region.},
}
@article {pmid40370256,
year = {2025},
author = {Wachino, JI},
title = {Horizontal Gene Transfer Systems for Spread of Antibiotic Resistance in Gram-Negative Bacteria.},
journal = {Microbiology and immunology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1348-0421.13222},
pmid = {40370256},
issn = {1348-0421},
abstract = {Antibiotic-resistant bacteria have become a significant global threat to public health due to the increasing difficulty in treatment. These bacteria acquire resistance by incorporating various antibiotic resistance genes (ARGs) through specialized gene transfer mechanisms, allowing them to evade antibiotic attacks. Conjugation, transformation, and transduction are well-established mechanisms that drive the acquisition and dissemination of ARGs in Gram-negative bacteria. In particular, the horizontal transfer of plasmids carrying multiple ARGs is highly problematic, as it can instantly convert susceptible bacteria into multidrug-resistant ones. Transduction, mediated by bacteriophages that package ARG-containing chromosomal DNA from host cells, also plays a crucial role in ARG spread without requiring direct cell-to-cell contact. Recently, a novel horizontal gene transfer (HGT) mechanism involving outer membrane vesicles (OMVs) has been identified as a key player in ARG dissemination. OMVs-nanoscale, spherical structures produced by bacteria during growth-have been found to carry small plasmids and chromosomal DNA fragments containing ARGs from their host bacteria. This newly discovered transfer process, termed "vesiduction," enables intercellular DNA exchange and further contributes to the spread of antibiotic resistance. Additionally, mobile genetic elements such as transposons, insertion sequences, and site-specific recombination systems like integrons facilitate rearrangement of ARGs, including their translocation between chromosomes and plasmids. This review explores the molecular mechanisms underlying the HGT of ARGs, with a particular focus on clinically isolated antibiotic-resistant Gram-negative bacteria.},
}
@article {pmid40368010,
year = {2025},
author = {Liu, H and Wang, L and Dong, Z and Wen, S and Liu, C and Wang, J and Wang, J and Zhu, L and Kim, YM and Wang, J},
title = {Insights into the drivers of antibiotic resistance gene migration in soil-lettuce system with manure application from different sources.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126444},
doi = {10.1016/j.envpol.2025.126444},
pmid = {40368010},
issn = {1873-6424},
abstract = {The application of livestock manure serves as a significant source of ARGs in soils. To study the impact of manure application on the migration of ARGs in the soil-plant system, we set different application ratios (1%, 3%, 8%) of chicken and cow manure for treatment. The study's results demonstrated that the application of organic fertilizers increased the quantity of resistance genes in soil, root, and leaf zones. This change was influenced by the type and proportion of the organic fertilizers used. ARGs and MGEs exhibited the highest absolute enrichment levels in leaf tissues (2.53 and 2.01 times, respectively) with the 3% cow manure treatment. In contrast, chicken manure exhibited the highest enrichment levels after the 1% addition (2.51 and 1.81 times, respectively). The applied manure exhibited a high degree of similarity in bacterial community composition with the soil-lettuce system, indicating that ARGs may spread through microorganisms in this system. This study demonstrated that the evolution of bacterial community structure plays a pivotal role in mediating and driving the migration of ARGs within manure-amended soil-plant ecosystems, providing a theoretical basis for understanding the transmission of ARGs in soils and plants due to agricultural production activities.},
}
@article {pmid40366029,
year = {2025},
author = {Rojas-Villalobos, C and Ossandon, FJ and Castillo-Vilcahuaman, C and Sepúlveda-Rebolledo, P and Castro-Salinas, D and Zapata-Araya, A and Arisan, D and Perez-Acle, T and Issotta, F and Quatrini, R and Moya-Beltrán, A},
title = {MOBHunter: a data integration platform for identification and classification of mobile genetic elements in microbial genomes.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf396},
pmid = {40366029},
issn = {1362-4962},
support = {1221035//ANID/ ; ANID/BASAL/FB210008//ANID/ ; 32300527//PROYECTO FONDECYT POSTDOCTORADO/ ; 3140005//PROYECTO FONDECYT POSTDOCTORADO/ ; 21241467//ANID/BECAS/DOCTORADO NACIONAL/ ; USS-FIN-24-CNGD-26//Fondo VRID apoyo a congresos/ ; //VRID-Universidad San Sebasti&#xe1;n PROYECTO/USS-FIN-23-PDOC-03USS/ ; //Vicerrector&#xed;a de Investigaci&#xf3;n y Postgrado - Escuela de Postgrado - Universidad Tecnol&#xf3;gica Metropolitana/ ; USS-FIN-25-APCS-20//Vicerrector&#xed;a de Investigaci&#xf3;n y Doctorados de la Universidad San Sebasti&#xe1;n - Fondo/ ; },
abstract = {Horizontal gene transfer plays a critical role in microbial genome evolution and adaptation. Integrated foreign DNA fragments encompass various types of mobile genetic elements (MGEs), ranging from small transposons to conspicuous integrative and conjugative elements. These regions often confer advantageous traits, including antibiotic resistance or novel metabolic capabilities, and contain foreign sequence signatures and hallmark genes such as transposases, integrases, etc. While bioinformatic tools target specific MGE subsets using alignments, compositional signatures, or diagnostic gene mapping, no single platform offers a unified framework for comprehensive, evidence-based, MGE identification and classification. To address this challenge, we developed MOBHunter, an advanced bioinformatic pipeline that consolidates standalone tools and in-house algorithms. Unlike basic tool concatenation, MOBHunter yields consensus identifications, score-supported classifications, and enhanced web visualizations. The platform reduces end user analysis time by integrating data collection, processing, and interpretation into a unified workflow. It delivers robust classifications of MGEs into distinct families and provides a comprehensive overview of the flexible regions of any given input genome. URL: https://informatica.utem.cl/mobhunter/.},
}
@article {pmid40362661,
year = {2025},
author = {Rybak, B and Werbowy, O and Debowski, K and Plotka, M and Kocot, AM},
title = {Coagulase-Negative Staphylococci Determined as Blood Culture Contamination Have High Virulence Characteristic Including Transfer of Antibiotic Resistance Determinants to Staphylococcus aureus and Escherichia coli.},
journal = {International journal of molecular sciences},
volume = {26},
number = {9},
pages = {},
doi = {10.3390/ijms26094424},
pmid = {40362661},
issn = {1422-0067},
mesh = {Biofilms/drug effects/growth &amp; development ; Humans ; *Escherichia coli/genetics/drug effects/pathogenicity ; *Staphylococcus aureus/drug effects/pathogenicity/genetics/isolation &amp; purification ; Coagulase/metabolism ; Anti-Bacterial Agents/pharmacology ; *Blood Culture ; *Drug Resistance, Bacterial/genetics ; Virulence/genetics ; Microbial Sensitivity Tests ; *Staphylococcus/drug effects/pathogenicity/genetics/isolation &amp; purification ; Staphylococcal Infections/microbiology ; Gene Transfer, Horizontal ; },
abstract = {This study aimed to evaluate the virulence of 36 clinical isolates estimated as blood culture contaminants (BCCs). MALDI-TOF MS classified all isolates as coagulase-negative staphylococci (CoNS) with the highest percentage of S. epidermidis (77.78%). All tested strains formed biofilms with greater ability at room temperature than 37 °C. CoNS were sensitive to vancomycin (0% resistance) and had relatively low resistance to linezolid and rifampicin (8.33 and 22.22% resistance). The highest resistance was observed for penicillin (94.44%). Moreover, we observed the transfer of antibiotic resistance genes from the tested CoNS to S. aureus and even to E. coli, although with lower efficiency. CoNS in planktonic form were completely combated by antiseptics after 10 and 60 s exposition, and activity against biofilms was time-dependent. The complete elimination of biofilms was observed after a 180 s exposure to Kodan and CITROclorex, and this exposure to Rivanol and Octenidyne showed still viable cells (>0.9 log CFU/mL). Our findings showed that a careful selection of antiseptics and extending the exposure time before blood collection can reduce the occurrence of blood culture contamination. However, our most important finding is the indication that CoNS naturally occurring on human skin and mucous membranes exhibit antibiotic resistance, and what is more, determinants of antibiotic resistance are transferred to both closely related Gram-positive bacteria and phylogenetically distant Gram-negative bacteria. Thus, our findings shed new light on CoNS-they indicate the necessity of their control due to the effective transfer of mobile genetic elements harboring antibiotic resistance genes, which may contribute to the spread of resistance genes and deepening the antibiotic crisis.},
}
@article {pmid40359552,
year = {2025},
author = {Otten, L and Liu, H and Meeprom, N and Linan, A and Puglisi, C and Chen, K},
title = {Accumulation of numerous cellular T-DNA sequences in the genus Diospyros by multiple rounds of natural transformation.},
journal = {The Plant journal : for cell and molecular biology},
volume = {122},
number = {3},
pages = {e70202},
doi = {10.1111/tpj.70202},
pmid = {40359552},
issn = {1365-313X},
support = {32370382//National Natural Science Foundation of China/ ; (G242406 to KC)//Shanghai landscaping and city appearance administrative bureau/ ; },
mesh = {*Diospyros/genetics ; *DNA, Bacterial/genetics ; *Gene Transfer, Horizontal/genetics ; *Transformation, Genetic ; Genome, Plant/genetics ; Phylogeny ; Agrobacterium/genetics ; },
abstract = {Horizontal gene transfer (HGT) is an important phenomenon in the evolutionary history of plants. Natural transformation by Agrobacterium is a special case of HGT and leads to the insertion of cellular T-DNA (cT-DNA) sequences, for example, in Diospyros lotus. The genus Diospyros contains about 795 species with economically important members, like different types of persimmon (D. kaki, D. lotus, and D. virginiana) and ebony (e.g., D. ebenum). Whole genome sequences (WGS) from D. kaki, D. oleifera, D. lotus, and D. virginiana were investigated for cT-DNAs. These four species belong to one clade and contain 15 different cT-DNAs (DiTA to DiTO). The hexaploid species D. kaki cv. "Xiaoguo-tianshi" contains seven types of cT-DNA (DiTA to DiTG) on 27 of 42 homeologs, adding up to 628 kb of cT-DNA. Five of these seven cT-DNAs are non-fixed, as shown by empty chromosomal insertion sites. The evolutionary history of the Diospyros cT-DNAs was reconstructed using the divergence of their inverted repeats. Insert age varied from 3 to 12 million years. Partial cT-DNA sequences were detected in 35 additional species from five Diospyros clades. Our data highlight the unexpectedly large scale of natural Agrobacterium transformation in Diospyros and demonstrate the necessity of whole genome approaches for studies on the origin and evolution of cT-DNAs.},
}
@article {pmid40359213,
year = {2025},
author = {Zhai, K and Yin, K and Lin, Y and Chen, S and Bi, Y and Xing, R and Ren, C and Chen, Z and Yu, Z and Chen, Z and Zhou, S},
title = {Free Radicals on Aging Microplastics Regulated the Prevalence of Antibiotic Resistance Genes in the Aquatic Environment: New Insight into the Effect of Microplastics on the Spreading of Biofilm Resistomes.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12699},
pmid = {40359213},
issn = {1520-5851},
abstract = {The spread of antibiotic resistance genes (ARGs) by microplastics has received a great concern in coexisting "hotspots". Despite most microplastics suffering from natural aging, little is known about the effect of aging microplastics (A-MPs) on ARGs dissemination. Here, we demonstrated significant suppression of A-MPs on ARGs dissemination in natural rivers. Although ARGs and mobile genetic elements (MGEs) were effectively enriched on A-MPs, the relative abundance of ARGs and MGEs on A-MPs as well as in receiving water decreased by approximately 21.4% to 42.3% during a period of 30 days of dissemination. Further investigation revealed that [•]OH was consistently generated on A-MPs with a maximum value of 0.2 μmol/g. Importantly, scavenging of [•]OH significantly increased the relative abundance of ARGs and MGEs both on A-MPs and in receiving water 1.4-29.1 times, indicating the vital role of [•]OH in suppressing ARGs dissemination. Microbial analysis revealed that [•]OH inhibited the potential antibiotic-resistant bacteria in surface biofilms, such as Pseudomonas and Acinetobacter (with a decrease of 68.8% and 89.3%). These results demonstrated that [•]OH was extensively produced on A-MPs, which greatly reduced both the vertical and horizontal gene transfer of ARGs. This study provided new insights into the dissemination of ARGs through microplastics in natural systems.},
}
@article {pmid40358144,
year = {2025},
author = {Mukherjee, SD and Suryavanshi, M and Knight, J and Lange, D and Miller, AW},
title = {Metagenomic and phylogenetic analyses reveal gene-level selection constrained by bacterial phylogeny, surrounding oxalate metabolism in the gut microbiota.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0091324},
doi = {10.1128/msphere.00913-24},
pmid = {40358144},
issn = {2379-5042},
abstract = {The gut microbiota is critical for neutralizing dietary toxins. Oxalate is a toxin commonly produced by plants to deter herbivory and is widely consumed in the human diet. Excess levels of systemic or urinary oxalate increase risk of multiple urologic and cardiometabolic diseases. The current study employed multiple amplicon-based and shotgun metagenomic methodologies, alongside comparative phylogenetic analyses, to interrogate evolutionary radiation surrounding microbial oxalate degradation within the human gut microbiome. In conservative genome-based estimates, over 30% of gut microbial species harbored at least one oxalate-handling gene, with the specific pathways used dependent on bacterial phylum. Co-occurrence analyses revealed interactions between specialist genes that can metabolize oxalate or its by-products, but not multi-functional genes that can act in more than one oxalate-related pathway. Specialization was rare at the genome level. Amplicon-based metagenomic sequencing of the oxalate-degrading gene, formyl-CoA transferase (frc), coupled with molecular clock phylogenetic analyses are indicative of rapid evolutionary divergence, constrained by phylum. This was corroborated by paired analyses of non-synonymous to synonymous substitutions (dN/dS ratios), which pointed toward neutral to positive selection. Sequence similarity network analyses of frc sequences suggest extensive horizontal gene transferring has occurred with the frc gene, which may have facilitated rapid divergence. The frc gene was primarily allocated to the Pseudomonodota phylum, particularly the Bradyrhizobium genus, which is a species capable of utilizing oxalate as a sole carbon and energy source. Collectively evidence provides strong support that, for oxalate metabolism, evolutionary selection occurs at the gene level, through horizontal gene transfer, rather than at the species level.IMPORTANCEA critical function of the gut microbiota is to neutralize dietary toxins, such as oxalate, which is highly prevalent in plant-based foods and is not degraded by host enzymes. However, little is known about the co-evolutionary patterns of plant toxins and the mammalian gut microbiota, which are expected to exhibit features of an evolutionary arms race. In the current work, we present molecular evidence that microbial genes for oxalate degradation are highly prevalent in humans, potentially driven by extensive horizontal gene transfer events. Phylogenetic analyses reveal that oxalate-degrading genes are under a positive selection pressure and have historically undergone rapid diversification events, which has led to diverse ecological strategies for handling oxalate by gut bacteria. Collectively, data shed light on potential evolutionary relationships between the diet and the gut microbiota that occur relatively independently of the mammalian host.},
}
@article {pmid40118050,
year = {2025},
author = {Berridge, MV and Zobalova, R and Boukalova, S and Caicedo, A and Rushworth, SA and Neuzil, J},
title = {Horizontal mitochondrial transfer in cancer biology: Potential clinical relevance.},
journal = {Cancer cell},
volume = {43},
number = {5},
pages = {803-807},
doi = {10.1016/j.ccell.2025.03.002},
pmid = {40118050},
issn = {1878-3686},
mesh = {Humans ; *Neoplasms/genetics/pathology/metabolism ; *Mitochondria/genetics/metabolism ; *Gene Transfer, Horizontal ; Animals ; DNA, Mitochondrial/genetics ; Clinical Relevance ; },
abstract = {Recent research highlights horizontal mitochondrial transfer as a key biological phenomenon linked to cancer onset and progression. The transfer of mitochondria and their genomes between cancer and non-cancer cells shifts our understanding of intercellular gene trafficking, increasing the metabolic fitness of cancer cells and modulating antitumor immune responses. This process not only facilitates tumor progression but also presents potential therapeutic opportunities.},
}
@article {pmid40356790,
year = {2025},
author = {, and Casacuberta, J and Barro, F and Braeuning, A and de Maagd, R and Epstein, MM and Frenzel, T and Gallois, JL and Koning, F and Messéan, A and Moreno, FJ and Nogué, F and Savoini, G and Schulman, AH and Tebbe, C and Veromann, E and Ardizzone, M and De Sanctis, G and Dumont, AF and Ferrari, A and Gennaro, A and Gómez Ruiz, J&#xc1; and Goumperis, T and Kagkli, DM and Lewandowska, A and Camargo, AM and Franco, MN and Piffanelli, P and Raffaello, T and Rodrigues, M and Sánchez-Brunete, E},
title = {Assessment of genetically modified sugar beet KWS20-1 (application GMFF-2023-14732).},
journal = {EFSA journal. European Food Safety Authority},
volume = {23},
number = {5},
pages = {e9381},
doi = {10.2903/j.efsa.2025.9381},
pmid = {40356790},
issn = {1831-4732},
abstract = {Genetically modified sugar beet KWS20-1 was developed to confer tolerance to glyphosate-, dicamba- and glufosinate-ammonium-based herbicides. These properties were achieved by introducing the cp4 epsps, dmo and pat expression cassettes. The molecular characterisation data and bioinformatic analyses do not identify issues requiring further safety assessment. None of the identified differences in the agronomic/phenotypic and compositional characteristics tested between sugar beet KWS20-1 and its conventional counterpart need further assessment, except for pectin in roots, which underwent additional evaluation and was found not to raise any safety or nutritional concerns. The GMO Panel does not identify safety concerns regarding the potential toxicity and allergenicity of the CP4 EPSPS, DMO and PAT proteins as expressed in sugar beet KWS20-1, and finds no evidence that the genetic modification would change the overall safety of sugar beet KWS20-1 as food and feed. In the context of this application, the consumption of food and feed from sugar beet KWS20-1 does not represent a nutritional concern in humans and animals. The GMO Panel concludes that sugar beet KWS20-1 is as safe as the conventional counterpart and non-GM sugar beet reference varieties tested, and no post-market monitoring of food/feed is considered necessary. The scope of the application does not include cultivation and import of viable materials in the EU and the products would be expected to only contain residual amounts of DNA and protein. The environmental risk assessment was limited to the possible plant-to-bacteria horizontal gene transfer and the evaluation of potential interactions of KWS20-1 sugar beet products with biogeochemical cycles, and neither of them indicates a safety concern. The GMO Panel concludes that the sugar beet KWS20-1 is as safe as its conventional counterpart and the tested non-GM reference sugar beet varieties with respect to potential effects on human and animal health and the environment.},
}
@article {pmid40356278,
year = {2025},
author = {Watanabe, Y and Kunishi, K and Matsui, H and Sakata, N and Noutoshi, Y and Toyoda, K and Ichinose, Y},
title = {Genomic Islands of Pseudomonas syringae pv. tabaci 6605: Identification of PtaGI-1 as a Pathogenicity Island With Effector Genes and a Tabtoxin Cluster.},
journal = {Molecular plant pathology},
volume = {26},
number = {5},
pages = {e70087},
doi = {10.1111/mpp.70087},
pmid = {40356278},
issn = {1364-3703},
support = {22H0234814//Japan Society for the Promotion of Science/ ; },
mesh = {*Genomic Islands/genetics ; *Pseudomonas syringae/genetics/pathogenicity ; *Multigene Family/genetics ; Virulence/genetics ; Nicotiana/microbiology ; *Bacterial Toxins/genetics ; Plant Diseases/microbiology ; Genes, Bacterial ; Mutation/genetics ; },
abstract = {Genomic islands (GIs) are 20-500 kb DNA regions that are thought to be acquired by horizontal gene transfer. GIs that confer pathogenicity and environmental adaptation have been reported in Pseudomonas species; however, GIs that enhance bacterial virulence have not. Here, we identified 110 kb and 103 kb GIs in P. syringae pv. tabaci 6605 (Pta6605), the causative agent of tobacco wildfire disease, which has the ability to produce tabtoxin as a phytotoxin. These GIs are partially homologous to known genomic islands in Pseudomonas aeruginosa and P. syringae pv. phaseolicola and were designated PtaGI-1 and PtaGI-2. Both PtaGIs conserve core genes, whereas each GI possesses different accessory genes. PtaGI-1 contains a tabtoxin biosynthetic gene cluster and three type III effector genes among its accessory genes, whereas PtaGI-2 also contains homologous genes to hsvABC, pathogenicity-related genes in Erwinia amylovora. Inoculation revealed that the PtaGI-1 mutant, but not the PtaGI-2 mutant, lost the ability to biosynthesise tabtoxin and to cause disease. Therefore, PtaGI-1 is thought to be a pathogenicity island. Both PtaGI-1 and PtaGI-2 have a pseudogene of tRNA[Lys] on the left border and an intact tRNA[Lys] gene on the right border. In a colony of Pta6605, both GIs can be excised at tRNA[Lys], and PtaGI-1 and PtaGI-2 exist in a circular form. These results indicate that tabtoxin biosynthesis genes in PtaGI-1 are required for disease development, and PtaGI-1 is necessary for Pta6605 virulence.},
}
@article {pmid40351943,
year = {2025},
author = {Kumar, A and Sharma, A and Mehrishi, P and Solanki, S and Faujdar, SS and Khatun, A},
title = {Detection of the blaNDM-1 Gene in Carbapenem-Resistant Enterobacterales Causing Urinary Tract Infections in Patients at a Rural Teaching Hospital.},
journal = {Cureus},
volume = {17},
number = {4},
pages = {e81811},
pmid = {40351943},
issn = {2168-8184},
abstract = {BACKGROUND: Carbapenem-resistant Enterobacterales (CRE) pose a significant public health threat due to their resistance to last-line antibiotics. Urinary tract infections (UTIs) caused by multidrug-resistant organisms have become a major challenge in clinical settings. The spread of CRE is largely attributed to the acquisition of carbapenemase-encoding genes, horizontal gene transfer, and overuse of broad-spectrum antibiotics.<br><br>METHODOLOGY: A total of 9235 urine samples were analyzed, and more than 10[5] CFU/mL bacterial count was considered positive for UTI. These bacteria were identified and further screened for CRE and blaNDM-1 genes.<br><br>RESULTS: A total of 9235 urine samples were analyzed, out of which 555 were identified as Enterobacterales. Among these, 47 were confirmed as CRE, accounting for 8.5% of the Enterobacterales isolates. Out of 47 CRE, 28 were positive for the&#xa0;blaNDM-1 gene.<br><br>CONCLUSIONS: The study highlights the increasing burden of CRE and the urgent need for stringent antimicrobial stewardship, effective infection control measures, and the development of new therapeutic strategies to combat MDR infections. Additionally, risk factors associated with CRE infections, their implications on public health, and potential future therapeutic approaches are discussed.},
}
@article {pmid40350664,
year = {2025},
author = {Sarink, MJ and Grassi, L and Tielens, AGM and Verbon, A and Vos, MC and Goessens, W and Strepis, N and Klaassen, CHW and van Hellemond, JJ},
title = {Acanthamoeba castellanii Can Facilitate Plasmid Transfer Between Environmental Pseudomonas spp.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70051},
doi = {10.1002/jobm.70051},
pmid = {40350664},
issn = {1521-4028},
support = {//This work was funded by the Erasmus MC and the Netherlands Centre for One Health./ ; },
abstract = {The conditions in which antimicrobial resistance (AMR) genes are transferred in natural environments are poorly understood. Acanthamoeba castellanii (a cosmopolitan environmental amoeba) feeds on bacteria by phagocytosis, which places the consumed bacteria closely together in a food vacuole (phagosome) of the amoeba. This way, amoebae can facilitate genetic exchanges between intra-amoebal bacteria. We studied this phenomenon in the clinically relevant bacteria Pseudomonas oleovorans and Pseudomonas aeruginosa (strain 957). The internalization of both the plasmid donor and recipient bacteria was shown by confocal microscopy. In seven independent experiments, an on average 12-fold increase in transfer of the blaVIM-2 gene between these two Pseudomonas strains was observed in the presence of A. castellanii compared to its absence. Negligible or no plasmid transfer was observed from P. oleovorans to 18 other investigated strains of P. aeruginosa. AMR gene transfer via plasmids between Pseudomonas species is highly strain-dependent and A. castellanii can substantially enhance plasmid transfer. This process of plasmid transfer might also occur between other bacteria and predatory protozoa, such as amoebae that reside in the gut of humans and animals.},
}
@article {pmid40346915,
year = {2025},
author = {Chen, SY and Huang, K and He, ZH and Zhao, FJ},
title = {Ampicillin Exposure and Glutathione Deficiency Synergistically Promote Conjugative Transfer of Plasmid-Borne Antibiotic Resistance Genes.},
journal = {Environmental microbiology},
volume = {27},
number = {5},
pages = {e70106},
doi = {10.1111/1462-2920.70106},
pmid = {40346915},
issn = {1462-2920},
support = {42090062//National Natural Science Foundation of China/ ; 336168//Research Council of Norway/ ; },
mesh = {*Glutathione/deficiency/metabolism ; *Ampicillin/pharmacology ; *Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; *Conjugation, Genetic/drug effects ; Escherichia coli/genetics/drug effects ; Enterobacter/genetics/drug effects ; Oxidative Stress ; *Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal ; Soil Microbiology ; *Drug Resistance, Microbial/genetics ; },
abstract = {Plasmid-mediated conjugation is an important pathway for the spread of antibiotic resistance genes (ARGs), posing a significant risk to global public health. It has been reported that the conjugative transfer of ARGs could be enhanced by oxidative stress. Whether endogenous glutathione (GSH), a major non-protein thiol compound involved in cellular redox homeostasis, influences conjugative transfer is unknown. In this study, we show that the deletion of the GSH biosynthesis gene gshA and ampicillin exposure synergistically promoted the conjugative transfer of plasmid RP4 bearing multiple ARGs from the soil bacterium Enterobacter sp. CZ-1 to Escherichia coli S17-1λπ in co-culture experiments and to diverse soil bacteria belonging to eight phyla, including some potential human pathogens, in a soil incubation experiment. The deletion of gshA increased ROS generation and cell membrane permeability, and upregulated the expression of the genes involved in intracellular oxidative stress regulation, membrane permeability, plasmid replication, and the SOS response process, especially under ampicillin exposure. These results suggest that endogenous GSH is an important factor affecting the spread of plasmid-borne ARGs. Exposure to antibiotics and environmental stresses that cause a depletion of endogenous GSH in vivo are likely to increase the risk of ARG dissemination in the environment.},
}
@article {pmid40036506,
year = {2025},
author = {Lin, J and Ni, S and Li, B and Guo, Y and Gao, X and Liu, Y and Yi, L and Wang, P and Chen, R and Yao, J and Wood, TK and Wang, X},
title = {A noncanonical intrinsic terminator in the HicAB toxin-antitoxin operon promotes the transmission of conjugative antibiotic resistance plasmids.},
journal = {Nucleic acids research},
volume = {53},
number = {5},
pages = {},
pmid = {40036506},
issn = {1362-4962},
support = {42188102//National Science Foundation of China/ ; 2022FY100600//Science &amp; Technology Fundamental Resources Investigation Program/ ; 2022RC1169//Science and Technology Innovation Program of Hunan Province/ ; 2019BT02Y262//Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program/ ; SCSIO2023QY03//South China Sea Institute of Oceanology, Chinese Academy of Sciences/ ; //Ocean Negative Carbon Emissions Program/ ; },
mesh = {*Toxin-Antitoxin Systems/genetics ; *Operon ; *Plasmids/genetics ; *Conjugation, Genetic ; *Escherichia coli Proteins/genetics ; *Terminator Regions, Genetic ; Escherichia coli/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Promoter Regions, Genetic ; *Bacterial Toxins/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; },
abstract = {Conjugative plasmids, major vehicles for the spread of antibiotic resistance genes, often contain multiple toxin-antitoxin (TA) systems. However, the physiological functions of TA systems remain obscure. By studying two TA families commonly found on colistin-resistant IncI2 mcr-1-bearing plasmids, we discovered that the HicAB TA, rather than the StbDE TA, acts as a crucial addiction module to increase horizontal plasmid-plasmid competition. In contrast to the canonical type II TA systems in which the TA genes are cotranscribed and/or the antitoxin gene has an additional promoter to allow for an increased antitoxin/toxin ratio, the HicAB TA system with the toxin gene preceding the antitoxin gene employs internal transcription termination to allow for a higher toxin production. This intrinsic terminator, featuring a G/C-rich hairpin with a UUU tract, lies upstream of the antitoxin gene, introducing a unique mechanism for the enhancing toxin/antitoxin ratio. Critically, the hicAB TA significantly contributes to plasmid competition and plasmid persistence in the absence of antibiotic selection, and deleting this intrinsic terminator alone diminishes this function. These findings align with the observed high occurrence of hicAB in IncI2 plasmids and the persistence of these plasmids after banning colistin as a feed additive. This study reveals how reprogramming the regulatory circuits of TA operons impacts plasmid occupancy in the microbial community and provides critical targets for combating antibiotic resistance.},
}
@article {pmid40345346,
year = {2025},
author = {Zhang, Q and Yan, D and Chen, L},
title = {virK and mig-14 Constitute a PhoP-dependent Operon and Contribute to the Intracellular Survival and Polymyxin B Resistance of Salmonella Typhi.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107668},
doi = {10.1016/j.micpath.2025.107668},
pmid = {40345346},
issn = {1096-1208},
abstract = {In bacteria, adjacent and functionally similar genes are typically transcribed as operons. The virulence genes virK and mig-14 are acquired through horizontal gene transfer in Salmonella. Previous studies have reported that these two genes have similar functions in terms of bacterial survival within macrophages and resistance to antimicrobial peptides. Nevertheless, the specific expression characteristics of the two genes remain unclear. This study revealed that virK and mig-14 were transcribed as a single operon in Salmonella Typhi. The virK-mig-14 operon was found to be activated under conditions of early hyperosmotic stress and polymyxin B stimulation, and its activation was dependent on the presence of the regulator PhoP. The luminescence assay demonstrated that the activity of the virK promoter was markedly elevated in an environment conducive to operon activation, whereas the mig-14 promoter exhibited no discernible change. This suggests that mig-14 is predominantly transcribed as a component of the operon. In the PhoP activation environment, which has a mildly acidic pH, low Mg[2+] levels, and intracellular macrophages, the virK-mig-14 operon exhibited significant activation. The absence of virK or mig-14 resulted in the impaired survival of Salmonella Typhi within macrophages and decreased its tolerance to polymyxin B. Collectively, this study shows that virK and mig-14 constitute an operon whose activation depends on PhoP and that it promotes S. Typhi's survival in macrophages and resistance to polymyxin B.},
}
@article {pmid39988070,
year = {2025},
author = {Zhang, Y and Yang, C and Yao, J and Zhou, L and Zhang, X and Wang, H and Liu, L and Tu, Y and Li, X},
title = {Spread of the Fosfomycin resistance fosA3 gene via the IS26 mobile element between plasmids and the chromosome of carbapenem-resistant Escherichia coli in China.},
journal = {Journal of global antimicrobial resistance},
volume = {42},
number = {},
pages = {80-87},
doi = {10.1016/j.jgar.2025.02.011},
pmid = {39988070},
issn = {2213-7173},
mesh = {*Fosfomycin/pharmacology ; *Plasmids/genetics ; China ; *Escherichia coli/genetics/drug effects ; *Escherichia coli Proteins/genetics ; *Anti-Bacterial Agents/pharmacology ; Phylogeny ; Humans ; Whole Genome Sequencing ; Escherichia coli Infections/microbiology ; *Carbapenem-Resistant Enterobacteriaceae/genetics/drug effects ; Microbial Sensitivity Tests ; *Chromosomes, Bacterial/genetics ; *Interspersed Repetitive Sequences ; Carbapenems/pharmacology ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; },
abstract = {OBJECTIVE: This study investigated fosA3-positive strains selected from carbapenem-resistant Escherichia coli (CREC) and further characterized them through genomic and phenotypic analyses.<br><br>METHODS: fosA3-positive CREC strains were subjected to agar dilution. Whole-genome sequencing (WGS) was used to identify molecular mechanisms of fosfomycin resistance and to investigate plasmid structure characteristics through comparative analysis. Conjugative transfer experiments were used to evaluate plasmid transfer ability, followed by plasmid stability assessment. Growth rate analysis evaluated the fitness costs of transconjugants. Phylogenetic analysis was performed on fosA3-positive CREC strains. Furthermore, analysis of fos genes carrying E. coli sequence types (STs) from the NCBI database explored the evolution and spread of fosfomycin resistance.<br><br>RESULTS: Between 2016 and 2023, a total of 11.23% CREC strains (10/89) carrying fosA3 were collected from a hospital for further analysis. These ten fosA3-positive strains were also resistant to fluoroquinolones and ceftazidime-avibactam. The fosA3 gene was located within a similar genetic background (IS26-fosA3-1811bp-IS26) on plasmids or chromosomes. The fosA3-carrying IncFII(pHN7A8)-IncX3 cointegrate plasmid pEC00-2-145k was transferable, with fitness cost of 20% to host. Furthermore, three of ten fosA3-positive CREC strains belonged to ST156. Analysis of fos genes carrying E. coli strains from China in the NCBI database identified ST156 (5.39%, 147/2,725) and ST167 (5.21%, 142/2,725) as predominant STs.<br><br>CONCLUSIONS: This study revealed fosA3 in CREC strains was associated with IS26 and spreads fosfomycin resistance through horizontal transfer, occurring both on chromosomes and plasmids. The first fosA3-carrying cointegrate plasmid pHN7A8-IncX3-type in E. coli isolates was reported, highlighting a new route of fosfomycin resistance spread. Additionally, notable diversity of ST among fosA3-carrying E. coli strains highlights complexity of fosfomycin resistance dissemination and the importance of surveillance and control measures.},
}
@article {pmid39909367,
year = {2025},
author = {Zhang, G and Li, C and Li, X and Li, Y and Li, Y and Zeng, X and Xu, C and Wu, S and Dong, N},
title = {Ibuprofen prevents the conjugative transfer of plasmid-mediated antimicrobial resistance genes.},
journal = {Journal of global antimicrobial resistance},
volume = {42},
number = {},
pages = {10-14},
doi = {10.1016/j.jgar.2025.01.012},
pmid = {39909367},
issn = {2213-7173},
mesh = {*Plasmids/genetics ; *Conjugation, Genetic/drug effects ; *Ibuprofen/pharmacology ; *Drug Resistance, Multiple, Bacterial/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; Humans ; Microbial Sensitivity Tests ; Escherichia coli/genetics/drug effects ; *Gene Transfer, Horizontal/drug effects ; },
abstract = {Refractory infections caused by multidrug-resistant bacteria pose a significant threat to public health. Here we report that ibuprofen inhibits conjugation of the RP4 plasmid and plasmids from clinical strains carrying different resistance genes including mcr-1, blaNDM, blaKPC, tet(X4), and tmexCD1-toprJ1. Mechanistic studies suggest that ibuprofen reduces ATP production and inhibits conjugation-related genes. The inhibitory effect of ibuprofen on conjugation has significant clinical implications for preventing the spread of multidrug resistance, opening new therapeutic avenues to combat multidrug-resistant bacteria.},
}
@article {pmid40343121,
year = {2025},
author = {Liang, H and Qi, H and Wang, C and Wang, Y and Liu, M and Chen, J and Sun, X and Xia, T and Feng, S and Chen, C and Zheng, D},
title = {Analysis of the complete mitogenomes of three high economic value tea plants (Tea-oil Camellia) provide insights into evolution and phylogeny relationship.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1549185},
doi = {10.3389/fpls.2025.1549185},
pmid = {40343121},
issn = {1664-462X},
abstract = {INTRODUCTION: Tea-oil Camellia species play a crucial economic and ecological role worldwide, yet their mitochondrial genomes remain largely unexplored.<br><br>METHODS: In this study, we assembled and analyzed the complete mitochondrial genomes of Camellia oleifera and C. meiocarpa, revealing multi-branch structures that deviate from the typical circular mitochondrial genome observed in most plants. The assembled mitogenomes span 953,690 bp (C. oleifera) and 923,117 bp (C. meiocarpa), containing 74 and 76 annotated mitochondrial genes, respectively.<br><br>RESULTS: Comparative genomic analyses indicated that C. oleifera and C. meiocarpa share a closer genetic relationship, whereas C. drupifera is more distantly related. Codon usage analysis revealed that natural selection plays a dominant role in shaping codon bias in these mitochondrial genomes. Additionally, extensive gene transfer events were detected among the three species, highlighting the dynamic nature of mitochondrial genome evolution in Tea-oil Camellia. Phylogenetic reconstruction based on mitochondrial genes exhibited incongruence with chloroplast phylogenies, suggesting potential discordance due to hybridization events, incomplete lineage sorting (ILS), or horizontal gene transfer (HGT). Furthermore, we identified species-specific mitochondrial markers, which provide valuable molecular tools for distinguishing Tea-oil Camellia species.<br><br>DISCUSSION: Our findings enhance the understanding of mitochondrial genome evolution and genetic diversity in Tea-oil Camellia, offering essential genomic resources for phylogenetics, species identification, and evolutionary research in woody plants.},
}
@article {pmid40343117,
year = {2025},
author = {Meng, D and Lu, T and He, M and Ren, Y and Fu, M and Zhang, Y and Yang, P and Lin, X and Yang, Y and Zhang, Y and Yang, Y and Jin, X},
title = {Organelle genomes of two Scaevola species, S. taccada and S. hainanensis, provide new insights into evolutionary divergence between Scaevola and its related species.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1587750},
doi = {10.3389/fpls.2025.1587750},
pmid = {40343117},
issn = {1664-462X},
abstract = {Chloroplast and mitochondrial genomes harbor crucial information that can be utilized for elucidating plant evolution and environmental adaptation. The organellar genomic characteristics of Goodeniaceae, a sister family to Asteraceae, remain unexplored. Here, using a combination of short-read and long-read sequencing technologies, we successfully assembled the complete organellar genomes of two Goodeniaceae species native to China, Scaevola taccada and S. hainanensis. Chloroplast genome collinearity analysis revealed that Scaevola expanded its genome length through inverted repeat expansion and large single copy fragment duplication, resulting in 181,022 bp (S. taccada) and 182,726 bp (S. hainanensis), ~30 kb increase compared to its related species. Mitochondrial genomes of two Scaevola species exhibit multi-ring topology, forming dual mitochondrial chromosomes of 314,251 bp (S. taccada) and 276,175 bp (S. hainanensis). Sequence variation analysis demonstrated substantial chloroplast sequence divergence (Pi = 0.45) and an increase in gene copy number within the genus. Relative synonymous codon usage (RSCU) analysis revealed that Scaevola chloroplast has a higher bias for A/U-ending codons than mitochondria, with chloroplasts RSCU values ranging from 0.32 to 1.94, whereas mitochondrial RSCU values ranging from 0.38 to 1.62. Phylogenetic analyses support the monophyly of the Asteraceae-Goodeniaceae sister group, whereas the extended evolutionary branches of Scaevola, coupled with mitochondrial collinearity analysis, indicate rapid organellar genome evolution of Scaevola. Organellar-nuclear horizontal gene transfer analysis identified specific increased in the copy numbers of photosynthesis-related genes and chloroplast-nuclear transfer events in S. taccada. Our study not only provides insights for understanding environmental adaptation mechanisms of coastal plants, but also contributes to elucidating organellar genome evolution in Scaevola and Goodeniaceae.},
}
@article {pmid40341387,
year = {2025},
author = {Marin, MG and Quinones-Olvera, N and Wippel, C and Behruznia, M and Jeffrey, BM and Harris, M and Mann, BC and Rosenthal, A and Jacobson, KR and Warren, RM and Li, H and Meehan, CJ and Farhat, MR},
title = {Pitfalls of bacterial pan-genome analysis approaches: a case study of M. tuberculosis and two less clonal bacterial species.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf219},
pmid = {40341387},
issn = {1367-4811},
abstract = {UNLABELLED: Pan-genome analysis is a fundamental tool for studying bacterial genome evolution; however, the variety of methods used to define and measure the pan-genome poses challenges to the interpretation and reliability of results. Using Mycobacterium tuberculosis (Mtb)-characterized by clonal evolution, absence of horizontal gene transfer, and a small accessory genome-as a model system, we systematically evaluated sources of variability in pan-genome estimates. Our analysis revealed that differences in assembly type (short-read vs. hybrid), annotation pipeline, and pan-genome software, significantly impact predictions of core and accessory genome size. Extending our analysis to two additional bacterial species, Escherichia coli and Staphylococcus aureus, we observed consistent tool-dependent biases but species-specific patterns in pan-genome variability. Our findings highlight the need for robust quality control and careful methodological selection to accurately capture genome diversity and evolution. This work underscores the importance of integrating nucleotide- and protein-level analyses to improve the reliability and reproducibility of pan-genome studies across diverse bacterial populations.<br><br>AVAILABILITY: Panqc is freely available under an MIT license at https://github.com/maxgmarin/panqc.<br><br>CONTACT: maha_farhat@hms.harvard.edu.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid40339917,
year = {2025},
author = {Schuster, HJ and van Mansfeld, R and van der Reijden, WA and van Houdt, R and Matamoros, S},
title = {VanB transposon analysis detects horizontal gene transfer in vancomycin resistant Enterococcus faecium: description of two outbreaks.},
journal = {The Journal of hospital infection},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhin.2025.04.021},
pmid = {40339917},
issn = {1532-2939},
abstract = {BACKGROUND: Outbreaks with vancomycin resistant Enterococcus faecium (VRE) are common in hospitals worldwide. Whole genome MLST (wgMLST) is often used to identify outbreak strains, but VRE typing can still be challenging due to their limited genomic variation.<br><br>AIM: Developing a method for sequence analysis of vancomycin resistance genes in parallel to wgMLST and application of this new method for real-time investigation of two parallel VRE outbreaks.<br><br>METHODS: We developed a bioinformatics pipeline to compare the sequences of transposons containing vanB resistance genes. We used this pipeline in addition to wgMLST to investigate two separate ongoing VRE outbreaks. We also sequenced five separate colonies from 15 different samples and 10 vancomycin sensitive isolates.<br><br>FINDINGS: Of 46 strains collected during two outbreaks, we identified 26 and 9 strains to be part of the two outbreaks based on wgMLST clustering. In 6 strains we identified an identical vanB transposon but a different wgMLST cluster, indicating horizontal gene transfer. This potential outbreak spread would have been missed without transposon analysis. We found no variability in vanB transposon sequence or wgMLST profiles within different colonies from the same sample. We identified 1 vancomycin sensitive E. faecium in blood culture with a similar wgST as one of the outbreak strains.<br><br>CONCLUSIONS: Real-time analysis of transposons containing vancomycin resistance genes provides additional information for analysis of vanB-VRE outbreaks. It detects possible horizontal gene transfer which would not be detected using conventional methods. Transposon analysis is a valuable addition to whole genome sequence analysis during vanB-VRE outbreaks.},
}
@article {pmid40337914,
year = {2025},
author = {Robertson, HM and Walker, JF and Moyroud, E},
title = {CAnDI: a new tool to investigate conflict in homologous gene trees and explain convergent trait evolution.},
journal = {Systematic biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/sysbio/syaf028},
pmid = {40337914},
issn = {1076-836X},
abstract = {Phenotypic convergence is found across the tree of life, and morphological similarities in distantly related species are often presumed to have evolved independently. However, clarifying the origins of traits has recently highlighted the complex nature of evolution, as apparent convergent features often share similar genetic foundations. Hence, the tree topology of genes that underlie such traits frequently conflicts with the overall history of species relationships. This conflict, which usually results from incomplete lineage sorting, introgression or horizontal gene transfer, creates both a challenge for systematists and an exciting opportunity to investigate the rich, complex network of information that connects molecular trajectories with trait evolution. Here we present a novel conflict identification program named CAnDI (Conflict And Duplication Identifier), which enables the analysis of conflict in homologous gene trees rather than inferred orthologs. We demonstrate that the analysis of conflicts in homologous trees using CAnDI yields more comparisons than in ortholog trees in six datasets from across the eukaryotic tree of life. Using the carnivorous trap of Caryophyllales, a charismatic group of flowering plants, as a case study we demonstrate that analysing conflict on entire homolog trees can aid in inferring the contribution of standing genetic variation to trait evolution: by dissecting all gene relationships within homolog trees, we find genomic evidence that the molecular basis of the pleisiomorphic mucilaginous sticky trap was likely present in the ancestor of all carnivorous Caryophyllales. We also show that many genes whose evolutionary trajectories group species with similar trap devices code for proteins contributing to plant carnivory and identify a LATERAL ORGAN BOUNDARY DOMAIN transcription factor as a possible candidate for regulating sticky trap development.},
}
@article {pmid40332509,
year = {2025},
author = {Ye, T and Li, H and Hai, D and Zhaxi, Z and Duan, J and Lin, Y and Xie, J and Cheng, J and Li, B and Chen, T and Yu, X and Lyu, X and Xiao, X and Fu, Y and Jiang, D},
title = {A Hypovirulence-Associated Partitivirus and Re-Examination of Horizontal Gene Transfer Between Partitiviruses and Cellular Organisms.},
journal = {International journal of molecular sciences},
volume = {26},
number = {8},
pages = {},
doi = {10.3390/ijms26083853},
pmid = {40332509},
issn = {1422-0067},
support = {31861143043//ISF-NSFC/ ; AML2023A02//the funds of the National Key Laboratory of Agricultural Microbiology/ ; },
mesh = {*Gene Transfer, Horizontal ; *Ascomycota/virology/genetics ; Phylogeny ; *Fungal Viruses/genetics/pathogenicity ; *RNA Viruses/genetics ; RNA-Dependent RNA Polymerase/genetics ; Capsid Proteins/genetics ; Genome, Viral ; Virulence/genetics ; Animals ; },
abstract = {Previous research has unearthed the integration of the coat protein (CP) gene from alphapartitivirus into plant genomes. Nevertheless, the prevalence of this horizontal gene transfer (HGT) between partitiviruses and cellular organisms remains an enigma. In our investigation, we discovered a novel partitivirus, designated Sclerotinia sclerotiorum alphapartitivirus 1 (SsAPV1), from a hypovirulent strain of Sclerotinia sclerotiorum. Intriguingly, we traced homologs of the SsAPV1 CP to plant genomes, including Helianthus annuus. To delve deeper, we employed the CP and RNA-dependent RNA polymerase (RdRP) sequences of partitiviruses as "bait" to search the NCBI database for similar sequences. Our search unveiled a widespread occurrence of HGT between viruses from all five genera within the family Partitiviridae and other cellular organisms. Notably, numerous CP-like and RdRP-like genes were identified in the genomes of plants, protozoa, animals, fungi, and even, for the first time, in an archaeon. The majority of CP and RdRP genes were integrated into plant and insect genomes, respectively. Furthermore, we detected DNA fragments originating from the SsAPV1 RNA genome in some subcultures of virus-infected strains. It suggested that SsAPV1 RdRP may possesses reverse transcriptase activity, facilitating the integration of viral genes into cellular organism genomes, and this function requires further confirmation. Our study not only offers a hypovirulence-associated partitivirus with implications for fungal disease control but also sheds light on the extensive integration events between partitiviruses and cellular organisms and enhances our comprehension of the origins, evolution, and ecology of partitiviruses, as well as the genome evolution of cellular organisms.},
}
@article {pmid40328220,
year = {2025},
author = {Doremus, MR and Hunter, MS},
title = {Symbiosis: An escalating arms race between a butterfly and bacterium.},
journal = {Current biology : CB},
volume = {35},
number = {9},
pages = {R339-R341},
doi = {10.1016/j.cub.2025.03.061},
pmid = {40328220},
issn = {1879-0445},
abstract = {Symbiotic bacteria such as Wolbachia can dramatically affect the reproduction of their arthropod hosts, in some instances causing male progeny to die as embryos. A recent paper describes an escalating arms race over Wolbachia-mediated male-killing in a tropical butterfly, with butterfly suppression of male-killing being overcome by acquisition of an additional male-killing gene via phage-mediated horizontal gene transfer.},
}
@article {pmid40328153,
year = {2025},
author = {Chu, Y and Dong, X and Fang, S and Gan, L and Lee, X and Zhou, L},
title = {Viruses in human-impacted estuarine ecotones: Distribution, metabolic potential, and environmental risks.},
journal = {Water research},
volume = {282},
number = {},
pages = {123750},
doi = {10.1016/j.watres.2025.123750},
pmid = {40328153},
issn = {1879-2448},
abstract = {Estuaries, as dynamic ecological interfaces between marine and terrestrial systems, are characterized by high productivity and intricate microbial communities. Viruses exert critical regulatory effects on microbial processes, influencing ecological functions and contributing to environmental dynamics in estuarine ecosystems. Despite their significance, the diversity and ecological roles of estuarine viruses remain insufficiently understood. This study explored the viral biogeographic patterns, metabolic potential, and influencing factors in 30 subtropical estuaries in China. Few estuarine viruses (< 22 %) exhibited homology with known viruses, and the low overlap of virus clusters with other environments highlights their novelty and habitat specificity. Mantel tests and random forest analysis identified salinity, temperature, nutrients, and pollutants as key factors influencing viral composition and functional profiles. In addition, correlation analysis between virus and host confirmed significant virus-host interactions, while functional analyses highlighted the role of environmental conditions and horizontal gene transfer in shaping auxiliary metabolic genes linked to elemental biogeochemical cycles, particularly phosphorus, sulfur, and nitrogen. The detection of antibiotic resistance genes (ARGs) and virulence factors (VFs) within viral genomes underscores the role of viruses as reservoirs of ARGs and VFs in these ecosystems. These results demonstrate the profound influence of abiotic and host factors on viral community structures in subtropical estuarine ecotones and underscore the ecological significance of metabolic genes in biogeochemical cycling. By clarifying these interactions, this study advances the understanding of viral contributions to ecosystem functioning and biogeochemical dynamics in estuarine environments.},
}
@article {pmid40326718,
year = {2025},
author = {Naseef Pathoor, N and Valsa, V and Ganesh, PS and Gopal, RK},
title = {From resistance to treatment: the ongoing struggle with Acinetobacter baumannii.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-22},
doi = {10.1080/1040841X.2025.2497791},
pmid = {40326718},
issn = {1549-7828},
abstract = {Acinetobacter baumannii (A. baumannii) has become a major hospital-acquired pathogen, well-known for its rapid development of resistance to multiple antibiotics. The rising incidence of antibiotic-resistant A. baumannii presents a significant global public health challenge. Gaining a deep understanding of the mechanisms behind this resistance is essential for creating effective treatment options. This comprehensive review explores the understanding of various antibiotic resistance mechanisms in A. baumannii. It covers intrinsic resistance, acquired resistance genes, efflux pumps, changes in outer membrane permeability, alterations in drug targets, biofilm formation, and horizontal gene transfer. Additionally, the review investigates the role of mobile genetic elements and the clinical implications of antibiotic resistance in A. baumannii infections. The insights provided may inform the development of new antimicrobial agents and the design of effective infection control strategies to curb the spread of multidrug-resistant (MDR) A. baumannii strains in healthcare environments. Unlike previous reviews, this study offers a more integrative perspective by also addressing the pathogen's environmental resilience, with particular emphasis on its resistance to desiccation and the formation of robust biofilms. It further evaluates both established and emerging therapeutic strategies, thereby expanding the current understanding of A. baumannii persistence and treatment.},
}
@article {pmid40325439,
year = {2025},
author = {Urban, JM and Gerbi, SA and Spradling, AC},
title = {Chromosome-scale scaffolds of the fungus gnat genome reveal multi-Mb-scale chromosome-folding interactions, centromeric enrichments of retrotransposons, and candidate telomere sequences.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {443},
pmid = {40325439},
issn = {1471-2164},
support = {NIH/GM121455/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: The lower Dipteran fungus gnat, Bradysia (aka Sciara) coprophila, has compelling chromosome biology. Paternal chromosomes are eliminated during male meiosis I and both maternal X sister chromatids are retained in male meiosis II. Embryos start with three copies of the X chromosome, but 1-2 copies are eliminated from somatic cells as part of sex determination, and one is eliminated in the germline to restore diploidy. In addition, there is gene amplification in larval polytene chromosomes, and the X polytene chromosome folds back on itself mediated by extremely long-range interactions between three loci. These developmentally normal events present opportunities to study chromosome behaviors that are unusual in other systems. Moreover, little is known about the centromeric and telomeric sequences of lower Dipterans in general, and there are recent claims of horizontally-transferred genes in fungus gnats. Overall, there is a pressing need to learn more about the fungus gnat chromosome sequences.<br><br>RESULTS: We produced the first chromosome-scale models of the X and autosomal chromosomes where each somatic chromosome is represented by a single scaffold. Extensive analysis supports the chromosome identity and structural accuracy of the scaffolds, demonstrating they are co-linear with historical polytene maps, consistent with evolutionary expectations, and have accurate centromere positions, chromosome lengths, and copy numbers. The positions of alleged horizontally-transferred genes in the nuclear chromosomes were broadly confirmed by genomic analyses of the chromosome scaffolds using Hi-C and single-molecule long-read datasets. The chromosomal context of repeats shows family-specific biases, such as retrotransposons correlated with the centromeres. Moreover, scaffold termini were enriched with arrays of retrotransposon-related sequence as well as nucleosome-length (~ 175 bp) satellite repeats. Finally, the Hi-C data captured Mb-scale physical interactions on the X chromosome that are seen in polytene spreads, and we characterize these interesting "fold-back regions" at the sequence level for the first time.<br><br>CONCLUSIONS: The chromosome scaffolds were shown to be of exceptional quality, including loci harboring horizontally-transferred genes. Repeat analyses demonstrate family-specific biases and telomere repeat candidates. Hi-C analyses revealed the sequences of ultra-long-range interactions on the X chromosome. The chromosome-scale scaffolds pave the way for further studies of the unusual chromosome movements in Bradysia coprophila.},
}
@article {pmid40127991,
year = {2025},
author = {Barretto, LAF and Fowler, CC},
title = {Multifaceted Evolution of the PhoPQ Two-Component System in Salmonella enterica Enhanced the Expression of Horizontally Acquired Virulence Genes.},
journal = {Molecular microbiology},
volume = {123},
number = {5},
pages = {464-478},
doi = {10.1111/mmi.15355},
pmid = {40127991},
issn = {1365-2958},
support = {RGPIN-2020-03964//Natural Sciences and Engineering Research Council of Canada/ ; //NSREC CGS-M Scholarship/ ; //University of Alberta Faculty of Science/ ; },
mesh = {*Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Virulence/genetics ; *Salmonella enterica/genetics/pathogenicity/metabolism ; Escherichia coli/genetics/metabolism ; Escherichia coli Proteins/genetics/metabolism ; Evolution, Molecular ; *Virulence Factors/genetics ; Gene Transfer, Horizontal ; },
abstract = {For a bacterium to adapt to a new environmental niche, its regulatory networks must evolve to effectively sense and respond to cues within that niche. For bacterial pathogens, which encounter harsh and dynamic host niches that require efficient coordination between detecting host cues and regulating virulence genes, this process is a key aspect of how virulence properties evolve. Here, we investigate how a widely conserved two-component regulatory system (TCS), PhoP/PhoQ (PhoPQ), evolved in Salmonella enterica to adopt a new role as a master regulator of gene expression within its species-specific intracellular niche: the Salmonella-containing vacuole (SCV). By comparing Salmonella PhoPQ with the closely related Escherichia coli PhoPQ ortholog, we demonstrate that optimizing virulence gene expression in Salmonella required a multifaceted evolution of several PhoPQ functional domains and establish that distinct genetic differences and mechanisms enhance virulence gene expression for different inducing cues. Interestingly, we find that the increased activity of the Salmonella PhoPQ system has a much more profound impact on the expression of H-NS-repressed, horizontally acquired virulence genes than on the ancestral members of the PhoP regulon. We observe that the PhoPQ systems of other related bacteria exhibit activity levels similar to the E. coli system, suggesting that the differences we observe are the result of Salmonella-specific adaptations that produced a more active PhoPQ system when encountering SCV conditions. Collectively, this study offers a window into the evolutionary adaptations of a TCS that enable it to assume an expanded regulatory role in a unique environment.},
}
@article {pmid40319560,
year = {2025},
author = {Gross, N and Brodard, I and Overesch, G and Kittl, S},
title = {Genetic basis of β-lactam resistance in Corynebacterium auriscanis and association with otitis externa in dogs and cats.},
journal = {Veterinary microbiology},
volume = {305},
number = {},
pages = {110526},
doi = {10.1016/j.vetmic.2025.110526},
pmid = {40319560},
issn = {1873-2542},
abstract = {Corynebacterium (C.) auriscanis is an opportunistic pathogen regularly isolated from canine otitis externa, an important condition often hard to treat. We found a surprisingly high prevalence of β-lactam resistant isolates of C. auriscanis (47 %), even though β-lactams are not routinely used for otitis externa treatment in Switzerland. To determine the genetic base of this phenotype, a selection of isolates of C. auriscanis with high and low minimal inhibitory concentration values were subjected to whole genome sequencing. Comparative analysis revealed a gene cassette containing three genes (hdfR encoding a LysR-family transcriptional regulator, blaB encoding a β-lactamase related protein and pbp2c encoding a D,D-transpeptidase) as the likely resistance-encoding determinant in the isolates from otitis externa. This locus had previously been described in C. jeikeium as well as C. diphtheriae and was associated with mobile genetic elements. In our six C. auriscanis isolates the pbp2c locus was always associated with the same IS3 family transposase, an association also found on C. diphtheriae plasmid CP091096, indicating horizontal gene transfer between species. To elucidate the function of the three genes in the pbp2c locus, we constructed plasmids with different combinations of these genes, transformed β-lactam sensitive isolates with the plasmids and tested resistance in the mutants phenotypically. By doing so we confirmed Pbp2c to be the primary factor conferring β-lactam resistance and HdfR and BlaB being important for expression and regulation. Interestingly, resistance to all β-lactams including carbapenems was constitutive in one C. auriscanis transformant while an induction effect was visible for the other transformed C. auriscanis strain, C. glutamicum and C. rouxii as previously described for C. jeikeium. Therefore, testing of β-lactam resistance should be done in combination including induction in Corynebacterium spp.},
}
@article {pmid40318462,
year = {2025},
author = {Zhang, T and Fan, L and Zhang, YN},
title = {Antibiotic resistance genes in aquatic systems: Sources, transmission, and risks.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {284},
number = {},
pages = {107392},
doi = {10.1016/j.aquatox.2025.107392},
pmid = {40318462},
issn = {1879-1514},
abstract = {The widespread use of antibiotics has significantly contributed to the spread of antibiotic resistance genes (ARGs), which have become a major challenge to global ecological and public health. Antibiotic resistance not only proliferates in clinical settings but also persists in aquatic systems, where its residues and cross-domain spread pose a dual threat to both ecosystems and human health. ARGs spread rapidly within microbial communities through horizontal gene transfer (HGT) and vertical gene transfer (VGT). Aquatic systems are the key transmission medium. This review summarizes recent studies on the Source-Transport-Sink dynamics of ARGs in aquatic environments, along with their environmental and health risk assessments, with a particular focus on the potential ecotoxicity of ARGs transmission. It also examines the distribution characteristics of ARGs across different regions and the ecological risk assessment methods employed, highlighting the limitations of existing models when addressing the complex behaviors of ARGs. By analyzing the potential hazards of ARGs to aquatic ecosystems and public health, this article aims to provide a scientific foundation for future research and the development of public policies.},
}
@article {pmid40314822,
year = {2025},
author = {Bell I, PJ and Muniyan, R},
title = {Synergistic pathogenesis: exploring biofilms, efflux pumps and secretion systems in Acinetobacter baumannii and Staphylococcus aureus.},
journal = {Archives of microbiology},
volume = {207},
number = {6},
pages = {134},
pmid = {40314822},
issn = {1432-072X},
mesh = {*Biofilms/growth &amp; development ; *Acinetobacter baumannii/pathogenicity/drug effects/physiology/genetics ; Humans ; *Staphylococcus aureus/pathogenicity/drug effects/physiology/genetics/metabolism ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/metabolism/genetics ; Staphylococcal Infections/microbiology/drug therapy ; Drug Resistance, Multiple, Bacterial ; Cross Infection/microbiology ; *Membrane Transport Proteins/metabolism/genetics ; Bacterial Proteins/metabolism/genetics ; Acinetobacter Infections/microbiology ; },
abstract = {Antimicrobial resistance (AMR) is a growing global health crisis, particularly among ESKAPE pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species. Among them, A. baumannii and S. aureus are major contributors to nosocomial infections, with high prevalence in intensive care units and immunocompromised patients. Their ability to resist multiple antibiotic classes complicates treatment strategies, leading to increased morbidity and mortality. Key resistance mechanisms, including biofilm formation, efflux pump activity, and horizontal gene transfer, enhance their survival and persistence. Furthermore, interactions during polymicrobial infections intensify disease severity through synergistic effects that promote both virulence and resistance. The epidemiological burden of these pathogens highlights the urgent need for novel antimicrobial strategies and targeted interventions. This review explores their virulence factors, resistance mechanisms, pathogenic interactions, and clinical implications, emphasizing the necessity of innovative therapeutic approaches to combat their growing threat.},
}
@article {pmid40311358,
year = {2025},
author = {Gómez-Brandón, M and Aira, M and Probst, M and Liu, N and Zhang, Z and Zhu, YG and Domínguez, J},
title = {Earthworms attenuate antibiotic resistance genes and mobile genetic elements during vermicomposting of sewage sludge.},
journal = {Journal of environmental management},
volume = {384},
number = {},
pages = {125562},
doi = {10.1016/j.jenvman.2025.125562},
pmid = {40311358},
issn = {1095-8630},
abstract = {Sewage sludge is among the richest reservoirs of antibiotic resistance genes (ARGs) that may spread to urban environment. Further investigation is warranted for removal of sludge-borne ARGs in large-scale vermicomposting systems. Under this scenario, there is the necessity to unveil the role of the widely-used earthworm species Eisenia andrei, since the current body of literature mostly focuses on E. fetida. The present study sought to evaluate the changes in sludge-borne ARGs and mobile genetic elements in a pilot-scale vermireactor in the presence of E. andrei in response to both gut- and cast-associated processes (GAPs and CAPs, respectively), by coupling high-throughput quantitative PCR and Illumina sequencing. After gut transit, large decreases in the relative abundances and number of the genes conferring resistance to major antibiotic classes, including some specific genes classified as of potentially high risk to human health, were recorded in the fresh casts. Likewise, genes encoding resistance to heavy metals were about nine-times lower in the egested materials than in the initial sludge. Genes coding for integrases or insertional sequences also exhibited reduced abundance as a result of GAP and CAP processes, suggesting that vermicompost appears to be less prone to horizontal gene transfer than untreated sludge. These findings provide evidence about the capacity of the earthworm E. andrei to diminish the risk of ARG spread during vermicomposting, reinforcing its potential for bioremediation purposes by transforming large quantities of waste into an improved fertiliser. This is crucial to propel vermicomposting technology forward and achieve transition toward net zero-waste process.},
}
@article {pmid40310292,
year = {2025},
author = {Alejandre-Sixtos, JE and Aguirre-Martínez, K and Cruz-López, J and Mares-Rivera, A and Álvarez-Martínez, SM and Zamorano-Sánchez, D},
title = {Insights on the regulation and function of the CRISPR/Cas transposition system located in the pathogenicity island VpaI-7 from Vibrio parahaemolyticus RIMD2210633.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0016925},
doi = {10.1128/iai.00169-25},
pmid = {40310292},
issn = {1098-5522},
abstract = {CRISPR/Cas-mediated transposition is a recently recognized strategy for horizontal gene transfer in a variety of bacterial species. However, our understanding of the factors that control their function in their natural hosts is still limited. In this work, we report our initial genetic characterization of the elements associated with the CRISPR/Cas-transposition machinery (CASTm) from Vibrio parahaemolyticus (VpaCASTm), which are encoded within the pathogenicity island VpaI-7. Our results revealed that the components of the VpaCASTm and their associated CRISPR arrays (VpaCAST system) are transcriptionally active in their native genetic context. Furthermore, we were able to detect the presence of polycistrons and several internal promoters within the loci that compose the VpaCAST system. Our results also suggest that the activity of the promoter of the atypical CRISPR array is not repressed by the baseline activity of its known regulator VPA1391 in V. parahaemolyticus. In addition, we found that the activity of the promoter of tniQ was modulated by a regulatory cascade involving ToxR, LeuO, and H-NS. Since it was previously reported that the activity of the VpaCAST system was less efficient than that of the VchCAST system at promoting transposition of a miniaturized CRISPR-associated transposon (mini-CAST) in Escherichia coli, we analyzed if the transposition efficiency mediated by the VpaCAST system could be enhanced inside its natural host V. parahaemolyticus. We provide evidence that this might be the case, suggesting that there could be host induction factors in V. parahaemolyticus that could enable more efficient transposition of CASTs.IMPORTANCEMobile genetic elements such as transposons play important roles in the evolutionary trajectories of bacterial genomes. The success of transposon dissemination depends on their ability to carry selectable markers that improve the fitness of the host cell or loci with addictive traits such as the toxin-antitoxin systems. Here we aimed to characterize a transposon from Vibrio parahaemolyticus that carries and could disseminate multiple virulence factors. This transposon belongs to a recently discovered family of transposons whose transposition is guided by crRNA. We showed that the transposition machinery of this transposon is transcribed in V. parahaemolyticus and that there are likely host-associated factors that favor transposition in the natural host V. parahaemolyticus over transposition in Escherichia coli.},
}
@article {pmid40307209,
year = {2025},
author = {Song, X and Wang, Y and Wang, Y and Zhao, K and Tong, D and Gao, R and Lv, X and Kong, D and Ruan, Y and Wang, M and Tang, X and Li, F and Luo, Y and Zhu, Y and Xu, J and Ma, B},
title = {Rhizosphere-triggered viral lysogeny mediates microbial metabolic reprogramming to enhance arsenic oxidation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4048},
pmid = {40307209},
issn = {2041-1723},
support = {42277283//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42090060//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41991334//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Rhizosphere ; *Arsenic/metabolism ; Oxidation-Reduction ; *Oryza/microbiology/virology/metabolism ; Soil Microbiology ; *Lysogeny/genetics ; Microbiota/genetics ; Gene Transfer, Horizontal ; Metagenome ; Plant Roots/microbiology/virology ; Oxidoreductases/genetics/metabolism ; Metabolic Reprogramming ; },
abstract = {The rhizosphere is a critical hotspot for metabolic activities involving arsenic (As). While recent studies indicate many functions for soil viruses, much remains overlooked regarding their quantitative impact on rhizosphere processes. Here, we analyze time-series metagenomes of rice (Oryza sativa L.)rhizosphere and bulk soil to explore how viruses mediate rhizosphere As biogeochemistry. We observe the rhizosphere favors lysogeny in viruses associated with As-oxidizing microbes, with a positive correlation between As oxidation and the prevalence of these microbial hosts. Moreover, results demonstrate these lysogenic viruses enrich both As oxidation and phosphorus co-metabolism genes and mediated horizontal gene transfers (HGTs) of As oxidases. In silico simulation with genome-scale metabolic models (GEMs) and in vitro validation with experiments estimate that rhizosphere lysogenic viruses contribute up to 25% of microbial As oxidation. These findings enhance our comprehension of the plant-microbiome-virome interplay and highlight the potential of rhizosphere viruses for improving soil health in sustainable agriculture.},
}
@article {pmid40306591,
year = {2025},
author = {Sam-On, MFS and Mustafa, S and Mohd Hashim, A and Abdul Malek, AZ},
title = {Probiogenomic insights into Bacillus velezensis MFSS1 for controlling aquaculture pathogens.},
journal = {Microbial pathogenesis},
volume = {205},
number = {},
pages = {107645},
doi = {10.1016/j.micpath.2025.107645},
pmid = {40306591},
issn = {1096-1208},
abstract = {Bacillus velezensis MFSS1 (previously known as B. subtilis FS6) was reported to have good probiotic criteria and antibacterial activity against Vibrio spp. and Aeromonas spp., through phenotypic analysis. However, whole genome sequencing is required for commercialising a new probiotic, especially due to reports on probiotics that can cause horizontal gene transfer towards the host microbiome. Therefore, this study aims to investigate the comprehensive genomic characteristics of B. velezensis MFSS1, focusing on its antimicrobial genes against aquaculture pathogens, its probiotic traits, and safety assessment. The bacterial genome was sequenced using Oxford Nanopore sequencing, resulting in 7 contigs with a total length of 3,914,361 base pairs and an average G + C content of 46.58 %. The analysis using ContEst16S and average nucleotide identity revealed that the bacterium previously reported as B. subtilis is actually B. velezensis. Additionally, secondary metabolites against pathogens were predicted using the antiSMASH website, which identified eight secondary metabolites: Bacillibactin, Bacilysin, Surfactin, Difficidin, Fengycin, Bacillaene, Macrolactin H, and Plantazolicin. Furthermore, several probiotic markers were detected, functioning in acid tolerance, bile salt tolerance, adhesion, osmotic stress, and intestinal persistence during the delivery of the bacteria to the host. Interestingly, the in silico safety assessment of the bacterium revealed a lack of 96 antibiotic resistance genes and confirmed it as non-pathogenic to humans, compared with genomic bacteria from ATCC. The study indicates that B. velezensis MFSS1 is a good probiotic through genomic analysis and can be commercialised to control aquaculture pathogens and reduce reliance on antibiotics.},
}
@article {pmid40306109,
year = {2025},
author = {Huang, X and Hou, Y and Zhao, M and Chen, J and Zhu, Z and Liu, H and Wang, M and Hua, L and Chen, H and Wu, B and Peng, Z},
title = {Identification of a broad-spectrum lytic Bordetella phage and assessments of its potential for combating Bordetella infections.},
journal = {Virology},
volume = {608},
number = {},
pages = {110545},
doi = {10.1016/j.virol.2025.110545},
pmid = {40306109},
issn = {1096-0341},
abstract = {Bordetella bronchiseptica (Bb) is a zoonotic respiratory pathogen that frequently causes infections in farming and companion animals, posing threats to agricultural economics and public health. However, Bb strains are intrinsically resistant to several antibiotics commonly used to treat respiratory infections. Phage therapy has been recognized as a promising strategy to combat bacterial infections. In this study, a novel Bordetella phage, designated PY223, was isolated using Bb strains as indicators. Genome network analysis with different phages showed PY223 was related to 15 viral clusters but was not included in any of these clusters. PY223 did not carry any known genes involved in lysogeny and/or horizontal gene transfer. Host range analysis showed that PY223 exhibited the capacity to lyse 70 Bb strains isolated from pigs and/or cats. Measurement of the one-step growth curve showed that PY223 had an incubation period of 10 min and a rapid growth period of 80 min. The burst size was estimated to be approximately 10[9] PFU/cell. In addition, PY223 displayed the capacity to inhibit the growth of Bb for up to 17 h. PY223 was stable under environmental temperatures ranging from 4 °C to 60 °C and/or pH values between 5.0 and 9.0. It remained stable even when exposed to UV light for 30 min. Notably, PY223 effectively eliminated Bb biofilms, inhibited the growth of prophage-harboring Bb strains, and cleared Bb from the environment. In vivo testing in mouse models highlighted its excellent potential for treating respiratory Bordetella infections.},
}
@article {pmid40304893,
year = {2025},
author = {Domingues, S and Lima, T and Escobar, C and Plantade, J and Charpentier, X and da Silva, GJ},
title = {Large DNA fragment ISEc9-mediated transposition during natural transformation allows interspecies dissemination of antimicrobial resistance genes.},
journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40304893},
issn = {1435-4373},
abstract = {PURPOSE: Antimicrobial resistance poses a significant global health challenge, contributing to a lack of effective therapeutic agents, especially against Gram-negative bacteria. Resistance dissemination is accelerated by horizontal gene transfer (HGT) mechanisms. The extended-spectrum beta lactamases CTX-M confer resistance to several beta-lactams, are usually embedded into plasmids and thought to be mainly disseminated by conjugation. However, an increasing number of isolates carry these enzyme-encoding genes in the chromosome, suggesting that they can spread by other means of HGT. In this study, we aimed to test the involvement of natural transformation in the chromosomal acquisition of a blaCTX-M gene.<br><br>METHODS: Natural transformation assays were performed during motility on wet surfaces. Acquisition of foreign DNA by transformants was screened by antimicrobial susceptibility testing, polymerase-chain reaction (PCR) and whole genome sequencing (WGS).<br><br>RESULTS: Acinetobacter baumannii A118, a naturally competent clinical strain, was transformed with naked DNA from Salmonella enterica serovar Typhimurium Sal25, which was isolated from swine meat. The transformation occurred at low frequency (2.7&#x2009;&#xd7;&#x2009;10[-&#x2009;8] &#xb1; 2.04&#x2009;&#xd7;&#x2009;10[-&#x2009;8] transformants per recipient) and blaCTX-M was acquired in one transformant, which was named ACI. WGS of the transformant revealed the acquisition of the blaCTX-M-32 as part of a ca. 36 Kb DNA fragment through an ISEc9-mediated transposition event; various mobile genetic elements and other resistance genes were co-transferred. The blaCTX-M-32 gene was subsequently transferred within A. baumannii at a higher frequency (1.8&#x2009;&#xd7;&#x2009;10[-&#x2009;6] &#xb1; 2.49&#x2009;&#xd7;&#x2009;10[-&#x2009;6] transformants per recipient).<br><br>CONCLUSION: Our results highlight the importance of natural transformation events in the dissemination of antimicrobial resistance genes and mobile genetic elements between and within species.},
}
@article {pmid40304813,
year = {2025},
author = {Qin, S and Wang, H and Wang, M and Shao, B and Ma, C and Yang, B and Jin, X},
title = {Mitochondrial genome evolution in the orchid subfamily Cypripedioideae (Orchidaceae).},
journal = {Functional &amp; integrative genomics},
volume = {25},
number = {1},
pages = {96},
pmid = {40304813},
issn = {1438-7948},
support = {2022YFF1301704)//National Key Research and Development Program of China/ ; },
mesh = {*Orchidaceae/genetics/classification ; *Evolution, Molecular ; *Genome, Mitochondrial ; Phylogeny ; },
abstract = {In this study, the mitogenomes of nine species in the subfamily Cypripedioideae were newly sequenced and assembled using both short and long reads for evolutionary analyses. Complete multi-chromosomal mitogenomes were obtained for Cypripedium subtropicum, C. henryi, Phragmipedium humboldtii, Phr. kovachii, and Paphiopedilum micranthum, and draft assemblies were obtained for four additional Paphiopedilum species. Thirty-nine protein-coding genes were annotated and shared in nine sampled species. sdh4 was discovered in all species of Cypripedioideae, and rpl10 was detected in four species of Paphiopedilum. These two genes might have been horizontally transferred from non-orchid plants at different times. Approximately 101 to 998 repeat sequences were identified with total lengths of 417,136 to 785,960 bp in the mitogenomes of Cypripedioideae. There were 634 and 662 RNA editing sites in C. subtropicum and Pa. gratrixianum, respectively, and C-to-U editing was dominant. The nad and ccm genes exhibited high frequencies of RNA editing. Our study revealed the complexity of orchid mitogenomes, including evidence for the horizontal transfer of rpl10 and sdh4.},
}
@article {pmid40303475,
year = {2025},
author = {Lu, J and Zhang, R and Yu, Y and Lou, H and Li, D and Bao, Q and Feng, C},
title = {Identification of a novel chromosome-encoded fosfomycin resistance gene fosC3 in Aeromonas caviae.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1577167},
pmid = {40303475},
issn = {1664-302X},
abstract = {BACKGROUND: Owing to the rapid emerging of multidrug-, even pandrug-resistant pathogens, and lack of new antibiotics, the older antibiotic, fosfomycin, has been reused in recent years in the clinical practice, especially for treatment of uropathogen infections. With the increased use of fosfomycin, bacterial resistance to it has also increased drastically. Elucidating the resistance mechanism to the antimicrobial has become an urgent task.<br><br>METHODS: The putative fosfomycin resistance gene fosC3 was cloned, and minimal inhibitory concentrations were determined by the agar dilution method. Enzyme kinetic parameters were measured by high-performance liquid chromatography. Bioinformatics analysis was applied to understand the evolutionary characteristics of FosC3.<br><br>RESULTS: The A. caviae strain DW0021 exhibited high level resistance to several antimicrobials including kanamycin, streptomycin, chloramphenicol, florfenicol, tetracycline, and especially higher to fosfomycin (> 1,024&#x202f;&#x3bc;g/mL), while genome annotation indicated that no function-characterized resistance gene was associated with fosfomycin resistance. A novel functional gene designated fosC3 responsible for fosfomycin resistance was identified in the chromosome of A. caviae DW0021. Among the function-characterized proteins, FosC3 shared the highest amino acid similarity of 58.65% with FosC2. No mobile genetic element (MGE) was found surrounding the fosC3 gene. The recombinant pMD19-fosC3/DH5&#x3b1; displayed a MIC value of 32&#x202f;&#x3bc;g/mL to fosfomycin, which revealed a 128-fold increase of MIC value to fosfomycin compared to the control pMD19/E. coli DH5&#x3b1; (0.25&#x202f;&#x3bc;g/mL). FosC3 was phylogenetically close to FosC2 and exhibited a k cat and K m of 82,442&#x202f;&#xb1;&#x202f;1,475&#x202f;s[-1], 70.99&#x202f;&#xb1;&#x202f;4.31&#x202f;&#x3bc;M, respectively, and a catalytic efficiency of (1.2&#x202f;&#xb1;&#x202f;0.3)&#x202f;&#xd7;&#x202f;10[3]&#x202f;&#x3bc;M[-1]&#xb7;s[-1].<br><br>CONCLUSION: In this work, a novel functional fosfomycin thiol transferase, FosC3, which shared the highest protein sequence similarity with FosC2, was identified in A. caviae. The fosfomycin inactivation enzyme FosC3 could effectively inactivate fosfomycin by chemical modification. It is implied that such mechanism facilitates A. caviae to respond to fosfomycin exposure, thereby enhancing survival. However, fosC3 was not related with any MGE, which differs from many other fosfomycin thiol transferase genes. As a result, fosC3 is not expected to be transmitted to other species through horizontal gene transfer mechanism. Our findings will contribute to the resistance mechanism of the common pathogenic A. caviae.},
}
@article {pmid40303018,
year = {2024},
author = {Jia, Y and Zheng, Z and Yang, B and Zhang, H and Wang, Z and Liu, Y},
title = {A Broad-Spectrum Horizontal Transfer Inhibitor Prevents Transmission of Plasmids Carrying Multiple Antibiotic Resistance Genes.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {7063673},
pmid = {40303018},
issn = {1865-1682},
mesh = {*Gene Transfer, Horizontal/drug effects ; *Plasmids/genetics/drug effects ; *Zidovudine/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Animals ; *Bacteria/drug effects/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {The dissemination of antimicrobial resistance (AMR) severely degrades the performance of antibiotics and constantly paralyzes the global health system. In particular, plasmid-mediated transfer of antibiotic resistance genes (ARGs) across bacteria is recognized as the primary driver. Therefore, antiplasmid transfer approaches are urgently warranted to resolve this intractable problem. Herein, we demonstrated the potential of azidothymidine (AZT), an FDA-approved anti-HIV drug, as a broad-spectrum horizontal transfer inhibitor to effectively prevent the transmission of multiple ARGs, including mcr-1, bla NDM-5, and tet(X4), both in vitro and in vivo. It was also noteworthy that the inhibitory effect of AZT was proved to be valid within and across bacterial genera under different mating conditions. Mechanistic studies revealed that AZT dissipated bacterial proton motive force, which was indispensable for ATP synthesis and flagellar motility. In addition, AZT downregulated bacterial secretion systems involving general and type IV secretion systems (T4SS). Furthermore, the thymidine kinase, which is associated with DNA synthesis, turned out to be the potential target of AZT. Collectively, our work demonstrates the broad inhibitory effect of AZT in preventing ARGs transmission, opening new horizons for controlling AMR.},
}
@article {pmid40302206,
year = {2025},
author = {Drebes Dörr, NC and Lemopoulos, A and Blokesch, M},
title = {Exploring Mobile Genetic Elements in Vibrio cholerae.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf079},
pmid = {40302206},
issn = {1759-6653},
abstract = {Members of the bacterial species Vibrio cholerae are known both as prominent constituents of marine environments and as the causative agents of cholera, a severe diarrheal disease. While strains responsible for cholera have been extensively studied over the past century, less is known about their environmental counterparts, despite their contributions to the species' pangenome. This study analyzed the genome compositions of 46 V. cholerae strains, including pandemic and non-pandemic, toxigenic, and environmental variants, to investigate the diversity of mobile genetic elements (MGEs), embedded bacterial defense systems, and phage-associated signatures. Our findings include both conserved and novel MGEs across strains, pointing to shared evolutionary pathways and ecological niches. The defensome analysis revealed a wide array of antiphage/anti-plasmid mechanisms, extending well beyond the traditional CRISPR-Cas and restriction-modification systems. This underscores the dynamic arms race between V. cholerae and MGEs and suggests that non-pandemic strains may act as reservoirs for emerging defense strategies. Moreover, the study showed that MGEs are integrated into genomic hotspots, which may serve as critical platforms for the exchange of defense systems, thereby enhancing V. cholerae's adaptive capabilities against phage attacks and other invading MGEs. Overall, this research offers new insights into V. cholerae's genetic complexity and potential adaptive strategies, offering a better understanding of the differences between environmental strains and their pandemic counterparts, as well as the possible evolutionary pathways that led to the emergence of pandemic strains.},
}
@article {pmid40301684,
year = {2025},
author = {Wagner, TM and Torres-Puig, S and Yimthin, T and Irobalieva, RN and Heller, M and Kaessmeyer, S and Démoulins, T and Jores, J},
title = {Extracellular vesicles of minimalistic Mollicutes as mediators of immune modulation and horizontal gene transfer.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {674},
pmid = {40301684},
issn = {2399-3642},
mesh = {*Extracellular Vesicles/immunology/metabolism ; *Gene Transfer, Horizontal ; Animals ; Cattle ; Plasmids/genetics ; *Tenericutes/genetics/immunology ; Mycoplasma/genetics/immunology ; Proteomics ; Mycoplasma mycoides/genetics/immunology ; *Immunomodulation ; },
abstract = {Extracellular vesicles (EVs) are central components of bacterial secretomes, including the small, cell wall-less Mollicutes. Although EV release in Mollicutes has been reported, EV proteomic composition and function have not been explored yet. We developed a protocol for isolating EVs of the pathogens Mycoplasma mycoides subsp. capri (Mmc) and Mycoplasma (Mycoplasmopsis) bovis and examined their functionality. Proteomic analysis demonstrated that EVs mirror the proteome of the EV-producing bacteria. EVs exhibited nuclease activity, effectively digesting both circular and linear DNA. Notably, M. bovis EVs elicited immune responses in bovine primary blood cells, like those induced by live M. bovis. Our findings reveal that EVs can carry plasmids and enable their horizontal transfer, known as vesiduction. Specifically, the natural plasmid pKMK1, with an unknown transmission route, was detected in EVs of Mmc 152/93 and the tetM-containing pIVB08 plasmid was associated with EVs released by an Mmc GM12 strain carrying this plasmid. pIVB08 could be transferred via homo- and heterologous vesiduction to Mmc, M. capricolum subsp. capricolum and M. leachii. Vesiduction was impeded by membrane disruption but resisted DNase and Proteinase K treatment, suggesting that EVs protect their cargo. These findings enhance our understanding of Mollicutes EVs, particularly in host interactions and horizontal gene transfer.},
}
@article {pmid40301564,
year = {2025},
author = {Xue, W and Hong, J and Zhao, R and Yao, H and Zhang, Y and Dai, Z and Wang, T},
title = {Spatial entropy drives the maintenance and dissemination of transferable plasmids.},
journal = {Molecular systems biology},
volume = {},
number = {},
pages = {},
pmid = {40301564},
issn = {1744-4292},
support = {2024YFA0920200//MOST | National Key Research and Development Program of China (NKPs)/ ; 32470701//MOST | National Natural Science Foundation of China (NSFC)/ ; HSE499011086//Shenzhen Institute of Synthetic Biology (iSynBio)/ ; },
abstract = {The dissemination of transferable plasmids, a major type of mobile genetic elements (MGEs), is one main driver of antibiotic resistance outbreaks. While the plasmid persistence condition in well-mixed environments has been extensively studied, most microbiota in nature are spatially heterogeneous. However, our knowledge regarding how spatial landscape shapes plasmid maintenance and dissemination remains limited. Here we establish a theoretical framework describing plasmid spread over a metacommunity of multiple patches. By analyzing the gene flow dynamics on randomly generated landscapes, we show that plasmid survival and dispersal are dictated by a simple feature of the landscape, spatial entropy. Reducing entropy speeds up plasmid range expansion and allows the global maintenance of many plasmids that are predicted to be lost by classic theories. The entropy's effects are experimentally validated in E. coli metacommunities transferring a conjugative plasmid. We further examine a vast collection of prokaryotic genomes and show that prokaryotes from low-entropy environments indeed carry more abundant MGEs and antibiotic resistance genes. Our work provides critical insights into the management and control of antimicrobial resistance.},
}
@article {pmid40301151,
year = {2025},
author = {Kaufmann, H and Salvador, C and Salazar, VW and Cruz, N and Dias, GM and Tschoeke, D and Campos, L and Sawabe, T and Miyazaki, M and Maruyama, F and Thompson, F and Thompson, C},
title = {Genomic Repertoire of Twenty-Two Novel Vibrionaceae Species Isolated from Marine Sediments.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {36},
pmid = {40301151},
issn = {1432-184X},
mesh = {*Geologic Sediments/microbiology ; *Vibrionaceae/genetics/classification/isolation &amp; purification ; *Genome, Bacterial ; Phylogeny ; Japan ; *Seawater/microbiology ; Genetic Variation ; },
abstract = {The genomic repertoire of vibrios has been extensively studied, particularly regarding their metabolic plasticity, symbiotic interactions, and resistance mechanisms to environmental stressors. However, little is known about the genomic diversity and adaptations of vibrios inhabiting deep-sea marine sediments. In this study, we investigated the genomic diversity of vibrios isolated from deep-sea core sediments collected using a manned submersible off Japan. A total of 50 vibrio isolates were obtained and characterized phenotypically, and by genome sequencing. From this total, we disclosed 22 novel species examining genome-to-genome distance, average amino acid identity, and phenotypes (Alivibrio: 1; Enterovibrio: 1; Photobacterium: 8; Vibrio: 12). The novel species have fallen within known clades (e.g., Fisheri, Enterovibrio, Profundum, and Splendidus) and novel clades (JAMM0721, JAMM0388, JAMM0395). The 28 remainder isolates were identified as known species: Aliivibrio sifiae (2), A. salmonicida (1), Enterovibrio baiacu (1), E. norvegicus (1), Photobacterium profundum (3), P. angustum (1), P. chitiniliticum (1), P. frigidiphilum (1), Photobacterium indicum (1), P. sanguinicancri (1). P. swingsii (2), Vibrio alginolyticus (3), V. anguillarum (1), V. campbellii (1), V. fluvialis (1), V. gigantis (1), V. lentus (1), V. splendidus (4), and V. tasmaniensis (1). Genomic analyses revealed that all 50 vibrios harbored genes associated with high-pressure adaptation, including sensor kinases, chaperones, autoinducer-2 (AI-2) signaling, oxidative damage repair, polyunsaturated fatty acid biosynthesis, and stress response mechanisms related to periplasmic and outer membrane protein misfolding under heat shock and osmotic stress. Additionally, alternative sigma factors, trimethylamine oxide (TMAO) respiration, and osmoprotectant acquisition pathways were identified, further supporting their ability to thrive in deep-sea environments. Notably, the genomes exhibited a high prevalence of antibiotic resistance genes, with antibiotic efflux pumps being the most abundant group. The ugd gene expanded in number in some novel species (Photobacterium satsumensis sp. nov. JAMM1754: 4 copies; Vibrio makurazakiensis sp. nov. JAMM1826: 3 copies). This gene may confer antibiotic (polymyxin) resistance to these vibrios.},
}
@article {pmid40300599,
year = {2025},
author = {Ba, F and Zhang, Y and Wang, L and Ji, X and Liu, WQ and Ling, S and Li, J},
title = {Integrase enables synthetic intercellular logic via bacterial conjugation.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101268},
doi = {10.1016/j.cels.2025.101268},
pmid = {40300599},
issn = {2405-4720},
abstract = {Integrases have been widely used in synthetic biology for genome engineering and genetic circuit design. They mediate DNA recombination to alter the genotypes of single cell lines in vivo, with these changes being permanently recorded and inherited via vertical gene transfer. However, integrase-based intercellular DNA messaging and its regulation via horizontal gene transfer remain underexplored. Here, we introduce a versatile strategy to design, build, and test integrase-based intercellular DNA messaging through bacterial conjugation. First, we screened conjugative plasmids and recipient cells for efficient conjugation. Then, we established a layered framework to describe the interactions among hierarchical E. coli strains and implemented dual-layer Boolean logic gates to demonstrate intercellular DNA messaging and management. Finally, we expanded the design to include four-layer single-processing pathways and dual-layer multi-processing systems. This strategy advances intercellular DNA messaging, hierarchical signal processing, and the application of integrase in systems and synthetic biology.},
}
@article {pmid40298586,
year = {2025},
author = {Niño-Vega, GA and Ortiz-Ramírez, JA and López-Romero, E},
title = {Novel Antibacterial Approaches and Therapeutic Strategies.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40298586},
issn = {2079-6382},
abstract = {The increase in multidrug-resistant organisms worldwide is a major public health threat driven by antibiotic overuse, horizontal gene transfer (HGT), environmental drivers, and deficient infection control in hospitals. In this article, we discuss these factors and summarize the new drugs and treatment strategies suggested to combat the increasing challenges of multidrug-resistant (MDR) bacteria. New treatments recently developed involve targeting key processes involved in bacterial growth, such as riboswitches and proteolysis, and combination therapies to improve efficacy and minimize adverse effects. It also tackles the challenges of the Gram-negative bacterial outer membrane, stressing that novel strategies are needed to evade permeability barriers, efflux pumps, and resistance mechanisms. Other approaches, including phage therapy, AMPs, and AI in drug discovery, are also discussed as potential alternatives. Finally, this review points out the urgency for continued research and development (R&amp;D), industry-academic partnerships, and financial engines to ensure that MDR microbes do not exceed the value of antibacterial therapies.},
}
@article {pmid40298491,
year = {2025},
author = {Karampatakis, T and Tsergouli, K and Behzadi, P},
title = {Carbapenem-Resistant Pseudomonas aeruginosa's Resistome: Pan-Genomic Plasticity, the Impact of Transposable Elements and Jumping Genes.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40298491},
issn = {2079-6382},
abstract = {Pseudomonas aeruginosa, a Gram-negative, motile bacterium, may cause significant infections in both community and hospital settings, leading to substantial morbidity and mortality. This opportunistic pathogen can thrive in various environments, making it a public health concern worldwide. P. aeruginosa's genomic pool is highly dynamic and diverse, with a pan-genome size ranging from 5.5 to 7.76 Mbp. This versatility arises from its ability to acquire genes through horizontal gene transfer (HGT) via different genetic elements (GEs), such as mobile genetic elements (MGEs). These MGEs, collectively known as the mobilome, facilitate the spread of genes encoding resistance to antimicrobials (ARGs), resistance to heavy metals (HMRGs), virulence (VGs), and metabolic functions (MGs). Of particular concern are the acquired carbapenemase genes (ACGs) and other β-lactamase genes, such as classes A, B [metallo-β-lactamases (MBLs)], and D carbapenemases, which can lead to increased antimicrobial resistance. This review emphasizes the importance of the mobilome in understanding antimicrobial resistance in P. aeruginosa.},
}
@article {pmid40298490,
year = {2025},
author = {Garcia-Torné, M and Falcó, I and Borrell, X and Bautista, A and Mazigh, R and Aznar, R and Sánchez, G and Farré, M and Llorca, M},
title = {Comprehensive Study of Antibiotics and Antibiotic Resistance Genes in Wastewater and Impacted Mediterranean Water Environments.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40298490},
issn = {2079-6382},
support = {869178-Aquatic Pollutants//Water JPI/ ; ON-HEALTH 2021 SGR 01150//Government of Catalonia/ ; CEX2021-001189-S//Spanish Ministry of Science and Innovation/ ; PRE2021-099409//Spanish Ministry of Science and Innovation/ ; MS21-006//Ministry of Universities of the Government of Spain, financed by the European Union (NextGeneration EU)/ ; },
abstract = {Background: The spread of antimicrobial resistance is a central public health problem. Wastewater treatment plants and impacted environments are well-known hotspots for antibiotic resistance. However, there is still limited knowledge regarding where antibiotic resistance genes (ARGs) acquire mobility. Method: In this study, we aimed to gather evidence on the seasonal patterns of ARG spread in two Mediterranean areas from NE and E of Spain (Ebro River and Ebro Delta, and Xúquer River and Albufera de València), correlating ARG presence, with special focus on the faecal bacteria Escherichia coli, with antibiotic residues and environmental conditions. The analytical methodology employed was based on a suspect screening approach, while a novel prioritisation approach for antibiotics was proposed to identify those areas more susceptible to the spread of ARG. Results: Our findings demonstrate that ARG levels in wastewater were similar across different seasons, although a greater diversity of ARGs was recorded in summer. We hypothesise that horizontal gene transfer among aquatic bacterial populations during the northeastern Mediterranean summer, when temperatures reach approximately 35~40 °C, could be a key driver of ARG dissemination. By contrast, the highest concentrations of antibiotics in winter samples, with temperatures around 5~10 °C, may promote the spread of microbial resistance. Conclusions: Our key findings highlight that water temperature and sunlight irradiation are crucial factors influencing antibiotic levels and microbial abundance, requiring further investigation in future studies.},
}
@article {pmid40294085,
year = {2025},
author = {Bellotti, G and Cortimiglia, C and Antinori, ME and Cocconcelli, PS and Puglisi, E},
title = {Comprehensive genome-wide analysis for the safety assessment of microbial biostimulants in agricultural applications.},
journal = {Microbial genomics},
volume = {11},
number = {4},
pages = {},
pmid = {40294085},
issn = {2057-5858},
mesh = {*Agriculture/methods ; Whole Genome Sequencing ; *Genome, Bacterial ; *Bacteria/genetics/drug effects ; Virulence Factors/genetics ; *Fertilizers/microbiology ; Interspersed Repetitive Sequences ; },
abstract = {Microbial biostimulants (MBs) offer a sustainable approach to agriculture by helping to reduce reliance on synthetic fertilizers. However, as MBs are intentionally released into the environment, their safety should be rigorously assessed. While taxa with qualified presumption of safety (QPS) benefit from established safety indications, non-QPS taxa lack such guidance. To address this gap, we propose a pipeline combining whole genome sequencing (WGS) and extensive literature search (ELS) data to evaluate microbial safety. We analysed public genomes of three QPS species (Rhodopseudomonas palustris, Bacillus velezensis, Priestia megaterium) and four non-QPS genera (Arthrobacter, Azotobacter, Azospirillum, Herbaspirillum), screening them for virulence factors (VFs), antimicrobial resistance (AMR) genes and mobile genetic elements (MGEs). Results confirmed the safety of QPS taxa, revealing no VFs and only a few intrinsic and non-clinically relevant AMRs. Among non-QPS taxa, VF hits were more prevalent in Azotobacter and Azospirillum spp., though they were mostly related to beneficial plant interactions rather than pathogenicity. AMR genes in non-QPS taxa were primarily associated with efflux pumps or were sporadically distributed. Notably, the only genus-wide pattern observed was that most Azospirillum and Herbaspirillum genomes harboured chromosomally encoded β-lactamases sharing similar genetic structures; however, the detected β-lactamase (bla) genes were distantly related to clinically relevant bla variants, and the absence of MGEs suggests a low risk of horizontal gene transfer, indicating the overall safety of these genera. In general, this WGS-ELS framework provides a robust tool for assessing the safety of non-QPS MBs, supporting regulatory decision-making and ensuring their safe use in sustainable agriculture while safeguarding public health.},
}
@article {pmid40289079,
year = {2025},
author = {Tsiklauri, R and Kobakhidze, S and Tsereteli, M and Jimsherishvili, L and Kakabadze, N and Koulouris, S and Kotetishvili, M},
title = {Genome data cross-contamination versus interdomain recombination: Equus caballus and Mus musculus genetic loci in the insertion sequence-rich genomes of two clonally related methicillin-resistant Staphylococcus aureus strains from China.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {251},
pmid = {40289079},
issn = {1471-2180},
mesh = {*Methicillin-Resistant Staphylococcus aureus/genetics/classification/isolation &amp; purification ; China ; *Genome, Bacterial ; Animals ; *Recombination, Genetic ; Staphylococcal Infections/microbiology/veterinary ; Horses/microbiology ; *DNA Transposable Elements ; DNA, Bacterial/genetics ; },
abstract = {BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) represents a significant global health threat, responsible for infections in both humans and animals. Determining genetic patterns associated with the genome plasticity of MRSA is critical for predicting the evolutionary trajectories of its emerging pathogenic clones.<br><br>RESULTS: The specific genetic loci of the MRSA strains WH3018 and WH9628 from Wuhan, China, ranging in size from 399 to 3,622 base pairs, were determined to be highly homologous (DNA identity: 90.95-100%) to corresponding chromosomal regions from Equus caballus and Mus musculus in the GenBank database. These eukaryotic-associated loci included the microsatellite DNAs or Y chromosome-specific regions from E. caballus, or 45&#xa0;S-28&#xa0;S ribosomal RNA/H19 loci from M. musculus, all exhibiting recurrent patterns across the genomes of both MRSA strains. The SplitsTree and RDP4 analyses did not reveal significant recombination signals for the eukaryotic-associated loci that had mimicked interdomain recombination events in the MRSA strains WH3018 and WH9628. The G&#x2009;+&#x2009;C content of these loci (47.6-65.0%) was notably higher than that of the S. aureus reference genome (32.5%). Furthermore, the MRSA genomes showed a significantly larger number and greater diversity of insertion sequences (ISs) (38 ISs per genome) compared to the S. aureus reference genome (16 ISs). Additionally, these genomes also exhibited an extensive decay of prophages and the accumulation of pseudo-transposases.<br><br>CONCLUSIONS: The recurring patterns of the eukaryotic-associated loci strongly suggested genome data contamination across the genomes of the MRSA strains WH3018 and WH9628. These MRSA genomes likely underwent extensive prophage decay and an increased proliferation of pseudo-transposases.},
}
@article {pmid40288735,
year = {2025},
author = {Wang, M and Masoudi, A and Wang, C and Feng, J and Yu, Z and Liu, J},
title = {Urban afforestation converges soil resistome and mitigates the abundance of human pathogenic bacteria.},
journal = {Environmental research},
volume = {278},
number = {},
pages = {121693},
doi = {10.1016/j.envres.2025.121693},
pmid = {40288735},
issn = {1096-0953},
abstract = {Afforestation has emerged as a nature-based strategy for climate mitigation and urban sustainability, yet its effects on antibiotic resistance genes (ARGs) in soils remain underexplored. This study investigates how the conversion of croplands into plantation forests affects the soil resistome, bacterial communities, and physicochemical properties in an urban environment. Using high-throughput metagenomic and 16S rRNA amplicon sequencing, we analyzed soil samples from croplands and afforested plots with Chinese pine (Pinus tabulaeformis) and Chinese scholar (Sophora japonica) trees, across two-time points post-afforestation. Our results show that afforestation promotes the convergence of both bacterial and ARG communities over time, accompanied by a significant reduction in the relative abundance of human pathogenic bacteria. Afforested soils exhibited a lower prevalence of high-risk ARGs (e.g., qnrA, qnrB from the quinolone class) and reduced co-occurrence between ARGs and mobile genetic elements (MGEs), particularly transposases and recombinases, suggesting diminished horizontal gene transfer. Additionally, afforestation-induced changes in soil pH and nutrient dynamics emerged as key ecological factors shaping ARG profiles. Differences between afforestation types were also observed, with Pinus plantations presenting lower ARG-derived risks than Sophora forests. This study supports afforestation as a nature-based solution for enhancing urban sustainability, reducing public health risks, and achieving resilient ecosystems under anthropogenic influence.},
}
@article {pmid40288673,
year = {2025},
author = {Kabeya, N and Ramos-Llorens, M and Nakano, Y and Gomes-Dos-Santos, A and Teixeira, A and Fujibayashi, M and Haro, JG and Navarro, JC and Castro, LFC and Haga, Y and Monroig, &#xd3;},
title = {Methyl-end desaturases determine the capability for de novo biosynthesis of polyunsaturated fatty acids in bivalves.},
journal = {Biochimica et biophysica acta. Molecular and cell biology of lipids},
volume = {1870},
number = {5},
pages = {159617},
doi = {10.1016/j.bbalip.2025.159617},
pmid = {40288673},
issn = {1879-2618},
abstract = {Recent studies have shown that many invertebrate species possess methyl-end desaturases (herein referred to as 'ωx'), enabling biosynthesis of polyunsaturated fatty acids (PUFA). However, the phylogenetic distribution of these enzymes across the animal kingdom remains puzzling, possibly due to horizontal gene transfer (HGT) and/or independent large-scale gene loss in certain invertebrate lineages. In molluscs, ωx genes have been identified in various cephalopods and gastropods but remain barely explored in bivalves. The increasing availability of genomic and transcriptomic resources enables a comprehensive exploration of the ωx gene repertoire in bivalves. To elucidate the distribution of ωx in bivalves, we conducted a broad homology search across existing genome and transcriptome assemblies, followed by functional characterisation of ωx in lineage representative species. Our results revealed no ωx-like sequences in any of the 65 Pteriomorphia species, suggesting gene loss in this clade. However, ωx-like sequences were found in Protobranchia, Palaeoheterodonta and Imparidentia. We analysed ωx from Solemya pusilla (Protobranchia), Lanceolaria oxyrhyncha and Margaritifera margaritifera (Palaeoheterodonta), and Ruditapes philippinarum and Tridacna crocea (Imparidentia). Except for M. margaritifera, which had two ωx genes, each species had a single ωx gene. Functional analysis showed Δ15Δ17Δ19 desaturase activity in the R. philippinarum and T. crocea ωx, while the L. oxyrhyncha ωx exhibited Δ15Δ17 activity but not Δ19. Both ωx from M. margaritifera showed no detectable activity in yeast. Interestingly, the S. pusilla ωx exhibited Δ12 desaturase activity. These findings highlight the diversity of ωx desaturation capabilities in bivalves, with significant gene loss in Pteriomorphia.},
}
@article {pmid40284824,
year = {2025},
author = {Silva, V and Caniça, M and de la Rivière, R and Barros, P and Cabral, JA and Poeta, P and Igrejas, G},
title = {Bats as Hosts of Antimicrobial-Resistant Mammaliicoccus lentus and Staphylococcus epidermidis with Zoonotic Relevance.},
journal = {Veterinary sciences},
volume = {12},
number = {4},
pages = {},
pmid = {40284824},
issn = {2306-7381},
abstract = {Bats are increasingly recognized as reservoirs for antimicrobial-resistant bacteria, playing a potential role in the dissemination of resistance genes across species and regions. In this study, 105 bats from 19 species in Portugal were sampled to investigate the presence, antimicrobial resistance, and genetic characteristics of Mammaliicoccus and Staphylococcus isolates. Thirteen Mammaliicoccus lentus and Staphylococcus epidermidis were recovered. Antimicrobial susceptibility testing revealed multidrug resistance in three isolates, with S. epidermidis carrying mph(C), msr(A), and dfrC genes, and M. lentus harboring salB, tet(K), and str. Notably, qacA was detected in S. epidermidis, highlighting its plasmid-associated potential for horizontal gene transfer to more pathogenic bacteria. Heavy metal resistance genes (arsB and cadD) were also identified, suggesting the role of environmental factors in co-selecting antimicrobial resistance. Molecular typing revealed the S. epidermidis strain as ST297, a clone associated with both healthy humans and invasive infections. These findings emphasize the need for monitoring bats as reservoirs of resistance determinants, particularly in the context of zoonotic and environmental health. The presence of mobile genetic elements and plasmids further underscores the potential for the dissemination of resistance. This study reinforces the importance of adopting a One Health approach to mitigate the risks associated with antimicrobial resistance.},
}
@article {pmid40284646,
year = {2025},
author = {Alglave, L and Faure, K and Mullié, C},
title = {Plasmid Dissemination in Multispecies Carbapenemase-Producing Enterobacterales Outbreaks Involving Clinical and Environmental Strains: A Narrative Review.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
pmid = {40284646},
issn = {2076-2607},
abstract = {Outbreaks involving carbapenemase-producing enterobacteria (CPE) have become a common occurrence in healthcare settings. While clonal dissemination is firmly established as a cause for these outbreaks, horizontal gene transfers (HGTs) between different species of Enterobacterales found in clinical and environmental isolates are less so. To gather evidence backing up this hypothesis, a review covering the 2013-2024 period was performed. HGTs between different species of clinical and environmental Enterobacterales were identified in thirteen papers, half of those published within the last three years. A combination of short- and long-read whole genome sequencing (WGS) was predominantly used to identify mobile genetic elements and plasmids. The more frequently reported carbapenemases were KPCs, followed by NDMs and IMPs. Predictably, broad-host-range plasmids were responsible for over 50% of HGTs, with the IncA/C group being in the lead. Klebsiella pneumoniae and Enterobacter cloacae complexes were the most frequent species identified in clinical samples, while Citrobacter freundii dominated environmental ones. Drains and pipework frequently constituted CPE reservoirs in protracted outbreaks, alternating epidemic outbursts with silent phases. Including WGS in a systematic environmental surveillance would help in swiftly identifying those CPE reservoirs and possibly help better control plasmid outbursts by allowing the implementation of adequate infection prevention and control measures.},
}
@article {pmid40284645,
year = {2025},
author = {González-Sánchez, A and Lozano-Aguirre, L and Jiménez-Flores, G and López-Sámano, M and García-de Los Santos, A and Cevallos, MA and Le Borgne, S},
title = {Physiology, Heavy Metal Resistance, and Genome Analysis of Two Cupriavidus gilardii Strains Isolated from the Naica Mine (Mexico).},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
pmid = {40284645},
issn = {2076-2607},
abstract = {Here, we report the characterization of two Cupriavidus strains, NOV2-1 and OV2-1, isolated from an iron-oxide deposit in an underground tunnel of the Naica mine in Mexico. This unique biotope, characterized by its high temperature (≈50 °C) and the presence of heavy metals, is no longer available for sampling at this time. The genomes of NOV2-1 and OV2-1 comprised two replicons: a chromosome of 3.58 and 3.53 Mb, respectively, and a chromid of 2.1 Mb in both strains. No plasmids were found. The average nucleotide identity and the core genome phylogeny showed that NOV2-1 and OV2-1 belonged to the Cupriavidus gilardii species. NOV2-1 and OV2-1 grew up to 48 °C, with an optimal temperature of 42 °C. Discrete differences were observed between C. gilardii CCUG38401[T], NOV2-1, and OV2-1 in the biochemical tests. NOV2-1 and OV2-1 presented resistance to zinc, lead, copper, cadmium, nickel, and cobalt. Several complete and incomplete gene clusters related to the resistance to these heavy metals (ars, czc, cop 1, sil-cop 2, cup, mmf, and mer) were detected in the genome of these strains. Although further studies are needed to determine the origin and role of the detected gene clusters, it is suggested that the czc system may have been mobilized by horizontal gene transfer. This study expands the extreme biotopes where Cupriavidus strains can be retrieved.},
}
@article {pmid40283102,
year = {2025},
author = {Zhao, Y and Wang, Y and Lu, J and Zhu, B and Li, AD},
title = {Exploring the Ecological Impacts of Herbicides on Antibiotic Resistance Genes and Microbial Communities.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
pmid = {40283102},
issn = {2075-1729},
support = {BK20230742//the Natural Science Foundation of Jiangsu Province/ ; GWJJ2024100202//2024 Annual Project of the National Health Commission (NHC) Capacity Building and Continuing Education Center/ ; M2022083//Scientific Research Project of Jiangsu Health Committee/ ; ZDXK202249//Jiangsu Provincial Medical Key Discipline/ ; 2024ZB315//Jiangsu Funding Program for Excellent Postdoctor/ ; },
abstract = {The widespread application of herbicides has profound ecological consequences, particularly regarding the distribution of antibiotic resistance genes (ARGs) and microbial communities. In this study, we analyzed herbicide-related metagenomic data to assess the impact of herbicide exposure on ARGs and microbial populations. Our results demonstrate that herbicide application significantly increased the abundance of ARGs, particularly those associated with multidrug resistance, sulfonamides, and bacitracin, with notable increases in subtypes such as bacA and sul1. Microbial community analyses revealed a dominance of Pseudomonadota and Actinomycetota, along with a significant down-regulation of genera like Fibrisoma, Gilsonvirus, Limnobacter, and Wilnyevirus in the experimental group. Additionally, herbicide exposure led to a marked reduction in biodiversity. When threshold values were relaxed, correlation analyses revealed a co-occurrence pattern between multiple genes and sul1, suggesting that horizontal gene transfer plays a pivotal role in the spread of antibiotic resistance in herbicide-contaminated soils. Moreover, environmental factors were found to significantly influence both microbial community composition and ARG distribution. These findings highlight the complex ecological effects of herbicides on microbial diversity and the dissemination of resistance genes, emphasizing the need for further research into the long-term environmental and public health implications of herbicide use.},
}
@article {pmid40280885,
year = {2025},
author = {Kaur, A and Sunny, A and Jones, JB and Goss, EM},
title = {Investigating Plasmids Diversity in X. euvesicatoria pv. perforans Population.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-02-25-0042-FI},
pmid = {40280885},
issn = {0031-949X},
abstract = {Plasmids are key drivers of horizontal gene transfer. These genetic elements promote diversification and rapid adaptation of bacterial populations to changing environments by transferring beneficial traits within and between bacterial species. Xanthomonas euvesicatoria pv. perforans is a devastating plant pathogen that causes bacterial spot disease in tomato and pepper. The pathogen population in Florida contains several distinct genetic lineages that differ in relative frequency. The objective of this study was to characterize plasmid diversity and gene content, and plasmid distribution in relation to chromosomal phylogeny. Our in silico-based plasmid prediction revealed the presence of diverse plasmids ranging from ~16 kb to ~235 kb. A network approach based on shared k-mer content uncovered ten distinct plasmid groups with high genetic similarity (cliques). Interestingly, these plasmid cliques were confined to specific phylogenetic clusters suggesting potential incompatibility or restricted plasmid movement between clusters. Some of the predicted plasmids carry virulence genes coding for type III secretion effectors (T3SEs), including transcriptional activator-like effectors (TALEs) and genes related to biocide resistance, such as copper. We also identified gene reshuffling between the plasmids, likely carried out by transposons present within them. Overall, these results provide foundational insights into plasmid diversity in Xanthomonas euvesicatoria pv. perforans with implications for the role of these mobile genetic elements in genome dynamics and pathogen adaptation.},
}
@article {pmid40279390,
year = {2025},
author = {Djermoun, S and Rode, DKH and Jiménez-Siebert, E and Netter, N and Lesterlin, C and Drescher, K and Bigot, S},
title = {Biofilm architecture determines the dissemination of conjugative plasmids.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {17},
pages = {e2417452122},
doi = {10.1073/pnas.2417452122},
pmid = {40279390},
issn = {1091-6490},
support = {ANR-19-ARMB-0006-01//Agence Nationale de la Recherche (ANR)/ ; 16GW0245//Bundesministerium f&#xfc;r Bildung und Forschung (BMBF)/ ; RF20200502684//Association Vaincre la Mucoviscidose (French CF Association)/ ; 955910//EC | H2020 | PRIORITY 'Excellent science' | H2020 Marie Sk&#x142;odowska-Curie Actions (MSCA)/ ; TMCG-3 _ 213801/SNSF_/Swiss National Science Foundation/Switzerland ; DR 982/6-1 part of SPP 2389//Deutsche Forschungsgemeinschaft (DFG)/ ; 57552336//Deutscher Akademischer Austauschdienst France (DAAD France)/ ; 47902YJ//Germaine de Stael swiss Academy of Engineering Sciences/ ; },
mesh = {*Biofilms/growth &amp; development ; *Plasmids/genetics ; *Escherichia coli/genetics/physiology ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; Microscopy, Fluorescence ; },
abstract = {Plasmid conjugation is a contact-dependent horizontal gene transfer mechanism that significantly contributes to the dissemination of antibiotic resistance among bacteria. While the molecular mechanisms of conjugation have been extensively studied, our understanding of plasmid transfer dynamics within spatially structured bacterial communities and the influence of community architecture on plasmid dissemination remains limited. In this study, we use live-cell fluorescence microscopy to investigate the propagation of the broad host range RP4 conjugative plasmid in Escherichia coli populations exhibiting varying levels of spatial organization. In high-density, two-dimensional cell monolayers, direct and tight contact between donors and recipients is not only necessary but also sufficient to trigger RP4 plasmid transfer, ensuring optimal plasmid propagation. In three-dimensional mature biofilms, the emergent community architecture limits the ability of donor cells to enter regions with high cell density, which hinders the establishment of direct contacts with recipients and impedes plasmid transfer in biofilms. In contrast, microcolonies, early-stage biofilms, and biofilms with a lower surface coverage leave open access points for donor cells in regions that later emerge as high-cell-density regions in mature biofilms, which facilitates plasmid transfer. These findings reveal the crucial role of bacterial community architecture in determining the efficiency of plasmid dissemination.},
}
@article {pmid40278619,
year = {2025},
author = {Pei, Y and Hamar, P and Pei, DS},
title = {Deciphering Multidrug-Resistant Pseudomonas aeruginosa: Mechanistic Insights and Environmental Risks.},
journal = {Toxics},
volume = {13},
number = {4},
pages = {},
pmid = {40278619},
issn = {2305-6304},
support = {CSTB2024TIAD-CYKJCXX0017//Sichuan-Chongqing Special Key Project/ ; },
abstract = {The rise of multidrug-resistant (MDR) Pseudomonas aeruginosa (P. aeruginosa) presents a significant challenge to clinical treatment and environmental risks. This review delves into the complex mechanisms underlying MDR development in P. aeruginosa, such as genetic mutations, horizontal gene transfer (HGT), and the interaction between virulence factors and resistance genes. It evaluates current detection methods, from traditional bacteriology to advanced molecular techniques, emphasizing the need for rapid and accurate diagnostics. This review also examines therapeutic strategies, including broad-spectrum antibiotics, novel drug candidates, combination therapies, and innovative approaches like RNA interference, CRISPR-Cas9 gene editing, and bridge RNA-guided gene editing. Importantly, this review highlights the distribution, migration, and environmental risks of MDR P. aeruginosa, underscoring its adaptability to diverse environments. It concludes by stressing the necessity for continued research and development in antimicrobial resistance, advocating for an integrated approach that combines genomics, clinical practice, and environmental considerations to devise innovative solutions and preserve antibiotic efficacy.},
}
@article {pmid40278556,
year = {2025},
author = {Zeng, Y and Feng, R and Huang, C and Liu, J and Yang, F},
title = {Antibiotic Resistance Genes in Agricultural Soils: A Comprehensive Review of the Hidden Crisis and Exploring Control Strategies.},
journal = {Toxics},
volume = {13},
number = {4},
pages = {},
pmid = {40278556},
issn = {2305-6304},
support = {42277033//the National Natural Science Foundation of China/ ; 202401AT070304//Basic Research Foundation of Yunnan Province of China/ ; Y2024QC28//Central Public-interest Scientific Institution Basal Research Fund/ ; 23JCYBJC00250//Tianjin Municipal Natural Science Foundation/ ; },
abstract = {This paper aims to review the sources, occurrence patterns, and potential risks of antibiotic resistance genes (ARGs) in agricultural soils and discuss strategies for their reduction. The pervasive utilization of antibiotics has led to the accumulation of ARGs in the soil. ARGs can be transferred among microorganisms via horizontal gene transfer, thereby increasing the likelihood of resistance dissemination and heightening the threat to public health. In this study, we propose that physical, chemical, and bioremediation approaches, namely electrokinetic remediation, advanced oxidation, and biochar application, can effectively decrease the abundance of ARGs in the soil. This study also highlights the significance of various control measures, such as establishing a strict regulatory mechanism for veterinary drugs, setting standards for the control of ARGs in organic fertilizers, and conducting technical guidance and on-farm soil monitoring to reduce the environmental spread of ARGs and protect public health.},
}
@article {pmid40275408,
year = {2025},
author = {Pérez-Carrascal, OM and Pratama, AA and Sullivan, MB and Küsel, K},
title = {Unveiling plasmid diversity and functionality in pristine groundwater.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {42},
pmid = {40275408},
issn = {2524-6372},
abstract = {BACKGROUND: Plasmids are key in creating a dynamic reservoir of genetic diversity, yet their impact on Earth's continental subsurface-an important microbial reservoir-remains unresolved. We analyzed 32 metagenomic samples from six groundwater wells within a hillslope aquifer system to assess the genetic and functional diversity of plasmids and to evaluate the role of these plasmids in horizontal gene transfer (HGT).<br><br>RESULTS: Our results revealed 4,609 non-redundant mobile genetic elements (MGEs), with 14% (664) confidently classified as plasmids. These plasmids displayed well-specific populations, with fewer than 15% shared across wells. Plasmids were linked to diverse microbial phyla, including Pseudomonadota (42.17%), Nitrospirota (3.31%), Candidate Phyla Radiation (CPR) bacteria (2.56%), and Omnitrophota (2.11%). The presence of plasmids in the dominant CPR bacteria is significant, as this group remains underexplored in this context. Plasmid composition strongly correlated with well-specific microbial communities, suggesting local selection pressures. Functional analyses highlighted that conjugative plasmids carry genes crucial for metabolic processes, such as cobalamin biosynthesis and hydrocarbon degradation. Importantly, we found no evidence of high confidence emerging antibiotic resistance genes, contrasting with findings from sewage and polluted groundwater.<br><br>CONCLUSIONS: Overall, our study emphasizes the diversity, composition, and eco-evolutionary role of plasmids in the groundwater microbiome. The absence of known antibiotic resistance genes highlights the need to preserve groundwater in its pristine state to safeguard its unique genetic and functional landscape.},
}
@article {pmid40275130,
year = {2025},
author = {Medina-Chávez, NO and Rodriguez-Cruz, UE and Souza, V and De la Torre-Zavala, S and Travisano, M},
title = {Salty secrets of Halobacterium salinarum AD88: a new archaeal ecotype isolated from Cuatro Cienegas Basin.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {399},
pmid = {40275130},
issn = {1471-2164},
support = {IG200319,IN204822//PAPIIT-DGAPA, UNAM/ ; NASA IDEAS16002//NASA IDEAS/ ; },
mesh = {*Halobacterium salinarum/genetics/isolation &amp; purification/classification/metabolism ; Phylogeny ; Genome, Archaeal ; Mexico ; Genomics ; },
abstract = {The Cuatro Cienegas Basin (CCB) in Mexico, represents a unique ecological habitat, characterized by extreme and fluctuating conditions, providing a window into ancient evolutionary processes. This basin, characterized by hypersalinity and phosphorus scarcity, harbors diverse microbial communities that exhibit remarkable adaptations to oligotrophic conditions. Among these, Halobacterium salinarum, a halophilic archaeon known for its polyploid genome and metabolic versatility, has been extensively studied as a model for extremophile survival. However, only a limited number of H. salinarum strains have been successfully cultured and characterized to date. Here, we report the isolation and genomic analysis of a novel Halobacterium salinarum strain, AD88, from microbial mats at the Archaean Domes site in the CCB. This strain displays unique genomic features, including smaller plasmid sizes and distinctive metabolic pathways for phosphorus and sulfur utilization. Comparative analyses with other Halobacterium strains revealed genetic innovations, such as genes involved in sulfolipid biosynthesis, enabling membrane stability in phosphorus-depleted environments, and adaptations for horizontal gene transfer, which facilitate genomic flexibility in response to environmental pressures. This study reveals that H. salinarum AD88 is the first recorded diploid strain of Halobacterium, a feature previously undocumented in this genus. Phylogenomic reconstruction positioned AD88 tightly within the Halobacterium clade, reflecting its evolutionary history within the genus. Pangenome analysis further highlighted the open nature of the Halobacterium genus, with AD88 contributing novel accessory genes linked to ecological specialization. These findings emphasize the evolutionary significance of the CCB as a natural laboratory for studying microbial adaptation and expand our understanding of archaeal genomic diversity and functional innovation under extreme conditions.},
}
@article {pmid40274494,
year = {2025},
author = {Good, BH and Bhatt, AS and McDonald, MJ},
title = {Unraveling the tempo and mode of horizontal gene transfer in bacteria.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.03.009},
pmid = {40274494},
issn = {1878-4380},
abstract = {Research on horizontal gene transfer (HGT) has surged over the past two decades, revealing its critical role in accelerating evolutionary rates, facilitating adaptive innovations, and shaping pangenomes. Recent experimental and theoretical results have shown how HGT shapes the flow of genetic information within and between populations, expanding the range of possibilities for microbial evolution. These advances set the stage for a new wave of research seeking to predict how HGT shapes microbial evolution within natural communities, especially during rapid ecological shifts. In this article, we highlight these developments and outline promising research directions, emphasizing the necessity of quantifying the rates of HGT within diverse ecological contexts.},
}
@article {pmid40273693,
year = {2025},
author = {Yan, X and Xin, Y and Zhu, L and Tang, Q and Chen, M and Wei, Y and Zhang, J and Richnow, HH},
title = {Neglected role of virus-host interactions driving antibiotic resistance genes reduction in an urban river receiving treated wastewater.},
journal = {Water research},
volume = {282},
number = {},
pages = {123627},
doi = {10.1016/j.watres.2025.123627},
pmid = {40273693},
issn = {1879-2448},
abstract = {Treated wastewater from wastewater treatment plants (WWTPs) is a major contributor to the transfer of antibiotic resistance genes (ARGs) into urban rivers. However, the role of viral communities in this process remains poorly understood. This study focused on North Canal in Beijing, China, which receives over 80 % of its water from treated wastewater, to investigate the impact of viral communities on ARGs transfer. Results showed significant seasonal variation in the abundance and composition of ARGs, with 30 high-risk ARGs detected, accounting for 1.50 % ± 1.28 % of total ARGs. The assembly of ARGs in North Canal followed a stochastic process of homogenizing dispersal, with conjugative mobility playing a key role in horizontal gene transfer with Pseudomonas as primary host for HGT. The potential conjugative mobility of ARGs is significantly higher in wet season (69.4 % ± 17.3 %) compared to dry season (42.9 % ± 17.1 %), with conjugation frequencies ranging from 1.18 × 10[-6] to 2.26 × 10[-4]. Viral species accumulation curves approaching saturation indicated the well captured viral diversity, and no phages carrying ARGs were found among 27,523 non-redundant viral operational taxonomic units. Most of the phages (89.2 % ± 3.8 %) were lytic in North Canal, which were observed to contribute to ARGs reduction by lysing their host bacteria, reflected by higher virus-host ratio and demonstrated by the phage lysis assays in treated wastewater and receiving river. We provided compelling evidence that phage-host interactions can reduce ARGs through host lysis, highlighting their potential role in mitigating ARG transmission in urban rivers receiving treated wastewater.},
}
@article {pmid40273218,
year = {2025},
author = {Urriza, M and Dimaria, G and de Oliveira, LO and Catara, V and Murillo, J},
title = {Comparative genomics of native plasmids from plant pathogenic Gammaproteobacteria.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {},
number = {},
pages = {},
doi = {10.1093/dnares/dsaf009},
pmid = {40273218},
issn = {1756-1663},
abstract = {Plasmids are key in the evolution and adaptation of plant pathogenic Gammaproteobacteria (PPG), yet their diversity and functional contributions remain underexplored. Here, comparative genomics revealed extensive variation in plasmid size, replicon types, mobility, and genetic content across PPG. Most plasmids are small (<200 kb), except in Pantoea, exhibiting high coding densities (76-78%). Five ancestral replicon types were identified across multiple orders, indicating vertical descent yet efficient horizontal transfer across taxa, although with limited genetic conservation. Virulence plasmids are widespread (56-68%) but differ in virulence gene content across orders: type III effector (T3E) genes are common in Pseudomonas and Xanthomonas, but rare in Enterobacterales and Xylella, aligning with their smaller effector repertoires. Plasmids frequently carry regulatory genes, highlighting their role in bacterial phenotype modulation. Distinct patterns were observed among orders: Enterobacterales plasmids often harbor thiamine biosynthesis operons and transcriptional regulators but lack post-transcriptional regulators, while Pseudomonas and Xanthomonas plasmids are highly mobile, enriched in T3E genes, and exhibit high insertion sequence densities, fostering DNA mobility. Resistance to ultraviolet light is common, but not to antimicrobial compounds. These findings highlight the dynamic role of plasmids in spreading adaptive traits, shaping virulence, and driving the evolution of plant pathogenic bacteria.},
}
@article {pmid40269132,
year = {2025},
author = {Kumar, T and Rekhi, A and Lee, Y and Tran, J and Nagtalon, AGD and Rohatgi, S and Cyphert, EL},
title = {Leveraging the microbiome to combat antibiotic resistant gynecological infections.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {32},
pmid = {40269132},
issn = {2731-8745},
abstract = {The vaginal resistome can be considered a collection of the resistant determinants in the vaginal microbiome. Here we review the vaginal resistome including the microbes and resistant genes harbored in common gynecological infections, vaginal microbes that participate in horizontal gene transfer, host factors that contribute to the resistome, and common therapies. Finally, we provide perspective on technologies that can be leveraged to study the vaginal resistome and remaining challenges.},
}
@article {pmid40268300,
year = {2025},
author = {Goyal, A and Chure, G},
title = {Paradox of the Sub-Plankton: Plausible Mechanisms and Open Problems Underlying Strain-Level Diversity in Microbial Communities.},
journal = {Environmental microbiology},
volume = {27},
number = {4},
pages = {e70094},
pmid = {40268300},
issn = {1462-2920},
mesh = {*Biodiversity ; *Microbiota ; *Bacteria/genetics/classification ; Gene Transfer, Horizontal ; Genetic Variation ; Ecosystem ; Biological Evolution ; },
abstract = {Microbial communities are often complex and highly diverse, typically with dozens of species sharing spatially-restricted environments. Within these species, genetic and ecological variation often exists at a much finer scale, with closely related strains coexisting and competing. While the coexistence of strains in communities has been heavily explored over the past two decades, we have no self-consistent theory of how this diversity is maintained. This question challenges our conventional understanding of ecological coexistence, typically framed around species with clear phenotypic and ecological differences. In this review, we synthesise plausible mechanisms underlying strain-level diversity (termed microdiversity), focusing on niche-based mechanisms such as nutrient competition, neutral mechanisms such as migration, and evolutionary mechanisms such as horizontal gene transfer. We critically assess the strengths and caveats of these mechanisms, acknowledging key gaps that persist in linking genetic similarity to ecological divergence. Finally, we highlight how the origin and maintenance of microdiversity could pose a major challenge to conventional ecological thinking. We articulate a call-to-arms for a dialogue between well-designed experiments and new theoretical frameworks to address this grand conceptual challenge in understanding microbial biodiversity.},
}
@article {pmid40267282,
year = {2025},
author = {Yang, Z and Chen, H and Zhong, GH and Liu, J},
title = {cAMP-Mediated Biofilm eDNA Transfer Facilitates the Resilience of Soil Microbiome to Agrochemical Stress.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c00961},
pmid = {40267282},
issn = {1520-5118},
abstract = {Soil microorganisms utilize extracellular DNA (eDNA)-based biofilms as a defense against xenobiotics. However, the specific effects and transfer pathways of eDNA under persistent agrochemical exposure remain unclear. This study examined the transfer dynamics of carbofuran-hydrolase gene pchA from Pseudomonas stutzeri PS21. During biofilm formation, pchA was released from eDNA, leading to an enrichment of beneficial microorganisms such as Acidobacteria and Elusimicrobia, which enhanced organic compound metabolism and improved soil microbiome resilience. An increase in the pchA-associated mobile genetic elements and the colocalization of pchA with other bacterial species indicated the potential horizontal gene transfer (HGT) under carbofuran exposure. Additionally, carbofuran triggered a cAMP-dependent apoptotic pathway, leading to a 59.6% increase in pchA copy number, which suggested that cAMP played a role in initiating HGT. In conclusion, the cAMP-mediated interspecific transfer of pchA could enhance microbial coadaptation to carbofuran contamination, thereby strengthening the collective defense of soil microbiome against agrochemical stress.},
}
@article {pmid40262895,
year = {2025},
author = {Lind, AL and McDonald, NA and Gerrick, ER and Bhatt, AS and Pollard, K},
title = {Contiguous and complete assemblies of Blastocystis gut microbiome-associated protists reveal evolutionary diversification to host ecology.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279080.124},
pmid = {40262895},
issn = {1549-5469},
abstract = {Blastocystis, an obligate host-associated protist, is the most common microbial eukaryote in the human gut and is widely distributed across vertebrate hosts. The evolutionary transition of Blastocystis from its free-living stramenopile ancestors to a radiation of host-associated organisms is poorly understood. To explore this, we cultured and sequenced eight strains representing the significant phylogenetic diversity of the genus using long-read, short-read, and Hi-C DNA sequencing, alongside gene annotation and RNA sequencing. Comparative genomic analyses revealed significant variation in gene content and genome structure across Blastocystis Notably, three strains from herbivorous tortoises, phylogenetically distant from human subtypes, have markedly larger genomes with longer introns and intergenic regions, and retain canonical stop codons absent in the human-associated strains. Despite these genetic differences, all eight isolates exhibit gene losses linked to the reduced cellular complexity of Blastocystis, including losses of cilia and flagella genes, microtubule motor genes, and signal transduction genes. Isolates from herbivorous tortoises contained higher numbers of plant carbohydrate-metabolizing enzymes, suggesting that like gut bacteria, these protists ferment plant material in the host gut. We find evidence that some of these carbohydrate-metabolizing enzymes were horizontally acquired from bacteria, indicating that horizontal gene transfer is an ongoing process in Blastocystis that has contributed to host-related adaptation. Together, these results highlight substantial genetic and metabolic diversity within the Blastocystis genus, indicating different lineages of Blastocystis have varied ecological roles in the host gut.},
}
@article {pmid40262702,
year = {2025},
author = {Zhang, S and Sun, C},
title = {Ecological divergence of marine bacteria Alteromonas mediterranea.},
journal = {Molecular phylogenetics and evolution},
volume = {208},
number = {},
pages = {108359},
doi = {10.1016/j.ympev.2025.108359},
pmid = {40262702},
issn = {1095-9513},
abstract = {Alteromonas mediterranea, originally designated as A. macleodii, is a deep-sea ecotype that plays an important ecological role in the ocean. However, a comprehensive understanding of their biogeographic distribution and evolutionary histories remains limited. In this study, our analysis indicated that A. mediterranea members could adapt contrasting marine ecosystems and flourish in nutrient-rich habitats such as feces and coral reefs. No significant correlations between the relative abundance of A. mediterranea members and the environmental variables were identified. Phylogenetic analysis and geographic patterns of A. mediterranea strains suggested that they could be clustered into two clades (clade Ⅰ and clade Ⅱ). In contrast, many distinct genomic traits exist between these clades, such as the complete genes encoding cytochrome o ubiquinol oxidase only involved in clade Ⅱ. Genes were more likely to be lost in the evolutionary history of A. mediterranea relatives. Gene loss might be a major force in all phylogenetic groups driving the distinct clades. Adaptation to different biotopes resulted in the functional differentiation of A. mediterranea members, with the loss of genes encoding carbohydrate-active enzymes. Genes acquired horizontally from unclassified bacteria, and Proteobacteria represented by Gammaproteobacteria played key roles in the functional diversification of A. mediterranea in marine habitats. Given these data, these results are useful for information supplementation of A. mediterranea strains, particularly for making significant advances in understanding marine microbial ecology within different clonal frames using genome-wide recruitments.},
}
@article {pmid40261943,
year = {2025},
author = {Gori, K and Baez-Ortega, A and Strakova, A and Stammnitz, MR and Wang, J and Chan, J and Hughes, K and Belkhir, S and Hammel, M and Moralli, D and Bancroft, J and Drydale, E and Allum, KM and Brignone, MV and Corrigan, AM and de Castro, KF and Donelan, EM and Faramade, IA and Hayes, A and Ignatenko, N and Karmacharya, R and Koenig, D and Lanza-Perea, M and Lopez Quintana, AM and Meyer, M and Neunzig, W and Pedraza-Ordoñez, F and Phuentshok, Y and Phuntsho, K and Ramirez-Ante, JC and Reece, JF and Schmeling, SK and Singh, S and Tapia Martinez, LJ and Taulescu, M and Thapa, S and Thapa, S and van der Wel, MG and Wehrle-Martinez, AS and Stratton, MR and Murchison, EP},
title = {Horizontal transfer of nuclear DNA in transmissible cancer.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {18},
pages = {e2424634122},
doi = {10.1073/pnas.2424634122},
pmid = {40261943},
issn = {1091-6490},
support = {102942/Z/13/A 222551/Z/21/Z//Wellcome Trust (WT)/ ; BB/Y514299/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {Animals ; *Gene Transfer, Horizontal ; Dogs ; *Dog Diseases/genetics ; *Venereal Tumors, Veterinary/genetics ; *Cell Nucleus/genetics ; Marsupialia/genetics ; *DNA/genetics ; },
abstract = {Horizontal transfer of nuclear DNA between cells of host and cancer is a potential source of adaptive variation in cancer cells. An understanding of the frequency and significance of this process in naturally occurring tumors is, however, lacking. We screened for this phenomenon in the transmissible cancers of dogs and Tasmanian devils and found an instance in the canine transmissible venereal tumor (CTVT). This involved introduction of a 15-megabase dicentric genetic element, composed of 11 fragments of six chromosomes, to a CTVT sublineage occurring in Asia around 2,000 y ago. The element forms the short arm of a small submetacentric chromosome and derives from a dog with ancestry associated with the ancient Middle East. The introduced DNA fragment is transcriptionally active and has adopted the expression profile of CTVT. Its features suggest that it may derive from an engulfed apoptotic body. Our findings indicate that nuclear horizontal gene transfer, although likely a rare event in tumor evolution, provides a viable mechanism for the acquisition of genetic material in naturally occurring cancer genomes.},
}
@article {pmid40261018,
year = {2025},
author = {Chi, W and Zhang, H and Li, X and Zhou, Y and Meng, Q and He, L and Yang, Y and Liu, S and Shi, K},
title = {Comparative genomic analysis of 255 Oenococcus oeni isolates from China: unveiling strain diversity and genotype-phenotype associations of acid resistance.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0326524},
doi = {10.1128/spectrum.03265-24},
pmid = {40261018},
issn = {2165-0497},
abstract = {Oenococcus oeni, the only species of lactic acid bacteria capable of fully completing malolactic fermentation under challenging wine conditions, continues to intrigue researchers owing to its remarkable adaptability, particularly in combating acid stress. However, the mechanism underlying its superior adaptation to wine stresses still remains elusive due to the lack of viable genetic manipulation tools for this species. In this study, we conducted genomic sequencing and acid resistance phenotype analysis of 255 O. oeni isolates derived from diverse wine regions across China, aiming to elucidate their strain diversity and genotype-phenotype associations of acid resistance through comparative genomics. A significant correlation between phenotypes and evolutionary relationships was observed. Notably, phylogroup B predominantly consisted of acid-resistant isolates, primarily originating from Shandong and Shaanxi wine regions. Furthermore, we uncovered a noteworthy linkage between prophage genomic islands and acid resistance phenotype. Using genome-wide association studies, we identified key genes correlated with acid resistance, primarily involved in carbohydrates and amino acid metabolism processes. This study offers profound insights into the genetic diversity and genetic basis underlying adaptation mechanisms to acid stress in O. oeni.IMPORTANCEThis study provides valuable insights into the genetic basis of acid resistance in Oenococcus oeni, a key lactic acid bacterium in winemaking. By analyzing 255 isolates from diverse wine regions in China, we identified significant correlations between strain diversity, genomic islands, and acid resistance phenotypes. Our findings reveal that certain prophage-related genomic islands and specific genes are closely linked to acid resistance, offering a deeper understanding of how O. oeni adapts to acidic environments. These discoveries not only advance our knowledge of microbial stress responses but also pave the way for selecting and engineering acid-resistant strains, enhancing malolactic fermentation efficiency and wine quality. This research underscores the importance of genomics in improving winemaking practices and addressing challenges posed by high-acidity wines.},
}
@article {pmid40259521,
year = {2025},
author = {Gatica-Soria, LM and Roulet, ME and Tulle, WD and Sato, HA and Barrandeguy, ME and Sanchez-Puerta, MV},
title = {Highly variable mitochondrial chromosome content in a holoparasitic plant due to recurrent gains of foreign circular DNA.},
journal = {Physiologia plantarum},
volume = {177},
number = {2},
pages = {e70231},
doi = {10.1111/ppl.70231},
pmid = {40259521},
issn = {1399-3054},
support = {06/A092-T1//Secretar&#xed;a de Investigaci&#xf3;n, Internacionales y Posgrado, Universidad Nacional de Cuyo/ ; PICT2020-01018//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICT2021 -GTR_TI-00435//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; },
mesh = {Gene Transfer, Horizontal/genetics ; DNA, Mitochondrial/genetics ; *Chromosomes, Plant/genetics ; *DNA, Circular/genetics ; *Genome, Mitochondrial/genetics ; Evolution, Molecular ; Phylogeny ; },
abstract = {Multichromosomal mitochondrial genomes (mtDNAs) in eukaryotes exhibit remarkable structural diversity, yet intraspecific variability and the origin of the individual chromosomes remain poorly understood. We focus on a holoparasitic angiosperm with an mtDNA consisting of 65 chromosomes largely composed of foreign DNA acquired by horizontal gene transfer (HGT) from its mimosoid hosts. The frequency, timing and population dynamics of these HGT events have not been examined. Here, we sampled different individuals of the holoparasite Lophophytum mirabile, along with their host plants, to assess mtDNA intraspecific variability and capture recent events that may bring insights into the HGT process. We also gathered mitochondrial data from 43 mimosoids to identify older and recent HGT events and assess precisely the proportion of foreign DNA. Through comparative genomic and evolutionary analyses, we uncovered great intraspecific variability in chromosome content and defined the mitochondrial pangenome of L. mirabile with 105 distinct chromosomes. The estimated foreign content reaches 93.5% of the mtDNA, including 73 fully foreign chromosomes that support the circle-mediated HGT model as a key mechanism for their acquisition. We inferred recurrent DNA transfers from the host plants, leading to new mitochondrial chromosomes that replicate autonomously. Our results emphasize the importance of adopting a pangenomic approach to fully capture the genetic diversity and evolution of multichromosomal mitochondrial genomes. This study shows that HGT can strongly influence the mtDNA content and generate enormous intraspecific variability even in geographically close individuals.},
}
@article {pmid40258067,
year = {2025},
author = {Christman, ND and Dalia, AB},
title = {The molecular basis for DNA-binding by competence T4P is distinct in a representative Gram-positive and Gram-negative species.},
journal = {PLoS pathogens},
volume = {21},
number = {4},
pages = {e1013128},
pmid = {40258067},
issn = {1553-7374},
support = {R35 GM128674/GM/NIGMS NIH HHS/United States ; },
mesh = {*Streptococcus pneumoniae/genetics/metabolism ; *Fimbriae, Bacterial/metabolism/genetics ; *DNA, Bacterial/metabolism/genetics ; *Fimbriae Proteins/metabolism/genetics ; *DNA-Binding Proteins/metabolism/genetics ; *Gram-Negative Bacteria/metabolism/genetics ; *DNA Transformation Competence ; Bacterial Proteins/metabolism/genetics ; *Gram-Positive Bacteria/metabolism/genetics ; Protein Binding ; },
abstract = {Competence type IV pili (T4P) are bacterial surface appendages that facilitate DNA uptake during horizontal gene transfer by natural transformation. These dynamic structures actively extend from the cell surface, bind to DNA in the environment, and then retract to import bound DNA into the cell. Competence T4P are found in diverse Gram-negative (diderm) and Gram-positive (monoderm) bacterial species. While the mechanism of DNA-binding by diderm competence T4P has been the recent focus of intensive study, relatively little is known about DNA-binding by monoderm competence T4P. Here, we use Streptococcus pneumoniae as a model system to address this question. Competence T4P likely bind to DNA via a tip-associated complex of proteins called minor pilins, and recent work highlights a high degree of structural conservation between the minor pilin tip complexes of monoderm and diderm competence T4P. In diderms, positively charged residues in one minor pilin, FimT, are critical for DNA-binding. We show that while these residues are conserved in ComGD, the FimT homolog of monoderms, they only play a minor role in DNA uptake for natural transformation. Instead, we find that two-positively charged residues in the neighboring minor pilin, ComGF (the PilW homolog of monoderms), play the dominant role in DNA uptake for natural transformation. Furthermore, we find that these residues are conserved in other monoderms, but not diderms. Together, these results suggest that the molecular basis for DNA-binding has either diverged or evolved independently in monoderm and diderm competence T4P.},
}
@article {pmid40253436,
year = {2025},
author = {Huang, J and Zheng, X and Yu, T and Ali, M and Wiese, J and Hu, S and Huang, L and Huang, Y},
title = {Diverse lifestyles and adaptive evolution of uncultured UBA5794 actinobacteria, a sister order of "Candidatus actinomarinales".},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {39},
pmid = {40253436},
issn = {2524-6372},
support = {92351301, 32470005, 42376238, and 32393970//National Natural Science Foundation of China/ ; 91751000//Major Research Plan of the National Natural Science Foundation of China/ ; GML20240002//the PI Project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; },
abstract = {Uncultured UBA5794 actinobacteria are frequently found in marine and inland water environments by using metagenomic approaches. However, knowledge about these actinobacteria is limited, hindering their isolation and cultivation, and they are always confused with "Candidatus Actinomarinales" based on 16S rRNA gene classification. Here, to conduct genomic characterization of them, we obtained three high-quality UBA5794 metagenome-assembled genomes (MAGs) from a hydrothermal sediment on the Carlsberg Ridge (CR) and retrieved 131 high-quality UBA5794 genomes from public datasets. Phylogenomic analysis confirms UBA5794 as an independent order within the class Acidimicrobiia. Genome-based metabolic predictions reveal that flexible metabolism and diversified energy acquisition, as well as heavy metal(loid) detoxification capacity, are crucial for the ability of UBA5794 to thrive in diverse environments. Moreover, there is separation between sponge-associated and free-living UBA5794 groups in phylogeny and functional potential, which can be attributed to the symbiotic nature of the sponge-associated group and the extensive horizontal gene transfer (HGT) events observed in these bacteria. Ancestral state reconstruction suggests that the UBA5794 clade may have originated from a free-living environment and then some members gradually migrated to the sponge host. Overall, our study sheds light on the ecological adaptation and evolutionary history of the ubiquitous but poorly understood UBA5794 actinobacteria.},
}
@article {pmid40251489,
year = {2025},
author = {Bini, F and Soffritti, I and D'Accolti, M and Mazziga, E and Caballero, JD and David, S and Argimon, S and Aanensen, DM and Volta, A and Bisi, M and Mazzacane, S and Caselli, E},
title = {Profiling the resistome and virulome of Bacillus strains used for probiotic-based sanitation: a multicenter WGS analysis.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {382},
pmid = {40251489},
issn = {1471-2164},
support = {INV-004891/GATES/Gates Foundation/United States ; },
mesh = {*Bacillus/genetics/isolation &amp; purification/drug effects/classification/pathogenicity ; *Probiotics ; *Whole Genome Sequencing ; *Genome, Bacterial ; Polymorphism, Single Nucleotide ; *Sanitation ; Humans ; *Drug Resistance, Bacterial/genetics ; },
abstract = {BACKGROUND: Healthcare-associated infections (HAIs) caused by microbes that acquire antimicrobial resistance (AMR) represent an increasing threat to human health worldwide. The high use of chemical disinfectants aimed at reducing the presence of pathogens in the hospital environment can simultaneously favor the selection of resistant strains, potentially worsening AMR concerns. In the search for sustainable ways to control bioburden without affecting this aspect, probiotic-based sanitation (PBS) using Bacillus spp. was proposed to achieve stable reduction of pathogens, AMR, and associated HAIs. Although Bacillus probiotics are classified as nonpathogenic, comprehensive data about the potential genetic alterations of these probiotics following prolonged contact with surrounding pathogens are not yet available. This study aimed to assess in depth the genetic content of PBS-Bacillus isolates to evaluate any eventual variations that occurred during their usage.<br><br>RESULTS: WGS analysis was used for the precise identification of PBS-Bacillus species and detailed profiling of their SNPs, resistome, virulome, and mobilome. Analyses were conducted on both the original PBS detergent and 172 environmental isolates from eight hospitals sanitized with PBS over a 30-month period. The two species B. subtilis and B. velezensis were identified in both the original product and the hospital environment, and SNP analysis revealed the presence of two clusters in each species. No virulence/resistance genes or mobile conjugative plasmids were detected in either the original PBS-Bacillus strain or any of the analyzed environmental isolates, confirming their high genetic stability and their low/no tendency to be involved in horizontal gene transfer events.<br><br>CONCLUSIONS: The data obtained by metagenomic analysis revealed the absence of genetic sequences associated with PBS-Bacillus and the lack of alterations in all the environmental isolates analyzed, despite their continuous contact with surrounding pathogens. These results support the safety of the Bacillus species analyzed. Further metagenomic studies aimed at profiling the whole genomes of these and other species of Bacillus, possibly during longer periods and under stress conditions, would be of interest since they may provide further confirmation of their stability and safety.},
}
@article {pmid40250499,
year = {2025},
author = {Yang, Y and Sun, Y and Zhou, Z and Song, Y and Zhu, Y and Zhou, W and Yue, M and Zhao, G and Jiang, H and Tang, B},
title = {Surveillance of Escherichia coli antimicrobial resistance in pig farms in Zhejiang province, China: high prevalence of multidrug resistance and risk-associated genes.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107598},
doi = {10.1016/j.micpath.2025.107598},
pmid = {40250499},
issn = {1096-1208},
abstract = {OBJECTIVES: The global rise in antimicrobial resistance (AMR) poses a critical threat to public health, with the overuse of antibiotics in livestock being a key driver of this escalating problem. However, research on livestock-associated AMR remains limited, with few systematic monitoring efforts. This study addresses this gap by presenting findings from our surveillance of Escherichia coli resistance in pig farms in Zhejiang Province, China.<br><br>METHODS: The minimum inhibitory concentrations were determined via broth microdilution-based antimicrobial susceptibility testing. The complete genome sequence was acquired using both Illumina NovaSeq 6000 platforms. In the plasmid conjugation experiment, sodium azide-resistant E. coli strain J53 served as the recipient. The E. coli genomes were analyzed for AMR genes, multi-locus sequence typing (MLST) types, plasmid types, and virulence genes using the ABRicate.<br><br>RESULTS: A total of 51 E. coli strains from 90 fecal samples collected across six farms. Resistance rates for amoxicillin/clavulanic acid and sulfamethoxazole exceeded 90%, while resistance to ampicillin, florfenicol, tetracycline, and trimethoprim/sulfamethoxazole was above 80%. The prevalence of multidrug-resistant strains was 89.24%. Whole-genome sequencing revealed 58 acquired AMR genes and 17 virulence-associated genes, notably including the astA gene. Two strains exhibited meropenem resistance and carried blaNDM-5, located on IncI1-I plasmids. These strains shared an identical genetic context, characterized by an "IS26-IS30-blaNDM-5-bleMBL-dsdD-IS91" structure, which may promote horizontal gene transfer of blaNDM-5. Additionally, six strains harbored the tet(X4) gene.<br><br>CONCLUSIONS: Despite ongoing antibiotic reduction efforts, the high prevalence of resistant E. coli in pigs underscores the urgent need for sustained surveillance of AMR in animal populations to mitigate the threat of resistance.},
}
@article {pmid40250277,
year = {2025},
author = {Han, Q and Yang, ML and Liu, ZS and Zhao, YH and Liu, XH and Ai, GM and Qin, WH and Liu, XY and Li, DF},
title = {Simultaneous high molecular weight PAHs degradation and chromate and arsenite detoxification by Altererythrobacter sp. H2.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138314},
doi = {10.1016/j.jhazmat.2025.138314},
pmid = {40250277},
issn = {1873-3336},
abstract = {The cooccurrence of high molecular weight PAHs and heavy metals Cr and As is frequently observed in soil and water and challenges public health and environmental management. Yet the limited microbial resources were reported to simultaneously detoxify PAHs, Cr(VI) and As(III), which restricts the bioremediation of co-contaminated soil by PAHs, Cr and As. Here, we isolated Altererythrobacter sp. H2 and found it could degrade various PAHs, including phenanthrene, fluoranthene, pyrene, benzo[a]anthracene, and benzo[a]pyrene, and tolerate and detoxify high concentrations of Cr(VI) and As(III). Genomic, transcriptomic, and biochemical assays reveal strain H2 degrades PAHs, reduces Cr(VI), and oxidize As(III) via a horizontally transferred RHO gene cluster, a chromate reductase ChrR, and a arsenite resistance gene cluster arsRBC. The horizontally transferred PAHs-degrading gene cluster encodes the Rieske dioxygenase three-component system and other enzymes required for PAHs degradation, which suggested those heavy metal-detoxifying bacteria could be excellent PAHs-degrading and heavy metal-detoxifying agents after accommodating a PAHs degradation gene cluster like strain H2 did. To our knowledge, strain H2 is the only reported Altererythrobacter member that uses a classical Rieske dioxygenase three-component system to initial PAHs degradation and the only one could simultaneously detoxify PAHs, Cr(VI), and As(III). Our study provides insights into the PAHs degradation mechanism of Altererythrobacter members and demonstrates the excellent potential of H2 in the bioremediation of both PAHs and heavy metal pollutants.},
}
@article {pmid40249581,
year = {2025},
author = {Deslauriers, N and Boulianne, M},
title = {Genetic Comparison of Enterococcus Species Isolated from Osteomyelitis Lesions and the Barn Environment of Successive Broiler Chicken Flocks.},
journal = {Avian diseases},
volume = {68},
number = {S1},
pages = {421-426},
doi = {10.1637/aviandiseases-D-24-00081},
pmid = {40249581},
issn = {1938-4351},
mesh = {Animals ; *Chickens ; *Osteomyelitis/veterinary/microbiology/epidemiology ; *Poultry Diseases/microbiology/epidemiology ; *Enterococcus/genetics/isolation &amp; purification/classification ; *Gram-Positive Bacterial Infections/veterinary/microbiology/epidemiology ; Quebec/epidemiology ; *Housing, Animal ; Virulence ; },
abstract = {Osteomyelitis caused by Enterococcus cecorum is an emerging disease in broiler chickens in Canada. Other Enterococcus species have been reported as causative agents in certain outbreaks. The epidemiology of this disease is unknown, but contaminated barns are affected by recurring episodes. A broiler chicken flock located in Quebec, Canada, exhibited osteomyelitis lesions positive for E. cecorum and Enterococcus faecalis. Surprisingly, the following lot, in the same barn, revealed the presence of E. faecalis- and Enterococcus raffinosus-positive lesions but no E. cecorum. To better understand the epidemiology of these two outbreaks, verify the persistence of pathogenic isolates in the barn, and identify the possible transfer of genetic material between the Enterococcus species isolated from both events, 16 isolates (1 E. cecorum, 13 E. faecalis, and 2 E. raffinosus isolates) were sequenced, and their genomes were compared. Interestingly, more than one Enterococcus species could be isolated from the same lesion, while other lesions also revealed several nonclonal isolates from the same species. This might suggest the opportunistic nature of Enterococcus spp. as there was no predominant isolate in the lesions. The number of virulence genes varied from 1 to 34 across three Enterococcus species with no common virulence gene. The number and nature of antimicrobial resistance genes among those isolates were worrisome because they indicate the presence of multidrug resistance on the farm. Both plasmids and phages were shared by different Enterococcus species, which suggests potential horizontal gene transfer of mobile genetic elements within this enterococci population.},
}
@article {pmid40249005,
year = {2025},
author = {Kerek, &#xc1; and Román, I and Szabó, &#xc1; and Kovács, D and Kardos, G and Kovács, L and Jerzsele, &#xc1;},
title = {Antibiotic resistance genes in Escherichia coli - literature review.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-35},
doi = {10.1080/1040841X.2025.2492156},
pmid = {40249005},
issn = {1549-7828},
abstract = {Antimicrobial resistance threatens humans and animals worldwide and is recognized as one of the leading global public health issues. Escherichia coli (E. coli) has an unquestionable role in carrying and transmitting antibiotic resistance genes (ARGs), which in many cases are encoded on plasmids or phage, thus creating the potential for horizontal gene transfer. In this literature review, the authors summarize the major antibiotic resistance genes occurring in E. coli bacteria, through the major antibiotic classes. The aim was not only listing the resistance genes against the clinically relevant antibiotics, used in the treatment of E. coli infections, but also to cover the entire resistance gene carriage in E. coli, providing a more complete picture. We started with the long-standing antibiotic groups (beta-lactams, aminoglycosides, tetracyclines, sulfonamides and diaminopyrimidines), then moved toward the newer groups (phenicols, peptides, fluoroquinolones, nitrofurans and nitroimidazoles), and in every group we summarized the resistance genes grouped by the mechanism of their action (enzymatic inactivation, antibiotic efflux, reduced permeability, etc.). We observed that the frequency of antibiotic resistance mechanisms changes in the different groups.},
}
@article {pmid40248430,
year = {2025},
author = {Chen, S and Liao, L and Wang, M},
title = {Editorial: Opportunistic pathogens: pathogenesis and multi-drug resistance mechanisms.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1597769},
doi = {10.3389/fmicb.2025.1597769},
pmid = {40248430},
issn = {1664-302X},
}
@article {pmid40246490,
year = {2025},
author = {Huang, L and Yang, Y and Xue, Y and Hu, S and Liang, T and Ye, J and Xue, X},
title = {A gene island from plasmid pkk5 of Burkholderia sp. KK1 confers arsenic resistance to Caballeronia jiangsuensis.},
journal = {Journal of environmental sciences (China)},
volume = {155},
number = {},
pages = {562-572},
doi = {10.1016/j.jes.2024.09.011},
pmid = {40246490},
issn = {1001-0742},
mesh = {*Arsenic/toxicity/metabolism ; *Burkholderia/genetics/metabolism ; *Plasmids/genetics ; Biodegradation, Environmental ; *Hypocreales/metabolism ; },
abstract = {Microorganisms play a critical role in the biotransformation of arsenic and the form which it exists in the environment. In this study, a methyl parathion-degrading bacterium Caballeronia jiangsuensis, isolated from an abandoned pesticide manufacturing plant, was used to analyze arsenic accumulation and transformation. The accumulation of trivalent organoarsenic compounds in C. jiangsuensis occurred to a greater extent than that of their pentavalent counterparts. The chromosome of C. jiangsuensis contains an arsenic gene island whose GC content is significantly lower than that of the genome, suggesting that the island was acquired via horizontal gene transfer. There was approximately 90 %-99 % similarity between the proteins encoded by the gene island and the corresponding sequence of the plasmid pkk5 from Burkholderia sp. KK1. The biotransformation of different arsenic species by C. jiangsuensis was subsequently analyzed. The results revealed that monomethylarsenic acid (MAs(V)) was rapidly demethylated to arsenate with very small amounts of intermediate monomethylarsonous acid (MAs(III)), whereas MAs(III) was largely oxidized to MAs(V) despite the occurrence of the gene arsI probably responsible for aerobic demethylation of MAs(III) in C. jiangsuensis. In addition, dimethylarsenic acid was partly demethylated to arsenate. Horizontal gene transfer of ars operon from a plasmid to other bacteria represents an adaptation to a specific environment. This study provides a new perspective for understanding arsenic biogeochemical cycling.},
}
@article {pmid40245502,
year = {2025},
author = {Zhong, Y and Teo, JQ and Guo, S and Schlundt, J and Kwa, AL and Ong, RT},
title = {Characterization of mobile resistance elements in extended-spectrum β-lactamase producing gram-negative bacteria from aquatic environment.},
journal = {The Science of the total environment},
volume = {978},
number = {},
pages = {179353},
doi = {10.1016/j.scitotenv.2025.179353},
pmid = {40245502},
issn = {1879-1026},
mesh = {*beta-Lactamases/genetics ; *Gram-Negative Bacteria/genetics ; *Interspersed Repetitive Sequences ; *Water Microbiology ; *Drug Resistance, Bacterial/genetics ; Singapore ; },
abstract = {Extended-spectrum β-lactamase producing (ESBL) bacteria from aquatic environments can pose potential threats to public health due to their capability of spreading antimicrobial resistance (AMR) genes through mobile genetic elements (MGEs), such as plasmids, insertion sequences (ISs), transposons, and integrons. Currently, there is no policy for routine monitoring of AMR genes in aquatic environments and their roles in transmission are therefore unknown. Previous metagenomic and PCR-based culture-independent approaches are limited in recovering AMR resistant aquatic bacteria isolates and the data resolution generated are not able to provide detailed genetic comparison with known human pathogens particularly for determining genetic islands harbouring AMR genes. To address these gaps, we thus investigated the genetic profiles of ESBL-producing gram-negative aquatic bacteria found from water body sites within Singapore, examining the AMR genes carried and their associated MGEs. In total, 16 ESBL-producing gram-negative bacteria were identified, of which 8 were Escherichia coli, 3 Klebsiella pneumoniae, and 5 Aeromonas spp. Whole genome sequencing (WGS) analysis revealed the presence of 12 distinct classes of AMR genes, including 16 distinct variants of β-lactamase, of which blaCTX-M was the dominant beta-lactamase genotype in all 11 Enterobacterales. The AMR genetic islands in the aquatic bacteria were also found to share similar genetic structures similar to those of circulating ESBL bacteria causing human infections. These findings underscore the potential role of aquatic ESBL bacteria as AMR reservoirs for human pathogens, suggesting that aquatic bacteria may facilitate the hidden transmission of AMR mediated by MGEs through horizontal gene transfer across different sources and species, highlighting the importance of integrating environmental AMR monitoring into local surveillance strategies.},
}
@article {pmid40243369,
year = {2025},
author = {Li, J and Chang, J and Ma, J and Zhou, W and Yang, Y and Wu, J and Guan, C and Yuan, X and Xu, L and Yu, B and Su, F and Ye, S and Chen, Y and Zhao, G and Tang, B},
title = {Genome-based assessment of antimicrobial resistance of Escherichia coli recovered from diseased swine in eastern China for a 12-year period.},
journal = {mBio},
volume = {},
number = {},
pages = {e0065125},
doi = {10.1128/mbio.00651-25},
pmid = {40243369},
issn = {2150-7511},
abstract = {The global rise of antimicrobial resistance (AMR), driven by antibiotic use in healthcare and agriculture, poses a major public health threat. While AMR in clinical settings is well studied, there is a gap in understanding the resistance profiles of Escherichia coli from diseased livestock, particularly regarding zoonotic transmission. This study analyzes 114 E. coli isolates from diseased swine over 12 years, revealing that 99.12% were multidrug-resistant. Resistance was highest for ampicillin and amoxicillin/clavulanic acid (100%), followed by ciprofloxacin (96.49%) and tetracycline (94.74%). Furthermore, 21.05% of isolates were resistant to colistin, and 1.75% to tigecycline. A total of 76 antimicrobial resistance genes (ARGs) were identified, with mcr-1 found in 18.42%, mcr-3 in 4.39%, and tet(X4) in 1.75%. Significant co-occurrence of ARGs and plasmids suggests potential for co-selective dissemination. This study is the first to report enterotoxigenic E. coli (ETEC) strains carrying both mcr-1 and mcr-3 genes. After the 2017 colistin ban in China, mcr-1 detection rates significantly decreased, while florfenicol resistance rates increased in 2018-2021 (94.29%) compared to 2010-2017 (79.55%). This work provides valuable insights into the AMR profiles of E. coli from diseased swine and highlights trends that can inform strategies for monitoring and controlling public health risks associated with zoonotic E. coli transmission.IMPORTANCEThis study highlights the critical role of diseased and deceased swine in the spread of antimicrobial resistance (AMR), providing new insights into the transmission of resistance genes in zoonotic contexts. By analyzing E. coli from diseased swine, we identify key resistance genes such as mcr-1, mcr-3, and tet(X4), which pose significant public health risks, especially regarding last-resort antibiotics like colistin. Moreover, the study identifies novel transmission patterns of mcr genes, including ETEC strains carrying the mcr-3 gene and strains harboring both mcr-1 and mcr-3 genes. The role of plasmids in horizontal gene transfer is also revealed, facilitating rapid AMR spread across species. The long-term persistence of resistant strains highlights the challenges in controlling AMR in livestock. These findings underscore the need for enhanced surveillance and a One Health approach to mitigate AMR risks across animal, human, and environmental health.},
}
@article {pmid40240954,
year = {2025},
author = {Feng, Y and Liu, Y and Han, J and Huang, Y and Lee, J and Kokubugata, G and Qi, Z and Yan, X},
title = {Decoding the mitogenome of rosemary (Salvia rosmarinus): insights into genome evolution, structural dynamics and prospects for mitochondrial engineering.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {488},
pmid = {40240954},
issn = {1471-2229},
support = {G242412, G252409//Special Fund for Scientific Research of Shanghai Landscaping &amp; City Appearance Administrative Bureau/ ; G242412, G252409//Special Fund for Scientific Research of Shanghai Landscaping &amp; City Appearance Administrative Bureau/ ; G242412, G252409//Special Fund for Scientific Research of Shanghai Landscaping &amp; City Appearance Administrative Bureau/ ; LY21C030008//Natural Science Foundation of Zhejiang Province/ ; LY21C030008//Natural Science Foundation of Zhejiang Province/ ; LY21C030008//Natural Science Foundation of Zhejiang Province/ ; },
mesh = {*Genome, Mitochondrial/genetics ; *Evolution, Molecular ; Phylogeny ; *Salvia/genetics ; RNA Editing ; *Genome, Plant ; Genetic Engineering ; },
abstract = {BACKGROUND: Rosemary (Salvia rosmarinus), an aromatic evergreen shrub of the Salvia (Lamiaceae), is native to the Mediterranean region, thriving in rocky or arid soils. Widely used in food, pharmaceuticals, and cosmetics, its clonal reproduction poses significant challenges for breeding and germplasm innovation. While mitogenome engineering holds promise for introducing heritable mutations, incomplete mitogenome information for rosemary has hindered such efforts. This study addresses this gap by assembling and analyzing the complete mitogenome of S. rosmarinus, focusing on its structure, repetitive sequences, RNA editing events, intracellular gene transfer (IGT), and phylogenetic relationships.<br><br>RESULTS: The S. rosmarinus mitogenome spans 384,113&#xa0;bp with a GC content of 44.8%, containing 34 unique protein-coding genes and 114 simple sequence repeats. Comparative analysis revealed 28 homologous segments shared between the mitogenome and plastome, totaling 18,675&#xa0;bp in length. Furthermore, homologous fragments between nuclear and organellar genomes were identified, including 1,069,255&#xa0;bp of organelle-derived sequences in the nuclear genome, with 194,689&#xa0;bp from nuclear plastid DNA transfers (NUPTs) and 15,192&#xa0;bp from nuclear mitochondrial DNA transfers (NUMTs). NUPTs were more abundant and contributed more significantly to the total length. Synteny analysis of eight Lamiales species revealed extensive mitogenomic recombination and structural rearrangements. These findings highlight the dynamic nature of mitogenomes, offering insights into genome evolution and supporting future breeding programs to enhance the genetic diversity and adaptability of S. rosmarinus.<br><br>CONCLUSIONS: This study provides the first complete mitogenome of S. rosmarinus, revealing dispersed repeats, RNA editing, and horizontal gene transfer between the nuclear and organelle genomes. The mitogenome exhibits a typical circular structure with evidence of frequent recombination, providing valuable insights into Salvia mitochondrial genetics, genome evolution, and molecular biology.},
}
@article {pmid40238219,
year = {2025},
author = {Cadamuro, RD and Elois, MA and Pilati, GVT and Savi, BP and Pessi, L and Jempierre, YFSH and Rodríguez-Lázaro, D and Fongaro, G},
title = {Role of Lysogenic Phages in the Dissemination of Antibiotic Resistance Genes Applied in the Food Chain.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
pmid = {40238219},
issn = {2304-8158},
abstract = {Bacteriophages, first discovered in 1915, have re-emerged as critical players in microbial ecosystems, particularly in food production. Their ability to lysogenize bacterial hosts raises concerns about their role in the horizontal transfer of antibiotic resistance genes (ARGs) and virulence factors, contributing to the global challenge of antimicrobial resistance. Key studies reveal that ARG-carrying phages are prevalent across various stages of the food chain, including soil, vegetables, meat, dairy, and wastewater associated with food production. These findings demonstrate the potential for lysogenic phages to act as vectors for resistance gene dissemination, posing risks to public health. The review also explores emerging genetic elements, such as phage-inducible chromosomal islands and gene transfer agents, that further enhance the mobility of resistance and virulence genes. Advancements in metagenomic tools have improved our understanding of phage-mediated gene transfer, but significant knowledge gaps remain. Future research should aim to quantify these processes in real-world settings and develop strategies to mitigate the risks associated with lysogenic phages in food systems.},
}
@article {pmid40236771,
year = {2025},
author = {Liu, W and Lau, HCH and Ding, X and Yin, X and Wu, WKK and Wong, SH and Sung, JJY and Zhang, T and Yu, J},
title = {Transmission of antimicrobial resistance genes from the environment to human gut is more pronounced in colorectal cancer patients than in healthy subjects.},
journal = {iMeta},
volume = {4},
number = {2},
pages = {e70008},
pmid = {40236771},
issn = {2770-596X},
abstract = {Antimicrobial resistance is a major global health concern. However, the source of gut resistome remains unsolved. We aimed to analyze the contribution of environmental antimicrobial resistance genes (ARGs) to colorectal cancer (CRC) patients. Here, we collected metagenomic data from 1,605 human stool samples (CRC = 748; healthy = 857) and 1,035 city-matched environmental samples, in which 110 CRC, 112 healthy, and 56 environmental samples were newly collected. Compared to healthy subjects, CRC patients had significantly higher ARG burden (p < 0.01) with increased levels of multidrug-resistant ARGs. Gut ARGs in CRC also had a closer similarity to environmental ARGs (p < 0.001). By comparing environmental and gut ARGs, 28 environmental ARGs were identified as CRC-specific ARGs, including SUL2 and MEXE, which were not identified in healthy subjects. Meanwhile, more mobile ARGs (mARGs) from the environment were observed in CRC patients compared to healthy subjects (p < 0.05). The hosts of mARGs were mainly pathogenic bacteria (e.g., Escherichia coli (E. coli) and Clostridium symbiosum (C. symbiosum)). Compared to healthy subjects, CRC patients showed elevated horizontal gene transfer efficiency from the environment to gut. Consistently, the abundance of pathobionts carrying specific mARGs (e.g., E. coli-SUL2 and C. symbiosum-SUL2) were significantly increased in CRC patients compared to healthy subjects (p < 0.05). We thus reveal a route of ARG dissemination from the environment into the gut of CRC patients.},
}
@article {pmid40234663,
year = {2025},
author = {Luk-In, S and Phopin, K and Bangmuangngam, S and Chatsuwan, T and Wannigama, DL and Shein, AMS and Plongla, R and Lawung, R and Yainoy, S and Eiamphungporn, W and Chatupheeraphat, C and Tantimongcolwat, T},
title = {Inhibitory effects of benzyl isothiocyanate on widespread mcr-1-harbouring IncX4 plasmid transfer.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12892},
pmid = {40234663},
issn = {2045-2322},
mesh = {*Plasmids/genetics ; *Klebsiella pneumoniae/genetics/drug effects ; *Escherichia coli/genetics/drug effects ; Colistin/pharmacology ; *Isothiocyanates/pharmacology ; *Escherichia coli Proteins/genetics ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Drug Resistance, Multiple, Bacterial/genetics/drug effects ; Humans ; Gene Transfer, Horizontal/drug effects ; Thailand ; },
abstract = {The global dissemination of mobile colistin resistance (mcr) genes represents a significant public health threat due to colistin's critical role in treating multidrug-resistant (MDR) bacterial infections. We identified high rates of carbapenem resistance in Escherichia coli (27.82%) and Klebsiella pneumoniae (57.98%) and colistin resistance in E. coli (7.52%) and K. pneumoniae (19.68%) among MDR clinical isolates in Thailand. We reported sequences of self-transferable IncX4 plasmids (~ 34 kb) that facilitated the spread of the mcr-1.1 gene among six diverse MDR strains, often co-transferring blaCTX-M-55. Additionally, E. coli ST101 was found to co-transfer mcr-1.1, mcr-3.5, blaCTX-M-55, and tet(X4) via three plasmids (~ 34-kb IncX4, ~ 84-kb IncFII, ~ 278-kb IncHI2), resulting in increases in MICs for colistin, ceftriaxone, and tigecycline. Core SNP analysis revealed that closely related IncX4 plasmids harbouring mcr-1 (< 35 SNP differences) were reported from at least 12 countries. We first demonstrated the inhibitory effects of benzyl isothiocyanate (BITC) on the conjugation of mcr-1-bearing IncX4 plasmids to 1.57 ± 1.00% to 48.86 ± 12.31% relative to control (100%), targeting VirB4 and VirB11 proteins, reducing ATPase activity by over 30%. This study highlights the widespread mcr-1-harbouring IncX4 plasmids and proposes BITC as a potential inhibitor to control the dissemination of colistin resistance.},
}
@article {pmid40230384,
year = {2025},
author = {Sousa, M and Machado, I and Simões, LC and Simões, M},
title = {Biocides as drivers of antibiotic resistance: A critical review of environmental implications and public health risks.},
journal = {Environmental science and ecotechnology},
volume = {25},
number = {},
pages = {100557},
pmid = {40230384},
issn = {2666-4984},
abstract = {The widespread and indiscriminate use of biocides poses significant threats to global health, socioeconomic development, and environmental sustainability by accelerating antibiotic resistance. Bacterial resistance development is highly complex and influenced significantly by environmental factors. Increased biocide usage in households, agriculture, livestock farming, industrial settings, and hospitals produces persistent chemical residues that pollute soil and aquatic environments. Such contaminants contribute to the selection and proliferation of resistant bacteria and antimicrobial resistance genes (ARGs), facilitating their dissemination among humans, animals, and ecosystems. In this review, we conduct a critical assessment of four significant issues pertaining to this topic. Specifically, (i) the role of biocides in exerting selective pressure within the environmental resistome, thereby promoting the proliferation of resistant microbial populations and contributing to the global spread of antimicrobial resistance genes (ARGs); (ii) the role of biocides in triggering transient phenotypic adaptations in bacteria, including efflux pump overexpression, membrane alterations, and reduced porin expression, which often result in cross-resistance to multiple antibiotics; (iii) the capacity of biocides to disrupt bacteria and make the genetic content accessible, releasing DNA into the environment that remains intact under certain conditions, facilitating horizontal gene transfer and the spread of resistance determinants; (iv) the capacity of biocides to disrupt bacterial cells, releasing intact DNA into the environment and enhancing horizontal gene transfer of resistance determinants; and (iv) the selective interactions between biocides and bacterial biofilms in the environment, strengthening biofilm cohesion, inducing resistance mechanisms, and creating reservoirs for resistant microorganisms and ARG dissemination. Collectively, this review highlights the critical environmental and public health implications of biocide use, emphasizing an urgent need for strategic interventions to mitigate their role in antibiotic resistance proliferation.},
}
@article {pmid40228732,
year = {2025},
author = {Zhang, R and Gong, C and Gao, Y and Chen, Y and Zhou, L and Lou, Q and Zhao, Y and Zhuang, H and Zhang, J and Shan, S and Wang, X and Qian, X and Lei, L and Wong, MH},
title = {Reducing antibiotic resistance genes in soil: The role of organic materials in reductive soil disinfestation.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {374},
number = {},
pages = {126245},
doi = {10.1016/j.envpol.2025.126245},
pmid = {40228732},
issn = {1873-6424},
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Genes, Bacterial ; },
abstract = {Increasing attention has been given to the role of reductive soil disinfestation (RSD) on antibiotic resistance genes (ARGs) in soil. The selection of organic materials in RSD is crucial to the effectiveness of the RSD method. However, the effects of distinct organic materials on ARGs remains unclear. In this study, we selected straw and rapeseed meal as the organic materials in RSD and explored their effects on ARGs. The results showed that using straw significantly reduced the abundance of ARGs, high-risk ARGs, and mobile genetic elements (MGEs) by 31.5 %-65.8 %, while using rapeseed meal led to ARGs enrichment. Structural equation modeling (SEM) analysis identified MGEs and microbial communities as the primary drivers of ARGS changes under different organic materials. The abundance of MGEs was effectively controlled in straw treatments, reducing the potential for horizontal gene transfer of ARGs. Bacterial diversity was significantly lower in the straw treatments compared to the rapeseed meal treatments, potentially leading to a reduced abundance of ARGs host bacteria. Network co-occurrence analysis further revealed that Symbiobacteraceae and Bacillus were potential bacterial hosts of ARGs. In straw treatments, these genera' abundance decreased by 12 %-100 % compared to the control (CK) and rapeseed meal groups, further inhibiting the spread of ARGs. These findings demonstrate that RSD with straw as the organic material is more effective in mitigating ARGs compared to rapeseed meal, providing insights into controlling soil antibiotic resistance risks and utilizing agricultural waste resources.},
}
@article {pmid40226105,
year = {2025},
author = {Wen, Y and Wu, J and You, L and Wei, X and Wang, J and Li, S},
title = {Genomic analyses reveal presence of extensively drug-resistant Salmonella enterica serovars isolated from clinical samples in Guizhou province, China, 2019-2023.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1532036},
pmid = {40226105},
issn = {1664-302X},
abstract = {BACKGROUND: The emergence of extensively drug-resistant (XDR) Salmonella in humans poses a significant public health and therapeutic challenge. However, limited data are available on XDR Salmonella isolates from Guizhou province, China. This study aimed to investigate the molecular epidemiology and resistance patterns of XDR Salmonella isolates from clinical samples in this region.<br><br>METHODS: A total of 931 Salmonella isolates were screened for XDR isolates through antimicrobial susceptibility testing. These XDR isolates were subjected to whole-genome sequencing (WGS) and bioinformatic analysis to further systematically investigating the molecular epidemiology and resistance patterns of XDR Salmonella isolates.<br><br>RESULTS: Between 2019 and 2023, 931 Salmonella isolates were collected from clinical samples in Guizhou. Of these isolates, 51 (5.5%) were identified as XDR and classified into 16 serovars. Among the serovars, 15 corresponded to a specific sequence type, except for S. Typhimurium serovars. The predominant serovars, S. 1,4,[5],12:i:-, S. Enteritidis, and S. Kentucky, were divided into ST34, ST11, and ST198, respectively. Genomic analysis showed that all XDR isolates harbored at least eight antimicrobial resistance genes (ARGs) and multidrug efflux pumps. Highly prevalent point mutations in gyrA (D87 and S83) and parC (S80I) were detected, along with eight plasmid-mediated quinolone resistance (PMQR) genes. The qnrS1 gene was the most common (43.1%), followed by oqxA, aac-(6')-lb-cr variant, qnrB4, qnrS2, qnrA1, qepA2, and oqxB. The predominant &#x3b2;-lactamase gene was blaTEM-1 (54.9%), and blaCTX-M-55 (35.3%) was the most prevalent extended-spectrum &#x3b2;-lactamase subtype. Notably, blaNDM-1 gene was identified for the first time in Salmonella from Guizhou, and one S. 1,4,[5],12:i:- isolate contained the mcr-1.1 gene. ARGs profiles varied by serovars, with S. 1,4,[5],12:i:- isolates carrying the highest number. Ten plasmid types were identified, predominantly IncHI2/IncHI2A (47.5%). Key resistance genes such as tetA, PMQR, blaCTX-M , mcr-1.1, and blaNDM-1 were located on IncHI2/IncHI2A plasmids. Notably, 75.0% of the conjugative plasmids belonged to IncHI2/IncHI2A, indicating that horizontal gene transfer through conjugation facilitates ARGs dissemination. Core genome multilocus sequence typing (cgMLST) analysis revealed significant genetic diversity, with 39 core genome sequence types (cgSTs) identified and no evidence of outbreaks.<br><br>CONCLUSION: The rising prevalence of XDR Salmonella in Guizhou province is concerning. Initial whole-genome sequencing (WGS) data provide critical insights for understanding and controlling XDR Salmonella infections, aiding public health officials in identifying emerging threats and trends.},
}
@article {pmid40223056,
year = {2025},
author = {Colp, MJ and Blais, C and Curtis, BA and Archibald, JM},
title = {The fate of artificial transgenes in Acanthamoeba castellanii.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {368},
pmid = {40223056},
issn = {1471-2164},
support = {GBMF5782//Gordon and Betty Moore Foundation/ ; },
mesh = {*Acanthamoeba castellanii/genetics ; *Transgenes/genetics ; Plasmids/genetics ; Transformation, Genetic ; },
abstract = {BACKGROUND: The soil amoeba Acanthamoeba castellanii is an emerging model organism with which to study a wide range of biomedical, microbiological, and evolutionary phenomena. While transformation systems were established for this organism more than two decades ago, the fate of artificial transgenes has not been well characterized. In this study, artificial transformation experiments were performed to investigate how the A. castellanii genome responds to foreign DNA presented in both circular and linear plasmid form.<br><br>RESULTS: Nanopore sequencing was used as a high throughput method to screen for transgene DNA in the resulting transformant cultures, and candidate transgene integrations were identified. Molecular biology experiments were performed to validate the sequence data and provide additional context on the fate of transgenes. A method was devised to estimate the rate of read chimerism in nanopore sequencing runs and accurately account for the effects of read chimerism in identifying putative transgene integrations. Based on the experimental data in hand, a potential mechanism for transgene maintenance in A. castellanii is proposed, one in which incoming foreign DNA is tandemly duplicated and telomeres are added to the ends.<br><br>CONCLUSIONS: Our results suggest that transformation of A. castellanii with foreign DNA leads to linear molecules that are maintained as telomere-containing, transgene-bearing minichromosomes, which may facilitate chromosomal integration. This process may allow lateral gene transfer by expanding the window of opportunity for exogenous DNA to be taken up and integrated into the A. castellanii genome. Similar mechanisms exist in other eukaryote groups, suggesting this may be a widespread feature of eukaryote genome biology.},
}
@article {pmid40220390,
year = {2025},
author = {Xiao, B and Pu, Q and Ding, G and Wang, Z and Li, Y and Hou, J},
title = {Synergistic effect of horizontal transfer of antibiotic resistance genes between bacteria exposed to microplastics and per/polyfluoroalkyl substances: An explanation from theoretical methods.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138208},
doi = {10.1016/j.jhazmat.2025.138208},
pmid = {40220390},
issn = {1873-3336},
abstract = {Microplastics (MPs) and per/polyfluoroalkyl substances (PFASs), as emerging pollutants widely present in aquatic environments, pose a significant threat to human health through the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Molecular dynamics simulations and machine learning can accurately capture the complex interactions between molecules. This study utilized them to identify the HGT risk between bacteria under MPs and PFASs stress. This study found that MPs and PFASs significantly increase the HGT risk between bacteria, up to 1.57 and 1.59 times, respectively. Notably, long-chain PFASs and perfluoroalkyl carboxylic acids increased the HGT risk by 1.38 and 1.40 times, respectively. Additionally, MPs primarily increase the HGT risk by enhancing hydrogen bonding interaction between key proteins in the HGT pathway and "active codons". The electronegativity and polarizability of PFASs critically influence the HGT risk, acting inversely and directly proportional, respectively. The HGT risk between bacteria under the combined stress from PP-MPs and PFASs exhibits a significant synergistic effect (synergistic effect value of 27.6), which markedly increases the HGT risk. Further analysis revealed that a smaller minimum distance and sharper RDF curve peaks between key proteins and "active codons" indicate higher HGT risk. This indicates that stronger interactions lead to higher HGT risk. This study identifies the characteristics of HGT risks between bacteria in aquatic environments under the individual and combined stresses from MPs and PFASs at the molecular level. It provides a theoretical basis for mitigating ARG transfer and comprehensively assessing the health risks posed by these emerging pollutants.},
}
@article {pmid40217451,
year = {2025},
author = {Hotor, P and Kotey, FCN and Donkor, ES},
title = {Antibiotic resistance in hospital wastewater in West Africa: a systematic review and meta-analysis.},
journal = {BMC public health},
volume = {25},
number = {1},
pages = {1364},
pmid = {40217451},
issn = {1471-2458},
support = {D43TW012487/TW/FIC NIH HHS/United States ; D43TW012487/TW/FIC NIH HHS/United States ; D43TW012487/TW/FIC NIH HHS/United States ; },
mesh = {Africa, Western ; *Wastewater/microbiology ; *Hospitals ; Humans ; *Drug Resistance, Microbial ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents ; },
abstract = {BACKGROUND: The occurrence of antibiotic-resistant bacteria (ARB) has become a global menace and therefore increases morbidity, mortality and healthcare costs. Globally, hospital wastewater (HWW) has been identified as a significant source of antibiotic-resistant elements.<br><br>OBJECTIVES: This review aims to systematically review and to perform meta-analyses from evidence on antibiotic resistance studies in HWW in West Africa.<br><br>METHODS: The review was conducted in compliance with PRISMA and included studies published between 1990 and 2024 in West Africa from the Scopus, PubMed, and Web of Science databases. Eligible studies that characterized resistant bacteria, genes, or antibiotic residues in HWW were included. Meta-analyses for resistant bacteria and genes as well risk of bias using the Newcastle-Ottawa scale were conducted.<br><br>RESULTS: Out of 23 studies reviewed, resistant bacteria were reported in 39% (E. coli), 26% (K. pneumoniae), and 17% (P. aeruginosa), while 17 studies reported ARGs, with blaTEM (29%), blaOXA- 48 (18%), blaSHV (18%), and mecA (18%) being the most common. Only 4% and 9% of studies focused on toxin genes and antibiotic residues, respectively. Meta-analysis showed pooled prevalence rates for resistant bacteria: E. coli 42.6% (95% CI: 26.7%-60.3%) and K. pneumoniae 32.1% (95% Cl: 28.8%- 36.5%), and ARGs: blaTEM 76.0% (95% CI =&#x2009;64.6%-84.6%) and blaSHV 59.3% (95% CI =&#x2009;19.5%-89.8%).<br><br>CONCLUSION: This systematic review highlights significant findings of high levels of ARGs and ARBs of public health concern in HWW in West Africa. This highlights the need to improve upon the monitoring of antibiotic resistance and treatment of HWW in West Africa.},
}
@article {pmid40216901,
year = {2025},
author = {Robinson, LR and McDevitt, CJ and Regan, MR and Quail, SL and Swartz, M and Wadsworth, CB},
title = {Revisiting the potential impact of doxycycline post-exposure prophylaxis on the selection of doxycycline resistance in Neisseria commensals.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12400},
pmid = {40216901},
issn = {2045-2322},
support = {R15 AI174182/AI/NIAID NIH HHS/United States ; R15AI174182/NH/NIH HHS/United States ; },
mesh = {*Doxycycline/pharmacology/therapeutic use ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Drug Resistance, Bacterial/genetics/drug effects ; *Post-Exposure Prophylaxis/methods ; *Neisseria/drug effects/genetics ; Gonorrhea/prevention &amp; control/microbiology ; Bacterial Proteins/genetics ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Female ; Male ; },
abstract = {Doxycycline post-exposure prophylaxis (doxy-PEP) is a strategy to reduce bacterial sexually transmitted infections. However, the impact of doxy-PEP on resistance emergence is as of yet unclear. Commensal Neisseria are known reservoirs of resistance for gonococci through horizontal gene transfer (HGT), and are more likely to experience bystander selection from doxy-PEP as they are universally carried. The consequences of doxycycline selection on commensal Neisseria will be critical to investigate to understand possible resistance mechanisms that may be transferred to an important human pathogen. Here, collection of commensals from human hosts demonstrated 46% of isolates carry doxycycline resistance; and doxycycline resistance was significantly greater in participants self-reporting doxycycline use in the past 6 months. High-level doxycycline resistance (> 8 µg/mL) was always associated with the ribosomal protection protein (tetM) and pConj. In vitro selection of Neisseria commensals (N. cinerea, N. canis, N. elongata, and N. subflava) resulted in 12 of 16 lineages evolving doxycycline resistance (> 1 µg/mL). An A46T substitution in the repressor of the Mtr efflux pump (MtrR) and a V57M substitution in the 30 ribosomal protein S10 were associated with elevated MICs. Mutations in ribosomal components also emerged (i.e., 16 S rRNA G1057C, RplX A14T). We find the MtrR 46T, RpsJ 57M, and RplX 14T in natural commensal populations. In vitro co-evolution of N. gonorrhoeae with Neisseria commensals demonstrated rapid transfer of the pConj plasmid to N. subflava and N. cinerea, and pbla to N. cinerea. This work underscores the importance of commensal Neisseria as reservoirs of doxycycline resistance, and demonstrates a link between doxycycline use and the emergence of resistance. Though novel chromosomal resistance mutations are nominated herein, resistance emergence in natural commensal populations appears to be mainly associated with acquisition of the tetM gene. A secondary danger to pConj acquisition, is spread of pbla and β-lactam resistance, which we demonstrate here in vitro. Ultimately, characterizing the contemporary prevalence of doxycycline resistance, and underlying resistance mechanisms, in commensal communities may help us to predict the long-term impact of doxy-PEP on Neisseria, and the likelihood of transferring resistance across species' boundaries.},
}
@article {pmid40216324,
year = {2025},
author = {Muteeb, G and Kazi, RNA and Aatif, M and Azhar, A and Oirdi, ME and Farhan, M},
title = {Antimicrobial resistance: Linking molecular mechanisms to public health impact.},
journal = {SLAS discovery : advancing life sciences R &amp; D},
volume = {33},
number = {},
pages = {100232},
doi = {10.1016/j.slasd.2025.100232},
pmid = {40216324},
issn = {2472-5560},
abstract = {BACKGROUND: Antimicrobial resistance (AMR) develops into a worldwide health emergency through genetic and biochemical adaptations which enable microorganisms to resist antimicrobial treatment. β-lactamases (blaNDM, blaKPC) and efflux pumps (MexAB-OprM) working with mobile genetic elements facilitate fast proliferation of multidrug-resistant (MDR) and exttreme drug-resistant (XDR) phenotypes thus creating major concerns for healthcare systems and community health as well as the agricultural sector.<br><br>OBJECTIVES: The review dissimilarly unifies molecular resistance pathways with public health implications through the study of epidemiological data and monitoring approaches and innovative therapeutic solutions. Previous studies separating their attention between molecular genetics and clinical outcomes have been combined into our approach which delivers an all-encompassing analysis of AMR.<br><br>KEY INSIGHTS: The report investigates the resistance mechanisms which feature enzymatic degradation and efflux pump overexpression together with target modification and horizontal gene transfer because these factors represent important contributors to present-day AMR developments. This review investigates AMR effects on hospital and community environments where it affects pathogens including MRSA, carbapenem-resistant Klebsiella pneumoniae, and drug-resistant Pseudomonas aeruginosa. This document explores modern AMR management methods that comprise WHO GLASS molecular surveillance systems and three innovative strategies such as CRISPR-modified genome editing and bacteriophage treatments along with antimicrobial peptides and artificial intelligence diagnostic tools.<br><br>CONCLUSION: The resolution of AMR needs complete scientific and global operational methods alongside state-of-the-art therapeutic approaches. Worldwide management of drug-resistant infection burden requires both enhanced infection prevention procedures with next-generation antimicrobial strategies to reduce cases effectively.},
}
@article {pmid40215939,
year = {2025},
author = {Chen, Y and Yan, Z and Su, P and Liu, S and Chen, X and Jiang, R and Lu, G and Yuan, S},
title = {Remediation strategy of biochar with different addition approaches on antibiotic resistance genes in riparian zones under dry wet alternation.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138207},
doi = {10.1016/j.jhazmat.2025.138207},
pmid = {40215939},
issn = {1873-3336},
abstract = {The global prevalence of antibiotic resistance genes (ARGs) has aroused increasing concern due to its threat to ecological security and human health. Although biochar has been widely used for pollution remediation including ARGs, little is known its regulation on antibiotics and ARGs propagation under riparian zones, where undergo frequent occurrence of dry and wet alternations (DWA) caused by water-level fluctuation. Therefore, this study investigated the regulative effects of biochar through different addition approaches on ARGs spread in riparian zone sediments. Under DWA, the presence of biochar (2 % w/w) inhibited microbial diversity and function expression, especially for tiled biochar. In addition, compared with DWA, the tiled biochar decreased ARGs abundance by 45.36 %, while the well-mixed increased that by 269.02 %. The ARGs abundance in sediments was positively correlated with mobile genetic element abundance (R[2]=0.996, p < 0.05), indicative of high horizontal gene transfer potential of ARGs. Metabolomics revealed that both DWA and biochar significantly altered microbial metabolism pathways in sediments, involving sulfur metabolism and histidine metabolism. Furthermore, ARGs propagation in riparian zones may be dominantly driven by MGEs, especially by transposases and integrase. These findings highlight the tiled biochar remediation effects on ARGs in riparian zones under DWA caused by global warming.},
}
@article {pmid40215278,
year = {2025},
author = {Dalia, TN and Machouri, M and Lacrouts, C and Fauconnet, Y and Guerois, R and Andreani, J and Radicella, JP and Dalia, AB},
title = {DprA recruits ComM to facilitate recombination during natural transformation in Gram-negative bacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {15},
pages = {e2421764122},
pmid = {40215278},
issn = {1091-6490},
support = {R35 GM128674/GM/NIGMS NIH HHS/United States ; ANR-22-CE44-0044//Agence Nationale de la Recherche (ANR)/ ; R35GM128674//HHS | National Institutes of Health (NIH)/ ; },
mesh = {*Bacterial Proteins/metabolism/genetics/chemistry ; *Vibrio cholerae/genetics/metabolism ; *Helicobacter pylori/genetics/metabolism ; *Recombination, Genetic ; *Transformation, Bacterial ; *DNA Helicases/metabolism/genetics/chemistry ; Gene Transfer, Horizontal ; *Gram-Negative Bacteria/genetics/metabolism ; Membrane Proteins ; },
abstract = {Natural transformation (NT) represents one of the major modes of horizontal gene transfer in bacterial species. During NT, cells can take up free DNA from the environment and integrate it into their genome by homologous recombination. While NT has been studied for >90 y, the molecular details underlying this recombination remain poorly understood. Recent work has demonstrated that ComM is an NT-specific hexameric helicase that promotes recombinational branch migration in Gram-negative bacteria. How ComM is loaded onto the postsynaptic recombination intermediate during NT, however, remains unclear. Another NT-specific recombination mediator protein that is ubiquitously conserved in both Gram-positive and Gram-negative bacteria is DprA. Here, we uncover that DprA homologs in Gram-negative species contain a C-terminal winged helix domain that is predicted to interact with ComM by AlphaFold. Using Helicobacter pylori and Vibrio cholerae as model systems, we demonstrate that ComM directly interacts with the DprA winged-helix domain, and that this interaction is critical for DprA to recruit ComM to the recombination site to promote branch migration during NT. These results advance our molecular understanding of recombination during this conserved mode of horizontal gene transfer. Furthermore, they demonstrate how structural modeling can help uncover unexpected interactions between well-studied proteins to provide deep mechanistic insight into the molecular coordination required for their activity.},
}
@article {pmid40215220,
year = {2025},
author = {Zhong, W and Zhou, Y and Che, M and Wang, L and Tian, X and Wang, C and Cheng, Y and Liu, H and Zhou, Z and Peng, G and Zhang, K and Luo, Y and Shi, K and Zhong, Z},
title = {Extended-spectrum β-lactamase-producing Escherichia coli isolated from captive primates: characteristics and horizontal gene transfer ability analysis.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0321514},
pmid = {40215220},
issn = {1932-6203},
mesh = {Animals ; *beta-Lactamases/genetics/metabolism ; *Gene Transfer, Horizontal ; *Escherichia coli/genetics/isolation &amp; purification/enzymology/drug effects ; *Escherichia coli Infections/microbiology/veterinary ; China ; Phylogeny ; *Primates/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Animals, Zoo/microbiology ; Microbial Sensitivity Tests ; },
abstract = {The rapid spread of extended-spectrum β-lactamases (ESBLs)-producing Escherichia coli (ESBL-EC) around the world has become a significant challenge for humans and animals. In this study, we aimed to examine the characteristics and horizontal gene transfer (HGT) capacity of ESBL-EC derived from captive primates. We screened for ESBL-EC among a total of 444 multidrug-resistant (MDR) E. coli strains isolated from 13 zoos in China using double-disk test. ESBL genes, mobile genetic elements (MGEs), and virulence-associated genes (VAGs) in ESBL-EC were detected through polymerase chain reaction (PCR). Furthermore, conjugation experiments were conducted to examine the HGT capacity of ESBL-EC, and the population structure (phylogenetic groups and MLST) was determined. Our results showed that a total of 69 (15.54%, 69/444) ESBL-EC strains were identified, and 5 variants of blaCTX and 3 variants of blaTEM were detected. The highest detection rate was blaCTX-M-55 (49.28%, 34/69), followed by blaCTX-M-15 (39.13%, 27/69). Ten MGEs were detected and the most prevalent was IS26 (78.26%, 54/69), followed by ISEcp1 (60.87%, 42/69). Eighteen combinations of MGEs were detected, in which ISEcp1 + IS26 was predominant (18.84%, n = 13). A total of 15 VAGs were detected and the most prevalent was fimC (84.06%, 58/69), followed by sitA (78.26%, 54/69). Furthermore, HGT ability analysis results showed that 40.58% (28/69) of ESBL-EC strains exhibited the ability to engage in conjugative transfer. Plasmid typing revealed that IncFIB (78.57%, 22/28) had the highest detection rates. Furthermore, antibiotic resistance genes (ARGs) of blaTEM-135, tetA and qnrS; MGEs of IS26, trbC and ISCR3/14 showed high rates of conjugative transfer. The population structure analysis showed that the phylogroup B1 and ST2161 were the most prevalent. ESBL-EC poses a potential threat to captive primates and may spread to other animals, humans, and the environment. It is imperative to implement measures to prevent the transmission of ESBL-EC among captive primates.},
}
@article {pmid40214801,
year = {2025},
author = {Sun, J and Wang, X and He, Y and Han, M and Li, M and Wang, S and Chen, J and Zhang, Q and Yang, B},
title = {Environmental fate of antibiotic resistance genes in livestock farming.},
journal = {Archives of microbiology},
volume = {207},
number = {5},
pages = {120},
pmid = {40214801},
issn = {1432-072X},
support = {32272444//National Natural Science Foundation of China/ ; },
mesh = {*Livestock/microbiology ; Animals ; Humans ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; Animal Husbandry ; Farms ; Manure/microbiology ; Genes, Bacterial ; },
abstract = {As emerging environmental pollutants, antibiotic resistance genes (ARGs) are prevalent in livestock farms and their surrounding environments. Although existing studies have focused on ARGs in specific environmental media, comprehensive research on ARGs within farming environments and their adjacent areas remains scarce. This review explores the sources, pollution status, and transmission pathways of ARGs from farms to the surrounding environment. Drawing on the "One Health" concept, it also discusses the potential risks of ARGs transmission from animals to human pathogens and the resulting impact on human health. Our findings suggest that the emergence of ARGs in livestock farming environments primarily results from intrinsic resistance and genetic mutations, while their spread is largely driven by horizontal gene transfer. The distribution of ARGs varies according to the type of resistance genes, seasonal changes, and the medium in which they are present. ARGs are disseminated into the surrounding environment via pathways such as manure application, wastewater discharge, and aerosol diffusion. They may be absorbed by humans, accumulating in the intestinal microbiota and subsequently affecting human health. The spread of ARGs is influenced by the interplay of microbial communities, antibiotics, heavy metals, emerging pollutants, and environmental factors. Additionally, we have outlined three control strategies: reducing the emergence of ARGs at the source, controlling their spread, and minimizing human exposure. This article provides a theoretical framework and scientific guidance for understanding the cross-media migration of microbial resistance in livestock farming environments.},
}
@article {pmid40210157,
year = {2025},
author = {Li, C and Zhu, YX and Shen, XX and Gao, Y and Xu, M and Chen, MK and An, MY},
title = {Exploring the distribution and transmission mechanism of ARGs in crab aquaculture ponds and ditches using metagenomics.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {374},
number = {},
pages = {126209},
doi = {10.1016/j.envpol.2025.126209},
pmid = {40210157},
issn = {1873-6424},
mesh = {*Aquaculture ; Ponds/microbiology ; Animals ; Metagenomics ; *Brachyura ; *Drug Resistance, Microbial/genetics ; China ; Bacteria/genetics ; Environmental Monitoring ; },
abstract = {Aquaculture provides notable economic benefits; however, the excessive use of antibiotics has resulted in the production and spread of antibiotic resistance genes (ARGs). The intricate pollution dynamics in aquaculture areas complicate the comprehension of the distribution and transmission of ARGs in aquaculture systems. Using metagenomic sequencing technology, this study used eight ponds and four ditches in a large crab aquaculture area in Taizhou City, where Proteobacteria (61.58 %) and Acidobacteria (6.04 %) were identified as the dominant phyla and Thiobacillus (1.84 %) and Lysobacter (0.99 %) were the dominant genera. Network and linear discriminant analysis effect size (LEfse) analyses showed that Proteobacteria and Lysobacter were the main host phyla of ARGs, and Lysobacter, which are key host bacteria in ponds, played an important role in determining the abundance of ARGs in ponds. Co-occurrence network analysis (spearman r > 0.7, p < 0.01) revealed that prophages can dominate the spread of ARGs by carrying several ARG subtypes (rsmA, OXA-21, THIN-B and lnuF). Analysis of variance demonstrated that functions related to the horizontal gene transfer (HGT) of ARGs, such as EPS synthesis (lptF), oxidative stress (gor and ompR), ATP synthesis (lapB and vcaM), and cell membrane permeability (yajC and gspJ), were significantly expressed in the pond (p < 0.05), confirming that ARGs had stronger transmission potential in the pond. The Mantel test and partial least squares path modeling (PLS-PM) analysis showed that ARGs exist in bacteria and spread among them through mobile genetic elements and HGT. This study revealed the distribution and transmission mechanism of ARGs in the ponds and ditches of a crab aquaculture system and provided a theoretical basis for controlling the spread of ARGs in crab aquaculture in this area.},
}
@article {pmid40209969,
year = {2025},
author = {Dündar, T and Köksal Çakırlar, F},
title = {Antimicrobial resistance in coagulase negative staphylococci: Genome analysis and role of horizontal gene transfer.},
journal = {Research in microbiology},
volume = {},
number = {},
pages = {104298},
doi = {10.1016/j.resmic.2025.104298},
pmid = {40209969},
issn = {1769-7123},
abstract = {Coagulase-negative staphylococci (CNS) are emerging as significant contributors to antimicrobial resistance, yet their genomic characteristics remain incompletely understood. This study presents a whole-genome analysis of 12 multidrug-resistant CNS strains (Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus hominis) isolated from blood cultures, focusing on antimicrobial resistance genes, mobile genetic elements (MGEs), and horizontal gene transfer (HGT) mechanisms. We identified 22 resistance genes conferring resistance to 11 antimicrobial classes, many of which were plasmid-associated. Notably, we report the first detection of the ISSha1 insertion sequence in S. hominis, along with novel resistance plasmids, including pGO1 and VRSAp in S. haemolyticus and pAMα1 in S. hominis. The identification of bacteriophage-derived sequences in S. haemolyticus and S. hominis suggests a role for phages in genetic exchange. CRISPR sequences and a Cas gene were detected in S. hominis, suggesting a potential but unconfirmed role in restricting gene transfer. Additionally, pGO1 was identified as a conjugative plasmid, while pAMα1 and VRSAp were determined to be mobilizable, reinforcing the role of CNS in resistance dissemination. These results highlight CNS as reservoirs of antimicrobial resistance genes and emphasize the importance of species-specific genomic surveillance. Proactive monitoring of CNS is crucial for controlling antimicrobial resistance in clinical settings.},
}
@article {pmid40209228,
year = {2025},
author = {Den Uyl, PA and Kiledal, EA and Errera, RM and Chaganti, SR and Godwin, CM and Raymond, HA and Dick, GJ},
title = {Genomic Identification and Characterization of Saxitoxin Producing Cyanobacteria in Western Lake Erie Harmful Algal Blooms.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {15},
pages = {7600-7612},
doi = {10.1021/acs.est.4c10888},
pmid = {40209228},
issn = {1520-5851},
mesh = {*Lakes/microbiology ; *Saxitoxin ; *Cyanobacteria/genetics ; *Harmful Algal Bloom ; },
abstract = {Saxitoxins (STXs), a group of closely related neurotoxins, are among the most potent natural toxins known. While genes encoding STX biosynthesis have been observed in Lake Erie, the organism(s) responsible for producing STXs in the Laurentian Great Lakes have not been identified. We identified a full suite of STX biosynthesis genes in a Dolichospermum metagenome-assembled genome (MAG). The content of sxt genes suggest that this organism can produce STX, decarbamoyl and deoxy-decarbamoyl saxitoxins, and other congeners. The absence of sxtX indicates this organism is unable to produce neosaxitoxin, a potent congener. However, a distinct, lower abundance sxt operon from an unidentified organism did contain sxtX, indicating neosaxitoxin biosynthesis potential. Metatranscriptomic data confirmed STX biosynthesis gene expression. We also recovered highly similar Dolichospermum MAGs lacking sxt genes, implying gene loss or horizontal gene transfer. sxtA was detected by quantitative polymerase chain reaction during 47 of 76 sampling dates between 2015 and 2019, demonstrating higher sensitivity than metagenomic approaches. sxtA gene abundance was positively correlated with temperature and particulate nitrogen:phosphorus ratio and negatively correlated with ammonium concentration. All Dolichospermum MAGs had genes required for nitrogen fixation. Collectively, this study provides a foundation for understanding potential new threats to Lake Erie water quality.},
}
@article {pmid40207493,
year = {2025},
author = {Swain, PP and Sahoo, RK},
title = {Blocking horizontal transfer of antibiotic resistance genes: an effective strategy in combating antibiotic resistance.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-20},
doi = {10.1080/1040841X.2025.2489463},
pmid = {40207493},
issn = {1549-7828},
abstract = {Antimicrobial resistance (AMR) poses a significant public health threat, with emerging and novel forms of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) potentially crossing international borders and challenging the global health systems. The rate of development of antibiotic resistance surpasses the development of new antibiotics. Consequently, there is a growing threat of bacteria acquiring resistance even to newer antibiotics further complicating the treatment of bacterial infections. Horizontal gene transfer (HGT) is the key mechanism for the spread of antibiotic resistance in bacteria through the processes of conjugation, transformation, and transduction. Several compounds, other than antibiotics, have also been shown to promote HGT of ARGs. Given the crucial role of HGT in the dissemination of ARGs, inhibition of HGT is a key strategy to mitigate AMR. Therefore, this review explores the contribution of HGT in bacterial evolution, identifies specific hotspots andhighlights the role of HGT inhibitors in impeding the spread of ARGs. By specifically focusing on the HGT mechanism and its inhibition, these inhibitors offer a highly promising approach to combating AMR.},
}
@article {pmid40207084,
year = {2025},
author = {Katonge, JH and Ally, ZK},
title = {Evolutionary relationships and genetic diversity in the BlaTEM gene among selected gram-negative bacteria.},
journal = {Biochemistry and biophysics reports},
volume = {42},
number = {},
pages = {101985},
pmid = {40207084},
issn = {2405-5808},
abstract = {This study investigates the genetic diversity and evolutionary relationships of the blaTEM gene, a major determinant of beta-lactam antibiotic resistance. We analyzed nucleotide sequences of 32 β-lactamase-producing strains from Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, Proteus mirabilis, and Acinetobacter baumannii obtained from public databases. Sequence analysis revealed 32 distinct sequences with 298 segregating sites and 303 mutations, indicating substantial genetic variability. A high level of haplotype diversity was observed, with 24 distinct haplotypes, reflecting evolutionary pressures and horizontal gene transfer. Phylogenetic analysis showed clear clades, suggesting the evolutionary relationships among blaTEM variants and interspecies gene transfer. The resistance profiles correlated with the genetic findings, particularly mutations. This analysis draws attention to the ongoing adaptive evolution of antibiotic resistance mechanisms, as well as the need for continued monitoring and novel therapeutic strategies. Further research with larger sample sizes and functional validation is needed to fully understand the implications of these variants in antibiotic resistance.},
}
@article {pmid40204742,
year = {2025},
author = {Napit, R and Gurung, A and Poudel, A and Chaudhary, A and Manandhar, P and Sharma, AN and Raut, S and Pradhan, SM and Joshi, J and Poyet, M and Groussin, M and Rajbhandari, RM and Karmacharya, DB},
title = {Metagenomic analysis of human, animal, and environmental samples identifies potential emerging pathogens, profiles antibiotic resistance genes, and reveals horizontal gene transfer dynamics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12156},
pmid = {40204742},
issn = {2045-2322},
mesh = {*Gene Transfer, Horizontal ; Animals ; Humans ; *Metagenomics/methods ; Feces/microbiology ; *Bacteria/genetics/drug effects ; Nepal ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; Virulence Factors/genetics ; Birds/microbiology ; Metagenome ; },
abstract = {Antimicrobial resistance (AMR) poses a significant threat to global health. The indiscriminate use of antibiotics has accelerated the emergence and spread of drug-resistant bacteria, compromising our ability to treat infectious diseases. A One Health approach is essential to address this urgent issue, recognizing the interconnectedness of human, animal, and environmental health. This study investigated the prevalence and transmission of AMR in a temporary settlement in Kathmandu, Nepal. By employing shotgun metagenomics, we analyzed a diverse range of samples, including human fecal samples, avian fecal samples, and environmental samples. Our analysis revealed a complex interplay of pathogenic bacteria, virulence factors (VF), and antimicrobial resistance genes (ARGs) across these different domains. We identified a diverse range of bacterial species, including potential pathogens, in both human and animal samples. Notably, Prevotella spp. was the dominant gut bacterium in human samples. Additionally, we detected a wide range of phages and viruses, including Stx-2 converting phages, which can contribute to the virulence of Shiga toxin-producing E. coli (STEC) strains. Our analysis revealed the presence of 72 virulence factor genes and 53 ARG subtypes across the studied samples. Poultry samples exhibited the highest number of ARG subtypes, suggesting that the intensive use of antibiotics in poultry production may contribute to the dissemination of AMR. Furthermore, we observed frequent horizontal gene transfer (HGT) events, with gut microbiomes serving as key reservoirs for ARGs. This study underscores the critical role of a One Health approach in addressing AMR. By integrating human, animal, and environmental health perspectives, we can better understand the complex dynamics of AMR and develop effective strategies for prevention and control. Our findings highlight the urgent need for robust surveillance systems, judicious antibiotic use, and improved hygiene practices to mitigate the impact of AMR on public health.},
}
@article {pmid40204671,
year = {2025},
author = {Luo, G and Fan, L and Liang, B and Guo, J and Gao, SH},
title = {Determining Antimicrobial Resistance in the Plastisphere: Lower Risks of Nonbiodegradable vs Higher Risks of Biodegradable Microplastics.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {15},
pages = {7722-7735},
doi = {10.1021/acs.est.5c00246},
pmid = {40204671},
issn = {1520-5851},
mesh = {*Microplastics ; Biodegradation, Environmental ; Biodegradable Plastics ; *Drug Resistance, Microbial/genetics ; },
abstract = {The plastisphere is a potential contributor to global antimicrobial resistance (AMR), posing potential threats to public and environmental health. However, comprehensively quantifying the contribution of microplastics with different biodegradability to AMR is lacking. In this study, we systematically quantified AMR risk mediated by biodegradable and nonbiodegradable microplastics using abundance-based methods and a custom AMR risk ranking framework that includes antimicrobial resistance genes (ARGs) abundance, mobility, and host pathogenicity. Our results demonstrated that biodegradable microplastics exhibited higher AMR risk compared to that of nonbiodegradable plastics. Key resistance genes, including those for multidrug, bacitracin, and aminoglycoside resistance, were predominant. Machine learning analysis identified cell motility as the most significant signature associated with AMR risk, highlighting its potential role in promoting ARGs dissemination. In addition, biodegradable microplastics promoted oxidative stress and SOS responses, which likely enhanced horizontal gene transfer (HGT) and AMR. Metagenome-assembled genomes (MAGs) analysis uncovered the colocalization of microplastic degradation genes, ARGs, and virulence factors (VFs), further supporting the elevated risk in biodegradable plastisphere. The proximity of ARGs to mobile genetic elements (MGEs) suggests that microplastic degradation processes might favor ARGs mobility. These findings would contribute critical insights into AMR dissemination in the plastisphere, emphasizing the need for integrated environmental and public health strategies under the context of One Health.},
}
@article {pmid40202301,
year = {2025},
author = {Mahillon, M and Debonneville, C and Groux, R and Roquis, D and Brodard, J and Faoro, F and Foissac, X and Schumpp, O and Dittmer, J},
title = {From insect endosymbiont to phloem colonizer: comparative genomics unveils the lifestyle transition of phytopathogenic Arsenophonus strains.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0149624},
doi = {10.1128/msystems.01496-24},
pmid = {40202301},
issn = {2379-5077},
abstract = {UNLABELLED: Bacteria infecting the plant phloem represent a growing threat worldwide. While these organisms often resist in vitro culture, they multiply both in plant sieve elements and hemipteran vectors. Such cross-kingdom parasitic lifestyle has emerged in diverse taxa via distinct ecological routes. In the genus Arsenophonus, the phloem pathogens "Candidatus Arsenophonus phytopathogenicus" (Ap) and "Ca. Phlomobacter fragariae" (Pf) have evolved from insect endosymbionts, but the genetic mechanisms underlying this transition have not been explored. To fill this gap, we obtained the genomes of both strains from insect host metagenomes. The resulting assemblies are highly similar in size and functional repertoire, rich in viral sequences, and closely resemble the genomes of several facultative endosymbiotic Arsenophonus strains of sap-sucking hemipterans. However, a phylogenomic analysis demonstrated distinct origins, as Ap belongs to the "Triatominarum" clade, whereas Pf represents a distant species. We identified a set of orthologs encoded only by Ap and Pf in the genus, including hydrolytic enzymes likely targeting plant substrates. In particular, both bacteria encode putative plant cell wall-degrading enzymes and cysteine peptidases related to xylellain, a papain-like peptidase from Xylella fastidiosa, for which close homologs are found in diverse Pseudomonadota infecting the plant vasculature. In silico predictions and gene expression analyses further support a role during phloem colonization for several of the shared orthologs. We conclude that the double emergence of phytopathogenicity in Arsenophonus may have been mediated by a few horizontal gene transfer events, involving genes acquired from other Pseudomonadota, including phytopathogens.<br><br>IMPORTANCE: We investigate the genetic mechanisms of a transition in bacterial lifestyle. We focus on two phloem pathogens belonging to the genus Arsenophonus: "Candidatus Arsenophonus phytopathogenicus" and "Ca. Phlomobacter fragariae." Both bacteria cause economically significant pathologies, and they have likely emerged among facultative insect endosymbionts. Our genomic analyses show that both strains are highly similar to other strains of the genus associated with sap-sucking hemipterans, suggesting a recent lifestyle shift. Importantly, although the phytopathogenic Arsenophonus strains belong to distant clades, they share a small set of orthologs unique in the genus pangenome. We provide evidence that several of these genes produce hydrolytic enzymes that are secreted and may target plant substrates. The acquisition and exchange of these genes may thus have played a pivotal role in the lifestyle transition of the phytopathogenic Arsenophonus strains.},
}
@article {pmid40199202,
year = {2025},
author = {Ferheen, I and Cimarelli, L and Marcheggiani, S and Klümper, U and Spurio, R},
title = {Plastic-mediated transformation: A new route to navigate plasmid-borne antibiotic resistance genes.},
journal = {The Science of the total environment},
volume = {976},
number = {},
pages = {179125},
doi = {10.1016/j.scitotenv.2025.179125},
pmid = {40199202},
issn = {1879-1026},
mesh = {*Plasmids/genetics ; *Plastics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Transformation, Bacterial ; },
abstract = {Among the anthropogenic sources of pollution, accumulation of plastic polymers in aquatic ecosystems is scaling at unprecedented rates and emerging as a new niche for bacterial colonization and horizontal gene transfer (HGT). The current study focuses on determining the ability of bacteria to acquire plasmid DNA from the extracellular environment under exposure to different treatments (soil, CaCl2 salt solution, soil plus CaCl2, Escherichia coli cell-free extract, and plastic debris) that simulate possible conditions experienced by microorganisms in natural environments. The transformation frequency of two plasmids (pACYC:Hyg and pBAV-1k) was tested following two experimental approaches: single species microcosm of E. coli cells (SSM) and bacterial consortium microcosm (BCM) of strains isolated from freshwater ecosystems. Plastic fragments (with consistent results obtained using polypropylene) proved to be remarkably efficient in increasing the bacterial competence towards plasmid DNA uptake as compared to the other conditions. Moreover, the effects of different plastic polymers and four incubation conditions on bacterial DNA transformation were analyzed to gain deeper insight into the exchange of genetic material. Our findings from both experimental approaches demonstrate that simultaneous incubation of microorganisms, plasmids, and plastic fragments enhances the bacterial ability to uptake plasmids and to express genes required for survival under stress conditions. The two microcosm models prove to be promising tools to mimic natural transformation events leading to the dissemination of antibiotic-resistant genes via HGT in the environment.},
}
@article {pmid40199074,
year = {2025},
author = {Li, ZY and Cui, YW and Liang, HK and Yan, HJ and Yang, RC},
title = {Tetracycline degradation by a mixed culture of halotolerant fungi-bacteria under static magnetic field: Mechanism and antibiotic resistance genes transfer.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138181},
doi = {10.1016/j.jhazmat.2025.138181},
pmid = {40199074},
issn = {1873-3336},
abstract = {Efficient antibiotics removal lowers the transmission risk of antibiotic resistance genes (ARGs). However, low efficiency limits the application of biological methods for antibiotics removal. Herein, a mixed culture of halotolerant fungi-bacteria was used for treatment of saline wastewater containing tetracycline (TC). Furthermore, static magnetic field (SMF) was used to increase TC removal. The study examined the effectiveness of SMF in removing antibiotics from saline wastewater and the associated risk of ARGs transmission. The results demonstrated that the application of a 40 mT SMF significantly improved the TC removal efficiency by 37.09 %, compared to the control (SMF=0) The TC was mainly removed through biodegradation and adsorption. In biodegradation, SMF enhanced electron transport system activity, and activities of lignin-degrading enzymes which led to higher TC biodegradation. The activity of lactate dehydrogenase and malondialdehyde decreased, lowering the damage of microbial cell membranes by TC. During the adsorption process, higher generation of extracellular polymeric substances was observed under SMF, which caused an increase in TC removal via adsorption. Microbial community analysis revealed that SMF facilitated the enrichment of TC-degrading microorganisms. Under SMF, vertical gene transfer of ARGs increased, while horizontal gene transfer risk decreased due to a reduction in mobile genetic elements (intl1) abundance. This study demonstrates that SMF is a promising strategy for enhancing TC removal efficiency, providing a basis for improved antibiotic wastewater management.},
}
@article {pmid40195311,
year = {2025},
author = {Rao, BD and Gomez-Gil, E and Peter, M and Balogh, G and Nunes, V and MacRae, JI and Chen, Q and Rosenthal, PB and Oliferenko, S},
title = {Horizontal acquisition of prokaryotic hopanoid biosynthesis reorganizes membrane physiology driving lifestyle innovation in a eukaryote.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3291},
pmid = {40195311},
issn = {2041-1723},
support = {ALTF 712-2022//European Molecular Biology Organization (EMBO)/ ; CC0102/ARC_/Arthritis Research UK/United Kingdom ; 103741/Z/14/Z//Wellcome Trust (Wellcome)/ ; 220790/Z/20/Z//Wellcome Trust (Wellcome)/ ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Schizosaccharomyces/genetics/metabolism/physiology ; *Gene Transfer, Horizontal ; Sterols/metabolism/biosynthesis ; *Intramolecular Transferases/genetics/metabolism ; *Cell Membrane/metabolism ; *Triterpenes/metabolism ; },
abstract = {Horizontal gene transfer is a source of metabolic innovation and adaptation to new environments. How new metabolic functionalities are integrated into host cell biology is largely unknown. Here, we probe this fundamental question using the fission yeast Schizosaccharomyces japonicus, which has acquired a squalene-hopene cyclase Shc1 through horizontal gene transfer. We show that Shc1-dependent production of hopanoids, mimics of eukaryotic sterols, allows S. japonicus to thrive in anoxia, where sterol biosynthesis is not possible. We demonstrate that glycerophospholipid fatty acyl asymmetry, prevalent in S. japonicus, is crucial for accommodating both sterols and hopanoids in membranes and explain how Shc1 functions alongside the sterol biosynthetic pathway to support membrane properties. Reengineering experiments in the sister species S. pombe show that hopanoids entail new traits in a naïve organism, but the acquisition of a new enzyme may trigger profound reorganization of the host metabolism and physiology.},
}
@article {pmid40190753,
year = {2025},
author = {Nahum, Y and Muhvich, J and Morones-Ramirez, JR and Casillas-Vega, NG and Zaman, MH},
title = {Biofilms as potential reservoirs of antimicrobial resistance in vulnerable settings.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1568463},
pmid = {40190753},
issn = {2296-2565},
mesh = {*Biofilms/drug effects/growth &amp; development ; Humans ; *Wastewater/microbiology ; *Drug Resistance, Bacterial ; *Vulnerable Populations ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial ; },
abstract = {Antimicrobial resistance is a major global health threat, characterized by the ability of microorganisms to withstand the effects of antimicrobial agents. Biofilms, as unique microbial communities, significantly contribute to this threat. They provide a protective environment for pathogens, facilitate horizontal gene transfer, and create an ideal setting for the persistence and evolution of resistant bacteria. This issue can be particularly important in low-income settings and vulnerable communities, such as formal and informal refugee and migrant camps. These settings usually have limited access to healthcare resources and appropriate treatments, contributing to the selective pressure that promotes the survival and proliferation of resistant bacteria. Thus, biofilms formed in wastewater in these areas can play a critical role in spreading antimicrobial resistance or acting as hidden reservoirs for future outbreaks. While emerging efforts focus on detecting antibiotic resistance genes and planktonic bacteria in wastewater, biofilms may be a source of under-appreciated antimicrobial resistance, creating a significant gap in our understanding of resistance dynamics in wastewater systems. Incorporating biofilm surveillance into wastewater monitoring strategies in vulnerable settings can help develop a more comprehensive understanding of resistance transmission and more effective intervention measures in these settings.},
}
@article {pmid40189939,
year = {2025},
author = {Wang, H and Wang, D and Shao, B and Li, J and Li, Z and Chase, MW and Li, J and Feng, Y and Wen, Y and Qin, S and Chen, B and Wu, Z and Jin, X},
title = {Unequally Abundant Chromosomes and Unusual Collections of Transferred Sequences Characterize Mitochondrial Genomes of Gastrodia (Orchidaceae), One of the Largest Mycoheterotrophic Plant Genera.},
journal = {Molecular biology and evolution},
volume = {42},
number = {4},
pages = {},
pmid = {40189939},
issn = {1537-1719},
support = {2022YFF1301704//National Key Research and Development Program of China/ ; 2023-QYCX-02//Linzhi Science and Technology Program/ ; 31870195//National Natural Science Foundation of China/ ; },
mesh = {*Genome, Mitochondrial ; *Chromosomes, Plant/genetics ; *Gastrodia/genetics ; Evolution, Molecular ; Phylogeny ; Genome, Plant ; DNA Copy Number Variations ; *Orchidaceae/genetics ; Heterotrophic Processes ; },
abstract = {The mystery of genomic alternations in heterotrophic plants is among the most intriguing in evolutionary biology. Compared to plastid genomes (plastomes) with parallel size reduction and gene loss, mitochondrial genome (mitogenome) variation in heterotrophic plants remains underexplored in many aspects. To further unravel the evolutionary outcomes of heterotrophy, we present a comparative mitogenomic study with 13 de novo assemblies of Gastrodia (Orchidaceae), one of the largest fully mycoheterotrophic plant genera, and its relatives. Analyzed Gastrodia mitogenomes range from 0.56 to 2.1 Mb, each consisting of numerous, unequally abundant chromosomes or contigs. Size variation might have evolved through chromosome rearrangements followed by stochastic loss of "dispensable" chromosomes, with deletion-biased mutations. The discovery of a hyper-abundant (∼15 times intragenomic average) chromosome in two assemblies represents the hitherto most extreme copy number variation in any mitogenomes, with similar architectures discovered in two metazoan lineages. Transferred sequence contents highlight asymmetric evolutionary consequences of heterotrophy: despite drastically reduced intracellular plastome transfers convergent across heterotrophic plants, their rarity of horizontally acquired sequences sharply contrasts parasitic plants, where massive transfers from their hosts prevail. Rates of sequence evolution are markedly elevated but not explained by copy number variation, extending prior findings of accelerated molecular evolution from parasitic to heterotrophic plants. Putative evolutionary scenarios for these mitogenomic convergence and divergence fit well with the common (e.g. plastome contraction) and specific (e.g. host identity) aspects of the two heterotrophic types. These idiosyncratic mycoheterotrophs expand known architectural variability of plant mitogenomes and provide mechanistic insights into their content and size variation.},
}
@article {pmid40188791,
year = {2025},
author = {Huang, X and Tan, Z and Wei, J and Bai, X},
title = {Super-robust synthetic microorganism can get chlorine resistance in advance and transfer their inserted DNA sequence in genome to indigenous bacteria in water.},
journal = {Water research},
volume = {281},
number = {},
pages = {123594},
doi = {10.1016/j.watres.2025.123594},
pmid = {40188791},
issn = {1879-2448},
abstract = {CRISPR-Cas gene editing tools have brought us to an era of synthetic biology that will change the world. Synthetic microorganisms (SMs) have brought enormous economic benefits and will contribute more in the future. Among them, super-robust SMs can overcome the stresses in bioproduction and further increase yield. However, when they are released into the environments, little is known about their fates and risks to human health. In this study, it was found that the gene editing super-robust SM could transfer its inserted DNA sequence in genome to the indigenous bacteria in surface water and showed stronger resistance to chlorine compared with wild-type bacteria. Chlorine disinfection did slight damage on cell membrane of super-robust SM, which decreased ATP leakage and DNA damage, and thereby promoted bacterial survival. Chlorine-injured super-robust SM retained high respiratory activity, and could resuscitate and regenerate. Less damage on super-robust SM cell membrane could prevent chlorine from entering the cells and resulted in lower ROS generation. Its DNA repair system and antioxidant system could still function under high concentrations of chlorine exposure. These findings provided new insights into the fates and environmental risks of SMs as an emerging biological pollutant in water supply system.},
}
@article {pmid40188040,
year = {2025},
author = {Yang, Y and Liu, W and Zhao, Z and Guo, K and Wang, X and Lou, Z and Yang, X and Gong, L and Wang, K and Liu, X and Xu, H and Liu, Q and Zheng, B and Jiang, X},
title = {Genomic insights and epidemiology of mcr-1-Carrying Escherichia albertii isolated from agricultural soil in China.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {344},
pmid = {40188040},
issn = {1471-2164},
mesh = {China/epidemiology ; *Soil Microbiology ; Phylogeny ; *Escherichia/genetics/isolation &amp; purification/drug effects/classification ; *Genomics ; Humans ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; *Escherichia coli Proteins/genetics ; Drug Resistance, Bacterial/genetics ; Agriculture ; },
abstract = {BACKGROUND: Polymyxins are critical in treating multidrug-resistant Gram-negative bacteria infections, yet their overuse has spurred the emergence of polymyxin-resistant pathogens globally. This study aims to analyze the genomic characteristics of the Escherichia albertii strain 6S-65-1 carrying the mcr-1 gene and to investigate the global epidemiology of mcr-1-carrying E. albertii strains.<br><br>RESULTS: In this study, we identified and analyzed a polymyxin-resistant Escherichia albertii strain (6S-65-1) carrying the mcr-1 gene, isolated from agricultural soil in China. Whole-genome sequencing and comparative genomic analyses revealed two chromosomal integrations of the mcr-1 gene within Tn6330 transposon structures, indicating its capacity for horizontal gene transfer. Strain 6S-65-1 also harbors other antimicrobial resistance genes, including tet(A), sul3, and aph (3')-Ia, enhancing its resistance profile. Comparative genomic analysis of E. albertii genomes in the NCBI database revealed that mcr-1-carrying E. albertii strains are geographically restricted to China and Japan, and have been isolated from both animals and humans. Phylogenetic analysis revealed that strain 6S-65-1 was most closely related to a human-derived strain from Japan (SAMD00164101), with both strains carried virulence genes (cdt, paa, and eae) that enable them to form attaching and effacing (A/E) lesions. Among all publicly available ST4619 E. albertii genomes, strain 6S-65-1 is the first to carry the mcr-1 gene.<br><br>CONCLUSION: Our findings offer new insights into the epidemiology and genomic features of mcr-1-carrying E. albertii, underscoring the need for targeted management strategies to curb its spread. These findings underscore the importance of "One Health" approaches to antimicrobial resistance, which require coordinated efforts across human, animal and the environmental health sectors.},
}
@article {pmid40186988,
year = {2025},
author = {Liu, L and Zhang, QH and Li, MZ and Li, RT and He, Z and Dechesne, A and Smets, BF and Sheng, GP},
title = {Single-cell analysis reveals antibiotic affects conjugative transfer by modulating bacterial growth rather than conjugation efficiency.},
journal = {Environment international},
volume = {198},
number = {},
pages = {109385},
doi = {10.1016/j.envint.2025.109385},
pmid = {40186988},
issn = {1873-6750},
mesh = {*Anti-Bacterial Agents/pharmacology ; Single-Cell Analysis ; *Conjugation, Genetic/drug effects ; *Escherichia coli/drug effects/genetics/growth &amp; development ; *Gene Transfer, Horizontal/drug effects ; Drug Resistance, Bacterial/genetics ; Plasmids ; },
abstract = {Antibiotic resistance genes (ARGs) pose a significant threat to human health and the environment. Quantifying the efficiency of horizontal gene transfer (HGT) is challenging due to diverse biological and environmental influences. Single-cell level approaches are well-suited for investigating conjugative transfer, given its reliance on cell-to-cell contact nature and its capacity to offer insights into population-level responses. This study introduces a self-developed system for automated time-lapse image acquisition and analysis. Using a custom dual-chamber microfluidic chip and Python-based image analysis pipeline, we dynamically quantify the ARGs conjugation efficiency at single-cell level. By combining experiments with individual-based modelling, we isolate the effects of subinhibitory antibiotic concentrations on conjugation efficiency from those related to bacterial growth dynamics. No significant variation in Escherichia coli conjugation efficiency was observed across kanamycin concentrations (0 to 50 mg l[-1]). Moreover, recipient cells with higher growth rates show a greater propensity for plasmid acquisition, suggesting the physiological state of cells pre-conjugation influences their susceptibility to gene transfer. Our methodology eliminates population growth bias, revealing the intrinsic nature of conjugation efficiency. This approach advances our understanding of the factors influencing HGT efficiency and holds promise for studying other microbial interactions. SYNOPSIS: This study employs single-cell analysis to reveal that subinhibitory concentrations of antibiotics affect the conjugative transfer of antibiotic resistance genes by modulating bacterial growth rate rather than conjugation efficiency.},
}
@article {pmid40183128,
year = {2025},
author = {Bolzoni, L and Scaltriti, E and Bracchi, C and Angelone, S and Menozzi, I and Taddei, R and Alba, P and Carfora, V and Diaconu, EL and Morganti, M and Dodi, A and Berni, M and Manni, L and Vinci, M and Tambassi, M and Mazzera, L and Venturelli, I and Ambretti, S and Battisti, A and Pongolini, S},
title = {Emergence of Salmonella enterica carrying bla OXA-181 carbapenemase gene, Italy, 2021 to 2024.},
journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin},
volume = {30},
number = {13},
pages = {},
pmid = {40183128},
issn = {1560-7917},
mesh = {*beta-Lactamases/genetics ; *Salmonella enterica/genetics/isolation &amp; purification/enzymology ; Humans ; Animals ; *Bacterial Proteins/genetics ; Italy/epidemiology ; Swine/microbiology ; Phylogeny ; Plasmids/genetics ; Microbial Sensitivity Tests ; *Salmonella Infections/microbiology/epidemiology ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; },
abstract = {Between 2021 and 2024, we detected carbapenemase gene blaOXA-181 in 16 of 11,398 Salmonella enterica (SE) isolates: 10 SE 1,4,[5],12:i:-, three Bovismorbificans, two London and one Rissen from pigs, humans, pork meat and wild roe deer. The gene was first detected in pig isolates, later in humans, suggesting zoonotic transmission. Phylogenetic analysis indicated that horizontal transfer, mainly through plasmids, contributed to the spread. These findings highlight a possible emerging public health threat and the importance of One Health surveillance.},
}
@article {pmid40173243,
year = {2025},
author = {Tsoi, R and Son, HI and Hamrick, GS and Tang, K and Bethke, JH and Lu, J and Maddamsetti, R and You, L},
title = {A predatory gene drive for targeted control of self-transmissible plasmids.},
journal = {Science advances},
volume = {11},
number = {14},
pages = {eads4735},
pmid = {40173243},
issn = {2375-2548},
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; Conjugation, Genetic ; *Gene Drive Technology/methods ; },
abstract = {Suppressing plasmid transfer in microbial communities has profound implications due to the role of horizontal gene transfer (HGT) in spreading and maintaining diverse functional traits such as metabolic functions, virulence factors, and antibiotic resistance. However, existing tools for inhibiting HGT are limited in their modes of delivery, efficacy, and scalability. Here, we present a versatile denial-of-spread (DoS) strategy to target and eliminate specific conjugative plasmids. Our strategy exploits retrotransfer, whereby an engineered DoS plasmid is introduced into host cells containing a target plasmid. Acting as a predatory gene drive, DoS propagates itself at the expense of the target plasmid, through competition or active elimination. Once the target plasmid is eradicated, DoS is removed via induced plasmid suicide, resulting in a community containing neither plasmid. The strategy is tunable and scalable for various conjugative plasmids, different mechanisms of plasmid inheritance interruption, and diverse environmental contexts. DoS represents a new tool for precise control of gene persistence in microbial communities.},
}
@article {pmid40173202,
year = {2025},
author = {Loyo, CL and Grossman, AD},
title = {A phage-encoded counter-defense inhibits an NAD-degrading anti-phage defense system.},
journal = {PLoS genetics},
volume = {21},
number = {4},
pages = {e1011551},
pmid = {40173202},
issn = {1553-7404},
support = {R35 GM122538/GM/NIGMS NIH HHS/United States ; R35 GM148343/GM/NIGMS NIH HHS/United States ; T32 GM007287/GM/NIGMS NIH HHS/United States ; },
mesh = {*Bacillus subtilis/virology/genetics ; *NAD/metabolism ; *Bacteriophages/genetics ; *Bacterial Proteins/genetics/metabolism ; *Bacillus Phages/genetics/pathogenicity ; Gene Transfer, Horizontal ; },
abstract = {Bacteria contain a diverse array of genes that provide defense against predation by phages. Anti-phage defense genes are frequently located on mobile genetic elements and spread through horizontal gene transfer. Despite the many anti-phage defense systems that have been identified, less is known about how phages overcome the defenses employed by bacteria. The integrative and conjugative element ICEBs1 in Bacillus subtilis contains a gene, spbK, that confers defense against the temperate phage SPβ through an abortive infection mechanism. Using genetic and biochemical analyses, we found that SpbK is an NADase that is activated by binding to the SPβ phage portal protein YonE. The presence of YonE stimulates NADase activity of the TIR domain of SpbK and causes cell death. We also found that the SPβ-like phage Φ3T has a counter-defense gene that prevents SpbK-mediated abortive infection and enables the phage to produce viable progeny, even in cells expressing spbK. We made SPβ-Φ3T hybrid phages that were resistant to SpbK-mediated defense and identified a single gene in Φ3T (phi3T_120, now called nip for NADase inhibitor from phage) that was both necessary and sufficient to block SpbK-mediated anti-phage defense. We found that Nip binds to the TIR (NADase) domain of SpbK and inhibits NADase activity. Our results provide insight into how phages overcome bacterial immunity by inhibiting enzymatic activity of an anti-phage defense protein.},
}
@article {pmid40173128,
year = {2025},
author = {Sichert, A},
title = {A single enzyme becomes a Swiss Army knife.},
journal = {PLoS biology},
volume = {23},
number = {4},
pages = {e3003072},
pmid = {40173128},
issn = {1545-7885},
mesh = {Gene Transfer, Horizontal ; *Diatoms/genetics/enzymology ; Photosynthesis/genetics ; Phaeophyceae/genetics/enzymology/metabolism ; Alginates/metabolism ; },
abstract = {An alga that abandoned photosynthesis? This Primer explores a PLOS Biology study showing that a single horizontal gene transfer event allowed the diatom Nitzschia sing1 to evolve a complete enzymatic machinery to break down alginate from brown algae, unlocking a new ecological niche.},
}
@article {pmid40168690,
year = {2025},
author = {Jaafar, T and Carvalhais, E and Shrestha, A and Cochrane, R and Meaney, J and Brumwell, S and Hamadache, S and Nasrollahi, V and Karas, BJ},
title = {Engineering conjugative plasmids for inducible horizontal DNA transfer.},
journal = {Canadian journal of microbiology},
volume = {71},
number = {},
pages = {1-9},
doi = {10.1139/cjm-2024-0241},
pmid = {40168690},
issn = {1480-3275},
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Conjugation, Genetic ; Promoter Regions, Genetic ; *Escherichia coli/genetics ; *Genetic Engineering/methods ; Arabinose/metabolism ; },
abstract = {Rapidly developing microbial resistance to existing antimicrobials poses a growing threat to public health and global food security. Current chemical-based treatments target cells by inhibiting growth or metabolic function, but their effectiveness is diminishing. To address the growing antimicrobial resistance crisis, there is an urgent need for innovative therapies. Conjugative plasmids, a natural mechanism of horizontal gene transfer in bacteria, have been repurposed to deliver toxic genetic cargo to recipient cells, showing promise as next-generation antimicrobial agents. However, the ecological risks posed by unintended gene transfer require robust biocontainment strategies. In this study, we developed inducible conjugative plasmids to solve these challenges. Utilizing an arabinose-inducible promoter, we evaluated 13 plasmids with single essential gene deletions, identifying trbC and trbF as strong candidates for stringent regulation. These plasmids demonstrated inducibility in both cis and trans configurations, with induction resulting in up to a 5-log increase in conjugation efficiency compared to uninduced conditions. Although challenges such as reduced conjugation efficiency and promoter leakiness persist, this work establishes a foundation for the controlled transfer of plasmids, paving the way for safer and more effective antimicrobial technologies.},
}
@article {pmid40168346,
year = {2025},
author = {Lim, ZH and Zheng, P and Quek, C and Nowrousian, M and Aachmann, FL and Jedd, G},
title = {Diatom heterotrophy on brown algal polysaccharides emerged through horizontal gene transfer, gene duplication, and neofunctionalization.},
journal = {PLoS biology},
volume = {23},
number = {4},
pages = {e3003038},
pmid = {40168346},
issn = {1545-7885},
mesh = {*Gene Transfer, Horizontal ; *Gene Duplication ; *Diatoms/genetics/metabolism ; *Polysaccharides/metabolism ; Phylogeny ; Heterotrophic Processes ; Alginates/metabolism ; Phaeophyceae/genetics ; Polysaccharide-Lyases/genetics/metabolism ; Evolution, Molecular ; },
abstract = {A major goal of evolutionary biology is to identify the genetic basis for the emergence of complex adaptive traits. Diatoms are ancestrally photosynthetic microalgae. However, in the genus Nitzschia, loss of photosynthesis led to a group of free-living secondary heterotrophs whose manner of acquiring chemical energy is unclear. Here, we sequence the genome of the non-photosynthetic diatom Nitzschia sing1 and identify the genetic basis for its catabolism of the brown algal cell wall polysaccharide alginate. N. sing1 obtained an endolytic alginate lyase enzyme by horizontal gene transfer (HGT) from a marine bacterium. Subsequent gene duplication through unequal crossing over and transposition led to 91 genes in three distinct gene families. One family retains the ancestral endolytic enzyme function. By contrast, the two others underwent domain duplication, gain, loss, rearrangement, and mutation to encode novel functions that can account for oligosaccharide import through the endomembrane system and the exolytic production of alginate monosaccharides. Together, our results show how a single HGT event followed by substantial gene duplication and neofunctionalization led to alginate catabolism and access to a new ecological niche.},
}
@article {pmid40166311,
year = {2025},
author = {Inglis, LK and Grigson, SR and Roach, MJ and Edwards, RA},
title = {Prophages as a source of antimicrobial resistance genes in the human microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40166311},
issn = {2692-8205},
support = {RC2 DK116713/DK/NIDDK NIH HHS/United States ; },
abstract = {Prophages-viruses that integrate into bacterial genomes-are ubiquitous in the microbial realm. Prophages contribute significantly to horizontal gene transfer, including the potential spread of antimicrobial resistance (AMR) genes, because they can collect host genes. Understanding their role in the human microbiome is essential for fully understanding AMR dynamics and possible clinical implications. We analysed almost 15,000 bacterial genomes for prophages and AMR genes. The bacteria were isolated from diverse human body sites and geographical regions, and their genomes were retrieved from GenBank. AMR genes were detected in 6.6% of bacterial genomes, with a higher prevalence in people with symptomatic diseases. We found a wide variety of AMR genes combating multiple drug classes. We discovered AMR genes previously associated with plasmids, such as blaOXA-23 in Acinetobacter baumannii prophages or genes found in prophages in species they had not been previously described in, such as mefA-msrD in Gardnerella prophages, suggesting prophage-mediated gene transfer of AMR genes. Prophages encoding AMR genes were found at varying frequencies across body sites and geographical regions, with Asia showing the highest diversity of AMR genes.},
}
@article {pmid40166188,
year = {2025},
author = {Gonçalves, C and Steenwyk, JL and Rinker, DC and Opulente, DA and LaBella, AL and Harrison, MC and Wolters, JF and Zhou, X and Shen, XX and Covo, S and Groenewald, M and Hittinger, CT and Rokas, A},
title = {Stable hypermutators revealed by the genomic landscape of DNA repair genes among yeast species.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40166188},
issn = {2692-8205},
support = {R01 AI153356/AI/NIAID NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; },
abstract = {Mutator phenotypes are short-lived due to the rapid accumulation of deleterious mutations. Yet, recent observations reveal that certain fungi can undergo prolonged accelerated evolution after losing DNA repair genes. Here, we surveyed 1,154 yeast genomes representing nearly all known yeast species of the subphylum Saccharomycotina to examine the relationship between reduced DNA repair repertoires and elevated evolutionary rates. We identified three distantly related lineages-encompassing 12% of species-with substantially reduced sets of DNA repair genes and the highest evolutionary rates in the entire subphylum. Two of these "faster-evolving lineages" (FELs)-a subclade within the order Pichiales and the Wickerhamiella/Starmerella (W/S) clade (order Dipodascales)-are described here for the first time, while the third corresponds to a previously documented Hanseniaspora FEL. Examination of DNA repair gene repertoires revealed a set of genes predominantly absent in these three FELs, suggesting a potential role in the observed acceleration of evolutionary rates. Genomic signatures in the W/S clade are consistent with a substantial mutational burden, including pronounced A|T bias and signatures of endogenous DNA damage. The W/S clade appears to mitigate UV-induced damage through horizontal acquisition of a bacterial photolyase gene, underscoring how gene loss may be offset by nonvertical evolution. These findings highlight how the loss of DNA repair genes gave rise to hypermutators that persist across macroevolutionary timescales, with horizontal gene transfer as an avenue for partial functional compensation.},
}
@article {pmid40166157,
year = {2025},
author = {Gozashti, L and Corbett-Detig, R},
title = {Double-stranded DNA viruses may serve as vectors for horizontal transfer of intron-generating transposons.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40166157},
issn = {2692-8205},
support = {R35 GM128932/GM/NIGMS NIH HHS/United States ; },
abstract = {Specialized transposable elements capable of generating introns, termed introners, are one of the major drivers of intron gain in eukaryotes. Horizontal gene transfer (HGT) is thought to play an important role in shaping introner distributions. Viruses could function as vehicles of introner HGT since they often integrate into host genomes and have been implicated in widespread HGT in eukaryotes. We annotated integrated viral elements in diverse dinoflagellate genomes with active introners and queried viral elements for introner sequences. We find that 25% of viral elements contain introners. The vast majority of viral elements represent maverick-polinton-like double-stranded DNA (dsDNA) viruses as well as giant dsDNA viruses. By querying a previously annotated set of maverick-polinton-like proviruses, we show that introners populate full-length elements with machinery required for transposition as well as viral infection. Introners in the vast majority of viral elements are younger than or similar in age to others in their host genome, suggesting that most viral elements acquired introners after integration. However, a subset of viral elements show the opposite pattern wherein viral introners are significantly older than other introners, possibly consistent with virus-to-host horizontal transfer. Together, our results suggest that dsDNA viruses may serve as vectors for HGT of introners between individuals and species, resulting in the introduction of intron-generating transposons to new lineages.},
}
@article {pmid40165783,
year = {2025},
author = {Herbert, A and Hancock, CN and Cox, B and Schnabel, G and Moreno, D and Carvalho, R and Jones, J and Paret, M and Geng, X and Wang, H},
title = {Corrigendum: Oxytetracycline and streptomycin resistance genes in Xanthomonas arboricola pv. pruni, the causal agent of bacterial spot in peach.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1580418},
doi = {10.3389/fmicb.2025.1580418},
pmid = {40165783},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2022.821808.].},
}
@article {pmid40165089,
year = {2025},
author = {Ma, Y and López-Pujol, J and Yan, D and Deng, Z and Zhou, Z and Niu, J},
title = {Complete mitochondrial genomes of the hemiparasitic genus Cymbaria (Orobanchaceae): insights into repeat-mediated recombination, phylogenetic relationships, and horizontal gene transfer.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {314},
pmid = {40165089},
issn = {1471-2164},
support = {31860106//National Natural Science Foundation of China/ ; 2019ZD008//Major Science and Technology Projects of Inner Mongolia Autonomous Region/ ; },
mesh = {*Genome, Mitochondrial ; *Phylogeny ; *Gene Transfer, Horizontal ; *Orobanchaceae/genetics/classification ; Recombination, Genetic ; RNA, Transfer/genetics ; Repetitive Sequences, Nucleic Acid ; Evolution, Molecular ; },
abstract = {BACKGROUND: The Orobanchaceae family is widely recognized as an exemplary model system for examining the evolutionary dynamics of parasitic plants. However, reports on the mitochondrial genome (mitogenome) of the hemiparasitic tribe Cymbarieae are currently lacking. Here, we sequenced, assembled and characterized the complete mitogenome of the genus Cymbaria L. sensu stricto (C. mongolica and C. daurica).<br><br>RESULTS: A total of 51 unique mitochondrial genes, including 33 protein-coding genes, three rRNA genes, and 15 tRNA genes, are shared by the mitogenomes of the two hemiparasitic plants, exhibiting the gene content characteristic of autotrophic plants. The mitogenomes of C. mongolica and C. daurica are characterized by a pentacyclic chromosome structure (their major conformation), with lengths of 1,576,465&#xa0;bp and 1,539,836&#xa0;bp, respectively. Moreover, we identified and validated the presence of four minor conformations mediated by four pairs of large repeats (>&#x2009;1000&#xa0;bp in size) in C. mongolica and eight minor conformations mediated by six large repeats in C. daurica. We further explored codon usage, RNA editing sites, selective pressure, and nucleotide diversity in two Cymbaria mitogenomes. Phylogenetic analyses of 26 species of Lamiales revealed that the two Cymbaria species form a sister clade to the other lineages of Orobanchaceae. Extensive mitogenomic rearrangements are also observed between Cymbaria and five closely related species. Although we identified mitochondrial plastid sequences in the Cymbaria mitogenomes, The mitochondrial plastid sequences (MTPTs) in their mitogenomes represent only 2.37% and 1.74%, respectively. Additionally, there is minimal evidence of intracellular and horizontal gene transfer, with only a few genes (rpl22, rps3, and ycf2) showing low bootstrap support (BS&#x2009;&#x2264;&#x2009;70%) for the relationships with the potential host plants Allium mongolicum, Leymus chinensis, and Saposhnikovia divaricata, respectively.<br><br>CONCLUSIONS: We reported the mitochondrial genome in hemiparasitic Cymbaria species for the first time, which are characterized by multiple repeat-mediated recombination and little to no intracellular and horizontal gene transfer. Our findings provide valuable genetic insights for further studies on the mitogenome evolution of hemiparasitic plants.},
}
@article {pmid40164788,
year = {2025},
author = {},
title = {Horizontal gene transfer of cold shock protein genes boosted wheat adaptation and expansion.},
journal = {Nature plants},
volume = {11},
number = {4},
pages = {676-677},
pmid = {40164788},
issn = {2055-0278},
}
@article {pmid40162837,
year = {2025},
author = {Major, SR and Polinski, JM and Penn, K and Rodrigue, M and Harke, MJ},
title = {Novel and diverse features identified in the genomes of bacteria isolated from a hydrothermal vent plume.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {4},
pages = {e0259324},
pmid = {40162837},
issn = {1098-5336},
support = {22-08846//Dalio Foundation/ ; },
mesh = {*Hydrothermal Vents/microbiology ; *Genome, Bacterial ; *Bacteria/genetics/isolation &amp; purification/classification ; Phylogeny ; Multigene Family ; Seawater/microbiology ; Gene Transfer, Horizontal ; },
abstract = {Hydrothermal vent plumes (HVPs), formed by high-temperature vent emissions, are rich in compounds that support chemosynthesis and serve as reservoirs of microbial diversity and genetic innovation. Through turbulence, mixing, and interaction with subsea currents, vent communities are thought to disperse across ocean basins. In this study, we focused on the plume of the Moytirra hydrothermal vent field, a relatively unexplored site, to investigate its microbial inhabitants. We cultured bacteria from the Moytirra HVP using 11 different media types and performed complete genome sequencing on 12 isolates. Our analyses revealed four putatively novel species from the Thalassobaculum, Sulfitobacter, Idiomarina, and Christiangramia genera. Comparative genomics identified unique genomic islands containing biosynthetic gene clusters, including a novel Non-Ribosomal Peptide Synthetase/Polyketide Synthase cluster, toxin-antitoxin systems, and evidence of horizontal gene transfer facilitated by prophages. These findings underscore the potential of HVPs as a source of novel microbial species and biotechnologically relevant genes, contributing to our understanding of the biodiversity and genetic complexity of these extreme environments.IMPORTANCEHydrothermal vents are dynamic environments that offer unique nutrients for chemosynthetic organisms to drive biology in the deep-sea. The dynamics of these ecosystems are thought to drive genomic innovation in resident populations. Hydrothermal vent plumes (HVPs) mix with surrounding water, carrying local microbiota with them and dispersing for hundreds of kilometers. This study isolated bacteria from a HVP to capture a genomic snapshot of the microbial community, revealing four putatively novel species of bacteria within three taxonomic classes. The addition of these genomes to public databases provides valuable insights into the genomic function, architecture, and novel biosynthetic gene clusters of bacteria found in these extreme environments.},
}
@article {pmid40161755,
year = {2025},
author = {Ratna, TA and Sharon, BM and Velin, CAB and Buttaro, BA and Palmer, KL},
title = {Factors affecting CRISPR-Cas defense against antibiotic resistance plasmids harbored by Enterococcus faecalis laboratory model strains and clinical isolates.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40161755},
issn = {2692-8205},
support = {R01 AI116610/AI/NIAID NIH HHS/United States ; },
abstract = {Enterococcus faecalis is a Gram-positive bacterium and opportunistic pathogen that acquires resistance to a wide range of antibiotics by horizontal gene transfer (HGT). The rapid increase of multidrug-resistant (MDR) bacteria including MDR E. faecalis necessitates the development of alternative therapies and a deeper understanding of the factors that impact HGT. CRISPR-Cas systems provide sequence-specific defense against HGT. From previous studies, we know that E. faecalis CRISPR-Cas provides sequence-specific anti-plasmid defense during agar plate biofilm mating and in the murine intestine. Those studies were mainly conducted using laboratory model strains with a single, CRISPR-targeted plasmid in the donor. MDR E. faecalis typically possess multiple plasmids that are diverse in sequence and may interact with each other to impact plasmid transfer and CRISPR-Cas efficacy. Here, we altered multiple parameters of our standard in vitro conjugation assays to assess CRISPR-Cas efficacy, including the number and genotype of plasmids in the donor; laboratory model strains as donor versus recent human isolates as donor; and the biofilm substrate utilized during conjugation. We found that the plasmids pTEF2 and pCF10, which are not targeted by CRISPR-Cas in our recipient, enhance the conjugative transfer of the CRISPR-targeted plasmid pTEF1 into both wild-type and CRISPR-Cas-deficient (via deletion of cas9) recipient cells. However, the effect of pTEF2 on pTEF1 transfer is much more pronounced, with a striking 6-log increase in pTEF1 conjugation frequency when pTEF2 is also present in the donor and recipients are deficient for CRISPR-Cas (compared to 4-log for pCF10). We also identified that E. faecalis Δcas9 has altered biofilm structure and thickness relative to the wild-type strain when cultured on a plastic substrate, but equivalent growth in the agar plate biofilms widely used for conjugation studies. Overall, this study provides insight about the interplay between plasmids and CRISPR-Cas defense, opening avenues for developing novel therapeutic strategies to curb HGT among bacterial pathogens, and highlighting pTEF2 as a plasmid for additional mechanistic study.},
}
@article {pmid40158280,
year = {2025},
author = {Zhang, L and Ye, M and Dong, Y and Yuan, L and Xiang, J and Yu, X and Liao, Q and Ai, Q and Qiu, S and Zhang, D},
title = {Strict relationship between phenotypic and plasmid-associated genotypic of multidrug-resistant Escherichia coli isolated from Taihe Black-Boned Silky Fowl farms.},
journal = {Poultry science},
volume = {104},
number = {6},
pages = {105082},
pmid = {40158280},
issn = {1525-3171},
abstract = {Taihe Black-Boned Silky Fowl (TBSF) is a unique breed in China, characterized by a high concentration of melanin deposited throughout its body. Compared to broiler chickens, many antibiotics exhibit significantly longer withdrawal periods in TBSF. Given that antibiotic exposure is widely recognized as the primary selective pressure driving the persistence and dissemination of antibiotic resistance genes (ARGs) across diverse environments, it is crucial to investigate the occurrence and prevalence of ARGs within TBSF farming systems. In this study, 34 Escherichia coli strains isolated from 22 TBSF farms were subjected to phenotypic and genotypic analyses. The isolates were tested for susceptibility to 28 antimicrobial drugs representing nine antibiotic classes to determine their antimicrobial resistance phenotypes. Draft genome sequences of these E. coli strains were obtained, and the ARGs carried by mobile genetic elements, particularly plasmids, were analyzed for their association with susceptibility phenotype. The genetic context of key ARGs in these E. coli isolates was further characterized. Network analysis was employed to investigate the correlations between ARGs, phenotypes, and drug residues. The results demonstrated that high rates of antimicrobial resistance were observed, with 100 % and 29.4 % of isolates exhibiting resistance to four or more and eight or more antibiotic classes, respectively. According to whole-genome sequencing, a total of 143 ARGs were identified. The antimicrobial resistance phenotypes were consistently correlated with the presence of corresponding ARGs in the 34 E. coli genomes. 100 % of the β-lactams antibiotics resistant mechanism could be attributed to the presence of the resistance gene blaTEM and/or blaOXA-10. Similarly, resistance to tetracyclines, chloramphenicols, aminoglycosides, and fluoroquinolones was fully explained by the presence of tetR and/or tetA, floR and/or cmlA, ant(3'')-IIa, aph(3'')-Ib, aph(6)-Id, aac(3)-IId, and aadA, and qnrS and/or mutant gyrA/parC/mdtH. The majority of these key ARGs were found to be plasmid-associated. This study verified and highlighted the prevalent horizontal gene transfer of ARGs in TBSF farms. Factors such as hygiene status, biosecurity measures, and other environmental conditions might play a more significant role than antimicrobial usage in facilitating the horizontal gene transfer of ARGs in TBSF farms. Appropriate measures should be taken to control the transmission and dissemination of these mobile genetic elements associated ARGs and prevent their entry into the human clinical environment from TBSF breeding environment.},
}
@article {pmid40155375,
year = {2025},
author = {von Rosen, T and Zdanowicz, R and El Hadeg, Y and Afanasyev, P and Boehringer, D and Leitner, A and Glockshuber, R and Weber-Ban, E},
title = {Substrates bind to residues lining the ring of asymmetrically engaged bacterial proteasome activator Bpa.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3042},
pmid = {40155375},
issn = {2041-1723},
support = {310030_215606//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; ETH-17 17-2//Eidgen&#xf6;ssische Technische Hochschule Z&#xfc;rich (Federal Institute of Technology Zurich)/ ; },
mesh = {*Proteasome Endopeptidase Complex/metabolism ; *Bacterial Proteins/metabolism/genetics/chemistry ; *Cryoelectron Microscopy ; Protein Binding ; Mycobacterium tuberculosis/metabolism/genetics ; Models, Molecular ; Mutagenesis, Site-Directed ; Binding Sites ; Proteolysis ; Substrate Specificity ; },
abstract = {Mycobacteria harbor a proteasome that was acquired by Actinobacteria through horizontal gene transfer and that supports the persistence of the human pathogen Mycobacterium tuberculosis within host macrophages. The core particle of the proteasome (20S CP) associates with ring-shaped activator complexes to degrade protein substrates. One of these is the bacterial proteasome activator Bpa that stimulates the ATP-independent proteasomal degradation of the heat shock repressor HspR. In this study, we determine the cryogenic electron microscopy 3D reconstruction of the complex between Bpa and its natural substrate HspR at 4.1 Å global resolution. The resulting maps allow us to identify regions of Bpa that interact with HspR. Using structure-guided site-directed mutagenesis and in vitro biochemical assays, we confirm the importance of the identified residues for Bpa-mediated substrate recruitment and subsequent proteasomal degradation. Additionally, we show that the dodecameric Bpa ring associates asymmetrically with the heptameric α-rings of the 20S CP, adopting a conformation resembling a hinged lid, while still engaging all seven docking sites on the proteasome.},
}
@article {pmid40154852,
year = {2025},
author = {He, L and Wang, W and Chen, H and Ma, L and Yu, L and Yang, Y and Qu, Y and Dai, P and Wang, D and Ma, X},
title = {Gene expressions of clinical Pseudomonas aeruginosa harboring RND efflux pumps on chromosome and involving a novel integron on a plasmid.},
journal = {Microbial pathogenesis},
volume = {203},
number = {},
pages = {107512},
doi = {10.1016/j.micpath.2025.107512},
pmid = {40154852},
issn = {1096-1208},
mesh = {*Pseudomonas aeruginosa/genetics/drug effects/isolation &amp; purification ; *Plasmids/genetics ; *Integrons/genetics ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Membrane Transport Proteins/genetics ; Humans ; Drug Resistance, Multiple, Bacterial/genetics ; Pseudomonas Infections/microbiology ; *Chromosomes, Bacterial/genetics ; Gene Expression Regulation, Bacterial ; Bacterial Proteins/genetics ; DNA Transposable Elements ; },
abstract = {The clinical strain of Pseudomonas aeruginosa XM8 harbored multiple RND-type antibiotic efflux pump genes and a novel integron In4881 on its plasmid pXM8-2, rendering it resistant to nearly all conventional antibiotics except colistin. The resistance was primarily attributed to the inactivation of the oprD gene and overexpression of several efflux pump genes, including mexAB-oprM, mexCD-oprJ, oprN-mexFE, and mexXY. In this study, the XM8 strain was comprehensively characterized using various methods. Antimicrobial susceptibility testing was performed using the BioMerieux VITEK2 system and manual double dilution methods. Gene expression levels of efflux pump-related genes were analyzed via quantitative real-time PCR. The bacterial chromosome and plasmid were sequenced using both Illumina and Nanopore platforms, and bioinformatics tools were employed to analyze mobile genetic elements associated with antibiotic resistance. The pXM8-2 plasmid containsed multiple mobile genetic elements, including integrons (In4881, In334, In413) and transposons (Tn3, TnAs1, TnAs3). Notably, In4881 was reported for the first time in this study. The presence of these elements highlights the potential for horizontal gene transfer and further spread of antibiotic resistance. Given the strong resistance profile of the XM8 strain, effective measures should be implemented to prevent the dissemination and prevalence of such multidrug-resistant bacteria.},
}
@article {pmid40154224,
year = {2025},
author = {Hao, X and Sang, W and Li, F and Shen, L and Zhu, L and Rong, L and Jiang, D and Bai, L},
title = {Regulation of antibiotic resistance gene rebound by degrees of microecological niche occupation by microbiota carried in additives during the later phases of swine manure composting.},
journal = {Ecotoxicology and environmental safety},
volume = {294},
number = {},
pages = {118112},
doi = {10.1016/j.ecoenv.2025.118112},
pmid = {40154224},
issn = {1090-2414},
mesh = {*Composting/methods ; *Manure/microbiology ; Animals ; *Drug Resistance, Microbial/genetics ; *Soil Microbiology ; Swine ; *Microbiota ; Bacteria/genetics ; Genes, Bacterial ; Soil/chemistry ; Gene Transfer, Horizontal ; },
abstract = {The occupation of microecological niches (MNs) by bacteria carrying lower antibiotic resistance genes (ARGs) has been demonstrated an effective strategy for reducing ARGs in compost, thereby mitigating the associated land use risks. In this study, humus soil (HS), matured compost (MC), and their respective isolated microbial agents (HSM and MCM), which exhibit varying abundances of ARGs, were introduced as additives after the thermophilic phase to investigate their influence on ARG removal and the mechanisms underlying effective MN occupation. The addition of HS resulted in the most favorable outcomes, including the highest carbon degradation, minimized nitrogen loss, and an 83.16 % reduction in ARG abundance during the later composting stages. In comparison, ARG rebound levels were 61.77 %-285.33 % across other treatments and 729.23 % in the control. Distinct dominant bacterial genera and potential ARG-host bacterial communities were observed, which varied with different additives and contributed to MN occupation dynamics. The addition of the HS additive intensified competition among non-host bacteria, and diversified the interactions both between genes and between bacteria. These changes suppressed horizontal gene transfer (HGT) mediated by mobile genetic elements (MGEs) and altered the abundance and composition of both dominant and non-dominant potential host species. Furthermore, it shifted the relative importance of key physicochemical parameters, collectively enhancing ARG removal during composting. These findings elucidate the mechanisms by which MN adjustments contribute to ARG reduction, providing actionable insights for designing composting strategies that mitigate environmental ARG dissemination risks more effectively.},
}
@article {pmid40151755,
year = {2025},
author = {Hota, S and Patil, SR and Mane, PM},
title = {Enterococcus: Understanding Their Resistance Mechanisms, Therapeutic Challenges, and Emerging Threats.},
journal = {Cureus},
volume = {17},
number = {2},
pages = {e79628},
pmid = {40151755},
issn = {2168-8184},
abstract = {The Enterococcus species originates as non-harmful bacteria indigenous to human intestines but has transformed into severe hospital-acquired pathogens due to antimicrobial resistance (AMR). The clinical species Enterococcus faecalis and Enterococcus faecium create the most relevant infections because they appear in urinary tract infections, bloodstream infections, endocarditis, and wound infections. Enterococcus species demonstrate multiple antibiotic class resistance and resistance determinant acquisition properties that make treatment difficult for medical professionals. Vancomycin-resistant enterococci (VRE) together with high-level aminoglycoside-resistant strains and resistance to both linezolid and daptomycin have exhausted available treatment options. The review investigates the development process of Enterococcus infections by examining virulence characteristics, which involve biofilm production and defense mechanisms against the immune response and transmission of resistance genes. A thorough investigation of medical publications used Google Scholar along with PubMed and ScienceDirect and Medical Subject Headings (MeSH) as appropriate search terms. The traditional classification of Enterococcus species from historical context to modern epidemiology and pathogenesis and available treatment and test approaches are explained in this review. This section examines two categories of resistance together with their mechanisms of action with a specific focus on vancomycin resistance produced by van gene clusters as well as its prevalence trends. An examination of how horizontal gene transfer functions in transferring resistance throughout healthcare facilities is included. The paper investigates the different symptoms of enterococcal infections together with diagnostic obstacles and treatment modalities. Drug-resistant Enterococcus infections continue to increase internationally, so healthcare professionals need new therapeutic methods, better antimicrobial policies, and stronger infection prevention measures. The examination surveys Enterococcus infections through an extensive evaluation of developing resistance patterns combined with emerging intervention requirements.},
}
@article {pmid40151212,
year = {2025},
author = {van Almsick, VF and Sobkowiak, A and Scherff, N and Schuler, F and Oehm, JB and Böing, C and Mellmann, A and Schwierzeck, V},
title = {In-depth characterization of Klebsiella pneumoniae carbapenemase (KPC)-encoding plasmids points at transposon-related transmission of resistance genes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1542828},
pmid = {40151212},
issn = {2235-2988},
mesh = {*Klebsiella pneumoniae/genetics/drug effects/enzymology ; *beta-Lactamases/genetics ; Humans ; *Plasmids/genetics ; *Klebsiella Infections/transmission/microbiology ; *DNA Transposable Elements/genetics ; *Bacterial Proteins/genetics/metabolism ; *Whole Genome Sequencing ; Germany ; Multilocus Sequence Typing ; Male ; Female ; Aged ; Middle Aged ; Anti-Bacterial Agents/pharmacology ; Tertiary Care Centers ; Cross Infection/microbiology/transmission ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Genome, Bacterial/genetics ; },
abstract = {Antimicrobial resistance (AMR) is a growing threat in healthcare systems, particularly in the management of infections in critically ill patients. This study highlights how to identify clusters and putative sharing of mobile genetic elements, such as transposons, in the hospital setting using long-read whole genome sequencing (lrWGS). The approach described here can be employed to investigate the transmission dynamics of KPC-3-positive Klebsiella pneumoniae at multiple levels, from the entire isolate down to individual plasmids and transposons. Here, a bla KPC-3 harboring transposon cluster was identified by using a Mash-based distance calculation for plasmids. This approach was used to investigate a local accumulation of KPC-3-positive Klebsiella pneumoniae on surgical and infectious disease wards of a tertiary care center in Germany over a time of six months. In total, seven patients were affected. Core genome multi-locus sequence typing analysis (cgMLST) identified two distinct genetic clusters: a sequence type (ST) 307 cluster (n = 5) and a ST101 cluster (n = 2). All isolates carried a bla KPC-3 carbapenemase. Further Mash distance-based plasmid analysis was not consistent with plasmid transfer due to genetic heterogeneity, but identified a transposon cluster across all isolates. Infection control evaluation of patient movements within their hospital admission supports a possible clonal transmission. Subsequent infection control measures, including point prevalence screening and enhanced contact precautions, successfully contained further transmissions. The study illustrates the value of in-depth plasmid analysis in understanding the transmission dynamics and epidemiology of AMR, particularly in hospital environments.},
}
@article {pmid40150788,
year = {2025},
author = {Müller, GA},
title = {The Transformation Experiment of Frederick Griffith I: Its Narrowing and Potential for the Creation of Novel Microorganisms.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {12},
number = {3},
pages = {},
pmid = {40150788},
issn = {2306-5354},
abstract = {The construction of artificial microorganisms often relies on the transfer of genomes from donor to acceptor cells. This synthetic biology approach has been considerably fostered by the J. Craig Venter Institute but apparently depends on the use of microorganisms, which are very closely related. One reason for this limitation of the "creative potential" of "classical" transformation is the requirement for adequate "fitting" of newly synthesized polypeptide components, directed by the donor genome, to interacting counterparts encoded by the pre-existing acceptor genome. Transformation was introduced in 1928 by Frederick Griffith in the course of the demonstration of the instability of pneumococci and their conversion from rough, non-pathogenic into smooth, virulent variants. Subsequently, this method turned out to be critical for the identification of DNA as the sole matter of inheritance. Importantly, the initial experimental design (1.0) also considered the inheritance of both structural (e.g., plasma membranes) and cybernetic information (e.g., metabolite fluxes), which, in cooperation, determine topological and cellular heredity, as well as fusion and blending of bacterial cells. In contrast, subsequent experimental designs (1.X) were focused on the use of whole-cell homogenates and, thereafter, of soluble and water-clear fractions deprived of all information and macromolecules other than those directing protein synthesis, including outer-membrane vesicles, bacterial prions, lipopolysaccharides, lipoproteins, cytoskeletal elements, and complexes thereof. Identification of the reasons for this narrowing may be helpful in understanding the potential of transformation for the creation of novel microorganisms.},
}
@article {pmid40149106,
year = {2025},
author = {Olsen, NS and Riber, L},
title = {Metagenomics as a Transformative Tool for Antibiotic Resistance Surveillance: Highlighting the Impact of Mobile Genetic Elements with a Focus on the Complex Role of Phages.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
pmid = {40149106},
issn = {2079-6382},
support = {NNF23OC0086264//Novo Nordisk Foundation/ ; },
abstract = {Extensive use of antibiotics in human healthcare as well as in agricultural and environmental settings has led to the emergence and spread of antibiotic-resistant bacteria, rendering many infections increasingly difficult to treat. Coupled with the limited development of new antibiotics, the rise of antimicrobial resistance (AMR) has caused a major health crisis worldwide, which calls for immediate action. Strengthening AMR surveillance systems is, therefore, crucial to global and national efforts in combating this escalating threat. This review explores the potential of metagenomics, a sequenced-based approach to analyze entire microbial communities without the need for cultivation, as a transformative and rapid tool for improving AMR surveillance strategies as compared to traditional cultivation-based methods. We emphasize the importance of monitoring mobile genetic elements (MGEs), such as integrons, transposons, plasmids, and bacteriophages (phages), in relation to their critical role in facilitating the dissemination of genetic resistance determinants via horizontal gene transfer (HGT) across diverse environments and clinical settings. In this context, the strengths and limitations of current bioinformatic tools designed to detect AMR-associated MGEs in metagenomic datasets, including the emerging potential of predictive machine learning models, are evaluated. Moreover, the controversial role of phages in AMR transmission is discussed alongside the potential of phage therapy as a promising alternative to conventional antibiotic treatment.},
}
@article {pmid40149092,
year = {2025},
author = {Hernández, M and Falcó-Prieto, &#xc1; and Ugarte-Ruiz, M and Miguela-Villoldo, P and Ocampo-Sosa, A and Abad, D and Pérez-Sancho, M and Álvarez, J and Cadamuro, RD and Elois, MA and Fongaro, G and Quesada, A and González-Zorn, B and Domínguez, L and Eiros, JM and Rodríguez-Lázaro, D},
title = {Genome Analysis of 6222 Bacterial Isolates from Livestock and Food Environments in Spain to Decipher the Antibiotic Resistome.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
pmid = {40149092},
issn = {2079-6382},
support = {AGL2016-74882-C3//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; },
abstract = {Background/Objectives: Antimicrobial resistance (AMR) poses a significant threat to global health and the economy, with projected costs ranging from $300 billion to $1 trillion annually and an estimated 10 million deaths per year by 2050. The food chain, from primary production to retail, represents a critical entry point for antimicrobial resistant bacteria into communities. This underscores the need for a coordinated "One Health" approach, integrating efforts in animal production, environmental health, and human healthcare to address this global concern. This study aimed to characterize the global resistome in Spanish primary production by sequencing 6222 bacterial genomes from animal origin. Methods and Results: Whole genome sequencing was performed on bacterial isolates collected from various farms and analyzed using a validated bioinformatic pipeline. The analysis revealed a diverse range of bacterial species, with Enterobacteriaceae being the most prevalent family. Escherichia coli was the most common species, followed by Salmonella enterica and Pseudomonas aeruginosa. This study identified 1072 antimicrobial resistance genes coding for 43 different classes of resistance, potentially conferring resistance to 81 antimicrobials. Additionally, 79 different plasmid types were detected, highlighting the potential for horizontal gene transfer. Conclusions: The resistome analysis revealed genes conferring resistance to various antibiotic classes, as well as antiseptics, disinfectants, and efflux pump-mediated resistance. This comprehensive characterization of AMR genes circulating in bacteria from primary production provides crucial insights into the ecology of AMR in Spanish livestock.},
}
@article {pmid40149046,
year = {2025},
author = {Mitsuwan, W and Boripun, R and Saengsawang, P and Intongead, S and Boonplu, S and Chanpakdee, R and Morita, Y and Boonmar, S and Rojanakun, N and Suksriroj, N and Ruekaewma, C and Tenitsara, T},
title = {Multidrug Resistance, Biofilm-Forming Ability, and Molecular Characterization of Vibrio Species Isolated from Foods in Thailand.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
pmid = {40149046},
issn = {2079-6382},
support = {SEAOHUN/2023-SC248//United States Agency for International Development (USAID) through the SEAOHUN 2023 One Health Research and Training (OHRT) Awards/ ; WU-CIA-03404/2024//Walailak University under the international research collaboration scheme/ ; },
abstract = {BACKGROUND: Vibrio species are common foodborne pathogens that cause gastrointestinal tract inflammation. Multidrug resistance (MDR) in Vibrio spp. is a global health concern, especially in aquaculture systems and food chain systems. This study aimed to detect Vibrio contamination in food collected from 14 markets in Nakhon Si Thammarat, Thailand, and determine their antibiotic susceptibility.<br><br>METHODS: One hundred and thirty-six food samples were investigated for Vibrio contamination. All isolates were tested for antibiogram and biofilm-forming ability. Moreover, the ceftazidime or cefotaxime resistance isolates were additionally investigated for extended-spectrum &#x3b2;-lactamase (ESBL) producers. The isolates were additionally examined for the presence of antibiotic resistance genes. The ESBL-suspected isolates with moderate-to-high biofilm-forming ability were further analyzed for their whole genome.<br><br>RESULTS: The prevalence of Vibrio contamination in food samples was 42.65%, with V. parahaemolyticus demonstrating the highest prevalence. Most isolates were resistant to &#x3b2;-lactam antibiotics, followed by aminoglycosides. The overall MDR of isolated Vibrio was 18.29%, with an average multiple antibiotic resistance (MAR) index of 16.41%. Most isolates were found to have &#x3b2;-lactam resistance-related genes (blaTEM) for 41.46%, followed by aminoglycoside resistance genes (aac(6')-Ib) for 18.29%. Most Vibrio showed moderate to strong biofilm-forming ability, particularly in MDR isolates (92.86%). Two ESBL-suspected isolates, one V. parahaemolyticus isolate and one V. navarrensis, were sequenced. Interestingly, V. parahaemolyticus was an ESBL producer that harbored the blaCTX-M-55 gene located in the mobile genetic element region. While V. navarrensis was not ESBL producer, this isolate carried the blaAmpC gene in the region of horizontal gene transfer event. Remarkably, the Inoviridae sp. DNA integration event was present in two Vibrio genomes.<br><br>CONCLUSIONS: These findings impact the understanding of antibiotic-resistant Vibrio spp. in food samples, which could be applied for implementing control measures in aquaculture farming and food safety plans.},
}
@article {pmid40148599,
year = {2025},
author = {Patra, M and Pandey, AK and Dubey, SK},
title = {Sludge amended soil induced multidrug and heavy metal resistance in endophytic Exiguobacterium sp. E21L: genomics evidences.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {4},
pages = {114},
pmid = {40148599},
issn = {1573-0972},
support = {R/Dev./Sch./UGC Non-NET Fellowship/2023-24/72267//University Grants Commission/ ; 6031//IOE/ ; },
mesh = {*Metals, Heavy/pharmacology ; *Sewage/microbiology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Soil Microbiology ; *Genome, Bacterial ; *Anti-Bacterial Agents/pharmacology ; *Genomics ; *Whole Genome Sequencing ; Phylogeny ; Microbial Sensitivity Tests ; Endophytes/genetics/isolation &amp; purification ; Gene Transfer, Horizontal ; },
abstract = {The emergence of multidrug-resistant bacteria in agro-environments poses serious risks to public health and ecological balance. In this study, Exiguobacterium sp. E21L, an endophytic strain, was isolated from carrot leaves cultivated in soil amended with sewage treatment plant-derived sludge. The strain exhibited resistance to clinically relevant antibiotics, including beta-lactams, fluoroquinolones, aminoglycosides, and macrolides, with a high Multi-Antibiotic Resistance Index of 0.88. Whole-genome sequencing revealed a genome of 3.06 Mb, encoding 3894 protein-coding genes, including antimicrobial resistance genes (ARGs) such as blaNDM, ermF, tetW, and sul1, along with heavy metal resistance genes (HMRGs) like czcD, copB, and nikA. Genomic islands carrying ARGs and stress-related genes suggested potential horizontal gene transfer. The strain demonstrated robust biofilm formation, high cell hydrophobicity (> 80%), and significant auto-aggregation (90% at 48 h), correlating with genes associated with motility, quorum sensing, and stress adaptation. Notably, phenotypic assays confirmed survival under simulated gastrointestinal conditions, emphasizing its resilience in host-associated environments. Comparative genomics positioned Exiguobacterium sp. E21L near Exiguobacterium chiriqhucha RW-2, with a core genome of 2716 conserved genes. Functional annotations revealed genes involved in xenobiotic degradation, multidrug efflux pumps, and ABC-type transporters, indicating versatile resistance mechanisms and metabolic capabilities. The presence of ARGs, HMRGs, and MGEs (mobile genetic elements) highlights the potential role of Exiguobacterium sp. E21L as a reservoir for resistance determinants in agricultural ecosystems. These findings emphasized the need for stringent regulations on sludge-based fertilizers and advanced sludge treatment strategies to mitigate AMR risks in agro-environments.},
}
@article {pmid40148598,
year = {2025},
author = {Wang, K and Guo, G and Bai, S and Ma, J and Zhang, Z and Xing, Z and Wang, W and Li, H and Liang, H and Li, Z and Si, X and Wang, J and Liu, Q and Xu, W and Yang, C and Song, RF and Li, J and He, T and Li, J and Zeng, X and Liang, J and Zhang, F and Qiu, X and Li, Y and Bu, T and Liu, WC and Zhao, Y and Huang, J and Zhou, Y and Song, CP},
title = {Horizontally acquired CSP genes contribute to wheat adaptation and improvement.},
journal = {Nature plants},
volume = {11},
number = {4},
pages = {761-774},
pmid = {40148598},
issn = {2055-0278},
support = {32230079//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Triticum/genetics/physiology ; *Gene Transfer, Horizontal ; *Plant Proteins/genetics/metabolism ; *Adaptation, Physiological/genetics ; Droughts ; Aegilops/genetics/physiology ; Photosynthesis ; Plants, Genetically Modified ; },
abstract = {Although horizontal gene transfer (HGT) often facilitates environmental adaptation of recipient organisms, whether and how they might affect crop evolution and domestication is unclear. Here we show that three genes encoding cold-shock proteins (CSPs) were transferred from bacteria to Triticeae, a tribe of the grass family that includes several major staple crops such as wheat, barley and rye. The acquired CSP genes in wheat (TaCSPs) are functionally conserved in their bacterial homologues by encoding a nucleic acid-binding protein. Experimental evidence indicates that TaCSP genes positively regulate drought response and improve photosynthetic efficiency under water-deficient conditions by directly targeting a type 1 metallothionein gene to increase reactive oxygen species scavenging, which in turn contributed to the geographic expansion of wheat. We identified an elite CSP haplotype in Aegilops tauschii, introduction of which to wheat significantly increased drought tolerance, photosynthetic efficiency and grain yields. These findings not only provide major insights into the role of HGT in crop adaptation and domestication, but also demonstrate that novel microbial genes introduced through HGT offer a stable and naturally optimized resource for transgenic crop breeding and improvement.},
}
@article {pmid40146211,
year = {2025},
author = {Hornok, S and Keve, G and Tuska-Szalay, B},
title = {Transmission route-dependent genetic diversity of selected protozoan parasites as reflected by the phylogenetic analysis of the 18S rRNA gene.},
journal = {Acta veterinaria Hungarica},
volume = {73},
number = {1},
pages = {64-72},
doi = {10.1556/004.2025.01128},
pmid = {40146211},
issn = {0236-6290},
mesh = {*RNA, Ribosomal, 18S/genetics ; *Genetic Variation ; *Phylogeny ; Animals ; *Protozoan Infections, Animal/parasitology/transmission/epidemiology ; *Eukaryota/genetics/classification ; },
abstract = {In this pilot study, the genetic diversity of protozoan parasites was analysed according to their different transmission routes (life cycle strategies), focusing on those species which were recently discovered or molecularly analysed for the first time in Hungary or its geographical region. The results showed that among four apicomplexan parasites (Babesia gibsoni, Cytauxzoon europaeus, Sarcocystis morae and Hepatozoon felis) the latter had the highest genetic diversity as reflected by its 18S rRNA gene sequences showing high (1.75%) maximum intraspecific pairwise distance, and also, based on its phylogenetic clustering. This is probably related to the long evolutionary history of H. felis, the absence of its intravascular division and other life cycle characteristics precluding direct transmission between hosts. On the other hand, among non-apicomplexan protozoa (Trichomonas gallinae, Pentatrichomonas hominis, Tritrichomonas foetus and Acanthamoeba castellanii), the latter proved to have the highest genetic diversity (7.73%), most likely due to its long evolutionary history, lateral gene transfer, homologous recombination and the absence of direct host-to-host dispersal. Transmission mode had a significant impact on the genetic diversity among protozoan parasites, depending on life cycle strategies and consequent frequency/chance of sexual reproduction vs binary fission. In particular, the absence of direct transmission between hosts is a common trait of H. felis and A. castellanii, contributing to their high genetic diversity.},
}
@article {pmid40142381,
year = {2025},
author = {Moriguchi, K and Nakamura, K and Takahashi, Y and Higo-Moriguchi, K and Kiyokawa, K and Suzuki, K},
title = {Genome-Wide Survey of Donor Chromosomal Genes Involved in Trans-Kingdom Conjugation via the RP4-T4SS Machinery.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
pmid = {40142381},
issn = {2076-2607},
support = {JP16K07200//Japan Society for the Promotion of Science/ ; No grant number (donation)//Consortium for the Exploration of Microbial Functions Ohsumi Frontier Science Foundation/ ; },
abstract = {Trans-kingdom conjugation (TKC)/inter-domain conjugation is a horizontal gene transfer phenomenon that transfers DNA from eubacteria to eukaryotes and archaebacteria via a type IV secretion system encoded in IncP1-type broad-host-range plasmids. Although TKC is considered a potential gene introduction tool, donor chromosomal genes that influence TKC efficiency have rarely been analyzed, hindering targeted donor breeding. To identify potential TKC-related genes on a donor chromosome, a genome-wide screening of TKC-deficient mutants was performed using a comprehensive collection of Escherichia coli gene knockout mutants (Keio collection) as donors and a Saccharomyces cerevisiae strain as a recipient. Out of 3884 mutants, two mutants (∆aceE, ∆priA) showed a severe decrease in TKC efficiency by more than two orders of magnitude but not in bacterial conjugation. The effect on TKC efficiency by the two mutants was partly recovered by a preculture with a fresh culture medium before the TKC reaction, regardless of the presence of antibiotics. These results suggest that no single chromosomal target gene is solely responsible for universally blocking IncP1-type conjugation by impeding its function. The results also suggest the existence of an unidentified recognition or transfer mechanism distinct from bacterial conjugation, highlighting the novel roles of aceE and priA.},
}
@article {pmid40142377,
year = {2025},
author = {Pazos, C and Gualoto, M and Oña, T and Velarde, E and Portilla, K and Cabrera-García, S and Banchón, C and Dávila, G and Hernández-Alomia, F and Bastidas-Caldes, C},
title = {Molecular Detection of blaTEM and blaSHV Genes in ESBL-Producing Acinetobacter baumannii Isolated from Antarctic Soil.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
pmid = {40142377},
issn = {2076-2607},
abstract = {The phenomenon of antimicrobial resistance (AMR) in cold environments, exemplified by the Antarctic, calls into question the assumption that pristine ecosystems lack clinically significant resistance genes. This study examines the molecular basis of AMR in Acinetobacter spp. Isolated from Antarctic soil, focusing on the blaTEM and blaSHV genes associated with extended-spectrum beta-lactamase (ESBL) production; Soil samples were collected and processed to isolate Antarctic soil bacteria. Molecular detection was then conducted using polymerase chain reaction (PCR) to identify the bacteria species by 16S rRNA/rpoB and 10 different beta-lactamase-producing genes. PCR amplicons were sequenced to confirm gene identity and analyze genetic variability. Acinetobacter baumannii were identified by both microbiological and molecular tests. Notably, both the blaTEM and blaSHV genes encoding the enzymes responsible for resistance to penicillins and cephalosporins were identified, indicating the presence of resistance determinants in bacteria from extreme cold ecosystems. The nucleotide sequence analysis indicated the presence of conserved ARGs, which suggest stability and the potential for horizontal gene transfer within microbial communities. These findings emphasize that AMR is not confined to human-impacted environments but can emerge and persist in remote, cold habitats, potentially facilitated by natural reservoirs and global microbial dispersal. Understanding the presence and role of AMR in extreme environments provides insights into its global dissemination and supports the development of strategies to mitigate the spread of resistance genes in both environmental and clinical contexts.},
}
@article {pmid40141150,
year = {2025},
author = {Rendueles, C and Garay-Novillo, JN and Rau, MH and Gaspar, P and Ruiz-Masó, J&#xc1; and Mahony, J and Rodríguez, A and Barra, JL and Del Solar, G and Martínez, B},
title = {A Plasmid-Encoded Surface Polysaccharide Partly Blocks Ceduovirus Infection in Lactococci.},
journal = {International journal of molecular sciences},
volume = {26},
number = {6},
pages = {},
pmid = {40141150},
issn = {1422-0067},
support = {PID2020-119697RB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; },
mesh = {*Lactococcus/genetics ; *Plasmids/genetics ; *Lactococcus lactis/genetics/virology ; Bacteriophages/genetics ; Polysaccharides, Bacterial/metabolism ; CRISPR-Cas Systems ; },
abstract = {Bacteriophages (or phages) remain the leading cause of failure in dairy fermentations. Thereby, phage-resistant Lactococcus lactis and Lactococcus cremoris dairy starters are in continuous demand. In this work, our goal was to identify phage defense mechanisms against ceduoviruses encoded by two wild isolates of dairy origin named L. lactis IPLA517 and IPLA1064. These strains were previously subjected to experimental evolution to select derivatives that are resistant to the bacteriocin Lcn972. It was observed that the Lcn972[R] derivatives became sensitive to phage infection; however, the underlying mechanism was not defined. The long-read sequencing technologies applied in this work reveal that all of the Lcn972[R] derivatives shared the loss of a 41 kb endogenous plasmid (p41) that harbors a putative exopolysaccharide (EPS) gene cluster with significant homology to one described in Lactococcus garvieae. Using a CRISPR-Cas9-based approach, p41 was selectively cured from L. lactis IPLA1064. Phage infection assays with three ceduoviruses demonstrated that curing p41 restored phage sensitivity at levels comparable to the Lcn972[R]-IPLA1064 derivatives. Phage adsorption to Δp41 cells was also increased, consistent with the hypothesis of EPS production hindering access to the phage receptor protein Pip. Our results reinforce the role of EPSs in protecting Lactococcus against phage infection, a phenomenon that is rarely reported for ceduoviruses. Moreover, the results also exemplify the likely horizontal gene transfer that can occur between L. lactis and L. garvieae in a dairy environment.},
}
@article {pmid40135944,
year = {2025},
author = {Zheng, Y and Zhu, X and Ding, C and Chu, W and Pang, X and Zhang, R and Ma, J and Xu, G},
title = {Multidrug-resistant hypervirulent Klebsiella pneumoniae: an evolving superbug.},
journal = {Future microbiology},
volume = {20},
number = {6},
pages = {499-511},
pmid = {40135944},
issn = {1746-0921},
mesh = {*Klebsiella pneumoniae/pathogenicity/drug effects/genetics ; Humans ; *Klebsiella Infections/microbiology/epidemiology ; *Drug Resistance, Multiple, Bacterial/genetics ; Virulence Factors/genetics ; Anti-Bacterial Agents/pharmacology ; Virulence ; China/epidemiology ; Asia/epidemiology ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Multidrug-resistant hypervirulent Klebsiella pneumoniae (MDR-hvKP) combines high pathogenicity with multidrug resistance to become a new superbug. MDR-hvKP reports continue to emerge, shattering the perception that hypervirulent K. pneumoniae (hvKP) strains are antibiotic sensitive. Patients infected with MDR-hvKP strains have been reported in Asia, particularly China. Although hvKP can acquire drug resistance genes, MDR-hvKP seems to be more easily transformed from classical K. pneumoniae (cKP), which has a strong gene uptake ability. To better understand the biology of MDR-hvKP, this review discusses the virulence factors, resistance mechanisms, formation pathways, and identification of MDR-hvKP. Given their destructive and transmissible potential, continued surveillance of these organisms and enhanced control measures should be prioritized.},
}
@article {pmid40133813,
year = {2025},
author = {Huang, X and Yu, C and Lu, L},
title = {Isolation and characterization of a roseophage representing a novel genus in the N4-like Rhodovirinae subfamily distributed in estuarine waters.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {295},
pmid = {40133813},
issn = {1471-2164},
mesh = {*Phylogeny ; *Bacteriophages/genetics/isolation &amp; purification/classification ; *Estuaries ; *Genome, Viral ; Rhodobacteraceae/genetics/virology/classification/isolation &amp; purification ; },
abstract = {BACKGROUND: Roseobacteraceae, often referred to as the marine roseobacter clade (MRC), are pivotal constituents of bacterial communities in coastal and pelagic marine environments. During the past two decades, 75 roseophages that infect various Roseobacteraceae lineages have been isolated. The N4-like roseophage clade, which encompasses 15 members, represents the largest clade among these roseophages. N4-like phages form a monophyletic group, classified as family Schitoviridae. And all N4-like roseophages form a unique clade within Schitoviridae and has been classified as the Rhodovirinae subfamily.<br><br>RESULTS: In this study, we isolated a novel roseophage, vB_DshP-R7L, that infects Dinoroseobacter shibae DFL12 from Xiamen Bay in the East China Sea. Conserved genes of Schitoviridae have been identified in the genome of vB_DshP-R7L, and following phylogenetic analysis suggests that the newly isolated phage is a member of the Rhodovirinae subfamily and represents the sole member of a novel genus, Gonggongvirus. The genome of vB_DshP-R7L harbors six auxiliary metabolic genes (AMGs), most of which potentially enhance DNA de novo synthesis. Additionally, a gene encoding ribosomal protein was identified. Comparative genomic analysis of AMG content among Rhodovirinae indicates a distinct evolutionary history characterized by independent ancient horizontal gene transfer events. Read-mapping analysis reveals the prevalence of vB_DshP-R7L and other Rhodovirinae roseophages in estuarine waters.<br><br>CONCLUSIONS: Our work illustrates the genomic features of a novel roseophage clade among the subfamily Rhodovirinae. The AMG content of vB_DshP-R7L is under severe purification selection, which reveals their possible ecological importance. We also demonstrated that vB_DshP-R7L and other Rhodovirinae roseophages are only detected in estuaries. Our isolation and characterization of this novel phage expands the understanding of the phylogeny, gene transfer history, and biogeography of Rhodovirinae infecting marine Roseobacteraceae.},
}
@article {pmid40131635,
year = {2025},
author = {Silva, UCM and da Silva, DRC and Cuadros-Orellana, S and Moreira, LM and Leite, LR and Medeiros, JD and Felestrino, EB and Caneschi, WL and Almeida, NF and Silva, RS and Oliveira-Paiva, CA and Dos Santos, VL},
title = {Genomic and phenotypic insights into Serratia interaction with plants from an ecological perspective.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {40131635},
issn = {1678-4405},
support = {N&#xb0; 477349/2013-7//CNPq/ ; N&#xb0; APQ-01819-13//Fapemig/ ; },
abstract = {We investigated the plant growth-promoting potential of two endophytic strains of Serratia marcescens, namely SmCNPMS2112 and SmUFMG85, which were isolated from the roots of the same maize (Zea mays) plant. The strains were evaluated in vitro for their ability to produce siderophores and indoleacetic acid, form biofilm, solubilize iron phosphate (Fe-P) and Araxá rock phosphate (RP), mineralize phytate, and for their ability to adhere and colonize host roots. Additionally, their plant growth-promoting potential was tested in vivo under greenhouse conditions using millet grown in soil under two fertilization schemes (triple superphosphate, TSP, or commercial rock phosphate, cRP). Both strains improved at least five physiological traits of millet or P content in soil. In order to elucidate the genetic basis of the plant growth-promoting ability of these strains, their genomes were compared. While both genomes exhibited a similar overall functional profile, each strain had unique features. SmCNPMS2112 contained genes related to arsenic and aromatic hydrocarbons degradation, whereas SmUFMG85 harbored genes related to rhamnolipid biosynthesis and chromium bioremediation. Also, we observe a unique repertoire of genes related to plant growth-promotion (PGP) in the SmUFMG85 genome, including oxalate decarboxylase (OxdC), associated with the catabolism of oxalic acid, and aerobactin siderophore (lucD) in the genome of SmCNPMS2112. The alkaline phosphatase was observed on two strains, but acid phosphatase was exclusive to SmUFMG85. Eighteen secondary metabolic gene clusters, such as those involved in the biosynthesis of macrolides and bacillomycin, among others, occur in both strains. Moreover, both genomes contained prophages, suggesting that viral-mediated horizontal gene transfer may be a key mechanism driving genomic variability in the endophytic environment. Indeed, the most genes unique and accessory of SmUFMG85 and SmCNPMS2112 were localized in genomic islands, highlighting genome plasticity and its underlying drivers. To investigate the ecological distribution of plant-interaction traits in the genus Serratia, the genomes of SmUFMG85 and SmCNPMS2112 strains were compared with those of other 19 Serratia strains of different species, which were isolated from different environments. We observe that many features for PGP are present in all genomes, regardless of niche, for instance: formation of flagella, fimbriae and pili, chemotaxis, biosynthesis of siderophores, indole-3-acetic acid (IAA) and volatile organic (VOC) and inorganic (VIC) compounds, such as acetoin and HCN. Also, all the analyzed genomes show an antimicrobial resistance repertoire of genes that confer resistance to several antibiotics belonging to the groups of aminoglycosides and quinolones, for instance. Also, from a niche partitioning perspective, secretion system preference and the ability to produce exopolysaccharides involved in biofilm formation are among the features that vary the most among strains, and most likely influence niche adaptation in Serratia spp., even though only the latter seems to be a feature specifically associated with virulence in the analyzed strains. Our results show that populations of bacteria sharing the same niche can present significant physiological and genomic differences, and reveal the intraspecific metabolic plasticity that underlie plant-bacteria interactions. Also, this study reveals the potential of two Serratia marcescens strains as bioinoculants in agriculture. Considering that Serratia spp. are regarded as low risk biological agents, despite the fact that they can be associated with human disease, we suggest that strain biosafety be evaluated using a combination of genome and phenotypic analyses, as presented herein.},
}
@article {pmid40121546,
year = {2025},
author = {Wang, Q and Liu, C and Sun, Y and Li, X and Gu, W and Wang, N and Sun, S and Luo, Y},
title = {Dietary intake of enrofloxacin promotes the spread of antibiotic resistance from food to simulated human gut.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf045},
pmid = {40121546},
issn = {1751-7370},
abstract = {Antibiotic residues are commonly found in food. The effect of dietary exposure to veterinary antibiotics on the transmission of antibiotic resistant bacteria and antibiotic resistance genes from food to humans is unknown. We found that dietary exposure to enrofloxacin reduced microbial diversity, interactions and the immune responses, weakened the colonization resistance of the resident microbiota, and promoted the colonization of exogenous Escherichia coli K-12 MG1655 in the simulated human intestine both in vitro and in vivo experiments in mice. In addition to the growth advantages for potential most likely bacterial hosts of ARGs under enrofloxacin exposure, the dietary exposure to enrofloxacin promoted horizontal transfer of resistance plasmids and altered the simulated human gut antibiotic resistome in a time-dependent manner. Collectively, these findings demonstrated that dietary intake of enrofloxacin promoted the colonization of E. coli K-12 MG1655 in the simulated human intestine and the horizontal transfer of antibiotic resistance genes, highlighting the risk of antibiotic resistance transmission from food to humans mediated by dietary exposure to veterinary antibiotics.},
}
@article {pmid40120959,
year = {2025},
author = {Wu, Z and Famous, M and Stoikidou, T and Bowden, FES and Dominic, G and Huws, SA and Godoy-Santos, F and Oyama, LB},
title = {Unravelling AMR dynamics in the rumenofaecobiome: Insights, challenges and implications for One Health.},
journal = {International journal of antimicrobial agents},
volume = {66},
number = {1},
pages = {107494},
doi = {10.1016/j.ijantimicag.2025.107494},
pmid = {40120959},
issn = {1872-7913},
abstract = {Antimicrobial resistance (AMR) is a critical global threat to human, animal and environmental health, exacerbated by horizontal gene transfer (HGT) via mobile genetic elements. This poses significant challenges that have a negative impact on the sustainability of the One Health approach, hindering its long-term viability and effectiveness in addressing the interconnectedness of global health. Recent studies on livestock animals, specifically ruminants, indicate that culturable ruminal bacteria harbour AMR genes with the potential for HGT. However, these studies have focused predominantly on using the faecobiome as a proxy to the rumen microbiome or using easily isolated and culturable bacteria, overlooking the unculturable population. These unculturable microbial groups could have a profound influence on the rumen resistome and AMR dynamics within livestock ecosystems, potentially holding critical insights for advanced understanding of AMR in One Health. In order to address this gap, this review of current research on the burden of AMR in livestock was undertaken, and it is proposed that combined study of the rumen microbiome and faecobiome, termed the 'rumenofaecobiome', should be performed to enhance understanding of the risks of AMR in ruminant livestock. This review discusses the complexities of the rumen microbiome and the risks of AMR transmission in this microbiome in a One Health context. AMR transmission dynamics and methodologies for assessing the risks of AMR in livestock are summarized, and future considerations for researching the impact of AMR in the rumen microbiome and the implications within the One Health framework are discussed.},
}
@article {pmid40120581,
year = {2025},
author = {Scarampi, A and Lawrence, JM and Bombelli, P and Kosmützky, D and Zhang, JZ and Howe, CJ},
title = {Polyploid cyanobacterial genomes provide a reservoir of mutations, allowing rapid evolution of herbicide resistance.},
journal = {Current biology : CB},
volume = {35},
number = {7},
pages = {1549-1561.e3},
doi = {10.1016/j.cub.2025.02.044},
pmid = {40120581},
issn = {1879-0445},
mesh = {*Polyploidy ; *Mutation ; *Genome, Bacterial ; *Herbicide Resistance/genetics ; *Synechocystis/genetics/drug effects/physiology ; *Herbicides/pharmacology ; Evolution, Molecular ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Adaptive mechanisms in bacteria, which are widely assumed to be haploid or partially diploid, are thought to rely on the emergence of spontaneous mutations or lateral gene transfer from a reservoir of pre-existing variants within the surrounding environment. These variants then become fixed in the population upon exposure to selective pressures. Here, we show that multiple distinct wild-type (WT) substrains of the highly polyploid cyanobacterium Synechocystis sp. PCC 6803 can adapt rapidly to the potent herbicide methyl viologen (MV). Genome sequencing revealed that the mutations responsible for adaptation to MV were already present prior to selection in the genomes of the unadapted parental strains at low allelic frequencies. This indicates that chromosomal polyploidy in bacteria can provide cells with a reservoir of conditionally beneficial mutations that can become rapidly enriched and fixed upon selection. MV-resistant strains performed oxygenic photosynthesis less efficiently than WTs when MV was absent, suggesting trade-offs in cellular fitness associated with the evolution of MV resistance and a possible role for balancing selection in the maintenance of these alleles under ecologically relevant growth conditions. Resistance was associated with reduced intracellular accumulation of MV. Our results indicate that genome polyploidy plays a role in the rapid adaptation of some bacteria to stressful conditions, which may include xenobiotics, nutrient limitation, environmental stresses, and seasonal changes.},
}
@article {pmid40118394,
year = {2025},
author = {Cuecas, A and Delgado, JA and Gonzalez, JM},
title = {Inferring inter-phylum gene transfer events from unique genes detected in Parageobacillus thermoglucosidasius.},
journal = {Molecular phylogenetics and evolution},
volume = {207},
number = {},
pages = {108329},
doi = {10.1016/j.ympev.2025.108329},
pmid = {40118394},
issn = {1095-9513},
mesh = {*Gene Transfer, Horizontal ; *Phylogeny ; Genome, Bacterial ; Evolution, Molecular ; Genes, Bacterial ; },
abstract = {A pan-genome includes the complete pool of genes of a species including those recently acquired. The new additions of genetic material to a genome are frequently linked to horizontal gene transfer (HGT) processes and can confer adaptive advantages improving the recipient functional response and growth. Previous studies have reported that Parageobacillus have frequent DNA exchange mainly with other members of the phylum Bacillota sharing similar environments. Nevertheless, the occurrence of transfer events between phylogenetically distant microorganisms is scarcely known. In this work, based on the pan-genome of Parageobacillus thermoglucosidasius, we detected a number of unique genes within the species which were used to carry out BLAST searches to find out similar genes in distant bacteria taxa. We aimed to infer potential inter-phylum HGT events. Results suggested genetic exchanges among different phyla. Among them Actinomycetota, Pseudomonadota and the Bacteroidota/Chlorobiota group were the dominant observed phyla. Those HGT events frequently involved ATP binding cassette transporters, enzymes of the C metabolism and transcriptional regulators. Based on the frequency of these genes within specific phyla, directional HGT events could be proposed. A dominant origin of the suggested HGT events could be within the Bacillota. This exploratory analysis indicates that Bacillota are frequent exporters of DNA both within the phylum and to phylogenetically distant groups. Long-distance HGT can assist to better understand microbial evolution, the relevance of HGT processes within the prokaryotes and the genomic plasticity of microorganisms.},
}
@article {pmid40113085,
year = {2025},
author = {Ding, J and Zhang, M and Chang, J and Hu, Z and He, P and Wang, J and Feng, L},
title = {Characterization of a multidrug-resistant hypovirulent ST1859-KL35 klebsiella quasipneumoniae subsp. similipneumoniae strain co-harboring tmexCD2-toprJ2 and blaKPC-2.},
journal = {Journal of global antimicrobial resistance},
volume = {42},
number = {},
pages = {253-261},
doi = {10.1016/j.jgar.2025.03.009},
pmid = {40113085},
issn = {2213-7173},
abstract = {OBJECTIVES: The rise of multidrug-resistant (MDR) Klebsiella pneumoniae is a significant public health threat. Klebsiella quasipneumoniae is often misidentified as K. pneumoniae, and its genetic and virulence traits remain underexplored. This study characterizes the genomic and phenotypic features of a K. quasipneumoniae subsp. similipneumoniae strain (KP24).<br><br>METHODS: Antibiotic susceptibility was tested using microbroth dilution assay. Virulence was evaluated through serum killing assay and Galleria mellonella infection model. Whole genome sequencing (WGS) and bioinformatics analysis determined sequence typing, resistance profiles, and plasmid types. Conjugation assays assessed plasmid transferability, while phylogenetic analysis explored genetic relationships.<br><br>RESULTS: KP24 exhibited an MDR phenotype, including resistance to carbapenems, ceftazidime/avibactam, and tigecycline. KP24 showed significantly higher serum survival and G. mellonella lethality than ATCC700603, though it was less virulent than the hypervirulent strain NUTH-K2044. WGS identified KP24 as ST1859 and KL35, harboring the aerobactin virulence gene cluster (iucABCDiutA) and multiple resistance genes, including tmexCD2-toprJ2, blaKPC-2, blaOXA-10, blaIMP-4, and qnrS1. Notably, the tmexCD2-toprJ2 and blaKPC-2 genes were located on the same plasmid (pKP24-1), an uncommon co-existence. Conjugation assays confirmed the independent transferability of pKP24-1 to Escherichia coli J53. Phylogenetic analysis revealed that ST1859 forms a distinct monoclade with low genetic diversity, closely related to ST334, suggesting regional expansion and potential global dissemination.<br><br>CONCLUSIONS: KP24 represents a hypovirulent yet multidrug-resistant strain of K. quasipneumoniae subsp. similipneumoniae, with a concerning combination of virulence and resistance determinants. The co-location of tmexCD2-toprJ2 and blaKPC-2 on a transferable plasmid highlights the potential for horizontal gene transfer of critical resistance mechanisms.},
}
@article {pmid40111106,
year = {2025},
author = {Kogay, R and Wolf, YI and Koonin, EV},
title = {Horizontal Transfer of Bacterial Operons into Eukaryote Genomes.},
journal = {Genome biology and evolution},
volume = {17},
number = {4},
pages = {},
pmid = {40111106},
issn = {1759-6653},
mesh = {*Gene Transfer, Horizontal ; *Operon/genetics ; Phylogeny ; *Bacteria/genetics ; Evolution, Molecular ; *Eukaryota/genetics ; *Genome, Bacterial ; *Genome ; },
abstract = {In prokaryotes, functionally linked genes are typically clustered into operons, which are transcribed into a single mRNA, providing for the coregulation of the production of the respective proteins, whereas eukaryotes generally lack operons. We explored the possibility that some prokaryotic operons persist in eukaryotic genomes after horizontal gene transfer (HGT) from bacteria. Extensive comparative analysis of prokaryote and eukaryote genomes revealed 33 gene pairs originating from bacterial operons, mostly encoding enzymes of the same metabolic pathways, and represented in distinct clades of fungi or amoebozoa. This amount of HGT is about an order of magnitude less than that observed for the respective individual genes. These operon fragments appear to be relatively recent acquisitions as indicated by their narrow phylogenetic spread and low intron density. In 20 of the 33 horizontally acquired operonic gene pairs, the genes are fused in the respective group of eukaryotes so that the encoded proteins become domains of a multifunctional protein ensuring coregulation and correct stoichiometry. We hypothesize that bacterial operons acquired via HGT initially persist in eukaryotic genomes under a neutral evolution regime and subsequently are either disrupted by genome rearrangement or undergo gene fusion which is then maintained by selection.},
}
@article {pmid40111082,
year = {2025},
author = {Maeda, K and Sumita, T and Nishi, O and Sushida, H and Higashi, Y and Nakagawa, H and Suzuki, T and Iwao, E and Fanani, MZ and Nishiya, Y and Iida, Y},
title = {Adaptive evolution of sesquiterpene deoxyphomenone in mycoparasitism by Hansfordia pulvinata associated with horizontal gene transfer from Aspergillus species.},
journal = {mBio},
volume = {16},
number = {4},
pages = {e0400724},
pmid = {40111082},
issn = {2150-7511},
support = {17H05022, 20H02993, 24K08919//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; //G-7 Scholarship Foundation/ ; },
mesh = {*Gene Transfer, Horizontal ; *Aspergillus/genetics/metabolism ; Solanum lycopersicum/microbiology ; Multigene Family ; *Sesquiterpenes/metabolism ; Plant Diseases/microbiology ; Cladosporium/drug effects ; *Evolution, Molecular ; Antifungal Agents/metabolism/pharmacology ; Phylogeny ; },
abstract = {UNLABELLED: Leaf mold caused by the ascomycete fungus Cladosporium fulvum is a devastating disease of tomato plants. The mycoparasitic fungus Hansfordia pulvinata is an effective biocontrol agent that parasitizes C. fulvum hyphae on leaves and secretes 13-deoxyphomenone, an eremophilane-type sesquiterpene, which was also identified as a sporulation-inducing factor in Aspergillus oryzae. Here, we identified deoxyphomenone biosynthesis (DPH) gene clusters conserved in both H. pulvinata and Aspergillus section Flavi, including A. oryzae and A. flavus. Functional disruption of DPH1 orthologous genes encoding sesquiterpene cyclase in H. pulvinata, A. oryzae, and its close relative A. flavus revealed that deoxyphomenone in H. pulvinata had exogenic antifungal activity against C. fulvum and controlled endogenic sporulation in Aspergillus species. Complete DPH clusters, highly similar to those in H. pulvinata, were exclusive to Aspergillus section Flavi, while species in other Aspergillus sections contained fragmented DPH clusters. A comparative genomics analysis revealed that these DPH gene clusters share a common origin and are horizontally transferred from an ancestor of Aspergillus to H. pulvinata. Our results suggest that after horizontal transfer, H. pulvinata maintained the DPH cluster as the inhibitory effect of deoxyphomenone on spore germination and mycelial growth contributed to its mycoparasitism on the host fungus C. fulvum.<br><br>IMPORTANCE: Tomato leaf mold disease caused by C. fulvum poses a significant economic threat to tomato production globally. Breeders have developed tomato cultivars with Cf resistance genes. C. fulvum frequently evolves new races that overcome these genetic defenses, complicating control efforts. Additionally, the pathogen has developed resistance to chemical fungicides, prompting the need for sustainable alternatives like biocontrol agents. The mycoparasitic fungus H. pulvinata is crucial as an effective agent against C. fulvum. Clarifying the mechanism of mycoparasitism is significant, as it enhances its application as a biocontrol agent against plant pathogens. This study revealed how H. pulvinata produces deoxyphomenone, an antifungal compound, through horizontal gene transfer from Aspergillus species. It is hypothesized that mycoparasitism could be one of the mechanisms that facilitated horizontal gene transfer between fungi. These insights facilitate the development of eco-friendly, sustainable agricultural practices by reducing dependence on chemical fungicides and promoting natural pathogen control methods.},
}
@article {pmid40110960,
year = {2025},
author = {Xu, P and Liu, X and Ke, L and Li, K and Wang, W and Jiao, Y},
title = {The genomic insights of intertidal adaptation in Bryopsis corticulans.},
journal = {The New phytologist},
volume = {246},
number = {4},
pages = {1691-1709},
doi = {10.1111/nph.70083},
pmid = {40110960},
issn = {1469-8137},
support = {2021YFA0909600//the National Key R&amp;D Program of China/ ; 2021YFA1300403//the National Key R&amp;D Program of China/ ; JCTD-2022-06//CAS Youth Interdisciplinary Team/ ; 32221001//the National Natural Science Foundation of China/ ; 32222007//the National Natural Science Foundation of China/ ; YSBR-093//CAS project for Young Scientists in Basic Research/ ; },
mesh = {*Adaptation, Physiological/genetics ; *Genomics ; Phylogeny ; *Genome, Plant ; Gene Transfer, Horizontal/genetics ; },
abstract = {Many marine green algae thrive in intertidal zones, adapting to complex light environments that fluctuate between low underwater light and intense sunlight. Exploring their genomic bases could help to comprehend the diversity of adaptation strategies in response to environmental pressures. Here, we developed a novel and practical strategy to assemble high-confidence algal genomes and sequenced a high-quality genome of Bryopsis corticulans, an intertidal zone macroalga in the Bryopsidales order of Chlorophyta that originated 678 million years ago. Comparative genomic analyses revealed a previously overlooked whole genome duplication event in a closely related species, Caulerpa lentillifera. A total of 100 genes were acquired through horizontal gene transfer, including a homolog of the cryptochrome photoreceptor CRY gene. We also found that all four species studied in Bryopsidales lack key photoprotective genes (LHCSR, PsbS, CYP97A3, and VDE) involved in the xanthophyll cycle and energy-dependent quenching processes. We elucidated that the expansion of light-harvesting antenna genes and the biosynthesis pathways for siphonein and siphonaxanthin in B. corticulans likely contribute to its adaptation to intertidal light conditions. Our study unraveled the underlying special genetic basis of Bryopsis' adaptation to intertidal environments, advancing our understanding of plant adaptive evolution.},
}
@article {pmid40108678,
year = {2025},
author = {Debroas, D},
title = {Global analysis of the metaplasmidome: ecological drivers and spread of antibiotic resistance genes across ecosystems.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {77},
pmid = {40108678},
issn = {2049-2618},
mesh = {*Plasmids/genetics ; *Ecosystem ; *Bacteria/genetics/drug effects/classification ; Humans ; *Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences/genetics ; Genes, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/genetics/drug effects ; },
abstract = {BACKGROUND: Plasmids act as vehicles for the rapid spread of antibiotic resistance genes (ARGs). However, few studies of the resistome at the community level distinguish between ARGs carried by mobile genetic elements and those carried by chromosomes, and these studies have been limited to a few ecosystems. This is the first study to focus on ARGs carried by the metaplasmidome on a global scale.<br><br>RESULTS: This study shows that only a small fraction of the plasmids reconstructed from 27 ecosystems representing 9 biomes are catalogued in public databases. The abundance of ARGs harboured by the metaplasmidome was significantly explained by bacterial richness. Few plasmids with or without ARGs were shared between ecosystems or biomes, suggesting that plasmid distribution on a global scale is mainly driven by ecology rather than geography. The network linking plasmids to their hosts shows that these mobile elements have thus been shared between bacteria across geographically distant environmental niches. However, certain plasmids carrying ARGs involved in human health were identified as being shared between multiple ecosystems and hosted by a wide variety of hosts. Some of these mobile elements, identified as keystone plasmids, were characterised by an enrichment in antibiotic resistance genes (ARGs) and CAS-CRISPR components which may explain their ecological success. The ARGs accounted for 9.2% of the recent horizontal transfers between bacteria and plasmids.<br><br>CONCLUSIONS: By comprehensively analysing the plasmidome content of ecosystems, some key habitats have emerged as particularly important for monitoring the spread of ARGs in relation to human health. Of particular note is the potential for air to act as a vector for long-distance transport of ARGs and accessory genes across ecosystems and continents. Video Abstract.},
}
@article {pmid40104036,
year = {2025},
author = {Yang, SM and Gruber, A and Jiroutová, K and Richtová, J and Vancová, M and Tesařová, M and Masařová, P and Dorrell, RG and Oborník, M},
title = {Localization of heme biosynthesis in the diatom Phaeodactylum tricornutum and differential expression of multi-copy enzymes.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1537037},
pmid = {40104036},
issn = {1664-462X},
abstract = {Heme is essential for all organisms. The composition and location of the pathway for heme biosynthesis, have been influenced by past endosymbiotic events and organelle evolution in eukaryotes. Endosymbioses led to temporary redundancy of the enzymes and the genes involved. Genes were transferred to the nucleus from different endosymbiotic partners, and their multiple copies were either lost or retained, resulting in a mosaic pathway. This mosaic is particularly complex in organisms with eukaryote-derived plastids, such as diatoms. The plastids of diatoms are clearly derived from red algae. However, it is not entirely clear whether they were acquired directly from a red algal ancestor or indirectly in higher-order endosymbioses. In the diatom Phaeodactylum tricornutum, most enzymes of the pathway are present in a single copy, but three, glutamyl-tRNA synthetase (GluRS), uroporphyrinogen decarboxylase (UROD) and coproporphyrinogen oxidase (CPOX), are encoded in multiple copies. These are not direct paralogs resulting from gene duplication within the lineage but were acquired horizontally during the plastid endosymbioses. While some iso-enzymes originate from the host cell, others originate either from the genome of the cyanobacterial ancestor of all plastids or from the nuclear genome of the eukaryotic ancestor of the diatom complex plastid, a rhodophyte or an alga containing rhodophyte-derived plastids, a situation known as pseudoparalogy. Using green fluorescent protein-tagged expression and immunogold labeling, we experimentally localized all enzymes of the pathway in P. tricornutum, and confirmed their localization in the plastid, with a few possible exceptions. Our meta-analyses of transcription data showed that the pseudoparalogs are differentially expressed in response to nitrate starvation, blue light, high light, high CO2, and the cell cycle. Taken together, our findings emphasize that the evolution of complex plastids via endosymbiosis has a direct impact not only on the genetics but also on the physiology of resulting organisms.},
}
@article {pmid40102781,
year = {2025},
author = {Yang, H and Gan, Y and Jiang, S and Zhu, X and Xia, Y and Gong, D and Xie, X and Gong, Y and Zhang, Y and Lei, Q and Wang, M and Li, J},
title = {Genomic alterations in Bacteroides fragilis favor adaptation in colorectal cancer microenvironment.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {269},
pmid = {40102781},
issn = {1471-2164},
support = {Guizhou Education Technology [2024] No. 335//Natural Science Research Project of Guizhou Education Department in 2024/ ; (Zunyi City, Kehe HZ character (2024) No. 303)//Zunyi city Science and Technology Program project/ ; Guizhou Science and Technology Platform Talents [2021]1350-038//Zunyi Medical University 2021 Special Project for Academic New Seedling Cultivation and Innovative Exploration/ ; No. gzwjkj2019-1-123//Science and Technology Fund Project of Guizhou Health Care Commission/ ; No. [2011]57//Governor's Special Fund for Outstanding Scientific and Technological Education Talents in Guizhou Province/ ; QJJ [2023] 019//Scientific Research Program of Guizhou Provincial Department of Education/ ; },
mesh = {*Bacteroides fragilis/genetics/pathogenicity/isolation &amp; purification ; Humans ; *Colorectal Neoplasms/microbiology/genetics/pathology ; *Tumor Microenvironment ; Genome, Bacterial ; Adaptation, Physiological/genetics ; Phylogeny ; Genomics ; Whole Genome Sequencing ; Virulence/genetics ; Enterotoxins/genetics/metabolism ; },
abstract = {BACKGROUND: The occurrence and development of colorectal cancer (CRC) is an incredibly long process that involves continuous changes in the tumor microenvironment. These constant changes may ultimately result in genetic alterations and changes in the metabolic processes of some symbiotic bacteria as a way to adapt to the changing environment. Patients with CRC exhibit an altered abundance of Bacteroides fragilis (B. fragilis) as indicated by several studies. To better understand the genomic characteristics and virulence spectrum of B. fragilis strains in tumor tissues, B. fragilis strains were isolated from tumor and paracancerous tissues of CRC patients.<br><br>METHODS: The isolates were identified using 16&#xa0;S rRNA sequencing, morphological analysis, physiological and biochemical characterization and PCR, and they were then subjected to whole genome sequencing (WGS) analysis.<br><br>RESULTS: A strain of B. fragilis enterotoxin (BFT) bft1-producing ZY0302 and a non-enterotoxin-producing B. fragilis ZY0804 were isolated from cancerous and paraneoplastic tissues, respectively. Analysis based on the core and nonessential genes showed that the genomic profiles of the isolates, ZY0302 and ZY0804, differed from those of B. fragilis from other tissue sources. This core and the co-evolution of non-essential genes may be the result of their adaptation to fluctuations in the tumor microenvironment and enhancing their survival. In addition, the ZY0302 and ZY0804 genomes underwent extensive horizontal gene transfer and varying degrees of genomic rearrangements, inversions, insertions, and deletion events, which may favor the enhancement of bacteria's ability to adapt to environmental changes. For instance, the virulence factors, such as the capsular biosynthesis gene clusters and components of the type IV secretion system, acquired through horizontal gene transfer, may facilitated B. fragilis in evading immune responses and managing oxidative stress. Moreover, our analysis revealed that multiple virulence factors identified in the isolates were mainly involved in bacterial adhesion and colonization, oxidative stress, iron acquisition, and immune evasion. This observation is worth noting given that enzymes such as neuraminidase, lipase, hemolysin, protease, and phosphatase, along with genes responsible for LPS biosynthesis, which are recognized for their association with the virulence of B. fragilis, were prevalent among the isolates.<br><br>CONCLUSIONS: In summary, it is our assertion that the alterations observed in both core and nonessential genes of B. fragilis, which have been isolated from tissues of colorectal cancer patients, along with significant instances of horizontal gene transfer to the genome, are likely intended to enhance adaptation to the evolving conditions of the tumor microenvironment. This study may provide new insights into the interaction between B. fragilis and the CRC microenvironment.},
}
@article {pmid40100768,
year = {2025},
author = {Chen, YW and Su, YC and Chen, WY and Wu, JH and Chen, JW and Su, SL and Chen, CS and Tsai, PF and Ko, WC and Chen, PL},
title = {Comprehensive Genomic Analysis of Antimicrobial Resistance in Aeromonas dhakensis.},
journal = {Microbial drug resistance (Larchmont, N.Y.)},
volume = {31},
number = {4},
pages = {97-106},
doi = {10.1089/mdr.2024.0212},
pmid = {40100768},
issn = {1931-8448},
mesh = {*Aeromonas/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; beta-Lactamases/genetics ; Microbial Sensitivity Tests/methods ; Humans ; Phylogeny ; Multilocus Sequence Typing ; Genome, Bacterial/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; Taiwan ; Gram-Negative Bacterial Infections/microbiology/drug therapy ; Genomics/methods ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Aeromonas dhakensis is prevalent in aquatic environments in Taiwan and known for its notable antimicrobial resistance. However, comprehensive pan-genomic studies for this species in Taiwan are limited. This study analyzed 28 clinical A. dhakensis isolates using single-molecule real-time sequencing technology, coupled with diverse databases, to elucidate the whole genomes. The focus was on phylogenetic relatedness, antimicrobial resistance genes, and mobile genetic elements. Genomic analysis and multilocus sequence typing were utilized to identify A. dhakensis strains of heterogeneous origins. The detection of various β-lactamase genes (blacphA, blaimiH, blaAQU, blaOXA, blaTEM-1, blaTRU-1, and blaVEB) in clinical A. dhakensis isolates raises concern, especially considering the use of carbapenems and third-generation cephalosporins in patients with severe infections. Notably, most A. dhakensis strains carry chromosome-encoded β-lactamases, including AmpC, metallo-β-lactamase, and oxacillinase, and were susceptible to cefepime in drug susceptibility tests. A. dhakensis strains were also susceptible to aminoglycosides, fluoroquinolones, tigecycline, and trimethoprim/sulfamethoxazole. Three of the 28 A. dhakensis isolates carried plasmids containing an array of drug resistance genes, suggesting this species is likely a recipient or donor of drug resistance genes through horizontal gene transfer. Our findings provide valuable insights into the antimicrobial resistance of A. dhakensis, highlighting the medical implications of its β-lactamase diversity and its potential role in the horizontal gene transfer of drug resistance genes.},
}
@article {pmid40098486,
year = {2025},
author = {Coluzzi, C and Rocha, EPC},
title = {The Spread of Antibiotic Resistance Is Driven by Plasmids Among the Fastest Evolving and of Broadest Host Range.},
journal = {Molecular biology and evolution},
volume = {42},
number = {3},
pages = {},
pmid = {40098486},
issn = {1537-1719},
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Host Specificity ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects ; Evolution, Molecular ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; },
abstract = {Microorganisms endure novel challenges for which other microorganisms in other biomes may have already evolved solutions. This is the case of nosocomial bacteria under antibiotic therapy because antibiotics are of ancient natural origin and resistances to them have previously emerged in environmental bacteria. In such cases, the rate of adaptation crucially depends on the acquisition of genes by horizontal transfer of plasmids from distantly related bacteria in different biomes. We hypothesized that such processes should be driven by plasmids among the most mobile and evolvable. We confirmed these predictions by showing that plasmid species encoding antibiotic resistance are very mobile, have broad host ranges, while showing higher rates of homologous recombination and faster turnover of gene repertoires than the other plasmids. These characteristics remain outstanding when we remove resistance plasmids from our dataset, suggesting that antibiotic resistance genes are preferentially acquired and carried by plasmid species that are intrinsically very mobile and plastic. Evolvability and mobility facilitate the transfer of antibiotic resistance, and presumably of other phenotypes, across distant taxonomic groups and biomes. Hence, plasmid species, and possibly those of other mobile genetic elements, have differentiated and predictable roles in the spread of novel traits.},
}
@article {pmid40094923,
year = {2025},
author = {Cinthi, M and Coccitto, SN and Simoni, S and Gherardi, G and Palamara, AT and Di Lodovico, S and Di Giulio, M and Du, XD and Vignaroli, C and Brenciani, A and Giovanetti, E},
title = {The optrA, cfr(D) and vanA genes are co-located on linear plasmids in linezolid- and vancomycin-resistant enterococcal clinical isolates in Italy.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {80},
number = {5},
pages = {1362-1370},
doi = {10.1093/jac/dkaf082},
pmid = {40094923},
issn = {1460-2091},
mesh = {*Plasmids/genetics ; *Linezolid/pharmacology ; Humans ; *Enterococcus faecium/genetics/drug effects/isolation &amp; purification ; *Enterococcus faecalis/genetics/drug effects/isolation &amp; purification ; *Gram-Positive Bacterial Infections/microbiology ; Anti-Bacterial Agents/pharmacology ; *Vancomycin-Resistant Enterococci/genetics/drug effects/isolation &amp; purification ; Microbial Sensitivity Tests ; *Drug Resistance, Multiple, Bacterial/genetics ; Italy ; *Bacterial Proteins/genetics ; *Carbon-Oxygen Ligases/genetics ; Genes, Bacterial ; Gene Transfer, Horizontal ; },
abstract = {OBJECTIVES: To characterize the optrA-, cfr(D)- and vanA-carrying linear plasmids detected in three MDR enterococcal clinical isolates.<br><br>METHODS: Enterococcus faecium (868), E. faecium (1001) and Enterococcus faecalis (2048), which were linezolid- and vancomycin-resistant due to the presence of optrA, cfr(D) and vanA genes, were tested for their susceptibility to several antibiotics. Characterization of the genetic elements carrying antibiotic resistance genes and ST determination were achieved using WGS data. The plasmid topology was evaluated by S1-PFGE. Resistance gene transferability was assessed by filter-mating experiments.<br><br>RESULTS: The linezolid- and vancomycin-resistant enterococci also showed resistance to tedizolid, chloramphenicol, tetracycline, erythromycin, ampicillin and levofloxacin. Both E. faecium 868 and E. faecium 1001 belonged to ST80 (included in clade A1), whereas E. faecalis 2048 was associated with ST6. WGS analysis revealed a plasmid co-localization of the optrA, cfr(D) and vanA genes. optrA was carried by Tn6674-like or Tn7695-like transposons; cfr(D) was associated with a truncated guaA gene, both flanked by IS1216 with opposite polarity; vanA was found on a Tn1546-like transposon containing IS1542 and IS1251 transposases. PFGE of S1 nuclease-treated and untreated DNAs displayed the linear topology of optrA-, cfr(D)- and vanA-harbouring plasmids. Only E. faecium 868 was able to transfer linezolid and vancomycin genes to an enterococcal recipient.<br><br>CONCLUSIONS: To the best of our knowledge this is the first report on the occurrence of a linear plasmid in E. faecalis. Linear plasmids can play a key role in the spread of oxazolidinone and glycopeptide resistance with serious consequences for public health.},
}
@article {pmid40093628,
year = {2025},
author = {Oh, H and Choi, Y and Lee, J},
title = {Antibiotic-Resistant Salmonella in Animal Products Jeopardize Human Health.},
journal = {Food science of animal resources},
volume = {45},
number = {2},
pages = {409-428},
pmid = {40093628},
issn = {2636-0780},
abstract = {Despite the significance of antibiotics in treating bacterial infections, antibiotic resistance is continuously increasing, thus posing a significant threat. In addition to strains resistant to individual drugs, multidrug-resistant (MDR) and pandrug-resistant strains, are emerging. Salmonella, a primary cause of global foodborne illness, is often transmitted through animal products. Antibiotic treatment is crucial for immunocompromised individuals, such as older adults and patients with weakened immune systems, due to their increased susceptibility to severe effects. MDR Salmonella, which can arise following antibiotic use in food animals, may transfer to humans, leading to significant health challenges. The emergence of Salmonella strains resistant to carbapenems, often considered a last-resort antibiotic class, is particularly concerning. Salmonella neutralizes antibiotics through mechanisms, such as horizontal gene transfer via plasmids, efflux/influx system regulation, and enzyme production that deactivate or alter antibiotics. The rise of megaplasmids in Salmonella is particularly alarming, as it may enable resistance to a broader range of antibiotics. This review summarizes the current state of the growing threat of MDR Salmonella and underscores the urgent need for a coordinated response.},
}
@article {pmid40092036,
year = {2025},
author = {Balta, I and Lemon, J and Gadaj, A and Cretescu, I and Stef, D and Pet, I and Stef, L and McCleery, D and Douglas, A and Corcionivoschi, N},
title = {The interplay between antimicrobial resistance, heavy metal pollution, and the role of microplastics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1550587},
pmid = {40092036},
issn = {1664-302X},
abstract = {Environmental pollution with heavy metals (HMs) and microplastics (MPs) could enhance the global health challenge antimicrobial resistance (AMR). Herein, we explore the complicated mechanics of how HMs, MPs, and AMR are interlinked within microbial ecosystems, as well as the co-selection and cross-resistance mechanisms. Unlike antibiotics, HMs have influenced microbial evolution for billions of years, promoting resistance mechanisms that predate antibiotic resistance genes (ARGs). At the same time, this conundrum is further complicated by the pervasive spread of MPs in the aquatic and terrestrial environments, acting as substrates for bacterial pathogenic biofilms and accelerates the horizontal gene transfer (HGT) of ARGs and heavy metal resistance genes (MRGs). This review highlights that HMs such as lead (Pb), mercury (Hg), arsenic (As), chromium (Cr), cadmium (Cd), and nickel (Ni) have persistently selected for resistance traits through efflux systems and genetic co-regulation. Together, these interactions are amplified by MPs that create genetic exchange hotspots due to biofilm formation. These dynamics are modulated by organic matter, which serves both as a nutrient source and a mediator of HM bioavailability, directly influencing ARG abundance. Soil and water ecosystems, including riverine systems and landfill leachate, are reservoirs for ARGs and ARG-MRG combinations, with notable contributions originating from anthropogenic activities. This review also emphasizes the urgent need for integrated environmental and public health strategies to mitigate pollutant-driven AMR. This work seeks to approach HMs and MPs as synergistic drivers of AMR such that both HMs and MPs are upstream (causes) levers, a foundation from which future research on sustainable environmental management practices and health policy (One Health Approach), aimed at curbing the spread of resistance determinants can proceed.},
}
@article {pmid40090954,
year = {2025},
author = {Lund, D and Parras-Moltó, M and Inda-Díaz, JS and Ebmeyer, S and Larsson, DGJ and Johnning, A and Kristiansson, E},
title = {Genetic compatibility and ecological connectivity drive the dissemination of antibiotic resistance genes.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2595},
pmid = {40090954},
issn = {2041-1723},
support = {2018-02835//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2018-05771//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2019-03482//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2022-00945//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; },
mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Humans ; *Phylogeny ; Wastewater/microbiology ; Genome, Bacterial ; Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Microbiota/genetics/drug effects ; Genes, Bacterial ; Metagenome ; Drug Resistance, Bacterial/genetics ; },
abstract = {The dissemination of mobile antibiotic resistance genes (ARGs) via horizontal gene transfer is a significant threat to public health globally. The flow of ARGs into and between pathogens, however, remains poorly understood, limiting our ability to develop strategies for managing the antibiotic resistance crisis. Therefore, we aim to identify genetic and ecological factors that are fundamental for successful horizontal ARG transfer. We used a phylogenetic method to identify instances of horizontal ARG transfer in ~1 million bacterial genomes. This data was then integrated with >20,000 metagenomes representing animal, human, soil, water, and wastewater microbiomes to develop random forest models that can reliably predict horizontal ARG transfer between bacteria. Our results suggest that genetic incompatibility, measured as nucleotide composition dissimilarity, negatively influences the likelihood of transfer of ARGs between evolutionarily divergent bacteria. Conversely, environmental co-occurrence increases the likelihood, especially in humans and wastewater, in which several environment-specific dissemination patterns are observed. This study provides data-driven ways to predict the spread of ARGs and provides insights into the mechanisms governing this evolutionary process.},
}
@article {pmid40090302,
year = {2025},
author = {Wang, J and Hu, Y and An, L and Wang, J and Wu, F and Gu, J and Wang, X and Tiedje, JM},
title = {An efficient strategy for bdd electrode drive electro-catalysis triggering active species on lincomycin and antibiotic resistance genes removal: Electron transfer based on calculation modeling.},
journal = {Journal of hazardous materials},
volume = {491},
number = {},
pages = {137915},
doi = {10.1016/j.jhazmat.2025.137915},
pmid = {40090302},
issn = {1873-3336},
abstract = {Identifying the degradation pathway and the final by-products is essential, as their ecological risks are pertinent to the advancement of this technology and its potential application in practical environmental pollution treatment. Elucidating the reaction mechanisms of the degradation system represents the most effective strategy for controlling this process. This study thoroughly revealed that indirect oxidation predominates throughout the electrochemical system, while direct oxidation serves a significant auxiliary role under the synergistic influence. It elucidates the critical importance of electron transfer behavior at the electrode surface for pollutant degradation and unveil potential mechanisms underlying primary degradation reactions via integrating charge density differences and Bader atomic charge analysis. In situ electrochemical infrared spectroscopy (In situ EC-FTIR) and density functional calculation (DFT) were used to analyze the final by-product generation path. It further elucidated the correlation between antibiotic resistance gene (ARGs) and binding strength among base pairs. The oxidative stress process of antibiotic resistance bacteria (ARB) was explained in detail. To comprehensively assess the impact of electrochemical treatment on environmental microbial communities, combined horizontal gene transfer (HGT) experiments were conducted to confirm that electrolytically treated wastewater does not induce ecological stress effects on microorganisms. Finally, a small cyclic electrochemical system was employed to evaluate both ecological impacts and economic benefits associated with wastewater treatment, thereby providing a novel theoretical framework for this domain.},
}
@article {pmid40086311,
year = {2025},
author = {Pereira, AP and Almeida-Santos, AC and Duarte, B and Antunes, P and Peixe, L and Freitas, AR and Novais, C},
title = {Insights towards the impact of subinhibitory chlorhexidine on antimicrobial susceptibility and horizontal gene transfer in Enterococcus faecium.},
journal = {The Science of the total environment},
volume = {972},
number = {},
pages = {179064},
doi = {10.1016/j.scitotenv.2025.179064},
pmid = {40086311},
issn = {1879-1026},
mesh = {*Enterococcus faecium/genetics/drug effects ; *Gene Transfer, Horizontal ; *Chlorhexidine/pharmacology ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; },
abstract = {Enterococcus faecium, a human and animal commensal broadly distributed in the environment, is currently one of the most challenging multidrug-resistant (MDR) healthcare-associated pathogens worldwide. It is often exposed to chlorhexidine (CHX), a broad-spectrum antiseptic, extensively used in healthcare, domestic, and food production settings, and a diffused polluter. However, the impact of gradients of CHX concentrations, including at subinhibitory levels, on E. faecium adaptation to various antimicrobials remains unclear. Our study aimed to explore the effects of subinhibitory CHX concentrations on biocides and antibiotics susceptibility as well as in the transfer of clinically relevant antibiotic resistance genes among E. faecium (n = 11) from diverse sources and clonal backgrounds. Serial exposure to increasing CHX concentrations resulted in strain-specific MICCHX and MBCCHX changes among six E. faecium studied. These strains presented different CHX genotypes, namely the P102H mutation in DNA-binding response regulator ChtR in two strains showing twofold increased MICCHX and/or MBCCHX, and an absent EfrEF transporter in a strain exhibiting increased CHX susceptibility after exposure. Whole-genome comparison between parental and CHX-adapted strains found no alterations in genes with a recognized role in CHX reduced susceptibility. Additionally, in a different assay, subinhibitory CHX exposure enhanced the transfer (up to 12.5-fold) of vancomycin or linezolid resistance genes among most E. faecium strains tested, except one lacking a functional EfrEF transporter. Our data suggest that subinhibitory CHX concentrations could have a role in Enterococcus adaptation to CHX and in the spread of antibiotic resistance through horizontal transfer events. Further investigation is warranted to elucidate the underlying mechanisms driving these phenomena in E. faecium, ensuring the continued effectiveness of both CHX and antibiotics, and safeguarding Public Health.},
}
@article {pmid40083414,
year = {2025},
author = {Shi, G and Dai, Y and Zhou, D and Chen, M and Zhang, J and Bi, Y and Liu, S and Wu, Q},
title = {An alignment- and reference-free strategy using k-mer present pattern for population genomic analyses.},
journal = {Mycology},
volume = {16},
number = {1},
pages = {309-323},
pmid = {40083414},
issn = {2150-1203},
abstract = {Pangenomes are replacing single reference genomes to capture all variants within a species or clade, but their analysis predominantly leverages graph-based methods that require multiple high-quality genomes and computationally intensive multiple-genome alignments. K-mer decomposition is an alternative to graph-based pangenomes. However, how to directly use k-mers for the population genetic analyses is unknown. Here, we developed a novel strategy that uses the variants of k-mer count in the genome for population analyses. To test the effectivity of this method, we compared it directly to the SNP-based method on the analysis of population structure and genetic diversity of 267 Saccharomyces cerevisiae strains within two simulated datasets and a real sequence dataset. The population structure identified with k-mers recapitulates that obtained using SNPs, indicating the effectiveness of k-mer-based approach, and higher genetic diversity within real dataset supported k-mers contained more genetic variants. Based on k-mer frequency, we found not only SNP but also some insertion/deletion and horizontal gene transfer (HGT) fragments related to the adaptive evolution of S. cerevisiae. Our study creates a framework for the alignment- and reference-free (ARF) method in population genetic analyses, which will be more pronounced in the species with no complete genome or highly diverged species.},
}
@article {pmid40081886,
year = {2025},
author = {Muleshkova, T and Bazukyan, I and Papadimitriou, K and Gotcheva, V and Angelov, A and Dimov, SG},
title = {Exploring the Multifaceted Genus Acinetobacter: the Facts, the Concerns and the Oppoptunities the Dualistic Geuns Acinetobacter.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2411043},
pmid = {40081886},
issn = {1738-8872},
mesh = {*Acinetobacter/genetics/classification/isolation &amp; purification ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genetic Variation ; Phylogeny ; Humans ; Biodegradation, Environmental ; Acinetobacter Infections/microbiology ; },
abstract = {In recent years, the research community has been interested in members of the Acinetobacter genus mainly because of their role as causative agents of nosocomial infections. However, this rich-in-species genus has been proven to play a significant role in several biotechnological processes, such as bioremediation and fermented foods production. To partially fill the lack of information on Acinetobacter's dualistic nature, in this review, based on literature data, we attempt to summarize the available information on the different roles the members of the genus play by considering their genetic constitution and metabolic properties. We analyzed reports of genetic divergence between the pathogenic and non-pathogenic species and isolates, which can be explained by their high adaptability to the different ecological niches. In turn, this adaptability could result from intrinsic genetic variability due to mechanisms of horizontal genetic transfer, as well as high mutability determined by the expression of error-prone DNA polymerases. Yet, we concluded that further studies are needed, especially whole-genome sequencing of non-pathogenic isolates, which for the moment are relatively scarce.},
}
@article {pmid40081035,
year = {2025},
author = {Qv, M and Dai, D and Wu, Q and Wang, W and Li, L and Zhu, L},
title = {Metagenomic insight into the horizontal transfer mechanism of fluoroquinolone antibiotic resistance genes mediated by mobile genetic element in microalgae-bacteria consortia.},
journal = {Journal of environmental management},
volume = {380},
number = {},
pages = {124946},
doi = {10.1016/j.jenvman.2025.124946},
pmid = {40081035},
issn = {1095-8630},
mesh = {*Microalgae/genetics ; *Gene Transfer, Horizontal ; *Fluoroquinolones ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; },
abstract = {Antibiotics could accumulate in the environment with the discharge of wastewater from families, hospitals and livestock farms, which intensifies the spread of resistance genes around the world. Although microalgae-bacteria consortia (MBC) can efficiently remove antibiotics, the horizontal transfer mechanism of antibiotics resistance genes in MBC is still rarely reported. In this study, the removal efficiency of ofloxacin, norfloxacin and enrofloxacin by MBC under different antibiotic concentrations was investigated, while resistance genes in the MBC were identified and the mechanism of horizontal transfer was disclosed. The results showed that norfloxacin removal efficiency (up to 56.35 %) surpassed that of ofloxacin and enrofloxacin. The abundance of the fluoroquinolone resistance gene QnrS8 was the highest at 1331. The horizontal transfer of resistance gene QnrS8 and QnrS11 were mainly mediated by transposons. Fluoroquinolones increased the abundance of Brevundimonas (<0.10 % up to 9.63 %) and Bosea (0.96 % up to 17.67 %) involved in antibiotic removal. Arthrobacter and Acidovorax might be potential hosts which carried fluoroquinolone resistance genes. Structural equation model indicated that the key factor influencing the fluoroquinolone resistance genes abundance in MBC was transposons. These findings drew an insightful understanding of MBC application for fluoroquinolone antibiotics removal and the horizontal transfer mechanism of fluoroquinolone resistance genes.},
}
@article {pmid40079731,
year = {2025},
author = {Elmarghani, ED and Pettersson, JH and Atterby, C and Hickman, RA and Seng, S and San, S and Osbjer, K and Magnusson, U and Mourkas, E and Järhult, JD},
title = {Genomic insights into extended-spectrum β-lactamase- and plasmid-borne AmpC-producing Escherichia coli transmission between humans and livestock in rural Cambodia.},
journal = {Journal of medical microbiology},
volume = {74},
number = {3},
pages = {},
pmid = {40079731},
issn = {1473-5644},
mesh = {Humans ; Cambodia/epidemiology ; *beta-Lactamases/genetics ; Animals ; *Escherichia coli/genetics/isolation &amp; purification/drug effects/classification/enzymology ; *Escherichia coli Infections/transmission/epidemiology/microbiology/veterinary ; *Plasmids/genetics ; *Livestock/microbiology ; *Phylogeny ; *Bacterial Proteins/genetics ; *Rural Population ; Male ; Female ; Adult ; Middle Aged ; Whole Genome Sequencing ; Feces/microbiology ; Multilocus Sequence Typing ; Young Adult ; Anti-Bacterial Agents/pharmacology ; Child ; Adolescent ; },
abstract = {Introduction. The global spread of extended-spectrum cephalosporinase-producing Escherichia coli (producing extended-spectrum β-lactamase or plasmid-borne AmpC, hereafter ESC-Ec) is a major public health concern. Whilst extensively studied in high-income countries, the transmission pathways between humans and animals in low- and middle-income countries (LMICs) remain unclear. In rural Cambodia, the asymptomatic carriage and transmission dynamics of ESC-Ec between humans and animals living in close proximity are poorly understood, highlighting the need for targeted research in this area.Gap statement. An enhanced understanding of the genetic epidemiology of ESC-Ec can enable mitigation strategies to reduce the burden of disease and drug-resistant infections in LMIC settings.Aim. This study aimed to investigate the genetic relatedness and genotypic antibiotic resistance profiles of ESC-Ec strains from humans and livestock in rural Cambodia and to identify patterns of antimicrobial resistance (AMR) gene transmission between hosts and across households and villages.Methodology. Faecal samples were collected from 307 humans and 285 livestock in 100 households in or near Kampong Cham Province in rural Cambodia. From these samples, 108 ESC-Ec strains were subjected to whole-genome sequencing. Core genome MLST (cgMLST) and phylogenetic analysis determined genetic relationships between strains. All strains were screened for the presence of antibiotic resistance genes and plasmids.Results. Human and livestock isolates were assigned to six phylogroups, with phylogroup A being the most common (56.5%). MLST identified 50 sequence types (STs), 17 of which were shared between humans and animals, with ST155 being the most prevalent. cgMLST revealed 97 distinct cgMLST sequence types (cgST), indicating strain sharing between humans and animals. Additionally, AMR gene analysis showed widespread resistance, with genes from the bla CTX-M group detected in 84.2% of isolates. Notably, AMR genes such as aph(3'')-Ib-sul2 co-occurred in 50% of isolates. Finally, plasmid analysis identified IncF plasmids in 75.9% of isolates, likely facilitating AMR gene transmission across hosts.Conclusions. Our findings demonstrate that ESC-Ec strains and their AMR genes are transmitted between humans and livestock in rural Cambodia, likely driven by both clonal spread and plasmid-mediated horizontal gene transfer. These results highlight the urgent need for antimicrobial stewardship and infection control strategies to mitigate the spread of multidrug-resistant pathogens in both human and animal populations.},
}
@article {pmid40078948,
year = {2024},
author = {Zhou, Z and Chen, H},
title = {Evaluating human exposure to antibiotic resistance genes.},
journal = {Biosafety and health},
volume = {6},
number = {2},
pages = {98-100},
pmid = {40078948},
issn = {2590-0536},
abstract = {Antibiotic resistance is an escalating global concern, leading to millions of annual fatalities. Antibiotic resistance genes (ARGs) present in bacteria equip them to withstand the effects of antibiotics. Intra- and interspecific ARGs transmission through horizontal gene transfer further exacerbates resistance dissemination. The presence of ARGs in the environment heightens the probability of human exposure via direct inhalation, ingestion, or contact with polluted air, food, or water, posing substantial biosafety and health hazards. Consequently, ARGs represent a critical focal point in public health and environmental safety and are classified as emerging contaminants. This perspective underscores the necessity to assess ARG exposure within the One Health framework and to accord greater attention to the mitigation strategies and tactics associated with ARGs.},
}
@article {pmid40078945,
year = {2024},
author = {Zhai, W and Wang, Y and Sun, H and Fu, B and Zhang, Q and Wu, C and Shen, J and Liu, D and Wang, Y},
title = {Epidemiology and genetic characterization of tet(X4)-positive Klebsiella pneumoniae and Klebsiella quasipneumoniae isolated from raw meat in Chengdu City, China.},
journal = {Biosafety and health},
volume = {6},
number = {2},
pages = {116-124},
pmid = {40078945},
issn = {2590-0536},
abstract = {The rapid spread of mobile tigecycline resistance presents a significant public health threat, particularly with the increasing prevalence of tet(X4)-positive Enterobacterales across various species. This study aimed to investigate the epidemic features and transmission dynamics of tet(X4)-positive Klebsiella pneumoniae (K. pneumoniae) through the analysis of 206 raw meats, including pork (n = 182), beef (n = 16), duck (n = 5), and chicken (n = 3). These samples were collected from schools, markets, and restaurants in Chengdu City, China. A total of 25 isolates were obtained from 13 administrative regions. All isolates exhibited resistance to tetracycline, tigecycline, ampicillin, chloramphenicol, and florfenicol. Over half of the isolates also demonstrated resistance to streptomycin (80 %), sulfamethoxazole/trimethoprim (72 %), ciprofloxacin (64 %), and ampicillin/sulbactam (56 %). Among these strains, 14 distinct sequence types (STs) were identified, revealing evidence of inter-regional clonal spread, notably among 9 K. pneumoniae ST3393. Phylogenetic analysis revealed the presence of two K. pneumoniae ST5 closely resembling hypervirulent K. pneumoniae from Jiangsu. Importantly, 12 isolates were capable of transferring tigecycline resistance to Escherichia coli J53. Further plasmid analysis showed that the tet(X4)-harboring plasmids in K. pneumoniae could be classified into four types, primarily belonging to the IncFIA(HI1)/HI1A/HI1B hybrid plasmid (n = 16) and IncFII plasmid (n = 7), which significantly contributed to the cross-species dissemination of tet(X4). In summary, this study highlights the prevalence of MDR tet(X4)-positive K. pneumoniae in Chengdu, driven predominantly by clonal expansion and plasmid-mediated horizontal gene transfer. These findings emphasize the importance of continuous surveillance of tet(X4)-positive K. pneumoniae in raw meat and the implementation of effective measures to control their spread.},
}
@article {pmid40076423,
year = {2025},
author = {Aguirre-Carvajal, K and Cárdenas, S and Munteanu, CR and Armijos-Jaramillo, V},
title = {Rampant Interkingdom Horizontal Gene Transfer in Pezizomycotina? An Updated Inspection of Anomalous Phylogenies.},
journal = {International journal of molecular sciences},
volume = {26},
number = {5},
pages = {},
pmid = {40076423},
issn = {1422-0067},
support = {PRG.BIO.23.14.01//Universidad de Las Am&#xe9;ricas/ ; },
mesh = {*Gene Transfer, Horizontal ; *Phylogeny ; *Ascomycota/genetics ; Evolution, Molecular ; Proteome/genetics ; },
abstract = {Horizontal gene transfer (HGT) is a significant source of diversity in prokaryotes and a key factor in their genome evolution. Although similar processes have been postulated for eukaryotes, the validity of HGT's impact remains contested, particularly between long-distance-related organisms like those from different kingdoms. Among eukaryotes, the fungal subphylum Pezizomycotina has been frequently cited in the literature for experiencing HGT events, with over 600 publications on the subject. The proteomes of 421 Pezizomycotina species were meticulously examined to identify potential instances of interkingdom HGT. Furthermore, the phylogenies of over 275 HGT candidates previously reported were revisited. Manual scrutiny of 521 anomalous phylogenies revealed that only 1.5% display patterns indicative of interkingdom HGT. Moreover, novel interkingdom HGT searches within Pezizomycotina yielded few new contenders, casting doubt on the prevalence of such events within this subphylum. Although the detailed examination of phylogenies suggested interkingdom HGT, the evidence for lateral gene transfer is not conclusive. The findings suggest that expanding the number of homologous sequences could uncover vertical inheritance patterns that have been misclassified as HGT. Consequently, this research supports the notion that interkingdom HGT may be an extraordinary occurrence rather than a significant evolutionary driver in eukaryotic genomes.},
}
@article {pmid40075357,
year = {2025},
author = {Donkor, ES and Odoom, A and Osman, AH and Darkwah, S and Kotey, FCN},
title = {A systematic review and meta-analysis on antibiotic resistance genes in Ghana.},
journal = {BMC medical genomics},
volume = {18},
number = {1},
pages = {47},
pmid = {40075357},
issn = {1755-8794},
support = {D43 TW012487/TW/FIC NIH HHS/United States ; D43TW012487//the Fogarty International Center of the National Institutes of Health through the Research and Capacity Building in Antimicrobial Resistance in West Africa (RECABAW) Training Programme/ ; },
mesh = {Ghana ; Humans ; Animals ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; Genes, Bacterial ; },
abstract = {BACKGROUND: Addressing antimicrobial resistance (AMR) poses a complex challenge, primarily because of the limited understanding of bacterial antibiotic resistance genes (ARGs) and the spread of these genes across different domains. To bridge this knowledge gap in Ghana, we undertook a comprehensive systematic review and meta-analysis to quantify and estimate the prevalence of circulating ARGs in bacteria isolated from human, animal, and environmental sources.<br><br>METHODS: A thorough literature search was conducted across three major databases-Web of Science, PubMed, and Scopus-to retrieve all relevant articles related to ARGs in Ghana from the inception of the databases to February 25, 2024. A risk-of-bias evaluation was performed using the Newcastle-Ottawa Scale (NOS), and the data analysis involved descriptive statistics and proportional meta-analysis.<br><br>RESULTS: Of the 371 articles initially obtained, 38 met the inclusion criteria. These studies adequately covered Ghana geographically. The most prevalent ESBL gene identified was blaCTX-M, with a prevalence of 31.6% (95% CI: 17.6-45.7), followed by blaTEM (19.5% [95% CI: 9.7-29.3]), and blaSHV (3.5% [95% CI: 0.3-6.6]). The pooled prevalence of carbapenemase genes ranged from 17.2% (95% CI: 6.9-27.6) for blaNDM to 10.3% (95% CI: 1.9-18.7) for blaOXA. Additionally, other ARGs, including sul1, qnrS, gyrA, erm(B), and mecA, were detected, with prevalence ranging from 3.9% (95% CI: 0.0-8.5) to 16.4% (95% CI: 3.1-29.8). Several ARGs were shared across human, animal, and environmental sources.<br><br>CONCLUSION: This review revealed that bacteria obtained from human, animal, and environmental samples in Ghana shared genes associated with AMR. This finding provides evidence on the interconnection of AMR across these three domains. Horizontal gene transfer, which enables the dissemination of ARGs between genetically diverse bacteria, can occur, necessitating a multidisciplinary approach to addressing antimicrobial resistance in Ghana.},
}
@article {pmid40073489,
year = {2025},
author = {Han, NN and Wang, XP and Jin, JA and Li, WH and Yang, WY and Fan, NS and Jin, RC},
title = {Underrated risk of antibiotic resistance genes dissemination mediated by bioaerosols released from anaerobic biological wastewater treatment system.},
journal = {Water research},
volume = {279},
number = {},
pages = {123463},
doi = {10.1016/j.watres.2025.123463},
pmid = {40073489},
issn = {1879-2448},
mesh = {*Wastewater/microbiology ; Aerosols ; *Drug Resistance, Microbial/genetics ; Anaerobiosis ; Anti-Bacterial Agents/pharmacology ; Waste Disposal, Fluid ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Antibiotic resistance has been recognized as one of the most prevalent public health problems. The bioaerosol-mediated spread of antibiotic resistance genes (ARGs) is an important but underrated pathway. Therefore, this work investigated the comprehensive resistome and pathogen-induced risk in bioaerosols released from anaerobic ammonium oxidation (anammox) process under antibiotic stress. The results showed that the bioaerosol oxidation potential increased by 2.7 times after the addition of sulfamethoxazole (SMX) into the anammox system. Based on the metagenomic analyses, abundant ARGs were enriched in bioaerosols, especially novA, olec, msbA and patA. There were many antibiotic resistance contigs carrying at least two mobile genetic elements (MGEs) in bioaerosols. Compared to the control, SMX caused the significant increase in ARGs proportion in plasmids from 11.4 % to 19.4 %. Similarly, the abundance of the type IV secretion system protein encoding genes (mtrA and mtrB) increased by 30.2 % and 31.5 %, respectively, which was conducive to gene transfer between bacteria. In addition, SMX stress induced the reactive oxygen species (ROS) production and the upregulation of genes related to membrane protein and DNA replication, further facilitating ARGs transfer. The co-occurrence networks showed that Aquamicrobium and Microbacterium probably were the hosts of most ARGs. Notably, four abundant human pathogens were detected in bioaerosols from the anammox system, which raised concerns on the health risk of resistant bioaerosol diffusion. These findings reveal the potential of horizontal gene transfer through bioaerosols and provide a guidance for systematically assessing the risk of environmental antibiotic resistance and relevant pathogens.},
}
@article {pmid40072588,
year = {2025},
author = {Zeng, Q and Liu, Q and Pu, Y and Gong, P and Li, Y and Sun, Y and Hao, Y and Yang, Q and Wu, Y and Yang, B and Shi, S and Gong, Z},
title = {Impacts of Naphthenic Acids (NAs) Exposure on Soil Bacterial Community and Antibiotic Resistance Genes (ARGs) Dissemination.},
journal = {Current microbiology},
volume = {82},
number = {5},
pages = {188},
pmid = {40072588},
issn = {1432-0991},
support = {2022-MS-311//Natural Science Foundation of Liaoning Province/ ; JYTMS20231059//Basic Scientific Research Project of Education Department of Liaoning Province/ ; H2022011//Horizontal Scientific Research Project (Microbial-enhanced treatment of petroleum hydrocarbon pollutants: Technical and engineering demonstration)/ ; },
mesh = {*Soil Microbiology ; *Bacteria/genetics/drug effects/classification/metabolism ; *Carboxylic Acids/metabolism/pharmacology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Denitrification ; Reactive Oxygen Species/metabolism ; Microbiota/drug effects/genetics ; Nitrification/drug effects ; },
abstract = {Naphthenic acids (NAs) are indigenous and complex components in petroleum. In the context of increasing global energy demand, the increasing extraction of fossil resources leads to increased environmental release of NAs, resulting in various environmental risks. However, the impact of NAs exposure on soil microorganisms remains still unclear. This study constructed a microcosm system to explore bacterial community structure and function, biological risk generation, and the mechanism of antibiotic resistance genes (ARGs) dissemination under NAs exposure. After 28 days of NAs stimulation, the denitrifying bacteria were enriched and the abundance of genes related to nitrogen cycle was up-regulated, enhancing nitrification and denitrification. Meanwhile, NAs stimulated the production of extracellular polymeric substances (EPS) and the accumulation of reactive oxygen species (ROS), as well as activated the glutathione antioxidant system. Furthermore, the cell metabolic, repair, and transfer regulatory pathways were enhanced under NAs exposure. The networks of ARGs with genera and mobile genetic elements (MGEs) indicated that NAs exposure promoted the enrichment of ARGs in hosts, the selective accumulation of MGEs, and the induction of horizontal gene transfer (HGT) of ARGs. This study will provide valuable perspectives of interactions between NAs and its microecological environment, as well as ARGs transfer mechanisms.},
}
@article {pmid40071515,
year = {2025},
author = {Medina, JS and Zhang, S and Narayanasamy, S and Wang, C and Al-Gashgari, B and Hong, PY},
title = {Metagenomic Insights in Antimicrobial Resistance Threats in Sludge from Aerobic and Anaerobic Membrane Bioreactors.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {11},
pages = {5636-5646},
pmid = {40071515},
issn = {1520-5851},
mesh = {*Sewage/microbiology ; *Bioreactors ; Anaerobiosis ; Metagenomics ; Aerobiosis ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; },
abstract = {Sludge is a biohazardous solid waste that is produced during wastewater treatment. It contains antibiotic resistance genes (ARGs) that pose significant antimicrobial resistance (AMR) threats. Herein, aerobic and anaerobic membrane bioreactors (AeMBRs and AnMBRs, respectively) were compared in terms of the volume of waste sludge generated by them, the presence of ARGs in the sludge, and the potential for horizontal gene transfer (HGT) events using metagenomics to determine which treatment process can better address AMR concerns associated with the generation of waste sludge. The estimated abundance of ARGs in the suspended sludge generated by the AnMBR per treated volume is, on average, 5-55 times lower than that of sludge generated by the AeMBR. Additionally, the ratio of potential HGT in the two independent runs was lower in the anaerobic sludge (0.6 and 0.9) compared with that in the aerobic sludge (2.4 and 1.6). The AnMBR sludge exhibited reduced HGT of ARGs involving potential opportunistic pathogens (0.09) compared with the AeMBR sludge (0.27). Conversely, the AeMBR sludge displayed higher diversity and more transfer events, encompassing genes that confer resistance to quinolones, rifamycin, multidrug, aminoglycosides, and tetracycline. A significant portion of these ARGs were transferred to Burkholderia sp. By contrast, the AnMBR showed a lower abundance of mobile genetic elements associated with conjugation and exhibited less favorable conditions for natural transformation. Our findings suggest that the risk of potential HGT to opportunistic pathogens is greater in the AeMBR sludge than in AnMBR sludge.},
}
@article {pmid40069391,
year = {2025},
author = {Huang, YX and Rao, HY and Su, BS and Lv, JM and Lin, JJ and Wang, X and Xu, LN and Kong, XD and Sun, Y},
title = {The pan-genome of Spodoptera frugiperda provides new insights into genome evolution and horizontal gene transfer.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {407},
pmid = {40069391},
issn = {2399-3642},
support = {32100355, 32100352, 31871964//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Spodoptera/genetics ; Animals ; *Gene Transfer, Horizontal ; *Evolution, Molecular ; *Genome, Insect ; Genetic Variation ; },
abstract = {Spodoptera frugiperda is a common and severely damaging agricultural pest. In-depth analysis of its population genomics and transcriptomics is crucial for providing references for pest control efforts. This study, focused on the extensive variation in the genome size of S. frugiperda, constructed its pan-genome and identified 1.37 Gb of non-reference sequences, highlighting significant genetic variation within the population. Analysis of Long Terminal Repeat (LTR) Presence/Absence Variation (PAV) suggests that LTR alterations may be one of the driving factors for genome size variation. Additionally, population gene PAV analysis revealed that variable genes are enriched in functions like acetyltransferase activity, which might be associated with detoxification, implying diverse selection pressures related to detoxification in different S. frugiperda populations. Moreover, 19 horizontal gene transfer (HGT) acquired genes were identified in the reference genome used in this study, which responded to 16 different treatments. Notably, three HGT-acquired genes (SFR02618, SFR05248, and SFR05249) co-expressed with heat shock protein family and responded under treatments with Avermectin and Cypermethrin. This may indicate their involvement in a detoxification mechanism coordinated with heat shock proteins. These results offering new insights into its genomic evolution and the potential functions of HGT-acquired genes.},
}
@article {pmid40069285,
year = {2025},
author = {Masuyer, G and Taverner, A and MacKay, J and Lima Marques, AR and Wang, Y and Hunter, T and Liu, K and Mrsny, RJ},
title = {Discovery of mono-ADP ribosylating toxins with high structural homology to Pseudomonas exotoxin A.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {413},
pmid = {40069285},
issn = {2399-3642},
mesh = {*Exotoxins/chemistry/metabolism/genetics ; *Bacterial Toxins/chemistry/metabolism/genetics ; *Pseudomonas aeruginosa Exotoxin A ; *ADP Ribose Transferases/chemistry/metabolism/genetics ; Crystallography, X-Ray ; Virulence Factors/chemistry/metabolism/genetics ; Amino Acid Sequence ; Humans ; Models, Molecular ; Phylogeny ; Bacterial Proteins/chemistry/metabolism/genetics ; },
abstract = {Mono-ADP-ribosyl transferase (mART) proteins are secreted virulence factors produced by several human pathogens, the founding member being diphtheria toxin (DT). Pseudomonas aeruginosa can also secrete a mART toxin, known as exotoxin A (PE), but with an organization of its three functional domains (receptor, translocation, and enzymatic elements) that is opposite to DT. Two additional PE-like toxins (PLTs) have been identified from Vibrio cholerae and Aeromonas hydrophila, suggesting more PLT family members may exist. Database mining discovered six additional putative homologues, considerably extending this group of PLTs across a wide range of bacterial species. Here, we examine sequence and structural information for these new family members with respect to previously identified PLTs. The X-ray crystal structures of four new homologues show the conservation of critical features responsible for structure and function. This study shows the potential of these newly described toxins for the development of novel drug delivery platforms. Additionally, genomic analysis suggests horizontal gene transfer to account for the wide distribution of PLTs across a range of eubacteria species, highlighting the need to monitor emerging pathogens and their virulence factors.},
}
@article {pmid40066988,
year = {2025},
author = {Mašlaňová, I and Kovařovic, V and Botka, T and Švec, P and Sedláček, I and Šedo, O and Finstrlová, A and Neumann-Schaal, M and Kirstein, S and Schwendener, S and Staňková, E and Rovňáková, K and Petráš, P and Doškař, J and Perreten, V and Pantůček, R},
title = {Evidence of in vitro mecB-mediated β-lactam antibiotic resistance transfer to Staphylococcus aureus from Macrococcus psychrotolerans sp. nov., a psychrophilic bacterium from food-producing animals and human clinical specimens.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {4},
pages = {e0165224},
pmid = {40066988},
issn = {1098-5336},
support = {LX22NPO5103, LM2023042, LM2023067, 90254//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; NIPH 75010330//Ministerstvo Zdravotnictv&#xed; Cesk&#xe9; Republiky/ ; MUNI/A/1603/2024//Masarykova Univerzita/ ; },
mesh = {Humans ; Animals ; *Staphylococcus aureus/genetics/drug effects ; Phylogeny ; *beta-Lactam Resistance/genetics ; *Anti-Bacterial Agents/pharmacology ; *Bacterial Proteins/genetics/metabolism ; Livestock/microbiology ; Whole Genome Sequencing ; Gene Transfer, Horizontal ; Genome, Bacterial ; *Enterococcaceae/genetics/isolation &amp; purification/drug effects ; Plasmids ; Staphylococcal Infections/microbiology ; },
abstract = {Macrococci are usually found as commensals on the skin and mucosa of animals and have been isolated from mammal-derived fermented foods; however, they can also act as opportunistic pathogens. Here, we used whole-genome sequencing, comparative genomics, extensive biotyping, MALDI-TOF mass spectrometry, and chemotaxonomy to characterize Macrococcus sp. strains isolated from livestock and human-related specimens. Based on the results of polyphasic taxonomy, we propose the species Macrococcus psychrotolerans sp. nov. (type strain NRL/St 95/376[T] = CCM 8659[T] = DSM 111350[T]) belonging to the Macrococcus caseolyticus phylogenetic clade. It grows at 4°C, and the core genome of the isolates contains suspected genes contributing to low-temperature tolerance. Variable genetic elements include prophages, chromosomal islands, a composite staphylococcal cassette chromosome island, and many plasmids that affect the overall genome expansion and adaptation to specific ecological settings of the studied isolates. Large plasmids carrying the methicillin resistance gene mecB were identified in M. psychrotolerans sp. nov. strains and confirmed as self-transmissible to Staphylococcus aureus in vitro. In addition to plasmids with circular topology, a 150-kb-long linear plasmid with 14.1-kb-long inverted terminal repeats, harboring many IS elements and putative genes for a type IV secretion system was revealed. The described strains were isolated from human clinical material, food-producing animals, meat, and a wooden cheese board and have the potential to proliferate at refrigerator temperatures. Their presence in the food chain and human infections indicates that attention needs to be paid to this potential novel opportunistic pathogen.IMPORTANCEThe study offers insights into the phenotypic and genomic features of a novel species of the genus Macrococcus that occurs in livestock, food, and humans. The large number of diverse mobile genetic elements contributes to the adaptation of macrococci to various environments. The ability of the described microorganisms to grow at refrigerator temperatures, enabled by genes that are predicted to contribute to low-temperature tolerance, raises food safety concerns. Confirmed in vitro conjugative transfer of plasmid-borne mecB gene to S. aureus poses a significant risk of spread of broad β-lactam resistance. In addition, the intergeneric plasmid transfer to S. aureus is indicative of horizontal gene transfer events that may be more frequent than generally accepted. Determining a complete sequence and gene content of linear megaplasmid with exceptional topology for the Staphylococcaceae family suggests its possible role in shuttling adaptive traits through an exchange of genetic information.},
}
@article {pmid40066273,
year = {2025},
author = {Han, B and Feng, C and Jiang, Y and Ye, C and Wei, Y and Liu, J and Zeng, Z},
title = {Mobile genetic elements encoding antibiotic resistance genes and virulence genes in Klebsiella pneumoniae: important pathways for the acquisition of virulence and resistance.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1529157},
pmid = {40066273},
issn = {1664-302X},
abstract = {Klebsiella pneumoniae is an opportunistic pathogen primarily associated with nosocomial infections, characterized by a propensity for multi-drug resistance and the potential evolution into hypervirulent strains. Based on its phenotypic and genotypic characteristics, K. pneumoniae can be classified into two types: classical K. pneumoniae (cKP) and hypervirulent K. pneumoniae (hvKP). The spread of mobile genetic elements (MGEs) in K. pneumoniae has led to the emergence of carbapenem-resistant K. pneumoniae (CRKP) and carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP). The emergence of CR-hvKP is particularly concerning due to its multidrug resistance, high pathogenicity, and increased transmissibility. This review summarizes the types of MGEs present in K. pneumoniae, the mechanisms of horizontal gene transfer (HGT) mediated by these mobile elements, their roles in the dissemination of antibiotic resistance genes (ARGs) and virulence genes, and the relationships among MGEs that resemble Russian dolls or exhibit hybrid characteristics. Additionally, the clinical treatment and epidemiological characteristics of CR-hvKP are discussed. Given the high variability and transmissibility of MGEs, continuous monitoring and control of the variation and transmission of such genetic material in K. pneumoniae should be prioritized.},
}
@article {pmid40064777,
year = {2025},
author = {Crespo-Bellido, A and Martin, DP and Duffy, S},
title = {Recombination Analysis of Geminiviruses Using Recombination Detection Program (RDP).},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2912},
number = {},
pages = {125-143},
pmid = {40064777},
issn = {1940-6029},
mesh = {*Geminiviridae/genetics ; *Recombination, Genetic ; Software ; Algorithms ; Sequence Alignment ; Genome, Viral ; Evolution, Molecular ; Computational Biology/methods ; Phylogeny ; },
abstract = {Geminiviruses are recombination-prone, and characterizing this evolutionary process within their genomes is a frequent goal of researchers. RDP is a stand-alone Windows program combining many algorithms that detect and characterize recombination. It has been widely used by the geminivirus community (and beyond). Here we describe the use of RDP4 and RDP5 for analysis of geminiviral nucleotide sequences including: (i) obtaining a reasonable dataset for analysis, (ii) making a credible multiple sequence alignment and (iii) analyzing an alignment with RDP on that alignment. RDP to both characterize recombination events and to produce statistically recombination-free datasets for other molecular evolution analyses.},
}
@article {pmid40063617,
year = {2025},
author = {Gaona, M and Corral, J and Sánchez Osuna, M and Campoy, S and Barbé, J and Pérez-Varela, M and Aranda, J},
title = {Reciprocal regulation between Acinetobacter baumannii and Enterobacter cloacae AdeR homologs: implications for antimicrobial resistance and pathogenesis.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0315428},
pmid = {40063617},
issn = {1932-6203},
mesh = {*Enterobacter cloacae/genetics/drug effects/pathogenicity ; *Acinetobacter baumannii/genetics/drug effects/pathogenicity ; *Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Anti-Bacterial Agents/pharmacology ; Animals ; Drug Resistance, Bacterial/genetics ; Promoter Regions, Genetic ; Microbial Sensitivity Tests ; Virulence/genetics ; Mice ; Membrane Transport Proteins ; },
abstract = {Acinetobacter baumannii and Enterobacter cloacae are phylogenetically distant Gram-negative bacterial pathogens that represent significant challenges in healthcare settings due to their remarkable ability to acquire antimicrobial resistance. This study investigates one of the most important efflux pump systems in A. baumannii, AdeABC-AdeRS, and identifies homologous components in E. cloacae. By constructing isogenic knockout mutants, we show that the AdeB pump component and the AdeR regulator are significant for antimicrobial resistance and pathogenicity in A. baumannii. Through in silico predictions, we identify homologs of AdeB and AdeR (ECL_01758 and ECL_01761, respectively) in E. cloacae. Notably, we demonstrate that while the inactivation of the E. cloacae gene encoding the AdeB protein does not impact on pathogenesis and only alters colistin susceptibility, a knockout mutant of the gene encoding the AdeR regulator significantly affects susceptibility to various antimicrobial classes, motility, and virulence. Additionally, we demonstrate that the AdeR regulators of A. baumannii and E. cloacae can functionally substitute for each other both in vitro and in vivo conditions. Electrophoretic mobility shift assays reveal that these regulators are capable of binding to the promoter regions of each other's species, where similar DNA motifs are present. Furthermore, cross-complementation tests show that the affected phenotypes in each species can be restored interchangeably. Moreover, phylogenomic analysis of previously published E.cloacae genomes and reconstructrion of ancestral states through the phylogenetic trees of the adeB and adeR genes suggest that these homologs are more likely derived from a common ancestor rather than through recent horizontal gene transfer. The findings of this work highlight that conserved regulatory functions concerning efflux pump expression can be maintained across species despite evolutionary divergence and open new perspectives for the control of bacterial infections.},
}
@article {pmid40061860,
year = {2025},
author = {Zhang, S and Yang, J and Abbas, M and Yang, Q and Li, Q and Liu, M and Zhu, D and Wang, M and Tian, B and Cheng, A},
title = {Threats across boundaries: the spread of ESBL-positive Enterobacteriaceae bacteria and its challenge to the "one health" concept.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1496716},
pmid = {40061860},
issn = {1664-302X},
abstract = {β-lactam antibiotics are essential medications for treating human diseases. The spread of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) exists globally in multiple reservoirs and the natural environment and poses an immense threat to public health. Plasmid incompatibility groups, such as IncFIA, IncI1, IncY, IncFIB, IncN, IncFIC, IncX4, IncB/O/K/Z, IncHI1/2, and IncA/C, which exist in humans, animals, and the environment, carrying bla CTX-M, bla TEM, and bla SHV genes. The ISEcp1 upstream and orf477 downstream of bla CTX-M genes, as well as other mobile genetic elements (MGEs) such as IS903 and IS26, are involved in capturing and mobilizing antibiotic-resistant genes (ARGs). The bla CTX-M-15 gene is the most common among all discussed reservoirs. The environmental reservoir and propagation mode of ESBL-PE are increasing and difficult to control. The reasons include but are not limited to bacterial adaptability and horizontal gene transfer (HGT) mediated by MGEs and plasmids. Conjugation is a pathway of HGT that is almost uncontrollable. MGEs and plasmids such as Tn3, IS1380 families, IncI1, IncK, and IncN are facilitating HGT of bla CTX-M genes. This review highlights the need to monitor trends in antimicrobial resistance (AMR) in the natural environment. Therefore, policies such as antibiotic management plans, training for healthcare providers and/or patients, cautious use of antibiotics, the need for epidemiological networks, pre-travel consultations, World Health Organization (WHO) infection control and biosafety guidelines, and other intervention measures are considered desirable.},
}
@article {pmid40058530,
year = {2025},
author = {Smykal, V and Tobita, H and Dolezel, D},
title = {Evolution of circadian clock and light-input pathway genes in Hemiptera.},
journal = {Insect biochemistry and molecular biology},
volume = {180},
number = {},
pages = {104298},
doi = {10.1016/j.ibmb.2025.104298},
pmid = {40058530},
issn = {1879-0240},
abstract = {Circadian clocks are timekeeping mechanisms that help organisms anticipate periodic alterations of day and night. These clocks are widespread, and in the case of animals, they rely on genetically related components. At the molecular level, the animal circadian clock consists of several interconnected transcription-translation feedback loops. Although the clock setup is generally conserved, some important differences exist even among various insect groups. Therefore, we decided to identify in silico all major clock components and closely related genes in Hemiptera. Our analyses indicate several lineage-specific alterations of the clock setup in Hemiptera, derived from gene losses observed in the complete gene set identified in the outgroup, Thysanoptera, which thus presents the insect lineage with a complete clock setup. Nilaparvata and Fulgoroidea, in general, lost the (6-4)-photolyase, while all Hemiptera lost FBXL3, and several lineage-specific losses of dCRY and jetlag were identified. Importantly, we identified non-canonical splicing variants of period and m-cry genes, which might provide another regulatory mechanism for clock functioning. Lastly, we performed a detailed reconstruction of Hemiptera's light input pathway genetic repertoire and explored the horizontal gene transfer of cryptochrome-DASH from plant to Bemisia. Altogether, this inventory reveals important trends in clock gene evolution and provides a reference for clock research in Hemiptera, including several lineages of important pest species.},
}
@article {pmid40057108,
year = {2025},
author = {Wang, Y and Song, Y and Zhang, D and Xing, C and Liang, J and Wang, C and Yang, X and Liu, Z and Zhao, Z},
title = {Effects of nitrogen-driven eutrophication on the horizontal transfer of extracellular antibiotic resistance genes in water-sediment environments.},
journal = {Environmental research},
volume = {274},
number = {},
pages = {121317},
doi = {10.1016/j.envres.2025.121317},
pmid = {40057108},
issn = {1096-0953},
mesh = {*Eutrophication ; *Nitrogen ; *Geologic Sediments/microbiology ; *Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Bacteria/genetics ; *Drug Resistance, Bacterial/genetics ; Water Pollutants, Chemical ; },
abstract = {Excessive nitrogen and other nutrients can trigger the eutrophication of freshwater bodies. Antibiotic resistance genes (ARGs) are now recognized as environmental pollutants, with extracellular ARGs (eARGs) being the dominant form in sediments. However, research on the propagation characteristics of eARGs remains limited. This study investigated the transfer characteristics of kanamycin resistance (KR) genes in the pEASY-T1 plasmid to intracellular DNA (iDNA) and extracellular DNA (eDNA) in water and sediment microenvironments under increasing nitrogen concentrations, as well as the community structure of free-living (FL) and particle-attached (PA) bacteria. The results revealed KR genes relative abundance in free extracellular DNA (f-eDNA) and adsorbed extracellular DNA (a-eDNA) of the water initially decreased and then increased with rising nitrogen concentrations. Its abundance in iDNA of the sediments decreased significantly with increasing nitrogen content, with relative abundance ranging from 5.09 × 10[-4] to 1.14 × 10[-3] copies/16SrRNA. The transfer from eDNA to iDNA in the water showed a rising and then falling trend as nitrogen concentration rose. The transfer of iDNA from the water to iDNA in sediments exhibited the opposite pattern. Additionally, copper (Cu) and zinc (Zn) were identified as key factors influencing the abundance of KR genes in the water, but total phosphorus (TP) was the primary determinant of KR gene distribution in sediments according to random forest analysis. These findings reveal novel mechanisms of eARG propagation in eutrophic environments, providing a theoretical foundation for managing antibiotic resistance in aquatic ecosystems.},
}
@article {pmid40056814,
year = {2025},
author = {Yasemi, M and Jalali, A and Asadzadeh, M and Komijani, M},
title = {Organophosphate pesticides and their potential in the change of microbial population and frequency of antibiotic resistance genes in aquatic environments.},
journal = {Chemosphere},
volume = {376},
number = {},
pages = {144296},
doi = {10.1016/j.chemosphere.2025.144296},
pmid = {40056814},
issn = {1879-1298},
mesh = {*Pesticides/toxicity ; *Drug Resistance, Microbial/genetics ; *Water Pollutants, Chemical/toxicity/analysis ; Lakes/microbiology ; Bacteria/drug effects/genetics ; Wetlands ; Organophosphates/toxicity ; Microbiota/drug effects/genetics ; Metals, Heavy/toxicity ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology/toxicity ; beta-Lactamases/genetics/metabolism ; Metagenomics ; },
abstract = {Heavy metals (HMs) and pesticides disrupt aquatic biodiversity and microbial communities, contributing to antibiotic resistance via cross-resistance and co-selection mechanisms. This study investigates the relationship between organophosphorus pesticides (OPs), HMs, microbial diversity, and antibiotic resistance genes (ARGs) in eight lakes and wetlands. Microbial communities were analyzed via metagenomics methods, and data were processed using CLC Genomics Workbench 22. ARGs, including tetA, tetB, qnrA, qnrS, CIT, Fox, KPC, CTX-M1, DHA, GES, OXA, IMP, VEB, NDM1, SHV, TEM, CTX-M, PER, and MOX, were identified through polymerase chain reaction (PCR). Element concentrations and pesticide were quantified using inductively coupled plasma mass spectrometry and gas chromatography-mass spectrometry, respectively. The results indicate that environmental elements and pesticides significantly influence microbial diversity. Proteobacteria (Gamma, Beta, Alpha) dominate over other bacteria in all locations. β-Lactamase resistance genes have a significant positive correlations with the concentrations of boron, iron, lithium, magnesium, sodium, and phosphorus (P-value<0.05). Positive correlations between phosphorus, iron, and beta-lactamase genes suggest that higher concentrations of these elements may increase resistance likelihood by promoting resistant bacterial growth or facilitating gene transfer. Additionally, tetA and tetB exhibited a significant positive correlation with parathion concentration. The results showed that OPs and HMs increase antibiotic resistance by causing gene mutations, altering gene expression, and promoting horizontal gene transfer, resulting in multidrug-resistant strains. This highlights the need for monitoring these pollutants as they affect microbial diversity and accelerate antibiotic resistance. Targeted measures, such as bioremediation and pollution control, are essential to mitigate risks to the environment and public health.},
}
@article {pmid40056564,
year = {2025},
author = {Singh, H and Bagra, K and Dixit, S and Singh, AK and Singh, G},
title = {Association of infrastructure and operations with antibiotic resistance potential in the dairy environment in India.},
journal = {Preventive veterinary medicine},
volume = {239},
number = {},
pages = {106497},
doi = {10.1016/j.prevetmed.2025.106497},
pmid = {40056564},
issn = {1873-1716},
mesh = {*Dairying/methods ; India ; Animals ; Cattle ; *Anti-Bacterial Agents/pharmacology ; Manure/microbiology ; *Drug Resistance, Microbial ; Wastewater/microbiology ; *Drug Resistance, Bacterial ; Soil Microbiology ; },
abstract = {The dairy industry in developing countries is often associated with inappropriate use of antibiotics and the subsequent contamination of the environment with co-selectors of antibiotic resistance. However, the specific factors in dairy farm environments that influence antibiotic resistance levels and the subsequent exposure risks to farm workers are unknown. We examined the link between the infrastructure and operations of the dairy farm and the antibiotic resistance potential in India, which is the highest producer and consumer of dairy products globally. We sampled sixteen dairy farms in the Dehradun district, India, that varied in their herd size, infrastructure, and operational features during winter, summer, and monsoon. We collected samples of dung, manure, wastewater, manure-amended, and control soil from these farms. We quantified six antibiotic resistance genes (ARGs) (sul1, sul2, parC, mcr5, ermF, and tetW), an integron integrase gene cassette (intI1), and 16S rRNA gene copies as an indicator for total bacterial count. We observed that the infrastructure and the operations of the dairy farms were significantly associated with antibiotic resistance potential in the dairy environment. For example, with increased ventilation and exposure to external weather, the levels of sul2 (x͂=10[-1.63]) and parC (x͂=10[-4.24]) in manure increased. When farmers administered antibiotics without veterinary consultation, the relative levels of intI1 (x͂=10[-2.36]), sul2 (x͂=10[-1.58]), and tetW (x͂=10[-3.04]) in manure were lower than the cases where professional advice was sought. Small-scale farms had lower relative ARG levels than medium- and large-scale farms, except for mcr5 (x͂=10[-3.98]) in wastewater. In different sample types, the relative ARG levels trended as manure-amended soil (x͂=10[-2.34]) > wastewater (x͂=10[-2.90])> manure (x͂=10[-3.39])> dung (x͂=10[-2.54]). ARGs correlated with the marker for horizontal gene transfer, intI1, which exacerbates overall antibiotic resistance levels. Exposure assessment showed that the agriculture farm workers working in manure-amended agriculture farms are exposed to higher antibiotic resistance potential than dairy farm workers, who manually handle dung. Our study showed that the link between the dairy infrastructure (ventilation and floor type) and operations (scale of operation and veterinary consultation) and the antibiotic resistance potential in the dairy farm environment was statistically significant. This knowledge paves the way for designing interventions that can minimize the antibiotic resistance potential on dairy farms and in affected environments and thus reduce the public health burden of antibiotic-resistant infections in the dairy industry and dairy workers in India.},
}
@article {pmid40056523,
year = {2025},
author = {Zhang, Q and Fan, Y and Qian, X and Zhang, Y},
title = {Unraveling the role of microplastics in antibiotic resistance: Insights from long-read metagenomics on ARG mobility and host dynamics.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137804},
doi = {10.1016/j.jhazmat.2025.137804},
pmid = {40056523},
issn = {1873-3336},
mesh = {*Microplastics/toxicity ; Biofilms ; Metagenomics ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; *Water Pollutants, Chemical/toxicity ; Plasmids/genetics ; Bacteria/genetics/drug effects ; Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; },
abstract = {As two emerging pollutants, microplastics (MPs) potentially serve as vectors for antibiotic resistance genes (ARGs) in aquatic environments, but the mechanisms driving ARG enrichment remain unclear. This study used long-read metagenomics to investigate ARG mobility and hosts dynamics within the biofilms of MPs and rocks in different water environments. We identified distinct enrichment patterns for microbial communities and ARGs, highlighting the significant role of horizontal gene transfer in ARG enrichment. Specifically, plasmid-encoded ARGs varied significantly among MP biofilms, rock biofilms, and water samples, while chromosome-encoded ARGs remained consistent across these environments, emphasizing the impact of plasmids on ARG enrichment. Despite this, 55.1 % of ARGs were on chromosomes, indicating that host organisms also play a crucial role. The related mechanisms driving ARG enrichment included enhanced cell adhesion, increased transmembrane transporter activity, and responses to environmental stressors, which led to an increased presence of plasmid-encoded ARGs on MP biofilms, facilitating more frequent horizontal gene transfer. Additionally, the diversity of hosts on MPs was notably lower compared to the water column, with specific bacteria, including Herbaspirillu, Limnohabitans, Polaromonas, Variovorax, Rubrivivax, and Thauera significantly driving ARG enrichment. This study highlights key mechanisms and bacterial taxa involved in ARG dynamics on MPs.},
}
@article {pmid40056518,
year = {2025},
author = {Zhu, Y and Li, R and Yan, S and Li, Y and Xie, S},
title = {Copper contamination determined the impact of phages on microbially-driven nitrogen cycling in coastal wetland sediments.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137870},
doi = {10.1016/j.jhazmat.2025.137870},
pmid = {40056518},
issn = {1873-3336},
mesh = {*Wetlands ; *Copper/toxicity/analysis ; *Geologic Sediments/microbiology/chemistry ; *Bacteriophages/physiology ; *Nitrogen Cycle/drug effects ; *Water Pollutants, Chemical/toxicity/analysis ; Nitrogen/metabolism ; Bacteria/metabolism/genetics ; Denitrification ; },
abstract = {Phages have garnered increasing attention due to their potential roles in biogeochemical cycling. However, their impacts on nitrogen cycling have primarily been inferred from the presence of putative auxiliary metabolic genes (AMGs) and the virus-host linkage, despite of very limited direct experimental evidence. In this study, a series of microcosms were established with the inoculation of either native or non-native phages to simulate coastal wetlands with different phage sources and different levels of copper (Cu) contamination. Metagenomics and metatranscriptomics were combined to reveal phages' regulation on microbially-driven nitrogen cycling and to explore how the effects were mediated by Cu stress. Phages significantly impacted denitrification-related genes, with their effects depending on Cu level. Phages inhibited nirK-type denitrification under Cu stress but led to up-regulation of nirS gene in the treatments without Cu addition. Non-native phages also promoted the transcription of genes related to nitrogen assimilation and organic nitrogen transformation. Detection of viral AMGs involved in glutamate synthesis suggested that horizontal gene transfer may be a crucial pathway for phages to facilitate microbial nitrogen uptake. Overall, these findings enhance the understanding of phages' impact on biogeochemical metabolism in coastal wetland, offering novel insights into the links of phages' regulation on microbial nitrogen cycling with Cu stress.},
}
@article {pmid40052062,
year = {2025},
author = {Liu, Y and Liu, L and Wang, X and Shao, M and Wei, Z and Wang, L and Li, B and Li, C and Luo, X and Li, F and Zheng, H},
title = {Microplastics enhance the prevalence of antibiotic resistance genes in mariculture sediments by enriching host bacteria and promoting horizontal gene transfer.},
journal = {Eco-Environment &amp; Health},
volume = {4},
number = {1},
pages = {100136},
pmid = {40052062},
issn = {2772-9850},
abstract = {Microplastics (MPs) and antibiotic resistance genes (ARGs) pose significant challenges to the One Health framework due to their intricate and multifaceted ecological and environmental impacts. However, the understanding of how MP properties influence ARG prevalence in mariculture sediments remains limited. Herein, the polystyrene (PS) and polyvinyl chloride (PVC) MPs with different sizes (20-120 μm and 0.5-2.0 mm) were selected to evaluate their impacts and underlying mechanisms driving ARGs dissemination. The results showed that PS and PVC MPs increased the relative abundance of ARGs by 1.41-2.50-fold and 2.01-2.84-fold, respectively, compared with control, particularly high-risk genes. The polymer type effect was identified as more influential than the size effect in driving the sediment resistome evolution. PVC shifted the microbial community assembly from stochastic to deterministic processes, thus enriching ARG host pathogens. Furthermore, the highly hydrophobic PS not only recruited the host bacteria colonization but also facilitated ARG exchange within the plastisphere. The exogenous additives released by PVC (e.g., heavy metals, bisphenol A, and tridecyl ester) and the particles synergistically promoted ARG conjugative transfer by inducing oxidative stress and enhancing cell membrane permeability. These findings revealed how MPs characteristics facilitated the spread of ARGs in marine benthic ecosystems, underscoring the importance of mitigating MPs pollution to maintain mariculture ecosystem health, prevent zoonotic diseases, and balance global mariculture with ecological health.},
}
@article {pmid40051841,
year = {2025},
author = {Vivekanandan, KE and Kumar, PV and Jaysree, RC and Rajeshwari, T},
title = {Exploring molecular mechanisms of drug resistance in bacteria and progressions in CRISPR/Cas9-based genome expurgation solutions.},
journal = {Global medical genetics},
volume = {12},
number = {2},
pages = {100042},
pmid = {40051841},
issn = {2699-9404},
abstract = {Antibiotic resistance in bacteria is a critical global health challenge, driven by molecular mechanisms such as genetic mutations, efflux pumps, enzymatic degradation of antibiotics, target site modifications, and biofilm formation. Horizontal gene transfer (HGT) further accelerates the spread of resistance genes across bacterial populations. These mechanisms contribute to the emergence of multidrug-resistant (MDR) strains, rendering conventional antibiotics ineffective. Recent advancements in CRISPR/Cas9-based genome editing offer innovative solutions to combat drug resistance. CRISPR/Cas9 enables precise targeting of resistance genes, facilitating their deletion or inactivation, and provides a potential method to eliminate resistance-carrying plasmids. Furthermore, phage-delivered CRISPR systems show promise in selectively killing resistant bacteria while leaving susceptible strains unaffected. Despite challenges such as efficient delivery, off-target effects, and potential bacterial resistance to CRISPR itself, ongoing research and technological innovations hold promise for using CRISPR-based antimicrobials to reverse bacterial drug resistance and develop more effective therapies. These abstract highlights the molecular mechanisms underlying bacterial drug resistance and explores how CRISPR/Cas9 technology could revolutionize treatment strategies against resistant pathogens.},
}
@article {pmid40051073,
year = {2025},
author = {Saranya, SV and Prathiviraj, R and Chellapandi, P},
title = {Mobilome-Mediated Speciation: Genomic Insights Into Horizontal Gene Transfer in Methanosarcina.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70013},
doi = {10.1002/jobm.70013},
pmid = {40051073},
issn = {1521-4028},
support = {//The authors express their gratitude to the Science and Engineering Research Board, Ministry of Science and Technology, Government of India (EEQ/2020/000095), and RUSA 2.0: Biological Science, Government of India (12/BDU/RUSA/TRP/BS) for their financial support. Funded by Department of Science and Technology, Ministry of Science and Technology, India, Science and Engineering Research Board, Grant/Award Number EEQ/2020/000095. Ministry of Education, India, Rashtriya Uchchatar Shiksha Abhiyan, RUSA 2.0: Biological Science, Government of India (12/BDU/RUSA/TRP/BS)./ ; },
abstract = {Speciation in prokaryotes is often driven by complex genetic exchanges such as horizontal gene transfer (HGT), which facilitates genomic divergence and adaptation. In this study, we inferred the evolutionary transitions of the mobilome (plasmids, transposons, and phages) between Methanosarcina and bacteria in driving speciation within the Methanosarcina genus. By conducting evolutionary and phylogenetic analyses of Methanosarcina acetivorans, M. barkeri, M. mazei, and M. siciliae, we identified key mobilome elements acquired through HGT from distantly related bacterial species. These mobile genetic elements have shaped genomic plasticity, enabling Methanosarcina to adapt to diverse environmental niches and potentially facilitating lineage divergence. The acquisition of mobilome-associated genes involved in antibiotic resistance, DNA repair, and stress responses suggests their significant role in the ecological speciation of Methanosarcina. Overall, we hypothesized that their mobile genetic element might have been acquired from distantly related bacteria by HGT and subsequently established as new functional homologs in the present lineage. This study provides insight into how mobilome-mediated gene flow contributes to genomic divergence and speciation within microbial populations, highlighting the broader significance of mobilome in microbial evolution and speciation processes.},
}
@article {pmid40051064,
year = {2025},
author = {Saranya, SV and Chellapandi, P},
title = {Convergent Evolution of Coenzyme Metabolism in Methanosarcina mazei: Insights Into Primitive Life and Metabolic Adaptations.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70015},
doi = {10.1002/jobm.70015},
pmid = {40051064},
issn = {1521-4028},
support = {//This paper was supported by Science and Engineering Research Board, Ministry of Science and Technology, Government of India and RUSA 2.0: Biological Science, Government of India./ ; },
abstract = {The convergent evolution of coenzyme metabolism in methanogens provides critical insights into primitive life and metabolic adaptations. This study investigated the molecular evolution and functional dynamics of eight coenzymes and cofactors in Methanosarcina mazei, a model methanogen essential for methane production and energy conservation in anaerobic environments. Phylogenetic and genetic diversity analyses of the 706 protein sequences revealed conserved evolutionary trajectories interspersed with lineage-specific adaptations driven by gene duplication, horizontal gene transfer, and selective pressures. Key findings included the purifying selection of methanofuran (Tajima's D = -2.9589) and coenzyme A (Tajima's D = -2.8555), indicating the conservation of critical metabolic functions. The coenzyme B biosynthesis pathway showed balanced selection (Tajima's D = 2.38602), reflecting its evolutionary plasticity. Phylogenetic analyses linked coenzyme F420 biosynthetic enzymes closely to Methanosarcina horonobensis, while coenzyme F430 enzymes highlighted prokaryotic specialization distinct from their eukaryotes. Coenzyme M biosynthetic genes have demonstrated unique evolutionary connections with species across domains, such as Methanothermobacter thermautotrophicus and Gekko japonicus, emphasizing their broad adaptive significance. These evolutionary trajectories reveal how M. mazei optimized its metabolic pathways to thrive in extreme anaerobic environments, bridging ancient metabolic systems from the Last Universal Common Ancestor with contemporary ecological adaptations.},
}
@article {pmid40050512,
year = {2025},
author = {Chacón, RD and Ramírez, M and Suárez-Agüero, D and Pineda, APA and Astolfi-Ferreira, CS and Ferreira, AJP},
title = {Genomic Differences in Antimicrobial Resistance and Virulence Among Key Salmonella Strains of Serogroups B and D1 in Brazilian Poultry.},
journal = {Current microbiology},
volume = {82},
number = {4},
pages = {173},
pmid = {40050512},
issn = {1432-0991},
support = {Finance Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; fellowship 1D//Conselho Nacional de Pesquisa e Desenvolvimento Tecnol&#xf3;gico/ ; },
mesh = {Animals ; Brazil ; *Salmonella/genetics/drug effects/classification/pathogenicity ; *Poultry/microbiology ; *Salmonella Infections, Animal/microbiology ; Virulence/genetics ; *Anti-Bacterial Agents/pharmacology ; *Serogroup ; *Poultry Diseases/microbiology ; *Genome, Bacterial ; *Virulence Factors/genetics ; *Drug Resistance, Bacterial/genetics ; Phylogeny ; Whole Genome Sequencing ; Microbial Sensitivity Tests ; Genomics ; },
abstract = {Salmonella is a significant threat to Brazilian poultry, causing economic losses and public health risks. This study analyzed 15 Salmonella isolates along with 45 retrieved complete genomes, including serovars Gallinarum, Pullorum, Enteritidis, Typhimurium, and Heidelberg. Biochemical characterization, antimicrobial susceptibility testing, whole-genome sequencing, and comparative genomics were performed. The studied strains exhibited high levels of antimicrobial resistance, particularly to tilmicosin, penicillin/novobiocin, nalidixic acid, and streptomycin. Genomic analysis revealed diverse virulence factors and antibiotic resistance genes (ARGs), with zoonotic strains showing higher virulence compared to avian-adapted strains. Multiple plasmid types carrying ARGs were identified, highlighting the potential for horizontal gene transfer. Pangenomic and phylogenomic analyses differentiated Salmonella strains from serogroup D1 from those from serogroup B. These findings emphasize the need for comprehensive surveillance and control measures to mitigate the impact of Salmonella on both animal and human health in Brazil.},
}
@article {pmid40048953,
year = {2025},
author = {Tamai, S and Okuno, M and Ogura, Y and Suzuki, Y},
title = {Genetic diversity of dissolved free extracellular DNA compared to intracellular DNA in wastewater treatment plants.},
journal = {The Science of the total environment},
volume = {970},
number = {},
pages = {178989},
doi = {10.1016/j.scitotenv.2025.178989},
pmid = {40048953},
issn = {1879-1026},
mesh = {*Wastewater ; *Waste Disposal, Fluid/methods ; *Genetic Variation ; DNA ; Environmental Monitoring ; Drug Resistance, Microbial/genetics ; Halogenation ; },
abstract = {Dissolved free extracellular DNA (free-exDNA) coexists with intracellular DNA (inDNA) in aquatic environments. Free-exDNA can be taken up by bacteria through transformation, and wastewater treatment plants (WWTPs) are positioned as potential hot spots for genetic contamination. However, studies comparing the composition of free-exDNA and inDNA is limited. This study employed colloidal adsorption and foam concentration method to recover free-exDNA from different WWTP stages and compared its diversity with inDNA via metagenomic analysis. Free-exDNA concentrations were observed to increase after chlorination. Genetic analysis revealed a higher abundance of specific genes following chlorination, suggesting that free-exDNA in effluent originated from bacterial death in secondary treated water. This result indicates that free-exDNA, which increases due to chlorination, is subsequently released into the catchment. Additionally, several high-risk antibiotic-resistance genes (ARGs) were detected that colocalized with mobile genetic elements. These ARGs were expected to have a high potential for gene transfer via transformation, and the risk was highlighted. Overall, these findings deepen our understanding of horizontal gene transfer risks in WWTPs.},
}
@article {pmid40045656,
year = {2025},
author = {Zhang, M and Zhao, X and Ren, X},
title = {Research Progress on the Mechanisms of Algal-Microorganism Symbiosis in Enhancing Large-Scale Lipid Production.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {11},
pages = {6345-6360},
doi = {10.1021/acs.jafc.4c11580},
pmid = {40045656},
issn = {1520-5118},
mesh = {*Microalgae/metabolism/genetics ; *Symbiosis ; Biofuels ; Bacteria/metabolism/genetics ; Lipids/biosynthesis ; Lipid Metabolism ; },
abstract = {Microalgae, characterized by their exceptional lipid content, rapid growth, and robust adaptability, represent a promising biological resource. In natural and engineered ecosystems, microalgae engage in intricate symbiotic relationships with diverse microorganisms, a dynamic interplay essential for ecological resilience and metabolic optimization. This review examines the role of symbiotic microorganisms in microalgal growth and lipid accumulation, with particular emphasis on the biological regulatory mechanisms that govern these processes. These include nutrient exchange, phytohormone-mediated growth stimulation, cofactors, and quorum-sensing-driven community coordination. The review highlights how these microbial interactions facilitate optimal lipid production by enhancing metabolic pathways, thereby improving the efficiency of lipid accumulation in microalgae. Furthermore, the review investigates horizontal gene transfer as an evolutionary driver that fortifies algal-microbial consortia against environmental stressors, enabling robust performance in fluctuating conditions. The integration of these biological insights holds transformative potential for advancing next-generation bioenergy platforms, where algal-microbial systems could play a pivotal role in enhancing biofuel production, wastewater treatment, and sustainable agriculture.},
}
@article {pmid40043931,
year = {2025},
author = {Li, HQ and Wang, WL and Shen, YJ and Su, JQ},
title = {Mangrove plastisphere as a hotspot for high-risk antibiotic resistance genes and pathogens.},
journal = {Environmental research},
volume = {274},
number = {},
pages = {121282},
doi = {10.1016/j.envres.2025.121282},
pmid = {40043931},
issn = {1096-0953},
mesh = {*Wetlands ; *Bacteria/genetics ; *Microplastics ; Geologic Sediments/microbiology ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; *Water Pollutants, Chemical ; },
abstract = {Microplastics (MPs) are critical vectors for the dissemination of antibiotic resistance genes (ARGs); however, the prevalence and ecological risks of high-risk ARGs in mangrove ecosystems-globally vital yet understudied coastal habitats-remain poorly understood. To address this gap, this study investigated polyethylene, polystyrene, and polyvinyl chloride incubated in mangrove sediments for one month, focusing on high-risk ARGs, virulence gene (VGs), and pathogenic antibiotic-resistant bacteria within the mangrove plastisphere. High-throughput PCR and metagenomic analyses revealed that high-risk ARGs, VGs, and mobile genetic elements (MGEs) were significantly enriched on MPs compared to surrounding sediments. Pathogenic bacteria and MGEs were also more abundant in the plastisphere, highlighting its role as a hotspot for ARG dispersal. Metagenome-assembled genome analysis identified Pseudomonas and Bacillus as key hosts for ARGs, MGEs, and VGs, particularly multidrug resistance genes, integrase genes, and adherence factors. Notably, polystyrene harbored the highest abundance of pathogenic bacteria carrying ARGs, MGEs, and VGs, and mangrove root exudates were found to amplify horizontal gene transfer on MPs, uncovering a previously overlooked mechanism driving antibiotic resistance in coastal ecosystems. These findings not only elucidate how MPs accelerate the spread of ARGs, but also underscore the urgent need for targeted mitigation strategies to address the adverse impacts microplastic pollution on human, animal, and environmental health.},
}
@article {pmid40038805,
year = {2025},
author = {Diricks, M and Maurer, FP and Dreyer, V and Barilar, I and Utpatel, C and Merker, M and Wetzstein, N and Niemann, S},
title = {Genomic insights into the plasmidome of non-tuberculous mycobacteria.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {19},
pmid = {40038805},
issn = {1756-994X},
support = {2004//German Cystic Fibrosis Association Mukoviszidose e.V/ ; EXC 2167//The Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germanys Excellence Strategy Precision Medicine in Inflammation/ ; },
mesh = {*Plasmids/genetics ; *Nontuberculous Mycobacteria/genetics ; *Genome, Bacterial ; *Genomics/methods ; Humans ; Phylogeny ; Mycobacterium Infections, Nontuberculous/microbiology ; },
abstract = {BACKGROUND: Non-tuberculous mycobacteria (NTM) are a diverse group of environmental bacteria that are increasingly associated with human infections and difficult to treat. Plasmids, which might carry resistance and virulence factors, remain largely unexplored in NTM.<br><br>METHODS: We used publicly available complete genome sequence data of 328 NTM isolates belonging to 125 species to study gene content, genomic diversity, and clusters of 196 annotated NTM plasmids. Furthermore, we analyzed 3755 draft genome assemblies from over 200 NTM species and 5415 short-read sequence datasets from six clinically relevant NTM species or complexes including M. abscessus, M. avium complex, M. ulcerans complex and M. kansasii complex, for the presence of these plasmids.<br><br>RESULTS: Between one and five plasmids were present in approximately one-third of the complete NTM genomes. The annotated plasmids varied widely in length (most between 10 and 400 kbp) and gene content, with many genes having an unknown function. Predicted gene functions primarily involved plasmid replication, segregation, maintenance, and mobility. Only a few plasmids contained predicted genes that are known to confer resistance to antibiotics commonly used to treat NTM infections. Out of 196 annotated plasmid sequences, 116 could be grouped into 31 clusters of closely related sequences, and about one-third were found across multiple NTM species. Among clinically relevant NTM, the presence of NTM plasmids showed significant variation between species, within (sub)species, and even among strains within (sub)lineages, such as dominant circulating clones of Mycobacterium abscessus.<br><br>CONCLUSIONS: Our analysis demonstrates that plasmids are a diverse and heterogeneously distributed feature in NTM bacteria. The frequent occurrence of closely related putative plasmid sequences across different NTM species suggests they may play a significant role in NTM evolution through horizontal gene transfer at least in some groups of NTM. However, further in vitro investigations and access to more complete genomes are necessary to validate our findings, elucidate gene functions, identify novel plasmids, and comprehensively assess the role of plasmids in NTM.},
}
@article {pmid40036335,
year = {2025},
author = {Bergman, S and Birk, C and Holmqvist, E},
title = {ProQ prevents mRNA degradation through inhibition of poly(A) polymerase.},
journal = {Nucleic acids research},
volume = {53},
number = {5},
pages = {},
doi = {10.1093/nar/gkaf103},
pmid = {40036335},
issn = {1362-4962},
support = {2016-03656//Swedish Research Council/ ; ICA16-0021//Swedish Foundation for Strategic Research/ ; },
mesh = {*Salmonella typhimurium/genetics/pathogenicity ; *Bacterial Proteins/metabolism/genetics ; *Polynucleotide Adenylyltransferase/metabolism/genetics ; *Sigma Factor/metabolism/genetics ; *RNA Stability ; *RNA, Messenger/metabolism/genetics ; *Biofilms/growth &amp; development ; *Gene Expression Regulation, Bacterial ; RNA-Binding Proteins/metabolism/genetics ; 3' Untranslated Regions/genetics ; Polyadenylation ; },
abstract = {The RNA-binding protein ProQ interacts with many transcripts in the bacterial cell. ProQ binding is associated with increased messenger RNA (mRNA) levels, but a mechanistic explanation for this effect has been lacking. In Salmonella Typhimurium, ProQ affects key traits associated with infection, including motility and intracellular survival. However, the direct links between ProQ activity and these phenotypes are not well understood. Here, we demonstrate that ProQ promotes biofilm formation, another virulence-associated phenotype. This effect is strictly dependent on sigma factor RpoS. ProQ increases both RpoS protein and rpoS mRNA levels, but neither affects rpoS transcription nor translation. The rpoS mRNA is a ProQ target, and expression of the rpoS 3'UTR alone is strongly dependent on ProQ. RpoS expression becomes independent of ProQ in strains lacking poly(A) polymerase I (PAPI), indicating that ProQ protects against 3' end-dependent decay. Indeed, purified ProQ inhibits PAPI-mediated polyadenylation at RNA 3' ends. Finally, PAPI is required for ProQ's effect on expression of genes involved in biofilm, motility, osmotic stress, and virulence, indicating that inhibition of polyadenylation is a general function of ProQ.},
}
@article {pmid40035762,
year = {2025},
author = {Raymond, JA},
title = {A horizontally transferred bacterial gene aids the freezing tolerance of Antarctic bdelloid rotifers.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {10},
pages = {e2421910122},
pmid = {40035762},
issn = {1091-6490},
support = {OPP-9814294//National Science Foundation (NSF)/ ; OPP-088000//National Science Foundation (NSF)/ ; },
mesh = {Antarctic Regions ; *Gene Transfer, Horizontal ; *Freezing ; Animals ; *Rotifera/genetics ; Genes, Bacterial ; Antifreeze Proteins/genetics/metabolism ; },
abstract = {Bdelloid rotifers are well known for their abilities to survive long periods of freezing as well as acquire foreign genes. Recently sequenced genomes of some bdelloid rotifers in England were found to encode several proteins similar to ice-binding proteins (IBPs) that are usually associated with freeze-thaw tolerance. Here, I describe bdelloid rotifers inhabiting an algal patch in Antarctica that have multiple homologs of these genes. Structures of the proteins predicted by AlphaFold show that they are well designed for ice-binding and a recombinant protein made for one of them showed strong ice-binding activity. The existence of multiple copies of these proteins is another characteristic of IBPs. Furthermore, multiple bdelloid rotifers in the algal patch were revived in less than an hour after storage at -25 °C for 24 y, an apparent record for laboratory-controlled studies. Several characteristics of these genes point to bacteria as their source: sequence homology, absence of introns, and a structural peculiarity so far found only in bacteria. The remarkable freezing tolerance of bdelloid rotifers can thus be at least partially attributed to horizontally acquired bacterial genes encoding IBPs.},
}
@article {pmid40035521,
year = {2025},
author = {Kanakapura Sundararaj, B and Goyal, M and Samuelson, J},
title = {Targets for the diagnosis of Acanthamoeba eye infections include four cyst wall proteins and the mannose-binding domain of the trophozoite mannose-binding protein.},
journal = {mSphere},
volume = {10},
number = {3},
pages = {e0094824},
pmid = {40035521},
issn = {2379-5042},
support = {R01 GM129324/GM/NIGMS NIH HHS/United States ; Emerging Pathogens Initiative (EPI)//Howard Hughes Medical Institute (HHMI)/ ; },
mesh = {*Acanthamoeba/genetics/metabolism ; *Microscopy, Confocal ; *Trophozoites/metabolism ; *Protozoan Proteins/genetics/metabolism ; Animals ; Rabbits ; Humans ; Mannose-Binding Lectin/genetics/metabolism ; Amebiasis/diagnosis/parasitology ; Antibodies, Protozoan/immunology ; Cell Wall/metabolism/chemistry ; Acanthamoeba Keratitis/diagnosis/parasitology ; },
abstract = {Acanthamoebae, which are free-living amoebae, cause corneal inflammation (keratitis) and blindness, if not quickly diagnosed and effectively treated. The walls of Acanthamoeba cysts contain cellulose and have two layers connected by conical ostioles. Cysts are identified by in vivo confocal microscopy of the eye or calcofluor-white- or Giemsa-labeling of corneal scrapings, both of which demand great expertise. Trophozoites, which use a mannose-binding protein to adhere to keratinocytes, are identified in eye cultures that delay diagnosis and treatment. We recently used structural and experimental methods to characterize cellulose-binding domains of Luke and Leo lectins, which are abundant in the inner layer and ostioles. However, no antibodies have been made to these lectins or to a Jonah lectin and a laccase, which are abundant in the outer layer. Here, confocal microscopy of rabbit antibodies (rAbs) to recombinant Luke, Leo, Jonah, and laccase supported localizations of GFP-tagged proteins in walls of transfected Acanthamoebae. rAbs efficiently detected calcofluor white-labeled cysts of 10 of the 11 Acanthamoeba isolates tested, including six T4 genotypes that cause most cases of keratitis. Further, laccase shed into the medium during encystation was detected by an enzyme-linked immunoassay. Structural and experimental methods identified the mannose-binding domain (ManBD) of the Acanthamoeba mannose-binding protein, while rAbs to the ManBD efficiently detected DAPI-labeled trophozoites from all 11 Acanthamoeba isolates tested. We conclude that antibodies to four cyst wall proteins and the ManBD efficiently identify Acanthamoeba cysts and trophozoites, respectively.IMPORTANCEFree-living amoeba in the soil or water cause Acanthamoeba keratitis, which is diagnosed by identification of unlabeled cysts by in vivo confocal microscopy of the eye or calcofluor-white (CFW) labeled cysts by fluorescence microscopy of corneal scrapings. Alternatively, Acanthamoeba infections are diagnosed by the identification of trophozoites in eye cultures. Here, we showed that rabbit antibodies (rAbs) to four abundant cyst wall proteins (Jonah, Luke, Leo, and laccase) each efficiently identify CFW-labeled cysts of 10 of the 11 Acanthamoeba isolates tested. Further, laccase released into the medium by encysting Acanthamoebae was detected by an enzyme-linked immunoassay. We also showed that rAbs to the mannose-binding domain (ManBD) of the Acanthamoeba mannose-binding protein, which mediates adherence of trophozoites to keratinocytes, efficiently identify DAPI-labeled trophozoites of all 11 Acanthamoeba isolates tested. In summary, four wall proteins and the ManBD appear to be excellent targets for the diagnosis of Acanthamoeba cysts and trophozoites, respectively.},
}
@article {pmid40032822,
year = {2025},
author = {Biller, SJ and Ryan, MG and Li, J and Burger, A and Eppley, JM and Hackl, T and DeLong, EF},
title = {Distinct horizontal gene transfer potential of extracellular vesicles versus viral-like particles in marine habitats.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2126},
pmid = {40032822},
issn = {2041-1723},
support = {OCE-2049004//National Science Foundation (NSF)/ ; OCE-2304066//National Science Foundation (NSF)/ ; 917971//Simons Foundation/ ; },
mesh = {*Gene Transfer, Horizontal ; *Extracellular Vesicles/metabolism ; *Ecosystem ; Seawater/microbiology/virology ; Interspersed Repetitive Sequences ; Viruses/genetics/metabolism ; },
abstract = {Horizontal gene transfer (HGT) is enabled in part through the movement of DNA within two broad groups of small (<0.2 µm), diffusible nanoparticles: extracellular vesicles (EVs) and virus-like particles (VLPs; including viruses, gene transfer agents, and phage satellites). The information enclosed within these structures represents a substantial portion of the HGT potential available in planktonic ecosystems, but whether some genes might be preferentially transported through one type of nanoparticle versus another is unknown. Here we use long-read sequencing to compare the genetic content of EVs and VLPs from the oligotrophic North Pacific. Fractionated EV-enriched and VLP-enriched subpopulations contain diverse DNA from the surrounding microbial community, but differ in their capacity and encoded functions. The sequences carried by both particle types are enriched in mobile genetic elements (MGEs) as compared with other cellular chromosomal regions, and we highlight how this property enables novel MGE discovery. Examining the Pelagibacter mobilome reveals >7200 distinct chromosomal fragments and MGEs, many differentially partitioned between EVs and VLPs. Together these results suggest that distinctions in nanoparticle contents contribute to the mode and trajectory of microbial HGT networks and evolutionary dynamics in natural habitats.},
}
@article {pmid40032228,
year = {2025},
author = {Jiang, Z and Zeng, J and Wang, X and Yu, H and Yue, L and Wang, C and Chen, F and Wang, Z},
title = {Biodegradable microplastics and dissemination of antibiotic resistance genes: An undeniable risk associated with plastic additives.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {372},
number = {},
pages = {125952},
doi = {10.1016/j.envpol.2025.125952},
pmid = {40032228},
issn = {1873-6424},
mesh = {*Microplastics/toxicity ; *Escherichia coli/genetics/drug effects ; *Gene Transfer, Horizontal ; *Polyesters ; *Drug Resistance, Microbial/genetics ; *Biodegradable Plastics ; Dibutyl Phthalate/toxicity ; Plasticizers/toxicity ; Biodegradation, Environmental ; },
abstract = {Biodegradable plastics (BDPs) represent a promising alternative to conventional plastics; however, the release of microplastics (MPs) during degradation necessitates an urgent investigation into their biological effects. The potential risks associated with MPs and additives released from BDPs, particularly in facilitating the dissemination of antibiotic resistance genes (ARGs), remain largely unknown. This study aims to investigate the effects of polylactic acid (PLA) MPs and their common plasticizer, dibutyl phthalate (DBP), on the horizontal gene transfer (HGT) of ARGs using conjugative transfer and transformation model systems. The viability of Escherichia coli (E. coli) cells after exposure to PLA MPs (0.01, 0.1, 1, and 10 mg L[-1]), DBP (0.01, 0.1, 1, and 10 μg L[-1]) alone, or in combination (1 mg L[-1] PLA MPs + 1 μg L[-1]DBP) remained unaffected. Exposure to PLA MPs at environmentally relevant concentrations did not promote the HGT of ARGs. However, the addition of DBP significantly enhanced the transfer frequency by 1.5-1.8 folds compared to exposure to PLA MPs alone. The accelerated dissemination of ARGs was primarily attributed to the elevated levels of reactive oxygen species (by 26.2%), increased membrane permeability (by 19.4%), and the up-regulation of genes involved in mating pair formation (by 1.6-3.8 folds) and DNA translocation (by 1.5-3.4 folds). These findings underscore the critical role of additives and highlight the potential accumulative effects associated with prolonged exposure to high concentrations of PLA MPs, which should be considered for a comprehensive risk assessment of BDPs.},
}
@article {pmid40029705,
year = {2025},
author = {Hong, J and Xue, W and Wang, T},
title = {Emergence of alternative stable states in microbial communities undergoing horizontal gene transfer.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {40029705},
issn = {2050-084X},
support = {12401660//National Natural Science Foundation of China/ ; HSE499011086//Shenzhen Institue of Synthetic Biology Scientific Research Program/ ; },
mesh = {*Gene Transfer, Horizontal ; *Microbiota/genetics ; Bacteria/genetics ; Models, Theoretical ; Microbial Interactions/genetics ; Interspersed Repetitive Sequences/genetics ; Ecosystem ; },
abstract = {Microbial communities living in the same environment often display alternative stable states, each characterized by a unique composition of species. Understanding the origin and determinants of microbiome multistability has broad implications in environments, human health, and microbiome engineering. However, despite its conceptual importance, how multistability emerges in complex communities remains largely unknown. Here, we focused on the role of horizontal gene transfer (HGT), one important aspect mostly overlooked in previous studies, on the stability landscape of microbial populations. Combining mathematical modeling and numerical simulations, we demonstrate that, when mobile genetic elements (MGEs) only affect bacterial growth rates, increasing HGT rate in general promotes multistability of complex microbiota. We further extend our analysis to scenarios where HGT changes interspecies interactions, microbial communities are subjected to strong environmental selections and microbes live in metacommunities consisting of multiple local habitats. We also discuss the role of different mechanisms, including interspecies interaction strength, the growth rate effects of MGEs, MGE epistasis and microbial death rates in shaping the multistability of microbial communities undergoing HGT. These results reveal how different dynamic processes collectively shape community multistability and diversity. Our results provide key insights for the predictive control and engineering of complex microbiota.},
}
@article {pmid40027803,
year = {2025},
author = {Christman, ND and Dalia, AB},
title = {The molecular basis for DNA-binding by competence T4P is distinct in Gram-positive and Gram-negative species.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.17.638644},
pmid = {40027803},
issn = {2692-8205},
abstract = {UNLABELLED: Competence type IV pili (T4P) are bacterial surface appendages that facilitate DNA uptake during horizontal gene transfer by natural transformation. These dynamic structures actively extend from the cell surface, bind to DNA in the environment, and then retract to import bound DNA into the cell. Competence T4P are found in diverse Gram-negative (diderm) and Gram-positive (monoderm) bacterial species. While the mechanism of DNA-binding by diderm competence T4P has been the recent focus of intensive study, relatively little is known about DNA-binding by monoderm competence T4P. Here, we use Streptococcus pneumoniae as a model system to address this question. Competence T4P likely bind to DNA via a tip-associated complex of proteins called minor pilins, and recent work highlights a high degree of structural conservation between the minor pilin tip complexes of monoderm and diderm competence T4P. In diderms, positively charged residues in one minor pilin, FimT, are critical for DNA-binding. We show that while these residues are conserved in ComGD, the FimT homolog of monoderms, they only play a minor role in DNA uptake for natural transformation. Instead, we find that two-positively charged residues in the neighboring minor pilin, ComGF (the PilW homolog of monoderms), play the dominant role in DNA uptake for natural transformation. Furthermore, we find that these residues are conserved in other monoderms, but not diderms. Together, these results suggest that the molecular basis for DNA-binding has either diverged or evolved independently in monoderm and diderm competence T4P.<br><br>AUTHOR SUMMARY: Diverse bacteria use extracellular structures called competence type IV pili (T4P) to take up DNA from their environment. The uptake of DNA by T4P is the first step of natural transformation, a mode of horizontal gene transfer that contributes to the spread of antibiotic resistance and virulence traits in diverse clinically relevant Gram-negative (diderm) and Gram-positive (monoderm) bacterial species. While the mechanism of DNA binding by competence T4P in diderms has been an area of recent study, relatively little is known about how monoderm competence T4P bind DNA. Here, we explore how monoderm competence T4P bind DNA using Streptococcus pneumoniae as a model system. Our results indicate that while monoderm T4P and diderm T4P likely have conserved structural features, the DNA-binding mechanism of each system is distinct.},
}
@article {pmid40027742,
year = {2025},
author = {Tabatabaee, Y and Zhang, C and Arasti, S and Mirarab, S},
title = {Species tree branch length estimation despite incomplete lineage sorting, duplication, and loss.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.20.639320},
pmid = {40027742},
issn = {2692-8205},
abstract = {UNLABELLED: Phylogenetic branch lengths are essential for many analyses, such as estimating divergence times, analyzing rate changes, and studying adaptation. However, true gene tree heterogeneity due to incomplete lineage sorting (ILS), gene duplication and loss (GDL), and horizontal gene transfer (HGT) can complicate the estimation of species tree branch lengths. While several tools exist for estimating the topology of a species tree addressing various causes of gene tree discordance, much less attention has been paid to branch length estimation on multi-locus datasets. For single-copy gene trees, some methods are available that summarize gene tree branch lengths onto a species tree, including coalescent-based methods that account for heterogeneity due to ILS. However, no such branch length estimation method exists for multi-copy gene family trees that have evolved with gene duplication and loss. To address this gap, we introduce the CASTLES-Pro algorithm for estimating species tree branch lengths while accounting for both GDL and ILS. CASTLES-Pro improves on the existing coalescent-based branch length estimation method CASTLES by increasing its accuracy for single-copy gene trees and extends it to handle multi-copy ones. Our simulation studies show that CASTLES-Pro is generally more accurate than alternatives, eliminating the systematic bias toward overestimating terminal branch lengths often observed when using concatenation. Moreover, while not theoretically designed for HGT, we show that CASTLES-Pro maintains relatively high accuracy under high rates of random HGT.<br><br>CODE AVAILABILITY: CASTLES-Pro is implemented inside the software package ASTER, available at https://github.com/chaoszhang/ASTER .<br><br>DATA AVAILABILITY: The datasets and scripts used in this study are available at https://github.com/ytabatabaee/CASTLES-Pro-paper .},
}
@article {pmid40027631,
year = {2025},
author = {Schmidt, H and Raphael, BJ},
title = {The tree labeling polytope: a unified approach to ancestral reconstruction problems.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40027631},
issn = {2692-8205},
support = {U24 CA248453/CA/NCI NIH HHS/United States ; U24 CA264027/CA/NCI NIH HHS/United States ; },
abstract = {MOTIVATION: Reconstructing unobserved ancestral states of a phylogenetic tree provides insight into the history of evolving systems and is one of the fundamental problems in phylogenetics. For a fixed phylogenetic tree, the most parsimonious ancestral reconstruction - a solution to the small parsimony problem - can be efficiently found using the dynamic programming algorithms of Fitch-Hartigan and Sankoff. Ancestral reconstruction is important in many applications including inferring the routes of metastases in cancer, deriving the transmission history of viruses, determining the direction of cellular differentiation in organismal development, and detecting recombination and horizontal gene transfer in phylogenetic networks. However, most of these applications impose additional global constraints on the reconstructed ancestral states, which break the local structure required in the recurrences of Fitch-Hartigan and Sankoff.<br><br>RESULTS: We introduce an alternative, polyhedral approach to ancestral reconstruction problems using the tree labeling polytope, a geometric object whose vertices represent the feasible ancestral labelings of a tree. This framework yields a polynomial-time linear programming algorithm for the small parsimony problem. More importantly, the tree labeling polytope facilitates the incorporation of additional constraints that arise in modern ancestral reconstruction problems. We demonstrate the utility of our approach by deriving mixed-integer programming algorithms with a small number of integer variables and strong linear relaxations for three such problems: the parsimonious migration history problem, the softwired small parsimony problem on phylogenetic networks, and the convex recoloring problem on trees. Our algorithms outperform existing state-of-the-art methods on both simulated and real datasets. For instance, our algorithm scales to trace routes of cancer metastases in trees with thousands of leaves, enabling the analysis of large trees generated by recent single-cell sequencing technologies. On a mouse model of metastatic lung adenocarcinoma, the tree labeling polytope allows us to infer simpler migration histories compared to previous results.<br><br>AVAILABILITY: Python implementations of the algorithms provided in this work are available at: github.com/raphael-group/tree-labeling-polytope.},
}
@article {pmid40024690,
year = {2025},
author = {Wajima, T and Tanaka, E and Uchiya, KI},
title = {Unique and Ingenious Mechanisms Underlying Antimicrobial Resistance and Spread of Haemophilus influenzae.},
journal = {Biological &amp; pharmaceutical bulletin},
volume = {48},
number = {3},
pages = {205-212},
doi = {10.1248/bpb.b23-00640},
pmid = {40024690},
issn = {1347-5215},
mesh = {*Haemophilus influenzae/drug effects ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Haemophilus Infections/drug therapy/microbiology ; *Drug Resistance, Bacterial/genetics ; Animals ; },
abstract = {Antimicrobial resistance (AMR) is a serious global concern. AMR pathogens are found in hospitals and communities. Haemophilus influenzae is a common pathogen associated with community-acquired infections. H. influenzae infections are usually treated with β-lactams, macrolides, and quinolones. However, the drug-resistant strains have emerged. The resistance mechanisms of H. influenzae are complex but are roughly characterized by the acquisition of a mutation in antimicrobial-targeting genes and exogenous resistant genes. Generally, the former cannot be transferred horizontally to a susceptible strain. However, several studies have demonstrated that, in the case of H. influenzae, both the former and the latter can be transferred horizontally. In this review, we provide an overview of the bacterial features and antimicrobial resistance of H. influenzae. We also summarize the unique and ingenious antimicrobial resistance mechanisms used by this pathogen based on the findings of recent studies. These are expected to facilitate the understanding of AMR pathogens in the community and develop strategies to combat infections.},
}
@article {pmid40023817,
year = {2025},
author = {Shao, Y and Chen, M and Cai, J and Doi, Y and Chen, M and Wang, M and Zeng, M and Guo, Q},
title = {Cefotaxime-Resistant Neisseria meningitidis Sequence Type 4821 Causing Fulminant Meningitis.},
journal = {Emerging infectious diseases},
volume = {31},
number = {3},
pages = {591-595},
pmid = {40023817},
issn = {1080-6059},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Cefotaxime/therapeutic use/pharmacology ; *Neisseria meningitidis/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Child, Preschool ; *Meningitis, Meningococcal/microbiology/drug therapy ; Microbial Sensitivity Tests ; China ; Male ; Drug Resistance, Bacterial ; },
abstract = {We explored the role of commensal Neisseria in the emergence of third-generation cephalosporin-resistant N. meningitidis. Cefotaxime resistance-conferring penA795 was prevalent among commensal Neisseria isolates in Shanghai, China, and was acquired by a serogroup C quinolone-resistant sequence type 4821 N. meningitidis, Nm507, causing fulminant meningitis in an unvaccinated 2-year-old child.},
}
@article {pmid40019366,
year = {2025},
author = {Hu, Y and Gong, C and Yang, Z and Han, H and Tian, T and Yang, X and Xie, W and Wang, S and Wu, Q and Zhou, X and Turlings, TCJ and Guo, Z and Zhang, Y},
title = {Functional Divergence of Plant-Derived Thaumatin-Like Protein Genes in Two Closely Related Whitefly Species.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {12},
number = {16},
pages = {e2502193},
pmid = {40019366},
issn = {2198-3844},
support = {2021YFD1400600//National Key R &amp; D Program of China/ ; GZB20240839//Postdoctoral Fellowship Program of CPSF/ ; Y2023XK15//Central Public-interest Scientific Institution Basal Research Fund/ ; Y2024XK01//Central Public-interest Scientific Institution Basal Research Fund/ ; //Beijing Key Laboratory for Pest Control and Sustainable Cultivation of Vegetables/ ; //Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences/ ; 788949//European Research Council Advanced/ ; CARS-23//Earmarked Fund for China Agriculture Research System/ ; 2024M753572//China Postdoctoral Science Foundation/ ; 32221004//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Hemiptera/genetics ; *Gene Transfer, Horizontal/genetics ; *Plant Proteins/genetics ; Phylogeny ; Insect Proteins/genetics ; Evolution, Molecular ; },
abstract = {The recent discovery that various insects have acquired functional genes through horizontal gene transfer (HGT) has prompted numerous studies into this puzzling and fascinating phenomenon. So far, horizontally transferred genes are found to be functionally conserved and largely retained their ancestral functions. It evidently has not yet been considered that horizontally transferred genes may evolve and can contribute to divergence between species. Here, it is first showed that the genomes of the two widespread and agriculturally important whiteflies Trialeurodes vaporariorum and Bemisia tabaci both contain a plant-derived thaumatin-like protein (TLP) gene, but with highly distinct functions in these closely related pests. In T. vaporariorum, TLP has maintained a function similar to that of the plant donor, acting as an antimicrobial protein to resist fungal infection; but in sharp contrast, in B. tabaci, TLP has evolved into an effector that suppresses plant defense responses. These findings reveal an as-yet undescribed scenario of cross-species functional differentiation of horizontally transferred genes and suggest that the HGT-mediated evolutionary novelty can contribute to ecotypic divergence and even speciation.},
}
@article {pmid40013789,
year = {2025},
author = {Jin, M and Rouxel, O and Quintin, N and Geslin, C},
title = {Molecular piracy in deep-sea hydrothermal vent: phage-plasmid interactions revealed by phage-FISH in Marinitoga piezophila.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {3},
pages = {e0230624},
pmid = {40013789},
issn = {1098-5336},
mesh = {*Hydrothermal Vents/microbiology/virology ; *Plasmids/genetics ; *Bacteriophages/genetics/isolation &amp; purification ; *In Situ Hybridization, Fluorescence ; Gene Transfer, Horizontal ; Seawater/virology/microbiology ; DNA, Viral/genetics ; },
abstract = {UNLABELLED: Prokaryotes and mobile genetic elements (MGEs, such as viruses and plasmids) interact extensively, leading to horizontal gene transfer (HGT) and consequent microbial evolution and diversity. However, our knowledge of the interactions between MGEs in deep-sea hydrothermal ecosystems is limited. In this study, we adapted a phage-fluorescence in situ hybridization (phage-FISH) approach to visualize and quantify the dynamics of phage-plasmid interactions in an anaerobic, thermophilic deep-sea bacterium, Marinitoga piezophila. Notably, our results revealed that plasmid signals were detected in viral particles released from lysed cells, indicating that mitomycin C not only induced plasmid replication but also its packaging into phage particles. Further analysis of the DNA content in purified virions showed that the phage capsids incorporated plasmid DNA even without induction, and the majority of capsids (up to 70%) preferentially packaged plasmid DNA rather than viral DNA after induction. Therefore, this study provided direct evidence of molecular piracy in the deep-sea hydrothermal ecosystem, highlighting the important roles of selfish MGEs in virus-host interactions and HGT in extreme marine environments.<br><br>IMPORTANCE: Deep-sea hydrothermal vents are hotspots for microbes. Several studies revealed that virus-mediated horizontal gene transfer (HGT) in deep-sea hydrothermal vent ecosystems may be crucial to the survival and stability of prokaryotes in these extreme environments. However, little is known about the interaction between viruses and other mobile genetic elements (MGEs, such as plasmids), and how their interactions influence virus-mediated HGT in these ecosystems. In this study, we adapted a phage-fluorescence in situ hybridization approach to directly monitor the dynamics of phage-plasmid-host interactions at the single-cell level in the Marinitoga piezophila model. Interestingly, our results indicate that plasmid DNA could not only be induced by mitomycin C to a great extent but also hijacked viral assembly machinery to facilitate its propagation and spread. Therefore, the data presented here imply that the interaction between the viruses and other MGEs could play profound roles in virus-host interaction and virus-mediated HGT in the deep-sea hydrothermal ecosystem.},
}
@article {pmid40012781,
year = {2025},
author = {Zhao, B and Zhang, R and Jin, B and Yu, Z and Wen, W and Zhao, T and Quan, Y and Zhou, J},
title = {Sludge water: a potential pathway for the spread of antibiotic resistance and pathogenic bacteria from hospitals to the environment.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1492128},
pmid = {40012781},
issn = {1664-302X},
abstract = {Hospitals play an important role in the spread of antibiotic resistance genes (ARGs) and antimicrobial resistance (AMR). The ARGs present in hospital wastewater tend to accumulate in activated sludge, with different ARGs exhibiting varying migration rates. As a result, sludge water produced during the activated sludge treatment process may be a significant source of ARGs entering the environment. Despite this, research into the behavior of ARGs during sludge concentration and dewatering remains limited. This study hypothesizes that ARGs might exhibit new behaviors in sludge water during sludge concentration. Using metagenomic analysis, we explored the distribution and migration risks of ARGs and human pathogenic bacteria (HPB) in sludge water, comparing them with those in hospital wastewater. The findings reveal a strong correlation between ARGs in sludge water and hospital wastewater, with subtypes such as arlR, efpA, and tetR showing higher abundance in sludge water. Although the horizontal gene transfer potential of ARGs is greater in hospital wastewater than in sludge water, the resistance mechanisms and migration pathways are similar even when their HPB host associations differ. ARGs in both environments are primarily transmitted through coexisting mobile genetic elements (MGEs). This suggests that sludge water serves as a critical route for the release of hospital-derived ARGs into the environment, posing potential threats to public health and ecological safety.},
}
@article {pmid40010677,
year = {2025},
author = {Lapadula, WJ and Cañadas, MG and Ayub, MJ},
title = {Characterization of Ribosome inactivating protein genes and their transcripts in Trialeurodes vaporariorum.},
journal = {Gene},
volume = {948},
number = {},
pages = {149356},
doi = {10.1016/j.gene.2025.149356},
pmid = {40010677},
issn = {1879-0038},
mesh = {Animals ; *Ribosome Inactivating Proteins/genetics/metabolism ; *Hemiptera/genetics ; Insect Proteins/genetics/metabolism ; Female ; Transcriptome ; Phylogeny ; },
abstract = {Ribosome-inactivating proteins (RIPs) are rRNA N-glycosylases (EC 3.2.2.22) that depurinate an adenine residue from the conserved alpha-sarcin/ricin loop in rRNA, blocking protein synthesis. In previous research, we demonstrated that whiteflies from the Aleyrodidae family (e.g., Bemisia tabaci), mosquitoes from the Culicinae subfamily (e.g., Aedes aegypti), and flies of Sciaroidea superfamily (e.g., Contarinia nasturtii) acquired these genes via three independent horizontal gene transfer events. The temporal expression profiles analyzed in mosquitoes and flies are consistent with the expected for immune effector molecules of insects. Notably, in A. aegypti, we found that these genes contribute to immunity. In whiteflies, codon analysis suggests that RIP genes have evolved under the influence of natural selection. Public transcriptomic experiments have shown that these genes are expressed in the adult stage of B. tabaci. Despite computational findings supporting RIP genes functionality in whiteflies, no experimental studies have been conducted. Furthermore, there is currently no publicly available RNA-seq data evaluating gene expression throughout ontogeny in the Aleyrodidae family. In this work, we experimentally demonstrated the presence of these foreign genes in the genome of Trialeurodes vaporariorum. We quantified their expression across the life cycle stages of this species and analyzed their untranslated regions. The results obtained contribute to a deeper understanding of the biological roles that these ribotoxin encoding genes may play in whiteflies and other insects.},
}
@article {pmid40010597,
year = {2025},
author = {Wang, X and Lin, Y and Li, S and Wang, J and Li, X and Zhang, D and Duan, D and Shao, Z},
title = {Metagenomic analysis reveals the composition and sources of antibiotic resistance genes in coastal water ecosystems of the Yellow Sea and Yangtze River Delta.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {371},
number = {},
pages = {125923},
doi = {10.1016/j.envpol.2025.125923},
pmid = {40010597},
issn = {1873-6424},
mesh = {China ; *Metagenomics ; *Seawater/microbiology ; *Drug Resistance, Microbial/genetics ; *Rivers/chemistry/microbiology ; Ecosystem ; Bacteria/genetics/drug effects ; Environmental Monitoring ; Genes, Bacterial ; },
abstract = {The rapid development of coastal areas has raised concerns about marine environmental pollution. In this study, metagenomics was employed to investigate antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial communities in the Yellow Sea and Yangtze River Delta in China. Multidrug resistance genes were the most abundant ARGs in these regions. Transposons and insertion_element_IS91 were the dominant MGEs, closely related to the horizontal gene transfer of ARGs. Temperature, dissolved oxygen, pH, and depth were identified as important environmental factors influencing the distribution of ARGs in seawater. Oil, agriculture, animal husbandry, and wastewater treatment plants are likely the primary sources of ARGs. From the perspective of ARG control, bacterial communities contributed the most to the development of the resistome and may carry ARGs, spreading from the Yangtze River Delta to the Yellow Sea along ocean currents. A comparison with Tara Oceans datasets revealed that the dominant ARG types and bacterial genera in coastal waters were consistent with global characteristics, with variations in ARG subtypes. This study expands knowledge on the distribution patterns of ARGs at an offshore scale and provides a reference for the prevention and control of resistant gene pollution in the Yellow Sea and Yangtze River Delta.},
}
@article {pmid40008406,
year = {2025},
author = {Heida, A and Hamilton, MT and Gambino, J and Sanderson, K and Schoen, ME and Jahne, MA and Garland, J and Ramirez, L and Quon, H and Lopatkin, AJ and Hamilton, KA},
title = {Population Ecology-Quantitative Microbial Risk Assessment (QMRA) Model for Antibiotic-Resistant and Susceptible E. coli in Recreational Water.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {9},
pages = {4266-4281},
doi = {10.1021/acs.est.4c07248},
pmid = {40008406},
issn = {1520-5851},
mesh = {*Escherichia coli/drug effects ; Risk Assessment ; Water Microbiology ; Humans ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Urinary Tract Infections/microbiology ; beta-Lactamases ; },
abstract = {Understanding and predicting the role of waterborne environments in transmitting antimicrobial-resistant (AMR) infections are critical for public health. A population ecology-quantitative microbial risk assessment (QMRA) model is proposed to evaluate urinary tract infection (UTI) development due to recreational waterborne exposures to Escherichia coli (E. coli) and antibiotic-resistant extended-spectrum β-lactamase-producing (ESBL) E. coli. The horizontal gene transfer (HGT) mechanism of conjugation and other evolutionary factors were modeled separately in the environment and the gut. Persistence/dilution dominated HGT in the environment; however, HGT highly impacted predicted ESBL populations in the body. Predicted disability life year (DALY) risks from exposure to ESBL E. coli at concentrations consistent with US recreational water criteria were less than the 10[-6] pppy benchmark value but greater than the susceptible E. coli DALY risks associated with a UTI health outcome. However, the prevailing susceptible dose-response relationship may underestimate ESBL risk if HGT rates in vivo approach those reported in vitro. A sensitivity analysis demonstrated that DALY values, E. coli/ESBL concentrations, and exposure parameters were influential on predicted risks. The model is a preliminary tool to begin the expansion of the QMRA paradigm to explore the impacts of evolutionary changes in AMR risk assessment.},
}
@article {pmid40007369,
year = {2025},
author = {Li, S and Liu, Y and Zhang, Y and Huang, P and Bartlam, M and Wang, Y},
title = {Stereoselective behavior of naproxen chiral enantiomers in promoting horizontal transfer of antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137692},
doi = {10.1016/j.jhazmat.2025.137692},
pmid = {40007369},
issn = {1873-3336},
mesh = {*Gene Transfer, Horizontal/drug effects ; *Naproxen/chemistry/pharmacology ; Stereoisomerism ; *Drug Resistance, Microbial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Genes, Bacterial ; Rivers/microbiology ; *Water Pollutants, Chemical/chemistry ; Bacteria/genetics/drug effects ; },
abstract = {Antibiotic resistance poses a global threat to public health, with recent studies highlighting the role of non-antibiotic pharmaceuticals in the transmission of antibiotic resistance genes (ARGs). This study provides insights into the comprehensive profile, horizontal gene transfer potential, hosts, and public health risks associated with antibiotic resistomes in river ecosystems exposed to chiral naproxen (NAP). Our findings demonstrate that NAP stress selectively enriches ARGs and mobile genetic elements (MGEs), thereby bolstering bacterial resistance to specific antibiotics. Importantly, the spatial variation of NAP chiral enantiomers influences the enantioselective response of bacterial communities to antibiotics. While (S)-NAP and (R)-NAP exhibit differing degrees of horizontal transfer potential, (S/R)-NAP notably facilitates microbial aggregation and DNA transport via type IV secretion system (T4SS)-related functional genes, promoting the conjugation of sul1. Moreover, (S/R)-NAP promotes the horizontal transfer of ARGs by stimulating ROS production and altering cell membrane permeability. Chiral NAP exposure induces pathogens to acquire ARGs and accelerates the proliferation of Burkholderia. ARG-Rank analysis indicates that the health risk posed by (R)-NAP exposure surpasses that of (S)-NAP, with the highest risk observed when both enantiomers are present. This study elucidates the horizontal transfer and transmission mechanisms of ARGs under chiral NAP stress, underscoring the potential health hazards associated with NAP chiral enantiomers.},
}
@article {pmid40007158,
year = {2025},
author = {Ma, S and Li, S and Lu, X and Zhang, Q and Dong, M and Wu, Y and Lv, D and Luo, L and Jin, W and Liu, X and Yang, W and Djalovic, I and Wang, T and Zhou, X and Chen, R},
title = {A transposon-based cargo system mediates gene trafficking and creates ultra-clean transgenic plants after stable transformation.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70017},
pmid = {40007158},
issn = {1469-8137},
support = {2023ZD0403005//Biological Breeding-Major Projects/ ; 32171453//National Natural Science Foundation of China/ ; 20220101//CAAS-Syngenta Innovation Expansion Project/ ; 2021YFD1200700//National Key Research and Development Program of China/ ; //Innovation Program of Chinese Academy of Agricultural Sciences/ ; },
abstract = {Genetically modified crops have profound impacts on cost savings and environmental friendliness conferred by new traits, such as resistance to insects and herbicides. Selectable marker genes are essential for screening transformed cells, but they are undesirable in the final product due to the risks of horizontal gene transfer and extensive safety assessment requirements. Generating marker- and backbone-free lines can enhance the public acceptance of transgenic crops. Here, we established a transposon-mediated ultra-clean selectable transformant (TRUST) system for generating marker- and backbone-free transformants in a visibly controllable manner, facilitated by the integration of transposon elements, fluorescence proteins, and the anthocyanin biosynthesis gene. This system creates ultra-clean transgenic events that retain only the expression cassette of the gene of interest with an average probability of 15.5%. Additionally, long-read whole-genome sequencing confirmed the integrity of the expression cassette boundaries. The TRUST system is not only a powerful method for producing backbone-free transgenic plants but also increases the number of transgenic events originating from one starting event, thereby potentially leading to advances in the genetic engineering of recalcitrant crop varieties.},
}
@article {pmid40005743,
year = {2025},
author = {Liu, F and Cheewangkoon, R and Zhao, RL},
title = {Discovery of a New Starship Transposon Driving the Horizontal Transfer of the ToxA Virulence Gene in Alternaria ventricosa.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
pmid = {40005743},
issn = {2076-2607},
support = {(Project ID: 31961143010,31970010,32300012)//National Natural Science Foundation of China/ ; },
abstract = {The virulence gene ToxA has been proposed to be horizontally transferred between three fungal wheat pathogens (Parastagonospora nodorum, Pyrenophora tritici-repentis, and Bipolaris sorokiniana) as part of a conserved ~14 kb ToxhAT transposon. Here, our analysis of 2137 fungal species-representative assemblies revealed that the ToxA gene is an isolate of Alternaria ventricosa and shows a remarkable 99.5% similarity to those found in B. sorokiniana and P. tritici-repentis. Analysis of the regions flanking ToxA within A. ventricosa revealed that it was embedded within a 14 kb genomic element nearly identical to the corresponding ToxhAT regions in B. sorokiniana, P. nodorum, and P. tritici-repentis. Comparative analysis further showed that ToxhAT in A. ventricosa resides within a larger mobile genetic element, which we identified as a member of the Starship transposon superfamily, named Frontier. Our analysis demonstrated that ToxhAT has been independently captured by three distinct Starships-Frontier, Sanctuary, and Horizon-which, despite having minimal sequence similarity outside of ToxhAT, facilitate its mobilization. These findings place Frontier, Sanctuary, and Horizon within a growing class of Starships implicated in the horizontal transfer of adaptive genes among fungal species. Moreover, we identified three distinct HGT events involving ToxA across these four fungal species, reinforcing the hypothesis of a single evolutionary origin for the ToxhAT transposon. These findings underscore the pivotal role of transposon-mediated HGT in the adaptive evolution of eukaryotic pathogens, offering new insights into how transposons facilitate genetic exchange and shape host-pathogen interactions in fungi.},
}
@article {pmid40001581,
year = {2025},
author = {Liu, Z and Fan, X and Wu, Y and Zhang, W and Zhang, X and Xu, D and Wang, Y and Sun, K and Wang, W and Ye, N},
title = {Comparative Genomics of Bryopsis hypnoides: Structural Conservation and Gene Transfer Between Chloroplast and Mitochondrial Genomes.},
journal = {Biomolecules},
volume = {15},
number = {2},
pages = {},
pmid = {40001581},
issn = {2218-273X},
mesh = {*Genome, Mitochondrial/genetics ; *Genome, Chloroplast/genetics ; *Phylogeny ; *Genomics/methods ; Codon Usage ; Evolution, Molecular ; Gene Transfer, Horizontal ; RNA, Transfer/genetics ; },
abstract = {Bryopsis hypnoides, a unicellular multinucleate green alga in the genus Bryopsis, plays vital ecological roles and represents a key evolutionary link between unicellular and multicellular algae. However, its weak genetic baseline data have constrained the progress of evolutionary research. In this study, we successfully assembled and annotated the complete circular chloroplast and mitochondrial genomes of B. hypnoides. The chloroplast genome has a total length of 139,745 bp and contains 59 protein-coding genes, 2 rRNA genes, and 11 tRNA genes, with 31 genes associated with photosynthesis. The mitochondrial genome has a total length of 408,555 bp and contains 41 protein-coding genes, 3 rRNA genes, and 18 tRNA genes, with 18 genes involved in oxidative phosphorylation. Based on the data, we conducted a genetic comparison involving repeat sequences, phylogenetic relationships, codon usage preferences, and gene transfer between the two organellar genomes. The major results highlighted that (1) the chloroplast genome favors A/T repeats, whereas the mitochondrial genome prefers C/G repeats; (2) codon usage preference analysis indicated that both organellar genomes prefer codons ending in A/T, with a stronger bias observed in the chloroplast genome; and (3) sixteen fragments with high sequence identity were identified between the two organellar genomes, indicating potential gene transfer. These findings provide critical insights into the organellar genome characteristics and evolution of B. hypnoides.},
}
@article {pmid40001396,
year = {2025},
author = {Sher, AA and Whitehead-Tillery, CE and Peer, AM and Bell, JA and Vocelle, DB and Dippel, JT and Zhang, L and Mansfield, LS},
title = {Dynamic Spread of Antibiotic Resistance Determinants by Conjugation to a Human-Derived Gut Microbiota in a Transplanted Mouse Model.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {2},
pages = {},
pmid = {40001396},
issn = {2079-6382},
support = {RN031097-DEHN//Albert C. and Lois E. Dehn Chair Endowment/ ; NC1202//United States Department of Agriculture/ ; GS100019//University Distinguished Professor Endowment, Michigan State University/ ; U19AI090872//National Institutes of Health, Enterics Research Investigational Network, Cooperative Research Center/ ; Stipend to Azam A. Sher//College of Veterinary Medicine/ ; },
abstract = {BACKGROUND: Antibiotic-resistant (AR) bacteria pose an increasing threat to public health, but the dynamics of antibiotic resistance gene (ARG) spread in complex microbial communities are poorly understood. Conjugation is a predominant direct cell-to-cell mechanism for the horizontal gene transfer (HGT) of ARGs. We hypothesized that commensal Escherichia coli donor strains would mediate the conjugative transfer of ARGs to phylogenetically distinct bacteria without antibiotic selection pressure in gastrointestinal tracts of mice carrying a human-derived microbiota with undetectable levels of E. coli. Our objective was to identify a mouse model to study the factors regulating AR transfer by conjugation in the gut.<br><br>METHODS: Two donor E. coli strains were engineered to carry chromosomally encoded red fluorescent protein, and an ARG- and green fluorescent protein (GFP)-encoding broad host range RP4 conjugative plasmid. Mice were orally gavaged with two donor strains (1) E. coli MG1655 or (2) human-derived mouse-adapted E. coli LM715-1 and their colonization assessed by culture over time. Fluorescence-activated cell sorting (FACS) and 16S rDNA sequencing were performed to trace plasmid spread to the microbiota.<br><br>RESULTS: E. coli LM715-1 colonized mice for ten days, while E. coli MG1655 was not recovered after 72 h. Bacterial cells from fecal samples on days 1 and 3 post inoculation were sorted by FACS. Samples from mice given donor E. coli LM715-1 showed an increase in cells expressing green but not red fluorescence compared to pre-inoculation samples. 16S rRNA gene sequencing analysis of FACS GFP positive cells showed that bacterial families Lachnospiraceae, Clostridiaceae, Pseudomonadaceae, Rhodanobacteraceae, Erysipelotrichaceae, Oscillospiraceae, and Butyricicoccaceae were the primary recipients of the RP4 plasmid.<br><br>CONCLUSIONS: Results show this ARG-bearing conjugative RP4 plasmid spread to diverse human gut bacterial taxa within a live animal where they persisted. These fluorescent marker strategies and human-derived microbiota transplanted mice provided a tractable model for investigating the dynamic spread of ARGs within gut microbiota and could be applied rigorously to varied microbiotas to understand conditions facilitating their spread.},
}
@article {pmid40001389,
year = {2025},
author = {Pandova, M and Kizheva, Y and Hristova, P},
title = {Relationship Between CRISPR-Cas Systems and Acquisition of Tetracycline Resistance in Non-Clinical Enterococcus Populations in Bulgaria.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {2},
pages = {},
pmid = {40001389},
issn = {2079-6382},
support = {project No BG-RRP-2.004-0008//European Union-NextGenerationEU, National Recovery and Resilience Plan of the Republic of Bulgaria, SUMMIT 3.2.4./ ; },
abstract = {Non-clinical enterococci are relatively poorly studied by means of acquired antibiotic resistance to tetracycline and by the distribution, functionality and role of their CRISPR systems. Background: In our study, 72 enterococcal strains, isolated from various non-clinical origins, were investigated for their phenotypic and genotypic (tet(M), tet(O), tet(S), tet(L), tet(K), tet(T) and tet(W)) tetracycline resistance. Methods: The genetic determinants for HGT (MGEs (Int-Tn and prgW), inducible pheromones (cpd, cop and cff), aggregation substances (agg, asa1, prgB and asa373) and CRISPR-Cas systems were characterized by PCR and whole-genome sequencing. Results: Four tet genes (tetM, tetO, tetS and tetT) were detected in 39% (n = 28) of our enterococcal population, with tetM (31%) being dominant. The gene location was linked to the Tn6009 transposon. All strains that contained tet genes also had genes for HGT. No tet genes were found in E. casseliflavus and E. gilvus. In our study, 79% of all tet-positive strains correlated with non-functional CRISPR systems. The strain E. faecalis BM15 was the only one containing a combination of a functional CRISPR system (cas1, cas2, csn2 and csn1/cas9) and tet genes. The CRISPR subtype repeats II-A, III-B, IV-A2 and VI-B1 were identified among E. faecalis strains (CM4-II-A, III-B and VI-B1; BM5-IV-A2, II-A and III-B; BM12 and BM15-II-A). The subtype II-A was the most present. These repeats enclosed a great number of spacers (1-10 spacers) with lengths of 31 to 36 bp. One CRISPR locus was identified in plasmid (p.Firmicutes1 in strain E. faecalis BM5). We described the presence of CRISPR loci in the species E. pseudoavium, E. pallens and E. devriesei and their lack in E. gilvus, E. malodoratus and E. mundtii. Conclusions: Our findings generally describe the acquisition of foreign DNA as a consequence of CRISPR inactivation, and self-targeting spacers as the main cause.},
}
@article {pmid40001375,
year = {2025},
author = {La Rosa, MC and Maugeri, A and Favara, G and La Mastra, C and Magnano San Lio, R and Barchitta, M and Agodi, A},
title = {The Impact of Wastewater on Antimicrobial Resistance: A Scoping Review of Transmission Pathways and Contributing Factors.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {2},
pages = {},
pmid = {40001375},
issn = {2079-6382},
abstract = {BACKGROUND/OBJECTIVES: Antimicrobial resistance (AMR) is a global issue driven by the overuse of antibiotics in healthcare, agriculture, and veterinary settings. Wastewater and treatment plants (WWTPs) act as reservoirs for antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). The One Health approach emphasizes the interconnectedness of human, animal, and environmental health in addressing AMR. This scoping review analyzes wastewater's role in the AMR spread, identifies influencing factors, and highlights research gaps to guide interventions.<br><br>METHODS: This scoping review followed the PRISMA-ScR guidelines. A comprehensive literature search was conducted across the PubMed and Web of Science databases for articles published up to June 2024, supplemented by manual reference checks. The review focused on wastewater as a source of AMR, including hospital effluents, industrial and urban sewage, and agricultural runoff. Screening and selection were independently performed by two reviewers, with conflicts resolved by a third.<br><br>RESULTS: Of 3367 studies identified, 70 met the inclusion criteria. The findings indicated that antibiotic residues, heavy metals, and microbial interactions in wastewater are key drivers of AMR development. Although WWTPs aim to reduce contaminants, they often create conditions conducive to horizontal gene transfer, amplifying resistance. Promising interventions, such as advanced treatment methods and regulatory measures, exist but require further research and implementation.<br><br>CONCLUSIONS: Wastewater plays a pivotal role in AMR dissemination. Targeted interventions in wastewater management are essential to mitigate AMR risks. Future studies should prioritize understanding AMR dynamics in wastewater ecosystems and evaluating scalable mitigation strategies to support global health efforts.},
}
@article {pmid40000989,
year = {2025},
author = {Zhao, M and Zhang, Y and Liu, S and Wang, F and Zhang, P},
title = {Eradication of Helicobacter pylori reshapes gut microbiota and facilitates the evolution of antimicrobial resistance through gene transfer and genomic mutations in the gut.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {90},
pmid = {40000989},
issn = {1471-2180},
support = {32201393//National Natural Science Foundation of China/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Humans ; *Helicobacter pylori/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Helicobacter Infections/microbiology/drug therapy ; *Gene Transfer, Horizontal ; *Feces/microbiology ; Mutation ; Metagenomics ; Klebsiella/genetics/drug effects ; Female ; Male ; Genome, Bacterial/genetics ; Adult ; Escherichia/genetics/drug effects ; Middle Aged ; Genes, Bacterial/genetics ; },
abstract = {Treating Helicobacter pylori (H. pylori) infection requires large quantities of antibiotics, thus dramatically promoting the enrichment and dissemination of antimicrobial resistance (AMR) in feces. However, the influence of H. pylori eradication on the AMR mobility and the gut microbiota evolution has yet to be thoroughly investigated. Here, a study involving 12 H. pylori-positive participants was conducted, and the pre- and post- eradication fecal samples were sequenced. Metagenomic analysis revealed that the eradication treatment drastically altered the gut microbiome, with the Escherichia and Klebsiella genera emerging as the predominant bacteria. Interestingly, the eradication treatment significantly increased the relative abundance and diversity of resistome and mobilome in gut microbiota. Eradication of H. pylori also enriched AMR genes (ARGs) conferring resistance to antibiotics not administered because of the co-location with other ARGs or mobile genetic elements (MGEs). Additionally, the Escherichia and Klebsiella genera were identified as the primary bacterial hosts of these highly transferable ARGs. Furthermore, the genomic variations associated with ARGs in Escherichia coli (E. coli) caused by the eradication treatment were profiled, including the parC, parE, and gyrA genes. These findings revealed that H. pylori eradication promoted the enrichment of ARGs and MGEs in the Escherichia and Klebsiella genera, and further facilitated bacterial evolution through the horizontal transfer of ARGs and genomic variations.},
}
@article {pmid39998220,
year = {2025},
author = {Kwak, Y and Argandona, JA and Miao, S and Son, TJ and Hansen, AK},
title = {A dual insect symbiont and plant pathogen improves insect host fitness under arginine limitation.},
journal = {mBio},
volume = {16},
number = {4},
pages = {e0358824},
pmid = {39998220},
issn = {2150-7511},
support = {S10 OD010786/OD/NIH HHS/United States ; 2019-70016-29066//U.S. Department of Agriculture (USDA)/ ; },
mesh = {Animals ; *Symbiosis ; *Hemiptera/microbiology/physiology ; *Arginine/metabolism/deficiency ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; *Liberibacter/physiology/genetics ; Plant Diseases/microbiology ; },
abstract = {Some facultative bacterial symbionts are known to benefit insects, but nutritional advantages are rare among these non-obligate symbionts. Here, we demonstrate that the facultative symbiont Candidatus Liberibacter psyllaurous enhances the fitness of its psyllid insect host, Bactericera cockerelli, by providing nutritional benefits. L. psyllaurous, an unculturable pathogen of solanaceous crops, also establishes a close relationship with its insect vector, B. cockerelli, increasing in titer during insect development, vertically transmitting through eggs, and colonizing various tissues, including the bacteriome, which houses the obligate nutritional symbiont, Carsonella. Carsonella supplies essential amino acids to its insect host but has gaps in some of its essential amino acid pathways that the psyllid complements with its own genes, many of which have been acquired through horizontal gene transfer (HGT) from bacteria. Our findings reveal that L. psyllaurous increases psyllid fitness on plants by reducing developmental time and increasing adult weight. In addition, through metagenomic sequencing, we reveal that L. psyllaurous maintains complete pathways for synthesizing the essential amino acids arginine, lysine, and threonine, unlike the psyllid's other resident microbiota, Carsonella, and two co-occurring Wolbachia strains. RNA sequencing reveals the downregulation of a HGT collaborative psyllid gene (ASL), which indicates a reduced demand for arginine supplied by Carsonella when the psyllid is infected with L. psyllaurous. Notably, artificial diet assays show that L. psyllaurous enhances psyllid fitness on an arginine-deplete diet. These results corroborate the role of L. psyllaurous as a beneficial insect symbiont, contributing to the nutrition of its insect host.IMPORTANCEUnlike obligate symbionts that are permanently associated with their hosts, facultative symbionts rarely show direct nutritional contributions, especially under nutrient-limited conditions. This study demonstrates, for the first time, that Candidatus Liberibacter psyllaurous, a facultative symbiont and a plant pathogen, enhances the fitness of its Bactericera cockerelli host by supplying an essential nutrient arginine that is lacking in the plant sap diet. Our findings reveal how facultative symbionts can play a vital role in helping their insect hosts adapt to nutrient-limited environments. This work provides new insights into the dynamic interactions between insect hosts, their symbiotic microbes, and their shared ecological niches, broadening our understanding of symbiosis and its role in shaping adaptation and survival.},
}
@article {pmid39993662,
year = {2025},
author = {Chen, M and Yan, X and Tang, Q and Liu, M and Yang, M and Chai, Y and Wei, Y and Shen, P and Zhang, J},
title = {Particle size transfer of antibiotic resistance genes in typical processes of municipal wastewater treatment plant.},
journal = {Bioresource technology},
volume = {424},
number = {},
pages = {132288},
doi = {10.1016/j.biortech.2025.132288},
pmid = {39993662},
issn = {1873-2976},
mesh = {*Particle Size ; *Sewage/microbiology ; *Wastewater ; *Water Purification/methods ; *Drug Resistance, Microbial/genetics ; Bioreactors ; Genes, Bacterial ; Gene Transfer, Horizontal ; Waste Disposal, Fluid/methods ; Cities ; },
abstract = {Occurrence and transfer of antibiotic resistance genes (ARGs) was investigated concerning sludge particle size in a typical wastewater treatment plant, and the roles of vertical (VGT) and horizontal gene transfer (HGT) in the spread of ARGs were explored. Results showed that although membrane bioreactor (MBR) effectively reduced the relative abundance of ARGs in the water phase, it concurrently enriched ARGs in MBR sludge, particularly for the largest-size particles (>150 μm). A decreasing trend in the relative abundance of ARGs was observed along with the decrease of sludge particle size, and larger-size particle sludge (>106 μm) formed a relatively stable composition of ARGs, while ARGs on smaller-size particle sludge (6.5-106 μm) fluctuate rapidly. Particle size does not affect the abundance distribution patterns or assembly mechanisms of ARGs as deterministic processes. The smallest-size particles were the primary attachment site for bacterial pathogens with highest diversity. Larger-size particle sludge (>106 μm) showed higher frequency of HGT, with Proteobacteria as the dominant hosts for this process.},
}
@article {pmid39990427,
year = {2025},
author = {Cai, L and Havird, JC and Jansen, RK},
title = {Recombination and retroprocessing in broomrapes reveal a universal roadmap for mitochondrial evolution in heterotrophic plants.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39990427},
issn = {2692-8205},
support = {R35 GM142836/GM/NIGMS NIH HHS/United States ; },
abstract = {The altered life history strategies of heterotrophic organisms often leave a profound genetic footprint on energy metabolism related functions. In parasitic plants, the reliance on host-derived nutrients and loss of photosynthesis in holoparasites have led to highly degraded to absent plastid genomes, but its impact on mitochondrial genome (mitogenome) evolution has remained controversial. By examining mitogenomes from 45 Orobanchaceae species including three independent transitions to holoparasitism and key evolutionary intermediates, we identified measurable and predictable genetic alterations in genomic shuffling, RNA editing, and intracellular (IGT) and horizontal gene transfer (HGT) en route to a nonphotosynthetic lifestyle. In-depth comparative analyses revealed DNA recombination and repair processes, especially RNA-mediated retroprocessing, as significant drivers for genome structure evolution. In particular, we identified a novel RNA-mediated IGT and HGT mechanism, which has not been demonstrated in cross-species and inter-organelle transfers. Based on this, we propose a generalized dosage effect mechanism to explain the biased transferability of plastid DNA to mitochondria across green plants, especially in heterotrophic lineages like parasites and mycoheterotrophs. Evolutionary rates scaled with these genomic changes, but the direction and strength of selection varied substantially among genes and clades, resulting in high contingency in mitochondrial genome evolution. Finally, we describe a universal roadmap for mitochondrial evolution in heterotrophic plants where increased recombination and repair activities, rather than relaxed selection alone, lead to differentiated genome structure compared to free-living species.},
}
@article {pmid39988254,
year = {2025},
author = {Hou, W and Yu, J and Shi, H and Xu, J and Chen, SS and Shaban, SS and Kim, Y and Bai, J},
title = {As a reservoir of antibiotic resistance genes and pathogens, the hydrodynamic characteristics drive their distribution patterns in Lake Victoria.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {370},
number = {},
pages = {125903},
doi = {10.1016/j.envpol.2025.125903},
pmid = {39988254},
issn = {1873-6424},
mesh = {*Lakes/microbiology/chemistry ; *Hydrodynamics ; *Bacteria/genetics ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Environmental Monitoring ; Drug Resistance, Bacterial/genetics ; },
abstract = {Antibiotic resistance genes (ARGs) and pathogenic bacteria pose significant challenges to human health, and hydrodynamic processes complicate their transmission mechanisms in lake ecosystems, particularly in tropical regions. Lake Victoria supports abundant water resources and provides livelihoods for millions of people, yet the environmental behavior of ARGs and pathogenic bacteria remains unclear. Herein, the novel insights into the co-occurrence patterns and transmission mechanisms of ARGs and pathogenic bacteria in Lake Victoria was investigated via molecular techniques and a hydrodynamic model. The results showed that as a large reservoir of ARGs and pathogenic bacteria, a total of 172 ARG subtypes and 93 pathogenic bacteria were identified in Lake Victoria. ARGs were spread through mobile genetic elements (tnpA4 and int2), enhancing the antibiotic resistance and virulence factors (secretion systems, regulatory factors, and toxins) of various pathogenic bacteria. The hydrodynamic model indicated that surface wind-driven currents and bottom compensatory flows shaped the outward dispersion of ARGs and pathogenic bacteria from the gulf. The NCM model suggested that water exchange accelerated the diffusion of antibiotics and pathogens, likely enhancing the deterministic assembly process of ARGs and the stochastic assembly process of pathogens. The PLS-PM model revealed that hydrodynamics directly influenced the accumulation of ARGs and pathogenic bacteria, and subsequently affected the diffusion and distribution patterns of ARGs and pathogens by facilitating the propagation of MGEs. Our study overcomes the limitations associated with lake and microenvironmental scale, providing insights and understanding into the transmission mechanisms of ARGs and pathogenic bacteria.},
}
@article {pmid39988071,
year = {2025},
author = {Le, NT and Hoang, PH and Nguyen, Q and Truong, MNH and Van Dang, C and Ho, TH and Hoang, PL and Truong, DQ and Nguyen, HTT and Van Le, C and Phan, TTP},
title = {Emergence of mcr-8.2-mediated colistin resistance in Klebsiella pneumoniae isolated from pediatric diarrhea cases in southern Vietnam.},
journal = {Journal of global antimicrobial resistance},
volume = {42},
number = {},
pages = {120-126},
doi = {10.1016/j.jgar.2025.02.007},
pmid = {39988071},
issn = {2213-7173},
abstract = {BACKGROUND: Colistin resistance poses a growing global challenge, particularly in low- and middle-income countries where antibiotic misuse is prevalent. This study investigates the prevalence of colistin resistance in Klebsiella spp. and characterizes the genetic features of resistant isolates, focusing on the mcr-8.2 gene identified in a Klebsiella pneumoniae isolate from pediatric diarrheal cases in southern Vietnam.<br><br>METHODS: Stool samples were collected from 500 pediatric patients (aged 0-5 years) hospitalized with diarrhea in two tertiary hospitals in Ho Chi Minh City between March and September 2022. Samples were cultured on Violet Red Bile Glucose Agar, then presumptive Klebsiella spp. colonies were selected, purified on nutrient agar, and identified using MALDI-TOF MS. Colistin resistance was determined via minimum inhibitory concentration testing, and the presence of mcr genes was confirmed through polymerase chain reaction. Whole-genome sequencing was performed on the Klebsiella pneumoniae strain harboring mcr-8.2 to elucidate resistance mechanisms. Strain characterization was performed using multi-locus sequence typing, while conjugation experiments assessed horizontal gene transfer potential.<br><br>RESULTS: Among 121 Klebsiella spp. isolates, 49 (40.5%) were resistant to colistin. The mcr-1 gene was detected in 31 isolates (25.6%), whereas the mcr-8 was identified in a single isolate (0.8%), with a colistin MIC of 16 &#xb5;g/mL. Genomic analysis revealed 34 antibiotic resistance genes, including mcr-8.2 and multiple &#x3b2;-lactamase genes, alongside plasmid types IncFIB and IncFII. Chromosomal mutations in phoP, phoQ, and lpxM were also implicated in colistin resistance.<br><br>CONCLUSIONS: This study documents the emergence of mcr-8.2-mediated colistin resistance in K. pneumoniae from pediatric diarrhea in Vietnam and highlights a high prevalence of multidrug resistance in Klebsiella spp.. Continuous surveillance of mcr genes and novel therapeutic strategies are urgently needed.},
}
@article {pmid39987875,
year = {2025},
author = {Pourrostami Niavol, K and Andaluri, G and Achary, MP and Suri, RPS},
title = {How does carbon to nitrogen ratio and carrier type affect moving bed biofilm reactor (MBBR): Performance evaluation and the fate of antibiotic resistance genes.},
journal = {Journal of environmental management},
volume = {377},
number = {},
pages = {124619},
doi = {10.1016/j.jenvman.2025.124619},
pmid = {39987875},
issn = {1095-8630},
mesh = {*Biofilms ; *Bioreactors ; *Nitrogen/metabolism ; *Carbon ; *Drug Resistance, Microbial/genetics ; Wastewater/microbiology ; Waste Disposal, Fluid/methods ; Denitrification ; Anti-Bacterial Agents/pharmacology ; },
abstract = {With the spread of antibiotic resistance genes (ARGs) in the environment, monitoring and controlling ARGs have become an emerging issue of concern in biological processes. Moving bed biofilm reactors (MBBR) have been gaining attention for application in wastewater treatment. Since the performance of MBBR depends on operational parameters and biocarriers, selection of suitable biocarriers and start-up conditions are vital for efficiency of MBBRs. This study investigates the effects of different carbon-to-nitrogen (C/N) ratios and carrier types on the fate of selected ARGs and microbial communities in four MBBR systems using two conventional (K3 and sponge biocarrier (SB)) and two modified carriers (Fe-Ca@SB and Ze-AC@SB). Results showed that the modified biocarriers achieved higher NH4-N removal and better simultaneous nitrification and denitrification (SND) performance (90%) at C/N of 20. However, as the C/N ratio decreased to 10 and 7, the performance of all bioreactors was approximately similar. Moreover, COD removal of 90% was achieved in all reactors regardless of C/N ratio and carrier type. Further studies on the fate of selected ARGs (tetA, blaTEM, ampR) showed that the C/N ratio could affect the abundance of target ARGs, especially for K3 biocarrier, with tetA being the most abundant gene. Also, as the C/N ratio decreased, intl1 was enriched using K3 and SB. However, for Ze-AC@SB, the increase in the abundance of ARGs and intl1 was the lowest making it a reliable carrier not only in MBBR performance but in the control of ARGs. Metagenomic studies showed that the C/N ratio and carrier type could alter the diversity and structure of the bacterial communities in different MBBR systems, with Proteobacteria being the most abundant phylum in all four systems.},
}
@article {pmid39987738,
year = {2025},
author = {Su, H and Xu, W and Hu, X and Xu, Y and Wen, G and Cao, Y},
title = {The impact of microplastics on antibiotic resistance genes, metal resistance genes, and bacterial community in aquaculture environment.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137704},
doi = {10.1016/j.jhazmat.2025.137704},
pmid = {39987738},
issn = {1873-3336},
mesh = {*Microplastics/toxicity ; Aquaculture ; *Water Pollutants, Chemical/toxicity ; *Bacteria/genetics/drug effects ; *Genes, Bacterial/drug effects ; *Drug Resistance, Microbial/genetics ; *Metals/pharmacology ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Microplastics are emerging contaminants. However, their effects on antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and the structure and abundance of bacterial communities, particularly pathogens, in aquaculture environments remains poorly understood. Therefore, this study investigated the effect of microplastics of different sizes on the abundance and distribution of ARGs, MRGs, and bacterial communities in aquaculture environments. The results revealed that, compared with pond water, large microplastics harbored significantly higher ARG abundances, particularly for multidrug-resistant genes; notably, level-I- and -II-risk ARGs were more prevalent on microplastics, highlighting the potential for horizontal gene transfer. Microplastics also exhibited a propensity to aggregate pathogenic bacteria such as Brucella and Pseudomonas, which could pose direct risks to aquatic product safety and public health. Network and differential network analyses revealed significant correlations between bacterial genera and ARG/MRG abundance, particularly on microplastics. Therefore, our findings suggest that microplastics act as vectors for the spread of ARGs, MRGs, and pathogens in aquaculture, potentially leading to the formation of complexes of these materials that threaten ecosystem health and human well-being. This study provides critical insights into the need for targeted management strategies to mitigate microplastic pollution in aquaculture settings.},
}
@article {pmid39981300,
year = {2025},
author = {Proença, M and Tanoeiro, L and Fox, JG and Vale, FF},
title = {Prophage dynamics in gastric and enterohepatic environments: unraveling ecological barriers and adaptive transitions.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf017},
pmid = {39981300},
issn = {2730-6151},
abstract = {Phage predation plays a critical role in shaping bacterial genetic diversity, with prophages playing a comparable role. However, the prevalence and genetic variability of prophages within the Helicobacter genus remain inadequately studied. Helicobacter species are clinically significant and occupy distinct digestive system regions, with gastric species (e.g. Helicobacter pylori) residing in the gastric mucosa and enterohepatic species colonizing the liver and intestines of various vertebrates. Here, we address this knowledge gap by analyzing prophage presence and diversity across 343 non-pylori Helicobacter genomes, mapping their distribution, comparing genomic features between gastric and enterohepatic prophages, and exploring their evolutionary relationships with hosts. We identified and analyzed a catalog of 119 new complete and 78 incomplete prophages. Our analysis reveals significant differences between gastric and enterohepatic species. Gastric prophages exhibit high synteny, and cluster in a few groups, indicating a more conserved genetic structure. In contrast, enterohepatic prophages show greater diversity in gene order and content, reflecting their adaptation to varied host environments. Helicobacter cinaedi stands out, harboring a large number of prophages among the enterohepatic species, forming a distinct cohesive group. Phylogenetic analyses reveal a co-evolutionary relationship between several prophages and their bacterial hosts-though exceptions, such as the enterohepatic prophages from H. canis, H. equorum, H. jaachi, and the gastric prophage from H. himalayensis-suggesting more complex co-evolutionary dynamics like host jumps, recombination, and horizontal gene transfer. The insights gained from this study enhance our understanding of prophage dynamics in Helicobacter, emphasizing their role in bacterial adaptation, virulence, and host specificity.},
}
@article {pmid39980242,
year = {2025},
author = {Yonemitsu, MA and Sevigny, JK and Vandepas, LE and Dimond, JL and Giersch, RM and Gurney-Smith, HJ and Abbott, CL and Supernault, J and Withler, R and Smith, PD and Weinandt, SA and Garrett, FES and Child, ZJ and Sigo, RLW and Unsell, E and Crim, RN and Metzger, MJ},
title = {Multiple Lineages of Transmissible Neoplasia in the Basket Cockle (C. nuttallii) With Repeated Horizontal Transfer of Mitochondrial DNA.},
journal = {Molecular ecology},
volume = {34},
number = {6},
pages = {e17682},
doi = {10.1111/mec.17682},
pmid = {39980242},
issn = {1365-294X},
support = {//National Research Council/ ; 2208081//Division of Ocean Sciences/ ; A19AP00215//Bureau of Indian Affairs/ ; },
mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Cardiidae/genetics ; *Phylogeny ; *Gene Transfer, Horizontal ; Neoplasms/genetics ; Washington ; },
abstract = {Transmissible cancers are clonal lineages of neoplastic cells able to infect multiple hosts, spreading through populations in the environment as an infectious disease. Transmissible cancers have been identified in Tasmanian devils, dogs, and bivalves. Several lineages of bivalve transmissible neoplasias (BTN) have been identified in multiple bivalve species. In 2019 in Puget Sound, Washington, USA, disseminated neoplasia was observed in basket cockles (Clinocardium nuttallii), a species that is important to the culture and diet of the Suquamish Tribe as well as other tribes with traditional access to the species. To test whether disseminated neoplasia in cockles is a previously unknown lineage of BTN, a nuclear locus was amplified from cockles from Agate Pass, Washington, and sequences revealed evidence of transmissible cancer in several individuals. We used a combination of cytology and quantitative PCR to screen collections of cockles from 11 locations in Puget Sound and along the Washington coastline to identify the extent of contagious cancer spread in this species. Two BTN lineages were identified in these cockles, with one of those lineages (CnuBTN1) being the most prevalent and geographically widespread. Within the CnuBTN1 lineage, multiple nuclear loci support the conclusion that all cancer samples form a single clonal lineage. However, the mitochondrial alleles in each cockle with CnuBTN1 are different from each other, suggesting mitochondrial genomes of this cancer have been replaced multiple times during its evolution, through horizontal transmission. The identification and analysis of these BTNs are critical for broodstock selection, management practices, and repopulation of declining cockle populations, which will enable continued cultural connection and dietary use of the cockles by Coast Salish Tribes.},
}
@article {pmid39979200,
year = {2025},
author = {Huisman, JS and Bernhard, A and Igler, C},
title = {Should I stay or should I go: transmission trade-offs in phages and plasmids.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.01.007},
pmid = {39979200},
issn = {1878-4380},
abstract = {Mobile genetic elements (MGEs), like temperate bacteriophages and conjugative plasmids, are major vectors of virulence and antibiotic resistance in bacterial populations. For reproductive success, MGEs must balance horizontal and vertical transmission. Yet, the cost of horizontal transmission (metabolic burden or host death) puts these transmission modes at odds. Using virulence-transmission trade-off (VTT) theory, we identify three groups of environmental variables affecting the balance between horizontal and vertical transmission: host density, host physiology, and competitors. We find that general theoretical predictions of the optimal response to environmental cues align with experimental evidence on the regulation of transmission by phages and plasmids. We further highlight gaps between theory and experiments, differences between phages and plasmids, and suggest areas for future research.},
}
@article {pmid39976625,
year = {2025},
author = {Lin, YJ and Chen, CH and Chang, IY and Chiang, RL and Wang, HY and Chiu, CH and Chen, YM},
title = {Genomic and transcriptomic insights into the virulence and adaptation of shock syndrome-causing Streptococcus anginosus.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {2},
pages = {},
doi = {10.1099/mic.0.001535},
pmid = {39976625},
issn = {1465-2080},
mesh = {*Streptococcus anginosus/genetics/pathogenicity ; *Genome, Bacterial ; Humans ; Virulence/genetics ; *Genomic Islands/genetics ; *Streptococcal Infections/microbiology ; Virulence Factors/genetics/metabolism ; Transcriptome ; Shock, Septic/microbiology ; Genomics ; Prophages/genetics ; Adolescent ; Gene Transfer, Horizontal ; Clustered Regularly Interspaced Short Palindromic Repeats ; Bacterial Proteins/genetics/metabolism ; Quorum Sensing/genetics ; },
abstract = {Streptococcus anginosus is a common isolate of the oral cavity and an opportunistic pathogen for systemic infections. Although the pyogenic infections caused by S. anginosus are similar to those caused by Streptococcus pyogenes, S. anginosus lacks most of the well-characterized virulence factors of S. pyogenes. To investigate the pathogenicity of S. anginosus, we analysed the genome of a newly identified S. anginosus strain, KH1, which was associated with toxic shock-like syndrome in an immunocompetent adolescent. The genome of KH1 contains nine genomic islands, two Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated systems and many phage-related proteins, indicating that the genome is influenced by prophages and horizontal gene transfer. Comparative genome analysis of 355 S. anginosus strains revealed a significant difference between the sizes of the pan genome and core genome, reflecting notable strain variations. We further analysed the transcriptomes of KH1 under conditions mimicking either the oral cavity or the bloodstream. We found that in an artificial saliva medium, the expression of a putative quorum quenching system and pyruvate oxidase for H2O2 production was upregulated, which could optimize the competitiveness of S. anginosus in the oral ecosystem. Conversely, in a modified serum medium, purine and glucan biosynthesis, competence and bacteriocin production were significantly upregulated, likely facilitating the survival of KH1 in the bloodstream. These findings indicate that S. anginosus can utilize diverse mechanisms to adapt to different environmental niches and establish infection, despite its lack of toxin production.},
}
@article {pmid39976429,
year = {2025},
author = {Smith, EP and Valdivia, RH},
title = {Chlamydia trachomatis: a model for intracellular bacterial parasitism.},
journal = {Journal of bacteriology},
volume = {207},
number = {3},
pages = {e0036124},
pmid = {39976429},
issn = {1098-5530},
support = {R21 AI173599/AI/NIAID NIH HHS/United States ; R21 AI173599-02//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {*Chlamydia trachomatis/genetics/physiology/pathogenicity ; Humans ; Animals ; *Chlamydia Infections/microbiology ; Virulence ; },
abstract = {Chlamydia comprises a diverse group of obligate intracellular bacteria that cause infections in animals, including humans. These organisms share fascinating biology, including distinct developmental stages, non-canonical cell surface structures, and adaptations to intracellular parasitism. Chlamydia trachomatis is of particular interest due to its significant clinical importance, causing both ocular and sexually transmitted infections. The strain L2/434/Bu, responsible for lymphogranuloma venereum, is the most common strain used to study chlamydial molecular and cell biology because it grows readily in cell culture and is amenable to genetic manipulation. Indeed, this strain has enabled researchers to tackle fundamental questions about the molecular mechanisms underlying Chlamydia's developmental transitions and biphasic lifecycle and cellular adaptations to obligate intracellular parasitism, including characterizing numerous conserved virulence genes and defining immune responses. However, L2/434/Bu is not representative of C. trachomatis strains that cause urogenital infections in humans, limiting its utility in addressing questions of host tropism and immune evasion in reproductive organs. Recent research efforts are shifting toward understanding the unique attributes of more clinically relevant C. trachomatis genovars.},
}
@article {pmid39975115,
year = {2025},
author = {Bean, EL and Smith, JL and Grossman, AD},
title = {Identification of insertion sites for the integrative and conjugative element Tn916 in the Bacillus subtilis chromosome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39975115},
issn = {2692-8205},
support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; R35 GM122538/GM/NIGMS NIH HHS/United States ; R35 GM148343/GM/NIGMS NIH HHS/United States ; },
abstract = {Integrative and conjugative elements (ICEs) are found in many bacterial species and are mediators of horizontal gene transfer. Tn916 is an ICE found in several Gram-positive genera, including Enterococcus, Staphylococcus, Streptococcus, and Clostridum. In contrast to the many ICEs that preferentially integrate into a single site, Tn916 can integrate into many sites in the host chromosome. The consensus integration motif for Tn916, based on analyses of approximately 200 independent insertions, is an approximately 16 bp AT-rich sequence. Here, we describe the identification and mapping of approximately 10[5] independent Tn916 insertions in the Bacillus subtilis chromosome. The insertions were distributed between 1,554 chromosomal sites, and approximately 99% of the insertions were in 303 sites and 65% were in only ten sites. One region, between ykuC and ykyB (kre), was a 'hotspot' for integration with ~22% of the insertions in that single location. In almost all of the top 99% of sites, Tn916 was found with similar frequencies in both orientations relative to the chromosome and relative to the direction of transcription, with a few notable exceptions. Using the sequences of all insertion regions, we determined a consensus motif which is similar to that previously identified for Clostridium difficile. The insertion sites are largely AT-rich, and some sites overlap with regions bound by the nucleoid-associated protein Rok, a functional analog of H-NS of Gram-negative bacteria. Rok functions as a negative regulator of at least some horizontally acquired genes. We found that the presence or absence of Rok had little or no effect on insertion site specificity of Tn916.},
}
@article {pmid39974991,
year = {2025},
author = {Hullinger, AC and Green, VE and Klancher, CA and Dalia, TN and Dalia, AB},
title = {Two transmembrane transcriptional regulators coordinate to activate chitin-induced natural transformation in Vibrio cholerae.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.30.615920},
pmid = {39974991},
issn = {2692-8205},
abstract = {UNLABELLED: Transcriptional regulators are a broad class of proteins that alter gene expression in response to environmental stimuli. Transmembrane transcriptional regulators (TTRs) are a subset of transcriptional regulators in bacteria that can directly regulate gene expression while remaining anchored in the membrane. Whether this constraint impacts the ability of TTRs to bind their DNA targets remains unclear. Vibrio cholerae uses two TTRs, ChiS and TfoS, to activate horizontal gene transfer by natural transformation in response to chitin by inducing the tfoR promoter (P tfoR). While TfoS was previously shown to bind and regulate P tfoR directly, the role of ChiS in P tfoR activation remains unclear. Here, we show that ChiS directly binds P tfoR upstream of TfoS, and that ChiS directly interacts with TfoS. By independently disrupting ChiS-P tfoR and ChiS-TfoS interactions, we show that ChiS-P tfoR interactions play the dominant role in P tfoR activation. Correspondingly, we show that in the absence of ChiS, recruitment of the P tfoR locus to the membrane is sufficient for P tfoR activation when TfoS is expressed at native levels. Finally, we show that the overexpression of TfoS can bypass the need for ChiS for P tfoR activation. All together, these data suggest a model whereby ChiS both (1) recruits the P tfoR DNA locus to the membrane for TfoS and (2) directly interacts with TfoS, thereby recruiting it to the membrane-proximal promoter. This work furthers our understanding of the molecular mechanisms that drive chitin-induced responses in V. cholerae and more broadly highlights how the membrane-embedded localization of TTRs can impact their activity.<br><br>AUTHOR SUMMARY: Living organisms inhabit diverse environments where they encounter a wide range of stressors. To survive, they must rapidly sense and respond to their surroundings. One universally conserved mechanism to respond to stimuli is via the action of DNA-binding transcriptional regulators. In bacterial species, these regulators are canonically cytoplasmic proteins that freely diffuse within the cytoplasm. In contrast, an emerging class of transmembrane transcriptional regulators (TTRs) directly regulate gene expression from the cell membrane. Prior work shows that two TTRs, TfoS and ChiS, cooperate to activate horizontal gene transfer by natural transformation in response to chitin in the facultative pathogen Vibrio cholerae . However, how these TTRs coordinate to activate this response has remained unclear. Here, we show that ChiS likely promotes TfoS-dependent activation of natural transformation by (1) relocalizing its target promoter to the membrane and (2) recruiting TfoS to the membrane proximal promoter through a direct interaction. Together, these results inform our understanding of both the V. cholerae chitin response and how TTR function can be impacted by their membrane localization.},
}
@article {pmid39970645,
year = {2025},
author = {Wang, W and Tao, J and Pang, R and Zhang, L and Zhang, Y and Su, Y and Li, W and Hong, S and Kim, H and Zhan, M and Xie, B},
title = {Effect of alkaline-thermal pretreatment on biodegradable plastics degradation and dissemination of antibiotic resistance genes in co-compost system.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137644},
doi = {10.1016/j.jhazmat.2025.137644},
pmid = {39970645},
issn = {1873-3336},
mesh = {Biodegradation, Environmental ; *Drug Resistance, Microbial/genetics ; *Composting ; *Biodegradable Plastics/chemistry/metabolism ; *Sodium Hydroxide/chemistry ; Genes, Bacterial ; Soil Microbiology ; Bacteria/genetics ; },
abstract = {Biodegradable plastics (BDPs) are an eco-friendly alternative to traditional plastics in organic waste, but their microbial degradation and impact on antibiotic resistance genes (ARGs) transmission during co-composting remain poorly understood. This study examines how alkaline-thermal pretreatment enhances BDPs degradation and influences the fate of ARGs and mobile genetic elements (MGEs) in co-composting. Pretreatment with 0.1 mol/L NaOH at 100℃ for 40 minutes increased the surface roughness and hydrophilicity of BDPs while reducing their molecular weight and thermal stability. Incorporating pretreated BDPs film (8 g/kg-TS) into the compost reduced the molecular weight of the BDPs by 59.70 % during the maturation stage, facilitating compost heating and prolonging the thermophilic stage. However, incomplete degradation of BDPs releases numerous smaller-sized microplastics, which can act as carriers for microorganisms, facilitating the dissemination of ARGs across environments and posing significant ecological and public health risks. Metagenomic analysis revealed that pretreatment enriched plastic-degrading bacteria, such as Thermobifida fusca, on BDPs surfaces and accelerated microbial plastic degradation during the thermophilic stage, but also increased ARGs abundance. Although pretreatment significantly reduced MGEs abundance (tnpA, IS19), the risk of ARGs dissemination remained. Three plastic-degrading bacteria (Pigmentiphaga sp002188465, Bacillus clausii, and Bacillus altitudinis) were identified as ARGs hosts, underscoring the need to address the risk of horizontal gene transfer of ARGs associated with pretreatment in organic waste management.},
}
@article {pmid39970091,
year = {2024},
author = {Sazykin, IS and Sazykina, MA and Litsevich, AR},
title = {[Distribution of Antibiotic Resistance Genes in Microbial Communities: The Impact of Anthropogenic Pollution].},
journal = {Molekuliarnaia biologiia},
volume = {58},
number = {6},
pages = {937-952},
pmid = {39970091},
issn = {0026-8984},
mesh = {*Bacteria/genetics/drug effects/classification/metabolism ; *Oxidative Stress/drug effects/genetics ; Drug Resistance, Bacterial/genetics/drug effects ; Gene Transfer, Horizontal ; Humans ; Anti-Bacterial Agents/pharmacology ; Environmental Pollution ; Microbiota/drug effects/genetics ; Drug Resistance, Microbial/genetics ; Animals ; Genes, Bacterial ; Wastewater/microbiology ; Evolution, Molecular ; },
abstract = {Issues related to the spread of antibiotic resistance genes in environmental microbial communities are considered. "Hotspots" of adaptive evolution, accumulation, and spread of antibiotic-resistant bacteria and genetic material of antibiotic resistance are highlighted. Such "hotspots" include anthropogenic ecosystems, such as municipal wastewater treatment plants, municipal solid waste landfills, livestock enterprises, and agrocenoses. The influence of various types of pollutants and biotic factors on enhancement of mutagenesis and horizontal transfer of antibiotic resistance genes is considered. The role of mobile genetic elements in mobilization and accelerated spread of resistance determinants is shown. Special attention is paid to the role of oxidative stress and stress regulons, which are activated for realization and control of molecular genetic mechanisms of adaptive evolution of bacteria and the horizontal distribution of genetic material in bacterial populations. Oxidative stress is identified as one of the main activators of genome destabilization and adaptive evolution of bacteria.},
}
@article {pmid39970089,
year = {2024},
author = {Shaskolskiy, BL and Kandinov, ID and Gryadunov, DA and Kravtsov, DV},
title = {[Unveiling Neisseria gonorrhoeae Survival: Genetic Variability, Pathogenesis, and Antimicrobial Drug Resistance].},
journal = {Molekuliarnaia biologiia},
volume = {58},
number = {6},
pages = {887-926},
pmid = {39970089},
issn = {0026-8984},
mesh = {*Neisseria gonorrhoeae/genetics/pathogenicity/drug effects/immunology ; Humans ; *Gonorrhea/drug therapy/microbiology/genetics/immunology ; *Drug Resistance, Bacterial/genetics ; Genetic Variation ; Female ; Gene Transfer, Horizontal ; Male ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Immune Evasion/genetics ; Type IV Secretion Systems/genetics ; },
abstract = {Despite nearly a century of therapy for gonococcal infection with a variety of antimicrobials, more than 80 million cases of the disease are reported annually worldwide. The gonorrhea pathogen, Neisseria gonorrhoeae, exhibits an exceptional capability of developing antimicrobial resistance due to its high genetic flexibility. As an obligate pathogen, the gonococcus has evolved mechanisms to evade host defenses by engaging with the innate and adaptive immune responses in both men and women. N. gonorrhoeae can establish residence within epithelial cells, macrophages, and neutrophils. Strains resistant to each of the drugs used in gonorrhea therapy have emerged via genetic variation and horizontal gene transfer. The type IV secretion system plays a critical role in horizontal gene transfer (HGT), driving the evolvement of antimicrobial resistance. The review explores the pathogenesis and immune evasion mechanisms, antimicrobial resistance, genetic variability, laboratory analysis methods for the pathogen, and emerging trends in diagnosis and treatment of gonococcal infections.},
}
@article {pmid39966712,
year = {2025},
author = {Hoile, AE and Holland, PWH and Mulhair, PO},
title = {Gene novelty and gene family expansion in the early evolution of Lepidoptera.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {161},
pmid = {39966712},
issn = {1471-2164},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *Lepidoptera/genetics ; *Evolution, Molecular ; *Phylogeny ; *Gene Duplication ; *Multigene Family ; Gene Transfer, Horizontal ; Insect Proteins/genetics ; },
abstract = {BACKGROUND: Almost 10% of all known animal species belong to Lepidoptera: moths and butterflies. To understand how this incredible diversity evolved we assess the role of gene gain in driving early lepidopteran evolution. Here, we compared the complete genomes of 115 insect species, including 99 Lepidoptera, to search for novel genes coincident with the emergence of Lepidoptera.<br><br>RESULTS: We find 217 orthogroups or gene families which emerged on the branch leading to Lepidoptera; of these 177 likely arose by gene duplication followed by extensive sequence divergence, 2 are candidates for origin by horizontal gene transfer, and 38 have no known homology outside of Lepidoptera and possibly arose via de novo gene genesis. We focus on two new gene families that are conserved across all lepidopteran species and underwent extensive duplication, suggesting important roles in lepidopteran biology. One encodes a family of sugar and ion transporter molecules, potentially involved in the evolution of diverse feeding behaviours in early Lepidoptera. The second encodes a family of unusual propeller-shaped proteins that likely originated by horizontal gene transfer from Spiroplasma bacteria; we name these the Lepidoptera propellin genes.<br><br>CONCLUSION: We provide the first insights into the role of genetic novelty in the early evolution of Lepidoptera. This gives new insight into the rate of gene gain during the evolution of the order as well as providing context on the likely mechanisms of origin. We describe examples of new genes which were retained and duplicated further in all lepidopteran species, suggesting their importance in Lepidoptera evolution.},
}
@article {pmid39966674,
year = {2025},
author = {Mondol, SM and Hossain, MA and Haque, FKM},
title = {Comprehensive genomic insights into a highly pathogenic clone ST656 of mcr8.1 containing multidrug-resistant Klebsiella pneumoniae from Bangladesh.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {5909},
pmid = {39966674},
issn = {2045-2322},
mesh = {*Klebsiella pneumoniae/genetics/drug effects/pathogenicity ; Bangladesh ; *Drug Resistance, Multiple, Bacterial/genetics ; *Genome, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Humans ; Genomics/methods ; Klebsiella Infections/microbiology ; Virulence Factors/genetics ; Microbial Sensitivity Tests ; Plasmids/genetics ; Colistin/pharmacology ; },
abstract = {Antimicrobial resistance (AMR) is a pressing global health issue, intensified by the spread of resistant pathogens like Klebsiella pneumoniae (K. pneumoniae), which frequently causes hospital-acquired infections. This study focuses on a multidrug-resistant K. pneumoniae sequence type (ST) 656 strain, isolated from canal water in Bangladesh. Whole-genome sequencing and comparative genomic analysis revealed extensive resistance mechanisms and genetic elements underlying its adaptability. The strain exhibited resistance to colistin and multiple β-lactam antibiotics, containing key resistance genes such as mcr8.1, blaLAP-2, blaTEM-1, blaSHV-11 and blaOXA-1, alongside genes for copper, zinc, and silver resistance, indicating survival capability in metal-rich environments. Virulence factor analysis identified genes supporting adhesion, biofilm formation, and immune evasion, amplifying its pathogenic potential. Plasmid and phage analyses revealed mobile genetic elements, highlighting the role of horizontal gene transfer in AMR dissemination. The study included a pangenome analysis using a dataset of 32 publicly available K. pneumoniae sequence type (ST) 656 genomes, demonstrating evidence of an expanding pangenome for K. pneumoniae ST656. This study emphasized the role of environmental sources in AMR spread and the importance of continued surveillance, particularly in settings with intensive antibiotic usage, to mitigate the spread of high-risk, multidrug-resistant clones like K. pneumoniae ST656.},
}
@article {pmid39965334,
year = {2025},
author = {Zhang, J and Lei, H and Huang, J and Wong, JWC and Li, B},
title = {Co-occurrence and co-expression of antibiotic, biocide, and metal resistance genes with mobile genetic elements in microbial communities subjected to long-term antibiotic pressure: Novel insights from metagenomics and metatranscriptomics.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137559},
doi = {10.1016/j.jhazmat.2025.137559},
pmid = {39965334},
issn = {1873-3336},
mesh = {*Anti-Bacterial Agents/pharmacology ; Chloramphenicol/pharmacology ; Metagenomics ; *Genes, Bacterial ; *Disinfectants/pharmacology ; *Bacteria/genetics/drug effects ; *Interspersed Repetitive Sequences ; Drug Resistance, Microbial/genetics ; Lincomycin/pharmacology ; Gene Transfer, Horizontal ; Transcriptome ; Metals/pharmacology ; *Drug Resistance, Bacterial/genetics ; },
abstract = {The burgeoning of antibiotic resistance has emerged as a pressing global challenge. To gain a deeper understanding of the interactions between antibiotic resistance genes (ARGs), biocide and metal resistance genes (BRGs&amp;MRGs), and mobile genetic elements (MGEs), this study utilized metagenomics and metatranscriptomics to investigate their co-occurrence and co-expression in two consortia subjected to long-term exposure to chloramphenicol and lincomycin. Long-term exposure to these antibiotics resulted in significant disparities in resistance profiles: ConsortiumCAP harbored 130 ARGs and 150 BRGs&amp;MRGs, while ConsortiumLIN contained 57 ARGs and 32 BRGs&amp;MRGs. Horizontal gene transfer (HGT) events were predicted at 125 and 300 instances in ConsortiumCAP and ConsortiumLIN, respectively, facilitating the emergence of multidrug-resistant bacteria, such as Caballeronia (10 ARGs, 2 BRGs&amp;MRGs), Cupriavidus (2 ARGs, 10 BRGs&amp;MRGs), and Bacillus (14 ARGs, 21 BRGs&amp;MRGs). Chloramphenicol exposure significantly enriched genes linked to phenicol resistance (floR, capO) and co-expressed ARGs and BRGs&amp;MRGs, while lincomycin exerted narrower effects on resistance genes. Additionally, both antibiotics modulated the expression of degradation genes and virulence factors, highlighting their role in altering bacterial substrate utilization and pathogenic traits. This study provides quantitative insights into the impact of antibiotics on microbial resistance profiles and functions at both DNA and RNA levels, highlighting the importance of reducing antibiotic pollution and limiting the spread of resistance genes in the environment.},
}
@article {pmid39965000,
year = {2025},
author = {Hullinger, AC and Green, VE and Klancher, CA and Dalia, TN and Dalia, AB},
title = {Two transmembrane transcriptional regulators coordinate to activate chitin-induced natural transformation in Vibrio cholerae.},
journal = {PLoS genetics},
volume = {21},
number = {2},
pages = {e1011606},
pmid = {39965000},
issn = {1553-7404},
support = {R35 GM128674/GM/NIGMS NIH HHS/United States ; },
mesh = {*Vibrio cholerae/genetics/metabolism ; *Chitin/metabolism/genetics ; *Gene Expression Regulation, Bacterial ; *Promoter Regions, Genetic/genetics ; *Bacterial Proteins/genetics/metabolism ; *Transcription Factors/genetics/metabolism ; Gene Transfer, Horizontal ; },
abstract = {Transcriptional regulators are a broad class of proteins that alter gene expression in response to environmental stimuli. Transmembrane transcriptional regulators (TTRs) are a subset of transcriptional regulators in bacteria that can directly regulate gene expression while remaining anchored in the membrane. Whether this constraint impacts the ability of TTRs to bind their DNA targets remains unclear. Vibrio cholerae uses two TTRs, ChiS and TfoS, to activate horizontal gene transfer by natural transformation in response to chitin by inducing the tfoR promoter (PtfoR). While TfoS was previously shown to bind and regulate PtfoR directly, the role of ChiS in PtfoR activation remains unclear. Here, we show that ChiS directly binds PtfoR upstream of TfoS, and that ChiS directly interacts with TfoS. By independently disrupting ChiS-PtfoR and ChiS-TfoS interactions, we show that ChiS-PtfoR interactions play the dominant role in PtfoR activation. Correspondingly, we show that in the absence of ChiS, recruitment of the PtfoR locus to the membrane is sufficient for PtfoR activation when TfoS is expressed at native levels. Finally, we show that the overexpression of TfoS can bypass the need for ChiS for PtfoR activation. All together, these data suggest a model whereby ChiS both (1) recruits the PtfoR DNA locus to the membrane for TfoS and (2) directly interacts with TfoS, thereby recruiting it to the membrane-proximal promoter. This work furthers our understanding of the molecular mechanisms that drive chitin-induced responses in V. cholerae and more broadly highlights how the membrane-embedded localization of TTRs can impact their activity.},
}
@article {pmid39964597,
year = {2025},
author = {Palanikumar, P and Nathan, B and Muthusamy, K and M, S and Natesan, S and Sampathrajan, V},
title = {Unravelling the Antibiotic Resistance: Molecular Insights and Combating Therapies.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {39964597},
issn = {1559-0291},
abstract = {Antibiotics, the full-stop of invasive bacteria, have been used in clinical setups from unthreatening fever to massive challenging therapies. Constant dependency on medication upsurges the evasion of microbes from antibiotics contemporarily along with ecological footprint. Thus, the infested pathogen became resilient to antibiotics, disguised as multidrug-resistant bacteria (MDR), pandrug-resistant bacteria (PDR), and extensively drug-resistant bacteria (XDR). The etymology of genetic modifications and horizontal gene transfer played an external influence on the arising resurgence. Also, intrinsic parameters, such as antibiotic efflux pumps and the formation of biofilms, encouraged intense resistance to antibiotic drugs. This aggravated resistance in microbes builds up resistome in the environment due to selective pressure; thereby drastic devastation of people suffering from disastrous diseases is mournful. Since novelite approaches for broad-spectrum antibiotics against drug resistance microbes are grueling challenges in these crucial times. This scientific study has come up with neoteric methodologies to elude immediate consequences and health hazards. Inculcating ancestral treatment towards pharmacognosy as adjuvants to the prevailing hi-fi nanotechnology, phage and algal therapy, genome mining, and bioinformatics databases are the optimizing inventions for actual and prospective living.},
}
@article {pmid39960880,
year = {2025},
author = {Zou, W and Ji, Y and Guan, J and Sun, Y},
title = {MOSTPLAS: a self-correction multi-label learning model for plasmid host range prediction.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {3},
pages = {},
pmid = {39960880},
issn = {1367-4811},
support = {11214924//Research Grants Council/ ; //City University of Hong Kong/ ; },
mesh = {*Plasmids/genetics ; *Algorithms ; Host Specificity ; Machine Learning ; Bacteria/genetics ; Computational Biology/methods ; Gene Transfer, Horizontal ; },
abstract = {MOTIVATION: Plasmids play an essential role in horizontal gene transfer, aiding their host bacteria in acquiring beneficial traits like antibiotic and metal resistance. There exist some plasmids that can transfer, replicate, or persist in multiple organisms. Identifying the relatively complete host range of these plasmids provides insights into how plasmids promote bacterial evolution. To achieve this, we can apply multi-label learning models for plasmid host range prediction. However, there are no databases providing the detailed and complete host labels of these broad-host-range plasmids. Without adequate well-annotated training samples, learning models can fail to extract discriminative feature representations for plasmid host prediction.<br><br>RESULTS: To address this problem, we propose a self-correction multi-label learning model called MOSTPLAS. We design a pseudo label learning algorithm and a self-correction asymmetric loss to facilitate the training of multi-label learning model with samples containing some unknown missing labels. We conducted a series of experiments on the NCBI RefSeq plasmid database, the PLSDB 2025 database, plasmids with experimentally determined host labels, the Hi-C dataset, and the DoriC dataset. The benchmark results against other plasmid host range prediction tools demonstrated that MOSTPLAS recognized more host labels while keeping a high precision.<br><br>MOSTPLAS is implemented with Python, which can be downloaded at https://github.com/wzou96/MOSTPLAS. All relevant data we used in the experiments can be found at https://zenodo.org/doi/10.5281/zenodo.14708999.},
}
@article {pmid39960859,
year = {2025},
author = {Chess, MM and Foley, S and Ettensohn, CA},
title = {Horizontal Transfer of msp130 Genes and the Evolution of Metazoan Biocalcification.},
journal = {Genome biology and evolution},
volume = {17},
number = {2},
pages = {},
pmid = {39960859},
issn = {1759-6653},
support = {P41 HD095831/HD/NICHD NIH HHS/United States ; IOS2004952//National Science Foundation/ ; P41HD095831/NH/NIH HHS/United States ; },
mesh = {*Gene Transfer, Horizontal ; Animals ; *Phylogeny ; *Evolution, Molecular ; Calcification, Physiologic/genetics ; Gene Duplication ; Bacteria/genetics ; },
abstract = {The formation of calcified skeletons is crucial for the development, physiology, and ecology of many marine metazoans. The evolutionary origins of the genetic toolkit required for biocalcification are widely debated. MSP130 proteins, originally identified through their expression specifically by sea urchin skeletal cells, have been hypothesized to have been acquired by metazoans from bacteria through horizontal gene transfer. Here, we provide support for a horizontal gene transfer-based origin of metazoan MSP130 proteins by conducting phylogenetic and in silico protein analyses utilizing high-quality genomes. We show that msp130 genes underwent duplications within almost all biocalcifying bilaterian phyla and identify highly conserved intron-exon junctions specific to bilaterian msp130 genes. The absence of MSP130 proteins in calcifying, nonbilaterian metazoans and other basal eukaryotes suggests that an ancestral msp130 gene underwent a horizontal gene transfer event that predates bilaterians, but not metazoans. We report striking structural similarities between bilaterian and bacterial MSP130 proteins, with each containing a seven-bladed, barrel-like motif that encompasses a choice-of-anchor domain, and identify highly conserved, predicted Ca2+-binding sites associated with the barrels. These findings point to a conserved, ancient function for MSP130 proteins in biocalcification and support the view that lateral transfer of bacterial genes supported the appearance of calcified animal skeletons.},
}
@article {pmid39955358,
year = {2025},
author = {Mahamud, SMI and Oishy, SH and Roy, S and Pal, K and Rubaiyat, RN and Ansary, MM},
title = {Comparative Genomic Analysis of 66 Bacteriophages Infecting Morganella morganii Strains.},
journal = {Current microbiology},
volume = {82},
number = {4},
pages = {137},
pmid = {39955358},
issn = {1432-0991},
mesh = {*Morganella morganii/virology/genetics ; *Bacteriophages/genetics/classification/isolation &amp; purification ; *Genome, Viral ; *Phylogeny ; *Genomics ; Host Specificity ; Base Composition ; Humans ; },
abstract = {Bacteriophages are viruses that specifically target bacteria and play a crucial role in influencing bacterial evolution and the transmission of antibiotic resistance. In this study, we explored the genomic profiles of 66 bacteriophages that infect Morganella morganii, an opportunistic pathogen associated with difficult-to-treat nosocomial and urinary tract infections. Our findings highlight the extraordinary diversity within this phage population, reflected in their genomic features, evolutionary relationships, and potential contributions to bacterial pathogenicity. The 66 phage genomes exhibited diversity in size, spanning from 6 to 115 kilobase pairs, reflecting a heterogeneous genetic material and coding potential. Their guanine-cytosine (G+C) content varied widely, from 43.3% to 64.6%, suggesting diverse evolutionary origins and adaptive strategies. Phylogenetic analysis identified ten distinct evolutionary clusters, some classified as singletons, highlighting unique evolutionary pathways. Several clusters included phages capable of infecting multiple M. morganii strains, indicating a broader host range and the potential for horizontal gene transfer. Genomic analysis also determined a substantial number of hypothetical proteins, underscoring the need for further investigation to clarify their functions. Importantly, we identified a wide array of antibiotic resistance and virulence-associated genes within these phage genomes, illuminating their potential to impact the treatment of M. morganii infections and develop new, more virulent strains. These findings highlight the critical role of phage-mediated gene transfer in shaping bacterial evolution and facilitating the transmission of antibiotic resistance.},
}
@article {pmid39954947,
year = {2025},
author = {Souza, HCA and Panzenhagen, P and Dos Santos, AMP and Portes, AB and Fidelis, J and Conte-Junior, CA},
title = {Unravelling the advances of CRISPR-Cas9 as a precise antimicrobial therapy: A systematic review.},
journal = {Journal of global antimicrobial resistance},
volume = {42},
number = {},
pages = {51-60},
doi = {10.1016/j.jgar.2025.02.002},
pmid = {39954947},
issn = {2213-7173},
abstract = {UNLABELLED: Antimicrobial resistance is a critical public health threat, compromising treatment effectiveness. The spread of resistant pathogens, facilitated by genetic variability and horizontal gene transfer, primarily through plasmids, poses significant challenges to health systems.<br><br>OBJECTIVE: This review explores the potential of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology and Cas9 nucleases in combating antimicrobial resistance.<br><br>METHODS: The literature review followed the PRISMA guidelines using PubMed, Embase, and Scopus databases until July 2023.<br><br>RESULTS: The Enterobacterales family, particularly Escherichia coli, was the main focus. The resistance genes targeted were mainly associated with &#x3b2;-lactam antibiotics, specifically bla genes, and colistin resistance linked to the mcr-1 gene. Plasmid vectors have been the primary delivery method for the CRISPR-Cas9 system, with conjugative plasmids resensitizing bacterial strains to various antimicrobials. Other delivery methods included electroporation, phage-mediated delivery, and nanoparticles. The efficacy of the CRISPR-Cas9 system in resensitizing bacterial strains ranged from 4.7% to 100%.<br><br>CONCLUSIONS: Despite challenges in delivery strategies and clinical application, studies integrating nanotechnology present promising approaches to overcome these limitations. This review highlights new perspectives for the clinical use of CRISPR-Cas9 as a specific and efficient antimicrobial agent, potentially replacing traditional broad-spectrum antimicrobials in the future.},
}
@article {pmid39954386,
year = {2025},
author = {Vilar, LC and Rego, ACS and Miguel, MAL and Paranhos, RPDR and Laport, MS and Rossi, CC and Giambiagi-deMarval, M},
title = {Staphylococcus spp. and methicillin-resistance gene mecA dispersion in seawater: A case study of Guanabara Bay's recreational and touristic waters.},
journal = {Comparative immunology, microbiology and infectious diseases},
volume = {118},
number = {},
pages = {102326},
doi = {10.1016/j.cimid.2025.102326},
pmid = {39954386},
issn = {1878-1667},
mesh = {*Staphylococcus/genetics/drug effects/isolation &amp; purification ; *Seawater/microbiology ; *Methicillin Resistance/genetics ; *Bacterial Proteins/genetics ; *Anti-Bacterial Agents/pharmacology ; Humans ; Brazil ; Microbial Sensitivity Tests ; CRISPR-Cas Systems ; Bays/microbiology ; Staphylococcal Infections/microbiology ; Penicillin-Binding Proteins/genetics ; Genetic Variation ; },
abstract = {Environmental Staphylococci, particularly coagulase-negative Staphylococci (CoNS), are known reservoirs of antimicrobial resistance genes and human-animal opportunistic pathogens, yet their role within the One Health framework remains underexplored. In this study, we isolated 12 species of CoNS from two sites 10 km apart in Guanabara Bay, Rio de Janeiro, with the most frequent species being the opportunistic Staphylococcus saprophyticus (30.3 %), Staphylococcus warneri (25.7 %), and Staphylococcus epidermidis (16.7 %). GTG5-PCR fingerprinting revealed significant genetic diversity, yet identical profiles persisted across both sites throughout the year, indicating strain dispersion and persistence. Among the 66 strains analyzed, 42 exhibited resistance to clinically significant antimicrobials, including methicillin-resistant strains harboring the mecA gene. Remarkably, 22.7 % of the strains carried CRISPR-Cas systems, a frequency unusually high for Staphylococcus spp., suggesting that bacteriophage pressure in the seawater environment may drive this increase. The presence of antimicrobial-resistant CoNS in Guanabara Bay, a popular recreational area, represents a potential public health risk.},
}
@article {pmid39952999,
year = {2025},
author = {Koper, P and Wysokiński, J and Żebracki, K and Decewicz, P and Dziewit, &#x141; and Kalita, M and Palusińska-Szysz, M and Mazur, A},
title = {Comparative analysis of Legionella lytica genome identifies specific metabolic traits and virulence factors.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {5554},
pmid = {39952999},
issn = {2045-2322},
support = {2019/03/X/NZ2/00976//Narodowe Centrum Nauki/ ; 2019/03/X/NZ2/00976//Narodowe Centrum Nauki/ ; 2019/03/X/NZ2/00976//Narodowe Centrum Nauki/ ; 2019/03/X/NZ2/00976//Narodowe Centrum Nauki/ ; 2019/03/X/NZ2/00976//Narodowe Centrum Nauki/ ; 2019/03/X/NZ2/00976//Narodowe Centrum Nauki/ ; },
mesh = {*Virulence Factors/genetics ; *Legionella/genetics/pathogenicity ; *Genome, Bacterial ; Plasmids/genetics ; Phylogeny ; Bacterial Proteins/genetics/metabolism ; Virulence/genetics ; Molecular Sequence Annotation ; },
abstract = {The complete genome of Legionella lytica PCM 2298 was sequenced and analyzed to provide insights into its genomic structure, virulence potential, and evolutionary position within the Legionella genus. The genome comprised a 3.2 Mbp chromosome and two plasmids, pLlyPCM2298_1 and pLlyPCM2298_2, contributing to a total genome size of 3.7 Mbp. Functional annotation identified 3,165 coding sequences, including genes associated with known virulence factors such as the major outer membrane protein (MOMP), the macrophage infectivity potentiator (Mip), and a comprehensive set of secretion systems (type II, type IVA, and type IVB Dot/Icm type IV secretion system). Notably, L. lytica contributed 383 unique genes to the Legionella pangenome, with 232 identified effector proteins, of which 35 were plasmid-encoded. The identification of unique genes, particularly those on plasmids, suggests an evolutionary strategy favoring horizontal gene transfer and niche adaptation. The effector repertoire included proteins with domains characteristic of host interaction strategies, such as ankyrin repeats and protein kinases. Comparative analyses showed that while L. lytica shares core virulence traits with other Legionella species, it has distinct features that may contribute to its adaptability and pathogenic potential. These findings underscore the genomic diversity within the genus and contribute to a deeper understanding of Legionella's ecological and clinical significance. A custom web application was developed using the R Shiny library, enabling users to interactively explore the expanded Legionella pangenome through UpSet plots.},
}
@article {pmid39952513,
year = {2025},
author = {Ke, F and Liu, AK and Zhang, QY},
title = {Extra peptidase of a cyanophage confers its stronger lytic effect on bloom-forming Microcystis aeruginosa.},
journal = {International journal of biological macromolecules},
volume = {304},
number = {Pt 2},
pages = {140979},
doi = {10.1016/j.ijbiomac.2025.140979},
pmid = {39952513},
issn = {1879-0003},
mesh = {*Microcystis/virology ; *Bacteriophages/genetics ; *Peptide Hydrolases/metabolism/genetics ; Harmful Algal Bloom ; Viral Proteins/genetics/metabolism ; },
abstract = {Microcystis covers important cyanobacteria species that causes harmful algal blooms. Cyanophages are viruses that infect and lyse cyanobacteria and have been considered as potential cyanobacteria control strategy. Present study isolated two cyanophage strains, MaMV-CH01 (CH01) and MaMV-CH02 (CH02), infecting M. aeruginosa. Growth curves showed that CH01 has a stronger proliferation ability and host cell lysis capability than CH02. Combined with genomic, gene structure and function analysis, as well as biologic testing including infectivity, we confirmed that there is widespread horizontal gene transfer between the cyanophages and cyanobacteria, enabling the cyanophages to carry a series of auxiliary metabolic genes (AMG) related to host's metabolism. Moreover, compared with CH02, the cyanophage CH01 carrying extra AMG, a peptidase encoding gene (82R), exhibited stronger lytic activity against its host. Expression of CH01 82R in vitro showed strong bacteriostatic activity. Further, testing the cyanophage's ability to form plaques showed that the CH01(AMG[+]), which encodes the aforementioned peptidase, can form larger plaques, with an area of about threefold than that formed by CH02(AMG[-]). Above results indicated that the cyanophages with specific peptidase possessed stronger algicidal efficiency, which provided a direction for finding efficient cyanophages to regulate the population of bloom-forming cyanobacteria.},
}
@article {pmid39952130,
year = {2025},
author = {Ding, L and Zhang, CM and Jiang, HY},
title = {Lipid-lowering drug clofibric acid promotes conjugative transfer of RP4 plasmid carrying antibiotic resistance genes by multiple mechanisms.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137560},
doi = {10.1016/j.jhazmat.2025.137560},
pmid = {39952130},
issn = {1873-3336},
mesh = {*Plasmids/genetics ; *Clofibric Acid/pharmacology ; *Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics/drug effects ; Reactive Oxygen Species/metabolism ; *Drug Resistance, Microbial/genetics ; *Gene Transfer, Horizontal/drug effects ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Conjugation, Genetic/drug effects ; },
abstract = {Antibiotic resistance represents a growing global health crisis, predominantly driven by the selective pressure imposed by antibiotics, which facilitates horizontal gene transfer. However, the potential role of non-antibiotic pharmaceuticals in promoting or enabling the spread of antibiotic resistance genes (ARGs) remains poorly understood. This study provided novel insights into the capacity of clofibric acid, a lipid-lowering drug, to enhance the conjugative transfer of ARGs, and deeply explored the underlying multiple mechanisms. The findings revealed that clofibric acid, at concentrations ranging from 0.01 to 1000 μg/L, significantly promoted the transfer efficiency of the RP4 plasmid carrying multiple ARGs. This enhancement was accompanied by a cascade of stress responses in bacterial cells, including elevated production of reactive oxygen species, increased secretion of extracellular polymeric substances, reduced bacterial surface zeta potential, and heightened cell membrane permeability. The physiological alterations were closely linked to significant changes in the expression of genes associated with these processes. Our results highlighted the potential of non-antibiotic pharmaceuticals to contribute to the dissemination of antibiotic resistance, offering a critical foundation for further research into the environmental and public health implications of such compounds.},
}
@article {pmid39952116,
year = {2025},
author = {Hirayama, A and Akase, H and Hayase, Y and Maeda, S},
title = {Subminimal inhibitory concentrations of antibiotics and anaerobic conditions promote Escherichia coli cell-to-cell plasmid transformation in biofilms.},
journal = {Biochemical and biophysical research communications},
volume = {752},
number = {},
pages = {151464},
doi = {10.1016/j.bbrc.2025.151464},
pmid = {39952116},
issn = {1090-2104},
mesh = {*Biofilms/drug effects/growth &amp; development ; *Escherichia coli/genetics/drug effects/metabolism ; *Plasmids/genetics/metabolism ; *Anti-Bacterial Agents/pharmacology ; Anaerobiosis ; Microbial Sensitivity Tests ; Transformation, Bacterial ; },
abstract = {In recent years, subminimal inhibitory concentrations (sub-MIC) of antibiotics have been found to exert unexpected physiological effects on bacterial cells, beyond their common growth-inhibition properties. Our previous research demonstrated that sub-MIC ampicillin, combined with mild mechanical stimulation using glass balls, significantly promotes intercellular plasmid transformation (cell-to-cell plasmid transformation) in Escherichia coli within air-solid biofilms. In this study, we investigated whether other antibiotics with diverse mechanisms of action similarly enhance plasmid transformation. Our findings revealed that various antibiotics indeed promote cell-to-cell plasmid transformation, and this effect was observed under both aerobic and anaerobic conditions. Interestingly, anaerobic conditions resulted in higher frequencies of plasmid transformation compared to aerobic conditions. Supporting these results, we found that several single-gene knockouts of aerobic respiratory chain components under aerobic conditions also enhanced plasmid transformation. This suggests that the unavailability of aerobic respiration may favor the process of intercellular plasmid transfer. Collectively, our results indicate that a wide range of sub-MIC antibiotics can stimulate horizontal plasmid transfer and that anaerobic conditions are particularly conducive to this process. Based on these findings, we hypothesize that the anaerobic gut environment of antibiotic-treated animals or humans, characterized by biofilm-like high cell densities of antibiotic-exposed bacteria and regular peristaltic and segmental movements, could serve as a favorable niche for horizontal gene transfer via intercellular plasmid transformation.},
}
@article {pmid39950610,
year = {2025},
author = {Jang, YJ and Oh, SD and Hong, JK and Park, JC and Lee, SK and Chang, A and Yun, DW and Lee, B},
title = {Impact of genetically modified herbicide-resistant maize on rhizosphere bacterial communities.},
journal = {GM crops &amp; food},
volume = {16},
number = {1},
pages = {186-198},
pmid = {39950610},
issn = {2164-5701},
mesh = {*Zea mays/genetics/microbiology/growth &amp; development/drug effects ; *Rhizosphere ; *Plants, Genetically Modified/genetics ; *Soil Microbiology ; *Bacteria/genetics/drug effects ; *Herbicides/pharmacology ; *RNA, Ribosomal, 16S/genetics ; Herbicide Resistance/genetics ; Acetyltransferases/genetics ; },
abstract = {Rhizosphere bacterial community studies offer valuable insights into the environmental implications of genetically modified (GM) crops. This study compared the effects of a non-GM maize cultivar, namely Hi-IIA, with those of a herbicide-resistant maize cultivar containing the phosphinothricin N-acetyltransferase gene on the rhizosphere bacterial community across growth stages. 16s rRNA amplicon sequencing and data analysis tools revealed no significant differences in bacterial community composition or diversity between the cultivars. Principal component analysis revealed that differences in community structure were driven by plant growth stages rather than plant type. Polymerase chain reaction analysis was conducted to examine the potential horizontal transfer of the introduced gene from the GM maize to rhizosphere microorganisms; however, the introduced gene was not detected in the soil genomic DNA. Overall, the environmental impact of GM maize, particularly on soil microorganisms, is negligible, and the cultivation of GM maize does not alter significantly the rhizosphere bacterial community.},
}
@article {pmid39947201,
year = {2025},
author = {Yang, SNN and Kertesz, MA and Coleman, NV},
title = {Phylogenetic and Functional Diversity of Soluble Di-Iron Monooxygenases.},
journal = {Environmental microbiology},
volume = {27},
number = {2},
pages = {e70050},
pmid = {39947201},
issn = {1462-2920},
support = {//University of Sydney/ ; },
mesh = {*Phylogeny ; *Mixed Function Oxygenases/genetics/metabolism/chemistry ; *Bacteria/enzymology/genetics/classification ; Biodegradation, Environmental ; Gene Transfer, Horizontal ; Substrate Specificity ; Oxidation-Reduction ; Oxygenases/genetics/metabolism ; Bacterial Proteins/genetics/metabolism/chemistry ; Iron/metabolism ; },
abstract = {Monooxygenase (MO) enzymes are responsible for the oxidation of hydrocarbons and other compounds in the carbon and nitrogen cycles, are important for the biodegradation of pollutants and can act as biocatalysts for chemical manufacture. The soluble di-iron monooxygenases (SDIMOs) are of interest due to their broad substrate range, high enantioselectivity and ability to oxidise inert substrates such as methane. Here, we re-examine the phylogeny and functions of these enzymes, using recent advances in the field and expansions in sequence diversity in databases to highlight relationships between SDIMOs and revisit their classification. We discuss the impact of horizontal gene transfer on SDIMO phylogeny, the potential of SDIMOs for the biodegradation of pollutants and the importance of heterologous expression as a tool for understanding SDIMO functions and enabling their use as biocatalysts. Our analysis highlights current knowledge gaps, most notably, the unknown substrate ranges and physiological roles of enzymes that have so far only been detected via genome or metagenome sequencing. Enhanced understanding of the diversity and functions of the SDIMO enzymes will enable better prediction and management of biogeochemical processes and also enable new applications of these enzymes for biocatalysis and bioremediation.},
}
@article {pmid39947132,
year = {2025},
author = {Wittmers, F and Poirier, C and Bachy, C and Eckmann, C and Matantseva, O and Carlson, CA and Giovannoni, SJ and Goodenough, U and Worden, AZ},
title = {Symbionts of predatory protists are widespread in the oceans and related to animal pathogens.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {2},
pages = {182-199.e7},
doi = {10.1016/j.chom.2025.01.009},
pmid = {39947132},
issn = {1934-6069},
mesh = {*Symbiosis ; Animals ; *Choanoflagellata/physiology ; *Oceans and Seas ; *Phylogeny ; Humans ; Bacteria/genetics/classification ; Gene Transfer, Horizontal ; Genome, Bacterial ; Fishes/microbiology ; Eukaryota/physiology/genetics ; Microbiota ; },
abstract = {Protists are major predators of ocean microbial life, with an ancient history of entanglements with prokaryotes, but their delicate cell structures and recalcitrance to culturing hinder exploration of marine symbioses. We report that tiny oceanic protistan predators, specifically choanoflagellates-the closest living unicellular relatives of animals-and uncultivated MAST-3 form symbioses with four bacterial lineages related to animal symbionts. By targeting living phagotrophs on ship expeditions, we recovered genomes from physically associated uncultivated Legionellales and Rickettsiales. The evolutionary trajectories of Marinicoxiellaceae, Cosmosymbacterales, Simplirickettsiaceae, and previously named Gamibacteraceae vary, including host-engagement mechanisms unknown in marine bacteria, horizontally transferred genes that mediate pathogen-microbiome interactions, and nutritional pathways. These symbionts and hosts occur throughout subtropical and tropical oceans. Related bacteria were detected in public data from freshwater, fish, and human samples. Symbiont associations with animal-related protists, alongside relationships to animal pathogens, suggest an unexpectedly long history of shifting associations and possibilities for host expansion as environments change.},
}
@article {pmid39946809,
year = {2025},
author = {Zeng, Q and Pu, Y and Liu, Q and Li, Y and Sun, Y and Hao, Y and Yang, Q and Yang, B and Wu, Y and Shi, S and Gong, Z},
title = {Effects of decabromodiphenyl ethane (DBDPE) exposure on soil microbial community: Nitrogen cycle, microbial defense and repair and antibiotic resistance genes transfer.},
journal = {Journal of environmental management},
volume = {376},
number = {},
pages = {124503},
doi = {10.1016/j.jenvman.2025.124503},
pmid = {39946809},
issn = {1095-8630},
mesh = {*Soil Microbiology ; *Nitrogen Cycle ; *Drug Resistance, Microbial/genetics ; Soil Pollutants/toxicity ; Bromobenzenes/toxicity ; Flame Retardants/toxicity ; Soil/chemistry ; Microbiota/drug effects ; },
abstract = {DBDPE, a widely used brominated flame retardant, is frequently detected in soil. However, the toxic effects of DBDPE on soil microbial communities remain unclear. This study investigated the effects of DBDPE on the microbial community shifts, the nitrogen cycle, microbial defense and repair, and antibiotic resistance genes (ARGs) transfer. After 28 days of DBDPE exposure, the soil microbial community was altered. Denitrifier were enriched by 4.07-78.22% under DBDPE exposure concentrations of 100-1000 ng/g. Additionally, the abundances of genes encoding enzymes involved in nitrification and denitrification processes were up-regulated at 100 ng/g DBDPE exposure, and further promoted at 1000 ng/g DBDPE exposure. Meanwhile, DBDPE exposure at concentrations of 100-1000 ng/g stimulated the production of extracellular polymers substances (EPS) (2155-2347 mg/kg), increased the accumulation of reactive oxygen species (ROS) (by 97.95-108.38%), and activated the antioxidant defense system of soil microorganisms, which correspondingly down-regulated catalase (CAT) genes (by 4.65-4.91%), while up-regulated superoxide dismutase (SOD) (by 0.52-2.63%) and glutathione (GSH) genes (by 19.03%-44.61%). Genes related to the tricarboxylic acid (TCA) cycle, glycerophospholipid metabolism, and peptidoglycan biosynthesis were up-regulated, enhancing cell membrane repair in response to DBDPE exposure. Moreover, the increase in DBDPE concentration selectively enriched and promoted the transmission of ARGs. The co-occurrence network of ARGs and mobile genetic elements (MGEs) revealed that DBDPE facilitated the horizontal gene transfer (HGT)-mediated transmission of transposase, ist, and insertion sequence-associated ARGs.},
}
@article {pmid39946805,
year = {2025},
author = {Xu, Z and Li, C and Xiong, J and Hu, S and Ma, Y and Li, S and Ren, X and Huang, B and Pan, X},
title = {The ecological security risks of phthalates: A focus on antibiotic resistance gene dissemination in aquatic environments.},
journal = {Journal of environmental management},
volume = {376},
number = {},
pages = {124488},
doi = {10.1016/j.jenvman.2025.124488},
pmid = {39946805},
issn = {1095-8630},
mesh = {*Phthalic Acids/toxicity ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Dibutyl Phthalate/toxicity ; Water Pollutants, Chemical/toxicity ; Anti-Bacterial Agents/toxicity ; },
abstract = {Antibiotic resistance genes (ARGs) have become a major focus in environmental safety and human health, with concerns about non-antibiotic substances like microplastics facilitating their horizontal gene transfer. Phthalate esters (PAEs), as ubiquitous plastic additives, are prevalent in aquatic environments, yet there remains a dearth of studies examining their impacts on ARG dissemination. This study focuses on dibutyl phthalate (DBP), a prototypical PAE, to assess its potential influence on the conjugative transfer of ARGs along with the related molecular mechanisms. The results revealed that DBP exposure at environmentally relevant concentrations significantly promoted the conjugative transfer of RP4 plasmid-mediated ARGs by up to 2.7-fold compared to that of the control group, whereas it severely suppressed the conjugation at a high concentration (100 μg/L). The promotion of conjugation transfer by low-concentration DBP (0.01-10 μg/L) was mainly attributed to the stimulation of ROS, enhanced membrane permeability, increased energy synthesis, increased polymeric substances secretion, and upregulation of conjugation-related genes. Conversely, high DBP exposure induced oxidative damage and reduced ATP synthesis, resulting in the suppression of ARG conjugation. Notably, donor and recipient bacteria responded differently to DBP-induced oxidative stress. This study explores the environmental behavior of DBP in the water environment from the perspective of ARG propagation and provides essential data and theoretical insights to raise public awareness about the ecological security risks of PAEs.},
}
@article {pmid39945525,
year = {2025},
author = {Chang, TH and Pourtois, JD and Haddock, NL and Furukawa, D and Kelly, KE and Amanatullah, DF and Burgener, E and Milla, C and Banaei, N and Bollyky, PL},
title = {Prophages are infrequently associated with antibiotic resistance in Pseudomonas aeruginosa clinical isolates.},
journal = {mSphere},
volume = {10},
number = {3},
pages = {e0090424},
pmid = {39945525},
issn = {2379-5042},
support = {//Cystic Fibrosis Foundation (CFF)/ ; R01 HL148184-01, R01 AI12492093, R01 DC019965//HHS | National Institutes of Health (NIH)/ ; BURGEN23G0, BURGEN24A0-KB//Cystic Fibrosis Foundation (CFF)/ ; R01 DC019965/DC/NIDCD NIH HHS/United States ; //SU | Stanford Bio-X/ ; 1K23HL169902-01//HHS | National Institutes of Health (NIH)/ ; R01 HL148184/HL/NHLBI NIH HHS/United States ; K23 HL169902/HL/NHLBI NIH HHS/United States ; },
mesh = {*Prophages/genetics ; *Pseudomonas aeruginosa/virology/drug effects/genetics ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Pseudomonas Infections/microbiology ; *Cystic Fibrosis/microbiology ; *Microbial Sensitivity Tests ; *Drug Resistance, Bacterial ; Lysogeny ; },
abstract = {Lysogenic bacteriophages can integrate their genome into the bacterial chromosome in the form of a prophage and can promote genetic transfer between bacterial strains in vitro. However, the contribution of lysogenic bacteriophages to the incidence of antimicrobial resistance (AMR) in clinical settings is poorly understood. Here, in a set of 186 clinical isolates of Pseudomonas aeruginosa collected from respiratory cultures from 82 patients with cystic fibrosis, we evaluate the links between prophage counts and both genomic and phenotypic resistance to six anti-pseudomonal antibiotics: tobramycin, colistin, ciprofloxacin, meropenem, aztreonam, and piperacillin-tazobactam. We identified 239 different prophages in total. We find that P. aeruginosa isolates contain on average 3.06 ± 1.84 (SD) predicted prophages. We find no significant association between the number of prophages per isolate and the minimum inhibitory concentration for any of these antibiotics. We then investigate the relationship between particular prophages and AMR. We identify a single lysogenic phage associated with phenotypic resistance to the antibiotic tobramycin and, consistent with this association, we observe that AMR genes associated with resistance to tobramycin are more likely to be found when this prophage is present. However, we find that they are not encoded directly on prophage sequences. Additionally, we identify a single prophage statistically associated with ciprofloxacin resistance but do not identify any genes associated with ciprofloxacin phenotypic resistance. These findings suggest that prophages are only infrequently associated with the AMR genes in clinical isolates of P. aeruginosa.IMPORTANCEAntibiotic-resistant infections of Pseudomonas aeruginosa (Pa), a leading pathogen in patients with cystic fibrosis (CF), are a global health threat. While lysogenic bacteriophages are known to facilitate horizontal gene transfer, their role in promoting antibiotic resistance in clinical settings remains poorly understood. In our analysis of 186 clinical isolates of P. aeruginosa from CF patients, we find that prophage abundance does not predict phenotypic resistance to key antibiotics but that specific prophages are infrequently associated with tobramycin resistance genes. In addition, we do not find antimicrobial resistance (AMR) genes encoded directly on prophages. These results highlight that while phages can be associated with AMR, phage-mediated AMR transfer may be rare in clinical isolates and difficult to identify. This work is important for future efforts on mitigating AMR in CFCF and other vulnerable populations affected by Pa infections and advances our understanding of bacterial-phage dynamics in clinical infections.},
}
@article {pmid39940717,
year = {2025},
author = {Subramanian, P and Kim, D and Ko, HR and Sim, JS and Mani, V and Lee, CM and Lee, SK and Park, S and Kim, DG and Yu, Y and Hahn, BS},
title = {Genomic and Transcriptomic Analysis of the Polyploidy Cyst Nematode, Heterodera trifolii, and Heterodera schachtii.},
journal = {International journal of molecular sciences},
volume = {26},
number = {3},
pages = {},
pmid = {39940717},
issn = {1422-0067},
support = {PJ01333201//Rural Development Administration/ ; },
mesh = {Animals ; *Polyploidy ; *Tylenchoidea/genetics ; Transcriptome/genetics ; Genome, Helminth ; Gene Expression Profiling/methods ; Genomics/methods ; Phylogeny ; Female ; Gene Transfer, Horizontal ; },
abstract = {Cyst nematodes remain a major threat to global agricultural production, causing huge losses. To understand the parasitism of the cyst nematodes Heterodera trifolii (HT) and Heterodera schachtii (HS), we constructed whole-genome assemblies using short- and long-read sequencing technologies. The nematode genomes were 379 Mb and 183 Mb in size, with the integrated gene models predicting 40,186 and 18,227 genes in HT and HS, respectively. We found more than half of the genes predicted in HT (64.7%) and HS (53.2%) were collinear to their nearest neighbor H. glycines (HG). Large-scale duplication patterns in HT and segmental duplications of more than half of the orthologous genes indicate that the genome of HT is polyploid in nature. Functional analysis of the genes indicated that 65.6% of the HG genes existed within the HT genome. Most abundant genes in HT and HS were involved in gene regulation, DNA integration, and chemotaxis. Differentially expressed genes showed upregulation of cuticle structural constituent genes during egg and female stages and cytoskeletal motor activity-related genes in juvenile stage 2 (J2). Horizontal gene transfer analyses identified four new vitamin biosynthesis genes, pdxK, pdxH, pdxS, and fabG, of bacterial origin, to be first reported in HT and HS. Mitogenomes of HT, HS, and HG showed similar structure, composition, and codon usage. However, rates of substitution of bases in the gene nad4l were significantly different between HT and HS. The described genomes, transcriptomes, and mitogenomes of plant-parasitic nematodes HT and HS are potential bio-resources used to identify several strategies of control of the nematode.},
}
@article {pmid39939755,
year = {2025},
author = {Subramanian, S and Kerns, HR and Braverman, SG and Doore, SM},
title = {The structure of Shigella virus Sf14 reveals the presence of two decoration proteins and two long tail fibers.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {222},
pmid = {39939755},
issn = {2399-3642},
support = {R01 AI170608/AI/NIAID NIH HHS/United States ; U24 GM116789/GM/NIGMS NIH HHS/United States ; AI170608//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; U24GM116789-03//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*Capsid Proteins/chemistry/metabolism/genetics ; *Bacteriophages/genetics/metabolism/chemistry ; Shigella flexneri/virology/genetics/metabolism ; Models, Molecular ; Phylogeny ; Capsid/metabolism/chemistry ; Protein Conformation ; },
abstract = {Bacteriophage Sf14 infects the human pathogen Shigella flexneri. A previous low-resolution structure suggested the presence of a decoration protein on its T = 9 icosahedral capsid. Here, we determined high-resolution structures of the Sf14 capsid and neck, along with a moderate-resolution structure of the whole Sf14 tail and baseplate. These structures indicate the capsid has not one, but two different types of decoration proteins: a trimeric β-tulip lattice that covers the entire capsid and a set of Hoc-like proteins that bind preferentially to hexamers at the quasi-3-fold axes of symmetry. The neck also contains two sets of whiskers oriented in opposite directions, and the tail has two types of long tail fibers which may bind different receptors. Based on homology and phylogenetic analysis, Sf14 may be the product of multiple horizontal gene transfer events. The structures presented here can be used to investigate further hypotheses of phage structure-function relationships and structural diversity.},
}
@article {pmid39939538,
year = {2025},
author = {Li, ZZ and Wang, Y and He, XY and Li, WG},
title = {The Taihangia mitogenome provides new insights into its adaptation and organelle genome evolution in Rosaceae.},
journal = {Planta},
volume = {261},
number = {3},
pages = {59},
pmid = {39939538},
issn = {1432-2048},
support = {31370434//National Natural Science Foundation of China/ ; },
mesh = {*Genome, Mitochondrial/genetics ; *Phylogeny ; *Rosaceae/genetics ; *Evolution, Molecular ; Genome, Plant/genetics ; Adaptation, Physiological/genetics ; Plastids/genetics ; Gene Transfer, Horizontal ; },
abstract = {We present the first Taihangia mitogenome, uncovering frequent rearrangements and significant length variation in Rosaceae, likely driven by hybridization and repeat content, alongside widespread mito-chloroplast phylogenetic conflicts. Taihangia, an ancient and endangered monotypic genus within the subfamily Rosoideae of the family Rosaceae, is endemic to cliffs and serves as an ideal material for studying the adaptations of cliff-dwelling plants and the evolutionary processes of the Rosaceae family. In this study, the mitogenome and plastome of T. rupestris var. ciliata were assembled, with lengths of 265,633 bp and 155,467 bp, both exhibiting typical circular structures. Positive selection was detected in the nad4L and sdh4 genes, likely playing a role in adaptation to harsh environments. Comparative genomic analysis indicated that repetitive sequences are likely the main contributors to genome size variation in Rosaceae and also influence horizontal gene transfer between organelle genomes. In T. rupestris var. ciliata, 20 mitochondrial plastid DNA sequences were identified, including 16 complete plastid genes. Moreover, frequent rearrangements were observed in the non-coding regions of mitogenome within the subfamily Rosoideae, potentially linked to the complex evolutionary history and the presence of repetitive sequences. In contrast, coding regions remained highly conserved (over 83% similarity) to maintain essential mitochondrial functions. Phylogenomic analysis of the two organelle genomes revealed conflicts in the phylogenetic relationships within Rosaceae, potentially due to the inconsistent mutation rates and frequent hybridization events in the evolutionary history of the family. In conclusion, the organelle genome analysis of Taihangia provides crucial genomic resources for understanding the evolution and adaptation of Rosaceae species.},
}
@article {pmid39937386,
year = {2025},
author = {Lindeberg, A and Hellmuth, M},
title = {Simplifying and Characterizing DAGs and Phylogenetic Networks via Least Common Ancestor Constraints.},
journal = {Bulletin of mathematical biology},
volume = {87},
number = {3},
pages = {44},
pmid = {39937386},
issn = {1522-9602},
mesh = {*Phylogeny ; *Mathematical Concepts ; *Models, Genetic ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Algorithms ; Animals ; },
abstract = {Rooted phylogenetic networks, or more generally, directed acyclic graphs (DAGs), are widely used to model species or gene relationships that traditional rooted trees cannot fully capture, especially in the presence of reticulate processes or horizontal gene transfers. Such networks or DAGs are typically inferred from observable data (e.g., genomic sequences of extant species), providing only an estimate of the true evolutionary history. However, these inferred DAGs are often complex and difficult to interpret. In particular, many contain vertices that do not serve as least common ancestors (LCAs) for any subset of the underlying genes or species, thus may lack direct support from the observable data. In contrast, LCA vertices are witnessed by historical traces justifying their existence and thus represent ancestral states substantiated by the data. To reduce unnecessary complexity and eliminate unsupported vertices, we aim to simplify a DAG to retain only LCA vertices while preserving essential evolutionary information. In this paper, we characterize LCA -relevant and lca -relevant DAGs, defined as those in which every vertex serves as an LCA (or unique LCA) for some subset of taxa. We introduce methods to identify LCAs in DAGs and efficiently transform any DAG into an LCA -relevant or lca -relevant one while preserving key structural properties of the original DAG or network. This transformation is achieved using a simple operator " ⊖ " that mimics vertex suppression.},
}
@article {pmid39936903,
year = {2025},
author = {Elena, AX and Orel, N and Fang, P and Herndl, GJ and Berendonk, TU and Tinta, T and Klümper, U},
title = {Jellyfish blooms-an overlooked hotspot and potential vector for the transmission of antimicrobial resistance in marine environments.},
journal = {mSystems},
volume = {10},
number = {3},
pages = {e0101224},
pmid = {39936903},
issn = {2379-5077},
support = {01DO2200, 01KI2404A//Bundesministerium f&#xfc;r Bildung und Forschung (BMBF)/ ; 16GW0355//Bundesministerium f&#xfc;r Bildung und Forschung (BMBF)/ ; 202004910327//China Scholarship Council (CSC)/ ; 793778//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; I04978//Austrian Science Fund (FWF)/ ; ARRS J7-2599, P1-0237//Javna Agencija za Raziskovalno Dejavnost RS (ARRS)/ ; Project ID: 57747282//DAAD/ ; Project ID: B|-DE/25-27-001//Public Agency for Scientific Research and Innovation of the Republic of Slovenia (ARIS)/ ; },
mesh = {Animals ; *Scyphozoa/microbiology/genetics ; RNA, Ribosomal, 16S/genetics ; Microbiota/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; Metagenome ; Bacteria/drug effects/genetics ; Zooplankton/drug effects/genetics ; Interspersed Repetitive Sequences/genetics ; },
abstract = {Gelatinous zooplankton (GZ) represents an important component of marine food webs, capable of generating massive blooms with severe environmental impact. When these blooms collapse, considerable amounts of organic matter (GZ-OM) either sink to the seafloor or can be introduced into the ocean's interior, promoting bacterial growth and providing a colonizable surface for microbial interactions. We hypothesized that GZ-OM is an overlooked marine hotspot for transmitting antimicrobial resistance genes (ARGs). To test this, we first re-analyzed metagenomes from two previous studies that experimentally evolved marine microbial communities in the presence and absence of OM from Aurelia aurita and Mnemiopsis leidyi recovered from bloom events and thereafter performed additional time-resolved GZ-OM degradation experiments to improve sample size and statistical power of our analysis. We analyzed these communities for composition, ARG, and mobile genetic element (MGE) content. Communities exposed to GZ-OM displayed up to fourfold increased relative ARG and up to 10-fold increased MGE abundance per 16S rRNA gene copy compared to the controls. This pattern was consistent across ARG and MGE classes and independent of the GZ species, indicating that nutrient influx and colonizable surfaces drive these changes. Potential ARG carriers included genera containing potential pathogens raising concerns of ARG transfer to pathogenic strains. Vibrio was pinpointed as a key player associated with elevated ARGs and MGEs. Whole-genome sequencing of a Vibrio isolate revealed the genetic capability for ARG mobilization and transfer. This study establishes the first link between two emerging issues of marine coastal zones, jellyfish blooms and ARG spread, both likely increasing with future ocean change. Hence, jellyfish blooms are a quintessential "One Health" issue where decreasing environmental health directly impacts human health.IMPORTANCEJellyfish blooms are, in the context of human health, often seen as mainly problematic for oceanic bathing. Here we demonstrate that they may also play a critical role as marine environmental hotspots for the transmission of antimicrobial resistance (AMR). This study employed (re-)analyses of microcosm experiments to investigate how particulate organic matter introduced to the ocean from collapsed jellyfish blooms, specifically Aurelia aurita and Mnemiopsis leidyi, can significantly increase the presence of antimicrobial resistance genes and mobile genetic elements in marine microbial communities by up to one order of magnitude. By providing abundant nutrients and surfaces for bacterial colonization, organic matter from these blooms enhances ARG proliferation, including transfer to and mobility in potentially pathogenic bacteria like Vibrio. Understanding this connection highlights the importance of monitoring jellyfish blooms as part of marine health assessments and developing strategies to mitigate the spread of AMR in coastal ecosystems.},
}
@article {pmid39935761,
year = {2025},
author = {Wijaya, AJ and Anžel, A and Richard, H and Hattab, G},
title = {Current state and future prospects of Horizontal Gene Transfer detection.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {1},
pages = {lqaf005},
pmid = {39935761},
issn = {2631-9268},
mesh = {*Gene Transfer, Horizontal ; *Artificial Intelligence ; Computational Biology/methods ; },
abstract = {Artificial intelligence (AI) has been shown to be beneficial in a wide range of bioinformatics applications. Horizontal Gene Transfer (HGT) is a driving force of evolutionary changes in prokaryotes. It is widely recognized that it contributes to the emergence of antimicrobial resistance (AMR), which poses a particularly serious threat to public health. Many computational approaches have been developed to study and detect HGT. However, the application of AI in this field has not been investigated. In this work, we conducted a review to provide information on the current trend of existing computational approaches for detecting HGT and to decipher the use of AI in this field. Here, we show a growing interest in HGT detection, characterized by a surge in the number of computational approaches, including AI-based approaches, in recent years. We organize existing computational approaches into a hierarchical structure of computational groups based on their computational methods and show how each computational group evolved. We make recommendations and discuss the challenges of HGT detection in general and the adoption of AI in particular. Moreover, we provide future directions for the field of HGT detection.},
}
@article {pmid39933461,
year = {2025},
author = {Mortezaei, Y and Gaballah, MS and Demirer, GN and Lammers, RW and Williams, MR},
title = {From wastewater to sludge: The role of microplastics in shaping anaerobic digestion performance and antibiotic resistance gene dynamics.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137413},
doi = {10.1016/j.jhazmat.2025.137413},
pmid = {39933461},
issn = {1873-3336},
mesh = {*Microplastics/analysis ; *Sewage/microbiology ; *Wastewater ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; *Water Pollutants, Chemical/analysis ; Waste Disposal, Fluid ; Bioreactors ; },
abstract = {The presence of microplastics (MPs) in wastewater treatment plants (WWTPs) disrupt processes and threaten the effectiveness of anaerobic digestion (AD), raising critical environmental and operational concerns. This review assesses MP occurrence in WWTPs and its effects on biogas production and the fate of antibiotic resistance genes (ARGs) during AD to understand their impact on process efficiency and environmental health. Polypropylene (PP) and polyethylene (PE) are the most prevalent types of MPs which are found in WWTP influent at an average concentration of 801.5 particles per liter (P/L), decrease to 38.3 P/L in effluent, and accumulate in sludge at 70.5 P/L. The effect of MPs on AD performance is influenced by MP type, concentration, size, and AD conditions (i.e., feed substrate, reactor configuration, temperature, and incubation time). For example, certain MPs (polyamide 7 (PA7) and PP) increase methane production by 39.5 %, while aged MPs decrease it by 47.2 %. The review also explores how AD drives MP degradation mechanisms like oxidation, hydrolysis, mechanical stress, and biodegradation. Additionally, MPs significantly impact ARGs, with abundance increasing by 0.4-514.4 %, especially with aged MPs. Mechanistic effects of MPs on ARGs dissemination were also discussed, including horizontal gene transfer (reactive oxygen species production, cell membrane permeability, extracellular polymeric substances secretion, and ATP dynamics), vertical gene transfer, microbial community, and adsorbing pollutants. This analysis provides insights into the complex interactions between MPs, microbial processes, and ARGs, highlighting their implications for wastewater treatment and biogas production systems.},
}
@article {pmid39932282,
year = {2025},
author = {Karki, S and Aylward, FO},
title = {Evolution of ubiquitin, cytoskeleton, and vesicular trafficking machinery in giant viruses.},
journal = {Journal of virology},
volume = {99},
number = {3},
pages = {e0171524},
pmid = {39932282},
issn = {1098-5514},
support = {2141862//National Science Foundation (NSF)/ ; },
mesh = {*Evolution, Molecular ; *Cytoskeleton/metabolism/virology ; *Ubiquitin/metabolism/genetics ; *Giant Viruses/genetics/metabolism ; Viral Proteins/metabolism/genetics ; Phylogeny ; Genome, Viral ; Gene Transfer, Horizontal ; DNA Viruses/genetics/metabolism ; },
abstract = {Members of the phylum Nucleocytoviricota, which include "giant viruses" known for their large physical dimensions and genome lengths, are a diverse group of dsDNA viruses that infect a wide range of eukaryotic hosts. The genomes of nucleocytoviruses frequently encode eukaryotic signature proteins (ESPs) such as RNA- and DNA-processing proteins, vesicular trafficking factors, cytoskeletal components, and proteins involved in ubiquitin signaling. Despite the prevalence of these genes in many nucleocytoviruses, the timing and number of gene acquisitions remains unclear. While the presence of DNA- and RNA-processing proteins in nucleocytoviruses likely reflects ancient gene transfers, the origins and evolutionary history of other proteins are largely unknown. In this study, we examined the distribution and evolutionary history of a subset of viral-encoded ESPs (vESPs) that are widespread in nucleocytoviruses. Our results demonstrate that most vESPs involved in vesicular trafficking were acquired multiple times independently by nucleocytoviruses at different time points after the emergence of the eukaryotic supergroups, while viral proteins associated with cytoskeletal and ubiquitin system proteins exhibited a more complex evolutionary pattern exhibited by both shallow and deep branching viral clades. This pattern reveals a dynamic interplay between the co-evoluton of eukaryotes and their viruses, suggesting that the viral acquisition of many genes involved in cellular processes has occurred both through ancient and more recent horizontal gene transfers. The timing and frequency of these gene acquisitions may provide insight into their role and functional significance during viral infection.IMPORTANCEThis research is pertinent for understanding the evolution of nucleocytoviruses and their interactions with eukaryotic hosts. By investigating the distribution and evolutionary history of viral-encoded eukaryotic signature proteins, the study reveals gene transfer patterns, highlighting how viruses acquire genes that allow them to manipulate host cellular processes. Identifying the timing and frequency of gene acquisitions related to essential cellular functions provides insights into their roles during viral infections. This work expands our understanding of viral diversity and adaptability, contributing valuable knowledge to virology and evolutionary biology, while offering new perspectives on the relationship between viruses and their hosts.},
}
@article {pmid39931631,
year = {2024},
author = {Zhou, X and Wagh, K and Lv, G and Sharma, D and Lei, W},
title = {Genome drafting of nosocomial infection CRE Klebsiella pneumoniae confirming resistance to colistin and eravacycline, carrying bla NDM-1, mcr-1, and bla KPC-2, in neonatology from November to December 2023.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1528017},
pmid = {39931631},
issn = {2235-2988},
mesh = {Humans ; *Klebsiella pneumoniae/genetics/drug effects/isolation &amp; purification ; *Klebsiella Infections/microbiology/epidemiology ; *Cross Infection/microbiology ; Infant, Newborn ; *Colistin/pharmacology ; *beta-Lactamases/genetics ; *Anti-Bacterial Agents/pharmacology ; *Whole Genome Sequencing ; *Intensive Care Units, Neonatal ; *Disease Outbreaks ; *Genome, Bacterial/genetics ; *Microbial Sensitivity Tests ; Drug Resistance, Multiple, Bacterial/genetics ; Plasmids/genetics ; Neonatology ; Bacterial Proteins/genetics ; Carbapenem-Resistant Enterobacteriaceae/genetics/isolation &amp; purification/drug effects ; Male ; },
abstract = {BACKGROUND: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a critical pathogen in healthcare settings, associated with high mortality due to its extensive antibiotic resistance. In this study, we report an outbreak of CRKP in a neonatal intensive care unit (NICU) within a 200-bed tertiary hospital. The main goal of this study was to characterize the phenotypic and genomic profiles of the CRKP isolates involved in the outbreak and to gain insights into their resistance mechanisms and transmission dynamics within the NICU.<br><br>METHODS: The study was conducted between November and December 2023 in a 5-bed NICU. Monthly surveillance cultures were performed to monitor colonization and infection with multidrug-resistant organisms. CRKP isolates were obtained from blood and nasal swabs of affected neonates. Identification and antimicrobial susceptibility testing were initially conducted using the Vitek[&#xae;]2 system with an N-395 card and further confirmed by 16S rRNA sequencing. Whole-genome sequencing (WGS) and antimicrobial resistance (AMR) profiling were performed to identify resistance genes and virulence factors. For genetic analysis, both Illumina short-read and Nanopore long-read sequencing were used, followed by hybrid assembly for enhanced genome resolution. Plasmid and resistance gene profiles were determined using AMRFinder and PlasmidFinder databases.<br><br>RESULTS: A total of three CRKP isolates (designated Kp1, Kp2, and Kp3) were identified. Kp1 and Kp2 belonged to sequence type (ST) ST23 and were genetically near-identical, differing by a single allele, while Kp3 was of a distinct sequence type, ST2096, with 245 allelic differences from Kp1 and Kp2. All isolates were resistant to colistin and carried resistance genes, including mcr-1 and bla NDM-1, bla KPC2 confirming carbapenem resistance. Efflux pump genes and aminoglycoside resistance genes were also detected, providing a multifaceted defence against antibiotics. Plasmid analysis identified several incompatibility groups (IncFI, IncHI, IncFIB, IncX), indicating the potential for horizontal gene transfer of resistance determinants.<br><br>CONCLUSION: This study highlights the complexity of CRKP outbreaks in neonatal care, with isolates exhibiting resistance mechanisms that complicate treatment. The plasmid profiles suggest these strains are reservoirs for multidrug-resistant genes, emphasizing the need for strict infection control and ongoing genomic surveillance. For neonatal care, these resistance challenges increase the risk of treatment failures and mortality, underscoring the importance of enhanced infection prevention and novel therapeutic strategies.},
}
@article {pmid39929813,
year = {2025},
author = {Liang, H and Xu, Y and Sahu, SK and Wang, H and Li, L and Chen, X and Zeng, Y and Lorenz, M and Friedl, T and Melkonian, B and Wong, GK and Melkonian, M and Liu, H and Wang, S},
title = {Chromosome-level genomes of two Bracteacoccaceae highlight adaptations to biocrusts.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1492},
pmid = {39929813},
issn = {2041-1723},
mesh = {*Gene Transfer, Horizontal ; Adaptation, Physiological/genetics ; Phylogeny ; Stress, Physiological/genetics ; Chromosomes/genetics ; },
abstract = {Biological soil crusts (biocrusts) cover the majority of the world's dryland ground and are a significant component of the vegetation-free surface of the planet. They consist of an intimate association of microbial organisms, lichens, bryophytes and fungi. Biocrusts are severely endangered by anthropogenic disturbances despite their importance. The genus Bracteacoccus (Sphaeropleales, Chlorophyta) is a ubiquitous component of biocrusts from extreme environments. Here, we present the chromosome-level genome sequences of two Bracteacoccus species, B. bullatus and B. minor. Genome comparisons with other Archaeplastida identify genomic features that highlight the adaptation of these algae to abiotic stresses prevailing in such environments. These features include horizontal gene transfer events mainly from bacteria or fungi, gains and expansions of stress-related gene families, neofunctionalization of genes following gene duplications and genome structural variations. We also summarize transcriptional and metabolic responses of the lipid pathway of B. minor, based on multi-omics analyses, which is important for balancing the flexible conversion of polar membrane lipids and non-polar storage lipids to cope with various abiotic stresses. Under dehydration and high-temperature stress conditions B. minor differs considerably from other eukaryotic algae. Overall, these findings provide insights into the genetic basis of adaptation to abiotic stress in biocrust algae.},
}
@article {pmid39927357,
year = {2024},
author = {Al-Bukhalifa, MA and Al-Tameemi, HM},
title = {First whole genome sequencing of Staphylococcus aureus isolates from Iraq: Insights into zoonotic relations and biofilm-related genes.},
journal = {Open veterinary journal},
volume = {14},
number = {12},
pages = {3269-3288},
pmid = {39927357},
issn = {2218-6050},
mesh = {*Biofilms ; Animals ; *Staphylococcus aureus/genetics/isolation &amp; purification/physiology ; Humans ; *Staphylococcal Infections/veterinary/microbiology ; *Whole Genome Sequencing ; Cats ; Iraq ; *Genome, Bacterial ; Dogs ; Cattle ; Sheep ; Zoonoses/microbiology ; },
abstract = {BACKGROUND: Staphylococcus aureus is a significant zoonotic pathogen capable of causing infections in both humans and animals. The bacterium's capacity to develop biofilms and resistance to many different antibiotics has raised significant concerns for public health. Furthermore, studies have demonstrated that horizontal gene transfer enables the transfer of deleterious features between strains found in humans and animals, consequently rendering treatment and control efforts more challenging.<br><br>AIM: This study aimed to investigate the relationships between human and animal isolates and biofilm-associated genes in local S. aureus strains using whole genome sequencing technique.<br><br>METHODS: We examined 111 suspected cases of S. aureus infection in humans and in animals and screened all S. aureus -positive isolates (11 isolates) for biofilm formation and antimicrobial profiles. Additionally, we sequenced and studied five S. aureus genomes isolated from humans, cows, sheep, cats, and dogs for significant biofilm-related genes and predicted their loci following annotation and deposition in the NCBI database.<br><br>RESULTS: The study showed that the isolates have genome sizes between 2.7 and 2.8 megabases, a GC content of 32.8%-33.1%, and a coding sequence count between 2,718 and 2,838. The cow isolate (MHB) and cat isolate (MHF) exhibited substantial genomic similarities with human isolates of S. aureus (N315) and the type strain of S. aureus (DSM 20231). The genomes of the human isolate (MHH) and the dog isolate (MHC) were comparable to S. aureus (N315). The sheep isolate (MHO) showed lesser genomic similarity and was closely related to S. aureus subsp. anaerobius. The genomes were submitted to the NCBI database with the following accession numbers: MHB (GCA_040196135.1), MHH (GCA_040196155.1), MHO (GCA_040195495.1), MHF (GCA_040195555.1), and MHC (GCA_040195445.1). The isolates were categorized by PubMLST typing into MHC (ST-1156), MHB (ST-6), MHF (ST-6), and MHO (a unique ST). We identified the accession numbers, locations, and lengths of biofilm-associated genes and regulators within the studied genomes.<br><br>CONCLUSION: The study is the first to conduct complete genome sequencing of Staphylococcus aureus in Iraq, allowing analysis of biofilm-associated genes in local isolates. It provides the first large-scale genomic investigation of genetic relationships among animal and human isolates in Iraq.},
}
@article {pmid39922005,
year = {2025},
author = {Iqbal, S and Begum, F and Manishimwe, C and Rabaan, AA and Sabour, AA and Alshiekheid, MA and Shaw, P},
title = {Allelochemicals degradation and multifarious plant growth promoting potential of two Bacillus spp.: Insights into genomic potential and abiotic stress alleviation.},
journal = {Chemosphere},
volume = {373},
number = {},
pages = {144191},
doi = {10.1016/j.chemosphere.2025.144191},
pmid = {39922005},
issn = {1879-1298},
mesh = {*Bacillus/metabolism/physiology/genetics ; *Pheromones ; *Stress, Physiological ; *Soil Microbiology ; Biodegradation, Environmental ; Volatile Organic Compounds/metabolism ; Triticum/growth &amp; development/metabolism ; Plant Development/drug effects ; Soil Pollutants/metabolism/toxicity ; Germination/drug effects ; Plant Roots/growth &amp; development/metabolism/microbiology ; Bacillus subtilis ; Benzoic Acid/metabolism ; },
abstract = {The deposition of allelochemicals poses a challenge to continuous cropping. Microbial degradation is an efficient approach to degrade these hazardous compounds. The current study employed an integrated approach to explore the allelochemical degradation potential of Bacillus subtilis RS10 and Bacillus pumilus SF-4 and concurrently validate their capabilities to enhance plant growth and alleviate abiotic stress in pot experiments. During initial in vitro screening, both strains utilized more than 45% of benzoic acid within 60 h of incubation and showed maximum growth after 72 h. Meanwhile, the wheat seed germination rate was increased by 34.33% and 30% when treated with strain RS10 and SF-4, respectively. In addition, both strains demonstrated the capacity to promote wheat growth in terms of root length, shoot length, and plant weight in soil contaminated with p-hydroxybenzoic acid. To determine the associated mechanism of plant growth-promoting and allelochemical degradation, the culture extract of RS10 and SF-4 were analyzed using gas chromatography-mass spectrometry, which showed several plant growth-promoting volatile organic compounds, including propanediol and butanone. Genome-wide analysis unveiled several genetic loci associated with plant growth-promoting traits such as siderophore synthesis, phosphate solubilization, and biosynthesis of biocontrol compounds. Moreover, the in-depth comparative genome analysis, horizontal gene transfer, and strain-specific genes unveiled intriguing insight into the evolutionary dynamics of these strains and constraints driven by natural selection. In conclusion, the current study revealed the multifarious plant growth-promoting traits of strains RS10 and SF-4 and suggested an application of these strains as plant growth stimulators in soil contaminated with allelochemicals.},
}
@article {pmid39921128,
year = {2025},
author = {Lavergne, JP and Page, A and Polard, P and Campo, N and Grangeasse, C},
title = {Quantitative phosphoproteomic reveals that the induction of competence modulates protein phosphorylation in Streptococcus pneumonaie.},
journal = {Journal of proteomics},
volume = {315},
number = {},
pages = {105399},
doi = {10.1016/j.jprot.2025.105399},
pmid = {39921128},
issn = {1876-7737},
mesh = {*Streptococcus pneumoniae/metabolism ; *Bacterial Proteins/metabolism/genetics ; Phosphorylation ; *Proteomics/methods ; *Phosphoproteins/metabolism ; Proteome/metabolism ; Protein Processing, Post-Translational ; },
abstract = {Competence in the pathogenic bacterium Streptococcus pneumoniae (S. pneumoniae) is a developmental genetic program that is key for natural genetic transformation and consequently bacterial horizontal gene transfer. Phosphoproteomic studies have revealed that protein phosphorylation on serine, threonine and tyrosine residues is a widespread regulatory post-translational modification in bacteria. In this study, we performed quantitative proteomic and phosphoproteomic analyses on S. pneumoniae as a function of competence induction. To calculate peptide abundance ratios between non-competent and competent samples we used dimethyl-tag labeling. Titanium dioxide (TiO2) beads were used for phosphopeptide enrichment and samples were analysed by LC-MS/MS. Our proteome analysis covers approximatively 63 % of the total bacterial protein content, identifying 82 proteins with significantly different abundance ratios, including some not previously linked to competence. 248 phosphopeptides were identified including 47 having different abundance ratios. Notably, the proteins with a change in phosphorylation in competent cells are different from the proteins with a change in expression, highlighting different pathways induced by competence and regulated by phosphorylation. This is the first report that phosphorylation of some proteins is regulated during competence in Streptococcus pneumoniae, a key pathway for the bacteria to evade vaccines or acquire antibiotic resistance. SIGNIFICANCE: S. pneumoniae is a prominent model for the study of competence that governs the development of natural genetic transformation. The latter largely accounts for the spread of antibiotic resistance and vaccine evasion in pneumococcal isolates. Many proteins specifically expressed during competence have been identified and extensively studied. However, the potential contribution of post-translational modifications, and notably phosphorylation, during the development of competence has never been investigated. In this study, we used a quantitative phosphoproteomic approach to determine both the protein expression and the protein phosphorylation patterns. Comparison of these patterns allows to highlight a series of proteins that are differentially phosphorylated in the two conditions. This result opens new avenues to decipher new regulatory pathways induced by competence and that are potentially key for natural genetic transformation. Interfering with theses regulatory pathways could represent a promising strategy to combat antibiotic resistance in the future.},
}
@article {pmid39921114,
year = {2025},
author = {Farooq, S and Talat, A and Dhariwal, A and Petersen, FC and Khan, AU},
title = {Transgenerational gut dysbiosis: Unveiling the dynamics of antibiotic resistance through mobile genetic elements from mothers to infants.},
journal = {International journal of antimicrobial agents},
volume = {65},
number = {5},
pages = {107458},
doi = {10.1016/j.ijantimicag.2025.107458},
pmid = {39921114},
issn = {1872-7913},
mesh = {Humans ; Female ; Infant ; *Gastrointestinal Microbiome/genetics ; Infant, Newborn ; *Dysbiosis/microbiology ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; Adult ; *Drug Resistance, Bacterial/genetics ; Mothers ; *Interspersed Repetitive Sequences ; Male ; *Bacteria/genetics/drug effects/isolation &amp; purification ; },
abstract = {OBJECTIVES: The initial microbial colonization of the gut is seeded by microbes transmitted from the mother's gut, skin, and vaginal tract. As the gut microbiome evolves, a few transmitted microbes persist throughout life. Understanding the impact of mother-to-neonate gut microbiome and antibiotic resistance genes (ARGs) transmission is crucial for establishing its role in infants' immunity against pathogens.<br><br>METHODS: This study primarily explores mother-neonate ARG transmission through 125 publicly available fecal metagenomes, isolated from eighteen mother-neonate pairs.<br><br>RESULTS: The core ARGs, detected in both mothers and their respective infants at all stages (birth, 1st, 2nd, 3rd, 4th, 8th and 12th months) included aminoglycosidases APH(3')-IIIa, Bifidobacterium adolescentis rpoB mutants conferring resistance to rifampicin, &#x3b2;-lactamases CblA-1, CfxA2, multidrug resistance gene CRP, diaminopyrimidine resistance gene dfrF, fluoroquinolone-resistance gene emrR, macrolide; lincosamide; streptogramin resistance gene ErmB, ErmG, macrolide resistance gene Mef(En2), nucleosidase SAT-4, and tetracycline-resistance genes tet(O), tet(Q), and tet(W). Most of these infants and mothers were not administered any antibiotics. In infants, ARGs were predominantly carried by Bacillota, Pseudomonadota, and Actinomycetota, similar to the mothers. The dominant ARG-carrying opportunistic pathogens were Escherichia coli, Klebsiella, and Streptococcus, found across all infant cohorts. All the core ARGs were associated with mobile genetic elements, signifying the role of horizontal gene transfer(HGT). We detected 132 virulence determinants, mostly E. coli-specific, including pilus chaperones, general secretion pathway proteins, type III secretion system effectors, and heme-binding proteins.<br><br>CONCLUSIONS: Maternal-neonate transmission of ARGs along with possible nosocomial infections, mode of delivery, breastfeeding versus formula feeding, and gestation period, must be considered for mother-neonate health.},
}
@article {pmid39919124,
year = {2025},
author = {Rodriguez-Grande, J and Ortiz, Y and Garcia-Lopez, D and Garcillán-Barcia, MP and de la Cruz, F and Fernandez-Lopez, R},
title = {Encounter rates and engagement times limit the transmission of conjugative plasmids.},
journal = {PLoS genetics},
volume = {21},
number = {2},
pages = {e1011560},
pmid = {39919124},
issn = {1553-7404},
mesh = {*Plasmids/genetics ; *Conjugation, Genetic ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Escherichia coli/genetics ; Bacteria/genetics ; },
abstract = {Plasmid conjugation is a major route for the dissemination of antibiotic resistances and adaptive genes among bacterial populations. Obtaining precise conjugation rates is thus key to understanding how antibiotic resistances spread. Plasmid conjugation is typically modeled as a density-dependent process, where the formation of new transconjugants depends on the rate of encounters between donor and receptor cells. By analyzing conjugation dynamics at different cell concentrations, here we show that this assumption only holds at very low bacterial densities. At higher cell concentrations, conjugation becomes limited by the engagement time, the interval required between two successful matings. Plasmid conjugation therefore follows a Holling´s Type II functional response, characterized by the encounter rate and the engagement time, which represent, respectively, the density and frequency-dependent limits of plasmid transmission. Our results demonstrate that these parameters are characteristic of the transfer machinery, rather than the entire plasmid genome, and that they are robust to environmental and transcriptional perturbation. Precise parameterization of plasmid conjugation will contribute to better understanding the propagation dynamics of antimicrobial resistances.},
}
@article {pmid39918226,
year = {2025},
author = {Prieto Farfan, AB and Llimpe Mitma de Barrón, Y and Mayorca Yarihuamán, MM and Príncipe Laines, FM and Paredes Pérez, MB and Calla Choque, JS and Barrón Pastor, HJ},
title = {Phylogenetic Analysis of Escherichia coli according to Phenotypic Resistance in Urinary Tract Infections in Children, Lima, Peru.},
journal = {Infection &amp; chemotherapy},
volume = {57},
number = {1},
pages = {93-101},
pmid = {39918226},
issn = {2093-2340},
support = {A18010321/UNMSM/Universidad Nacional Mayor de San Marcos/Peru ; },
abstract = {BACKGROUND: Phylogenetic studies are essential for understanding the virulence and resistance factors of bacteria, especially in evaluating their distribution within specific populations for effective infection control. Urinary tract infections (UTIs) caused by Escherichia coli are highly prevalent and pose significant health challenges from childhood to adulthood. The rising incidence of multidrug-resistant (MDR) strains highlights the urgent need for research aimed at developing preventive measures and epidemiological control strategies. This study aimed to analyze phylogenetically uropathogenic E. coli strains and their resistance phenotypes in children.<br><br>MATERIALS AND METHODS: A retrospective analysis was conducted on 111 urine culture samples collected from June 2023 to February 2024 at the Pediatric Emergency Hospital (PEH) in Lima, Peru. The phylogroups of E. coli were identified using Clermont's protocol based on polymerase chain reaction.<br><br>RESULTS: UTIs were predominantly observed in females (85.6%) and infants under two years old (42.3%). The most frequent uropathogenic E. coli phylogroups were B2 (30.6%), D (29.7%), and A (25.2%). These phylogroups showed significant correlation with MDR and the production of extended spectrum beta-lactamases (ESBL).<br><br>CONCLUSION: At PEH, UTIs in children are primarily caused by uropathogenic E. coli from the B2 and D phylogroups, which demonstrate high virulence and resistance factors. The correlation between these phylogroups, MDR, and ESBL production, along with the increasing infection rates associated with phylogroup A, suggests a potential for horizontal gene transfer. This underscores the urgent need for vigilant control measures.},
}
@article {pmid39913343,
year = {2025},
author = {Davidovich, C and Erokhina, K and Gupta, CL and Zhu, YG and Su, JQ and Djordjevic, SP and Wyrsch, ER and Blum, SE and Cytryn, E},
title = {Occurrence of "under-the-radar" antibiotic resistance in anthropogenically affected produce.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {39913343},
issn = {1751-7370},
mesh = {*Lactuca/microbiology ; *Wastewater/microbiology ; *Escherichia coli/genetics/drug effects/isolation &amp; purification ; *Manure/microbiology ; *Agricultural Irrigation ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Animals ; Plasmids/genetics ; Gene Transfer, Horizontal ; Poultry/microbiology ; Drug Resistance, Bacterial ; },
abstract = {With global climate change, treated-wastewater irrigation and manure amendment are becoming increasingly important in sustainable agriculture in water- and nutrient-stressed regions. Yet, these practices can potentially disseminate pathogens and antimicrobial resistance determinants to crops, resulting in serious health risks to humans through the food chain. Previous studies demonstrated that pathogen and antimicrobial resistance indicators from wastewater and manure survive poorly in the environment, suggesting that ecological barriers prevent their dissemination. However, we recently found that these elements can persist below detection levels in low quality treated wastewater-irrigated soil, and potentially proliferate under favorable conditions. This "under-the-radar" phenomenon was further investigated here, in treated wastewater-irrigated and poultry litter-amended lettuce plants, using an enrichment platform that resembles gut conditions, and an analytical approach that combined molecular and cultivation-based techniques. Enrichment uncovered clinically relevant multidrug-resistant pathogen indicators and a myriad of antibiotic resistance genes in the litter amended and treated wastewater-irrigated lettuce that were not detected by direct analyses, or in the enriched freshwater irrigated samples. Selected resistant E. coli isolates were capable of horizontally transferring plasmids carrying multiple resistance genes to a susceptible strain. Overall, our study underlines the hidden risks of under-the-radar pathogen and antimicrobial resistance determinants in anthropogenically affected agroenvironments, providing a platform to improve quantitative microbial risk assessment models in the future.},
}
@article {pmid39908756,
year = {2025},
author = {Xu, J and Ding, D and Fan, Y and Chen, R and Xia, Y and Liang, Y and Ding, Y and Feng, H},
title = {The overlooked risk of horizontal transfer of plasmid-borne antibiotic resistance genes induced by synthetic phenolic antioxidants.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137459},
doi = {10.1016/j.jhazmat.2025.137459},
pmid = {39908756},
issn = {1873-3336},
mesh = {*Gene Transfer, Horizontal ; *Plasmids/genetics ; *Antioxidants/pharmacology ; *Phenols/toxicity ; Wastewater ; Butylated Hydroxyanisole/pharmacology ; Drug Resistance, Bacterial/genetics/drug effects ; Drug Resistance, Microbial/genetics ; Microbiota/drug effects ; Conjugation, Genetic/drug effects ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Plasmid-borne conjugation transfer of antibiotic resistance genes (ARGs) triggered by non-antibiotic stresses has attracted widespread attention, known to motivate conjugation through well-recognized reactive oxygen species and SOS response. However, a notable knowledge gap remains on the potential risks of reductive compounds, such as synthetic phenolic antioxidants (SPAs), in facilitating horizontal gene transfer by the other mechanisms beyond intracellular ROS. Therefore, intragenus and wastewater indigenous microbiota conjugation models were established to examine conjugative transfer frequency of RP4 plasmid under exposure of four extensively detected SPAs. The mechanisms were elucidated utilizing fluorescence detection, RT-qPCR, and transcriptomic analysis with 3-tert-butyl-4-hydroxyanisole (BHA) serving as a representative SPA. Results demonstrated that conjugation transfer frequencies of both models were significantly promoted without triggering SOS responses under exposure to high doses of BHA. Furthermore, BHA exposure benefited conjugation progress through improving membrane permeability of donors and ameliorating cellular energy supply. In addition, BHA exposure activated the RP4-encoded transfer apparatus by regulating the expression of associated genes. This study highlighted and provided a stark reminder about the potential horizontal gene transfer risks posed by SPAs exposure, which were regarded as a neglected driver in the dissemination of ARGs.},
}
@article {pmid39908303,
year = {2025},
author = {Poncin, K and McKeand, SA and Lavender, H and Kurzyp, K and Harrison, OB and Roberti, A and Melia, C and Johnson, E and Maiden, MCJ and Greaves, DR and Exley, R and Tang, CM},
title = {Bacteriocin-like peptides encoded by a horizontally acquired island mediate Neisseria gonorrhoeae autolysis.},
journal = {PLoS biology},
volume = {23},
number = {2},
pages = {e3003001},
pmid = {39908303},
issn = {1545-7885},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Neisseria gonorrhoeae/metabolism/genetics/pathogenicity/physiology ; *Bacteriocins/metabolism/genetics ; Humans ; *Gene Transfer, Horizontal ; Bacteriolysis ; Genomic Islands ; Gonorrhea/microbiology ; },
abstract = {Neisseria gonorrhoeae is a human-specific pathogen that causes the important sexually transmitted infection, gonorrhoea, an inflammatory condition of the genitourinary tract. The bacterium is closely related to the meningococcus, a leading cause of bacterial meningitis. Both these invasive bacterial species undergo autolysis when in the stationary phase of growth. Autolysis is a form of programmed cell death (PCD) which is part of the life cycle of remarkably few bacteria and poses an evolutionary conundrum as altruistic death provides no obvious benefit for single-celled organisms. Here, we searched for genes present in these 2 invasive species but not in other members of the Neisseria genus. We identified a ~3.4 kb horizontally acquired region, we termed the nap island, which is largely restricted to the gonococcus and meningococcus. The nap island in the gonococcus encodes 3 cationic, bacteriocin-like peptides which have no detectable antimicrobial activity. Instead, the gonococcal Neisseria autolysis peptides (Naps) promote autolytic cell death when bacteria enter the stationary phase of growth. Furthermore, strains lacking the Naps exhibit reduced autolysis in assays of PCD. Expression of Naps is likely to be phase variable, explaining how PCD could have arisen in these important human pathogens. NapC also induces lysis of human cells, so the peptides are likely to have multiple roles during colonisation and disease. The acquisition of the nap island contributed to the emergence of PCD in the gonococcus and meningococcus and potentially to the appearance of invasive disease in Neisseria spp.},
}
@article {pmid39907470,
year = {2025},
author = {Wang, X and Koster, Ad and Koenders, BB and Jonker, M and Brul, S and Ter Kuile, BH},
title = {De novo acquisition of antibiotic resistance in six species of bacteria.},
journal = {Microbiology spectrum},
volume = {13},
number = {3},
pages = {e0178524},
pmid = {39907470},
issn = {2165-0497},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Mutation ; *Gene Transfer, Horizontal ; *Microbial Sensitivity Tests ; Whole Genome Sequencing ; Bacteria/drug effects/genetics/classification ; Drug Resistance, Bacterial/genetics ; Fluoroquinolones/pharmacology ; Animals ; Drug Resistance, Multiple, Bacterial/genetics ; DNA Gyrase/genetics ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Bacteria can become resistant to antibiotics in two ways: by acquiring resistance genes through horizontal gene transfer and by de novo development of resistance upon exposure to non-lethal concentrations. The importance of the second process, de novo build-up, has not been investigated systematically over a range of species and may be underestimated as a result. To investigate the DNA mutation patterns accompanying the de novo antibiotic resistance acquisition process, six bacterial species encountered in the food chain were exposed to step-wise increasing sublethal concentrations of six antibiotics to develop high levels of resistance. Phenotypic and mutational landscapes were constructed based on whole-genome sequencing at two time points of the evolutionary trajectory. In this study, we found that (1) all of the six strains can develop high levels of resistance against most antibiotics; (2) increased resistance is accompanied by different mutations for each bacterium-antibiotic combination; (3) the number of mutations varies widely, with Y. enterocolitica having by far the most; (4) in the case of fluoroquinolone resistance, a mutational pattern of gyrA combined with parC is conserved in five of six species; and (5) mutations in genes coding for efflux pumps are widely encountered in gram-negative species. The overall conclusion is that very similar phenotypic outcomes are instigated by very different genetic changes. The outcome of this study may assist policymakers when formulating practical strategies to prevent development of antimicrobial resistance in human and veterinary health care.IMPORTANCEMost studies on de novo development of antimicrobial resistance have been performed on Escherichia coli. To examine whether the conclusions of this research can be applied to more bacterial species, six species of veterinary importance were made resistant to six antibiotics, each of a different class. The rapid build-up of resistance observed in all six species upon exposure to non-lethal concentrations of antimicrobials indicates a similar ability to adjust to the presence of antibiotics. The large differences in the number of DNA mutations accompanying de novo resistance suggest that the mechanisms and pathways involved may differ. Hence, very similar phenotypes can be the result of various genotypes. The implications of the outcome are to be considered by policymakers in the area of veterinary and human healthcare.},
}
@article {pmid39904308,
year = {2025},
author = {Whiteman, NK},
title = {Insect herbivory: An inordinate fondness for plant cell wall degrading enzymes.},
journal = {Current biology : CB},
volume = {35},
number = {3},
pages = {R107-R109},
doi = {10.1016/j.cub.2024.12.045},
pmid = {39904308},
issn = {1879-0445},
mesh = {Animals ; *Herbivory/physiology ; *Cell Wall/metabolism/enzymology ; *Coleoptera/physiology/enzymology/genetics ; Symbiosis ; Gene Transfer, Horizontal ; },
abstract = {Tens of thousands of species of leaf beetles rely on plant cell wall degrading enzymes in order to make the most of nutritionally depauperate plant tissues. Many of the genes encoding these enzymes were acquired from microbial donors, either through horizontal gene transfer or by hosting microbial endosymbionts. A new study explores how these insects have leveraged this metabolic potential to diversify and expand into new niches.},
}
@article {pmid39902196,
year = {2024},
author = {Chen, R and Rao, R and Wang, C and Zhu, D and Yuan, F and Yue, L},
title = {Features and evolutionary adaptations of the mitochondrial genome of Garuga forrestii W. W. Sm.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1509669},
pmid = {39902196},
issn = {1664-462X},
abstract = {INTRODUCTION: Garuga forrestii W. W. Sm. is a tree species of the Burseraceae family, endemic to China, found in hot/warm-dry valleys. This species plays a crucial role in maintaining biodiversity in these ecosystems.<br><br>METHODS: We performed de novo assembly of the Garuga forrestii mitochondrial genome using PMAT (v.1.5.4), resulting in a typical circular molecule of 606,853 bp. The genome consists of 31 tRNA genes, 3 rRNA genes, 35 protein-coding genes, and 1 pseudogene. The study also investigates RNA editing sites and evolutionary patterns.<br><br>RESULTS: The mitochondrial genome exhibits a low proportion of repetitive sequences (3.30%), suggesting a highly conserved structure. A high copy number of the trnM-CAT gene (4 copies) is noted, which may contribute to genomic rearrangement and adaptive evolution. Among the 476 RNA editing sites, hydrophilic-hydrophobic and hydrophobic-hydrophobic editing events are most common, accounting for 77.10%. Negative selection predominates among most genes (Ka/Ks < 1), while a few genes (e.g., matR, nad3, rps1, rps12, and rps4) show signs of positive selection (Ka/Ks > 1), potentially conferring evolutionary advantages. Additionally, a significant A/T bias is observed at the third codon position. Phylogenomic analysis supports the APG IV classification, with no evidence of horizontal gene transfer.<br><br>DISCUSSION: This mitochondrial genome offers valuable insights into the adaptive mechanisms and evolutionary processes of Garuga forrestii. It enhances our understanding of the species' biogeography in tropical Southeast Asia and Southwest China, providing key information on the evolutionary history of this genus.},
}
@article {pmid39902180,
year = {2024},
author = {Li, X and Zhu, Y and Lu, Y and Wu, K and Che, Y and Wang, X and Wang, W and Gao, J and Gao, J and Liu, Z and Zhou, Z},
title = {Population genetic analysis of clinical Mycobacterium abscessus complex strains in China.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1496896},
pmid = {39902180},
issn = {2235-2988},
mesh = {China/epidemiology ; Humans ; *Mycobacterium abscessus/genetics/classification/isolation &amp; purification/drug effects ; *Mycobacterium Infections, Nontuberculous/microbiology/epidemiology ; Multilocus Sequence Typing ; Genome, Bacterial ; Virulence Factors/genetics ; Genetic Variation ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Genetics, Population ; Interspersed Repetitive Sequences ; Genomic Islands ; Genotype ; Phylogeny ; },
abstract = {BACKGROUND: To explore the genetic characteristics of the Mycobacterium abscessus complex (MABC) population in China, given its rising clinical importance among nontuberculous mycobacteria.<br><br>METHODS: We conducted population genetic analyses on 360 MABC genomes from China, focusing on core genome multilocus sequence typing (cgMLST), pan-genome characterization, population genetics, and antimicrobial resistance gene profiling.<br><br>RESULTS: Our analysis identified 273 M. abscessus subsp. abscessus (MabA) and 87 M. abscessus subsp. massiliense (MabM) isolates, uncovering 68 sequence types (STs), with ST5 being the most common. cgMLST classified 33.3% of isolates into six dominant circulating clones (DCCs) and 49.4% into 59 genomic clusters at a threshold of 25 different alleles, including 18 international clusters linking Chinese isolates with seven other countries. The MABC pan-genome is open, with MabA exhibiting greater accessory gene diversity and higher gene turnover compared to MabM. Mobile genetic elements (MGEs), such as prophages and genomic islands, were prevalent across all genomes. 139 to 151 virulence factors (VFs) were identified per genome, with distinct accessory VFs in MabA and MabM affecting immune modulation and metabolism. Resistance gene profiling revealed ubiquitous mtrA, RbpA, and bla MAB, with MabA-specific erm(41) conferring resistance to macrolides and &#x3b2;-lactams. Common rrs and rrl gene mutations indicated widespread resistance to aminoglycosides and macrolides, while gyrA mutations suggested emerging fluoroquinolone resistance. An acquired erm(46) gene, likely obtained via phage-mediated horizontal gene transfer, was detected in one MabA strain.<br><br>CONCLUSION: This study provides key genetic insights into the dynamics of MABC in China. The widespread distribution of DCCs, high genomic clustering rates, open pan-genome, and distinct resistance patterns between MabA and MabM, along with MGEs, highlight the need for targeted surveillance and tailored therapies to address emerging challenges in MABC infections.},
}
@article {pmid39901063,
year = {2025},
author = {Wiśniewska, MM and Kyslík, J and Alama-Bermejo, G and Lövy, A and Kolísko, M and Holzer, AS and Kosakyan, A},
title = {Comparative transcriptomics reveal stage-dependent parasitic adaptations in the myxozoan Sphaerospora molnari.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {103},
pmid = {39901063},
issn = {1471-2164},
support = {19-25536Y//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 19-28399X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 20-30321Y//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//ERD fund Centre for Research of Pathogenicity and Virulence Parasites/ ; },
mesh = {*Myxozoa/genetics/physiology/growth &amp; development ; Animals ; *Gene Expression Profiling ; *Transcriptome ; Carps/parasitology ; Host-Parasite Interactions/genetics ; Gills/parasitology ; *Adaptation, Physiological/genetics ; },
abstract = {BACKGROUND: Parasitism as a life strategy has independently evolved multiple times within the eukaryotic tree of life. Each lineage has developed mechanisms to invade hosts, exploit resources, and ensure replication, but our knowledge of survival mechanisms in many parasitic taxa remain extremely limited. One such group is the Myxozoa, which are obligate, dixenous cnidarians. Evidence suggests that myxozoans evolved from free-living ancestors to endoparasites around 600 million years ago and are likely one of the first metazoan parasites on Earth. Some myxozoans pose significant threats to farmed and wild fish populations, negatively impacting aquaculture and fish stocks; one such example is Sphaerospora molnari, which forms spores in the gills of common carp (Cyprinus carpio), disrupting gill epithelia and causing somatic and respiratory failure. Sphaerospora molnari undergoes sequential development in different organs of its host, with large numbers of morphologically distinct stages occurring in the blood, liver, and gills of carp. We hypothesize that these parasite life-stages differ in regards to their host exploitation, pathogenicity, and host immune evasion strategies and mechanisms. We performed stage-specific transcriptomic profiling to identify differentially expressed key functional gene groups that relate to these functions and provide a fundamental understanding of the mechanisms S. molnari uses to optimize its parasitic lifestyle. We aimed to identify genes that are likely related to parasite pathogenicity and host cell exploitation mechanisms, and we hypothesize that genes unique to S. molnari might be indicative of evolutionary innovations and specific adaptations to host environments.<br><br>RESULTS: We used parasite isolation protocols and comparative transcriptomics to study early proliferative and spore-forming stages of S. molnari, unveiling variation in gene expression between each stage. We discovered several apparent innovations in the S. molnari transcriptome, including proteins that are likely to function in the uptake of previously unknown key nutrients, immune evasion factors that may contribute to long-term survival in hosts, and proteins that likely improve adhesion to host cells that may have arisen from horizontal gene transfer. Notably, we identified genes that are similar to known virulence factors in other parasitic organisms, particularly blood and intestinal parasites like Plasmodium, Trypanosoma, and Giardia. Many of these genes are absent in published cnidarian and myxozoan datasets and appear to be specific to S. molnari; they may therefore represent potential innovations enabling Sphaerospora to exploit the host's blood system.<br><br>CONCLUSIONS: In order to address the threat posed by myxozoans to both cultured fish species and wild stocks, it is imperative to deepen our understanding of their genetics. Sphaerospora molnari offers an appealing model for stage-specific transcriptomic profiling and for identifying differentially expressed key functional gene groups related to parasite development. We identified genes that are thus far unique to S. molnari, which reveal their evolutionary novelty and likely role as adaptations to specific host niches. In addition, we describe the pathogenicity-associated genetic toolbox of S. molnari and discuss the implications of our discoveries for disease control by shedding light on specific targets for potential intervention strategies.},
}
@article {pmid39900484,
year = {2025},
author = {Van Etten, J and Stephens, TG and Bhattacharya, D},
title = {Genetic Transfer in Action: Uncovering DNA Flow in an Extremophilic Microbial Community.},
journal = {Environmental microbiology},
volume = {27},
number = {2},
pages = {e70048},
pmid = {39900484},
issn = {1462-2920},
support = {//U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231/ ; 10.46936/10.25585/60000481//Joint Genome Institute/ ; NJ01180//National Institute of Food and Agriculture/ ; 80NSSC19K1542/NASA/NASA/United States ; NASA (80NSSC19K0462)/NASA/NASA/United States ; },
mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics ; *Extremophiles/genetics ; *DNA, Bacterial/genetics ; Genome, Bacterial ; *Microbiota ; },
abstract = {Horizontal genetic transfer (HGT) is a significant driver of genomic novelty in all domains of life. HGT has been investigated in many studies however, the focus has been on conspicuous protein-coding DNA transfers that often prove to be adaptive in recipient organisms and are therefore fixed longer-term in lineages. These results comprise a subclass of HGTs and do not represent exhaustive (coding and non-coding) DNA transfer and its impact on ecology. Uncovering exhaustive HGT can provide key insights into the connectivity of genomes in communities and how these transfers may occur. In this study, we use the term frequency-inverse document frequency (TF-IDF) technique, that has been used successfully to mine DNA transfers within real and simulated high-quality prokaryote genomes, to search for exhaustive HGTs within an extremophilic microbial community. We establish a pipeline for validating transfers identified using this approach. We find that most DNA transfers are within-domain and involve non-coding DNA. A relatively high proportion of the predicted protein-coding HGTs appear to encode transposase activity, restriction-modification system components, and biofilm formation functions. Our study demonstrates the utility of the TF-IDF approach for HGT detection and provides insights into the mechanisms of recent DNA transfer.},
}
@article {pmid39898629,
year = {2025},
author = {Huang, S and Wei, DD and Hong, H and Chen, S and Fan, L-P and Huang, Q-S and Du, F-L and Xiang, T-X and Li, P and Zhang, W and Wan, L-G and Liu, Y},
title = {Capture of mobile genetic elements following intercellular conjugation promotes the production of ST11-KL64 CR-hvKP.},
journal = {Microbiology spectrum},
volume = {13},
number = {3},
pages = {e0134724},
pmid = {39898629},
issn = {2165-0497},
support = {82102411, 32370195, 82260403//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/metabolism ; *Klebsiella Infections/microbiology ; *Conjugation, Genetic ; *Plasmids/genetics ; Humans ; *Interspersed Repetitive Sequences ; Virulence/genetics ; Gene Transfer, Horizontal ; Animals ; Whole Genome Sequencing ; Mice ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Carbapenem-Resistant Enterobacteriaceae/genetics/isolation &amp; purification ; },
abstract = {UNLABELLED: Sequence type (ST)11 carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) can cause life-threatening infections and is therefore of global concern. Despite its importance, the evolutionary history and mechanism for the emergence of ST11 CR-hvKP are unclear. In recent years, the detection rate of ST11 CR-hvKP has increased in a teaching hospital. Based on its clonal transmission, a conjugation experiment was performed between a hvKP strain AP8555 and a ST11 CRKP strain, resulting in two ST11 CR-hvKP strains. Research had confirmed that the virulence plasmid pAP855 was horizontally transferred to the CRKP strain to form the conjugant S270-Tc, which was recombined by mobile genetic elements to evolve into the conjugant S270-Tc-R. The S270-Tc-R had high virulence, high plasmid stability, and greater adaptability. Interestingly, it had high homology to clinically prevalent ST11 CR-hvKP strains using pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS). This is the first demonstration that plasmid recombination in vitro has led to the formation of ST11 CR-hvKP strains. The clinical setting is a multi-factorial and multi-selection pressure environment that may stimulate the evolution of conjugant strains in the transition period to local strains in the stable period, and surveillance is urgently needed for infection control.<br><br>IMPORTANCE: The emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) heralded the onset of a new and rapidly worsening public health disaster on a global scale. More attention has been paid to its evolutionary history and mechanism, which currently remains unclear. In this study, a conjugation experiment was performed between a hvKP strain AP8555 and a ST11 CRKP strain, resulting in two ST11 CR-hvKP strains. We had confirmed that the virulence plasmid pAP855 was horizontally transferred to the CRKP strain to form the conjugant S270-Tc, which was recombined by mobile genetic elements to evolve into the conjugant S270-Tc-R. The S270-Tc-R had high virulence, high plasmid stability, and greater adaptability. Interestingly, it had high homology to clinically prevalent ST11 CR-hvKP strains using pulsed-field gel electrophoresis and whole-genome sequencing.},
}
@article {pmid39897699,
year = {2025},
author = {Theobald, S and Vesth, T and Nybo, JL and Frisvad, JC and Kjærbølling, I and Mondo, S and LaButti, K and Haridas, S and Riley, R and Kuo, AA and Salamov, AA and Pangilinan, J and Lipzen, A and Koriabine, M and Yan, M and Barry, K and Clum, A and Lyhne, EK and Drula, E and Wiebenga, A and Müller, A and Lubbers, RJM and Kun, RS and Dos Santos Gomes, AC and Mäkelä, MR and Henrissat, B and Simmons, BA and Magnuson, JK and Hoof, JB and Mortensen, UH and Dyer, PS and Momany, M and Larsen, TO and Grigoriev, IV and Baker, SE and de Vries, RP and Andersen, MR},
title = {Comparative genomics of Aspergillus nidulans and section Nidulantes.},
journal = {Current research in microbial sciences},
volume = {8},
number = {},
pages = {100342},
pmid = {39897699},
issn = {2666-5174},
abstract = {Aspergillus nidulans is an important model organism for eukaryotic biology and the reference for the section Nidulantes in comparative studies. In this study, we de novo sequenced the genomes of 25 species of this section. Whole-genome phylogeny of 34 Aspergillus species and Penicillium chrysogenum clarifies the position of clades inside section Nidulantes. Comparative genomics reveals a high genetic diversity between species with 684 up to 2433 unique protein families. Furthermore, we categorized 2118 secondary metabolite gene clusters (SMGC) into 603 families across Aspergilli, with at least 40 % of the families shared between Nidulantes species. Genetic dereplication of SMGC and subsequent synteny analysis provides evidence for horizontal gene transfer of a SMGC. Proteins that have been investigated in A. nidulans as well as its SMGC families are generally present in the section Nidulantes, supporting its role as model organism. The set of genes encoding plant biomass-related CAZymes is highly conserved in section Nidulantes, while there is remarkable diversity of organization of MAT-loci both within and between the different clades. This study provides a deeper understanding of the genomic conservation and diversity of this section and supports the position of A. nidulans as a reference species for cell biology.},
}
@article {pmid39894155,
year = {2025},
author = {Ren, B and Shi, X and Guo, J and Jin, P},
title = {Interaction of sulfate-reducing bacteria and methanogenic archaea in urban sewers, leads to increased risk of proliferation of antibiotic resistance genes.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {368},
number = {},
pages = {125777},
doi = {10.1016/j.envpol.2025.125777},
pmid = {39894155},
issn = {1873-6424},
mesh = {*Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; *Archaea/genetics ; Bacteria/genetics/metabolism ; Anti-Bacterial Agents ; Biofilms ; Sulfates/metabolism ; Sulfamethoxazole ; Biodegradation, Environmental ; Waste Disposal, Fluid ; Tetracycline ; Cities ; Genes, Bacterial ; },
abstract = {Sewers are considered a potential reservoir of antibiotic resistance. However, the generation of antibiotic resistance genes (ARGs) in microbial communities in pipeline biofilms under antibiotic stress remains unexplored. In this study, the biodegradation efficiency of tetracycline (TCY) and sulfamethoxazole (SMX) was evaluated in a pilot reactor of the sewers. The results showed that under TCY and SMX stress, the degradation efficiency of sewage water was inhibited. The most abundant ARGs detected in the biofilm samples were TCY-related genes (e.g., tetW/N/W, tetC, and tetM), accounting for 34.1%. The microbial community composition varied, and the correlation analysis showed that antibiotic stress had a certain impact on the biological metabolic activity and function of the urban sewers. The community structure and diversity of biofilms enabled the evaluation of the bioconversion of antibiotics. Notably, Anaerocella and Paludibacter directly influenced the methanogenesis and sulfate reduction processes, playing a key role in the interaction between sulfate-reducing bacteria and methanogenic archaea. These microorganisms facilitated the proliferation of ARGs (tet and sul) in the biofilms through horizontal gene transfer. This study provides insight into the front-end control of ARGs, further improving sewage treatment plant processes and reducing the environmental and health risks caused by antibiotic abuse.},
}
@article {pmid39883727,
year = {2025},
author = {Wielert, I and Kraus-Römer, S and Volkmann, TE and Craig, L and Higgins, PG and Maier, B},
title = {Pilin antigenic variants impact gonococcal lifestyle and antibiotic tolerance by modulating interbacterial forces.},
journal = {PLoS biology},
volume = {23},
number = {1},
pages = {e3003022},
pmid = {39883727},
issn = {1545-7885},
mesh = {*Neisseria gonorrhoeae/drug effects/genetics/physiology/immunology ; *Antigenic Variation ; *Fimbriae Proteins/genetics/immunology/metabolism/chemistry ; Anti-Bacterial Agents/pharmacology ; Humans ; Drug Resistance, Bacterial ; Fimbriae, Bacterial ; Bacterial Adhesion/drug effects ; Biofilms/growth &amp; development/drug effects ; Ciprofloxacin/pharmacology ; Antigens, Bacterial/genetics/immunology ; Gonorrhea/microbiology ; },
abstract = {Type 4 pili (T4P) are multifunctional filaments involved in adhesion, surface motility, biofilm formation, and horizontal gene transfer. These extracellular polymers are surface-exposed and, therefore, act as antigens. The human pathogen Neisseria gonorrhoeae uses pilin antigenic variation to escape immune surveillance, yet it is unclear how antigenic variation impacts most other functions of T4P. Here, we addressed this question by replacing the major pilin of a laboratory strain with pilins from clinical isolates. We reveal that the resulting strains vary substantially in their attractive forces. Strongly interacting bacteria form microcolonies while weakly interacting bacteria retain a planktonic lifestyle. In mixed microcolonies, different variant strains segregate in agreement with the differential strength of adhesion hypothesis. By combining structural predictions and laser tweezers experiments, we show that the C-terminal region of the pilin is crucial for attraction. Lifestyle affects growth kinetics and antibiotic tolerance. In the presence of ceftriaxone or ciprofloxacin, the killing kinetics indicate strongly increased tolerance of aggregating strains. We propose that pilin antigenic variation produces a mixed population containing variants optimized for growth, colonization, or survivability under external stress. Different environments select different variants, ensuring the survival and reproduction of the population as a whole.},
}
@article {pmid39882964,
year = {2025},
author = {Warren, JM and Ceriotti, LF and Sanchez-Puerta, MV and Sloan, DB},
title = {Fungal-Derived tRNAs Are Expressed and Aminoacylated in Orchid Mitochondria.},
journal = {Molecular biology and evolution},
volume = {42},
number = {2},
pages = {},
pmid = {39882964},
issn = {1537-1719},
mesh = {*RNA, Transfer/genetics/metabolism ; *Orchidaceae/genetics/metabolism ; Genome, Mitochondrial ; Gene Transfer, Horizontal ; Mitochondria/genetics/metabolism ; },
abstract = {Plant mitochondrial genomes (mitogenomes) experience remarkable levels of horizontal gene transfer, including the recent discovery that orchids anciently acquired DNA from fungal mitogenomes. Thus far, however, there is no evidence that any of the genes from this interkingdom horizontal gene transfer are functional in orchid mitogenomes. Here, we applied a specialized sequencing approach to the orchid Corallorhiza maculata and found that some fungal-derived tRNA genes in the transferred region are transcribed, post-transcriptionally modified, and aminoacylated. In contrast, all the transferred protein-coding sequences appear to be pseudogenes. These findings show that fungal horizontal gene transfer has altered the composition of the orchid mitochondrial tRNA pool and suggest that these foreign tRNAs function in translation. The exceptional capacity of tRNAs for horizontal gene transfer and functional replacement is further illustrated by the diversity of tRNA genes in the C. maculata mitogenome, which also include genes of plastid and bacterial origin in addition to their native mitochondrial counterparts.},
}
@article {pmid39881475,
year = {2025},
author = {Wang, P and Wang, H and Qi, S and Wang, W and Lu, H},
title = {Synergistic effects of quaternary ammonium compounds and antibiotics on the evolution of antibiotic resistance.},
journal = {Water research},
volume = {275},
number = {},
pages = {123206},
doi = {10.1016/j.watres.2025.123206},
pmid = {39881475},
issn = {1879-2448},
mesh = {*Quaternary Ammonium Compounds/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/drug effects ; Drug Synergism ; Wastewater/microbiology ; Escherichia coli/drug effects/genetics ; },
abstract = {The usage of quaternary ammonium compounds (QACs) as disinfectants has surged dramatically during the COVID-19 pandemic and thereafter. QACs can promote antimicrobial resistance, but the combined effects of QACs and antibiotics in driving resistance evolution were yet revealed. This study aimed to evaluate antibiotic resistance of wastewater microorganisms under coexposure to typical antibiotics and the most widely used QAC, dodecyl dimethyl benzyl ammonium chloride (DDBAC). DDBAC exhibited synergistic effects with multiple antibiotics (ampicillin, azithromycin, ciprofloxacin, kanamycin, polymyxin B) in enhancing activated sludge resistance by 1.53-6.67 folds, compared with antibiotics exposure alone. DDBAC-ampicillin coexposure enriched multidrug and aminoglycoside ARGs with relatively high horizontal gene transfer potential. The synergistic mechanism was further explored using sludge-isolated pathogenic E. coli. DDBAC at 1-10 mg/L alone did not induce notable resistance, but synergized with ampicillin on enhancing resistance by 6.56-22.90 folds. Based on mutation analysis and transcriptomics, DDBAC-enhanced resistance evolution was attributable to efflux pump upregulation, target modification, and inhibition of ATP synthesis (a less reported mechanism). Five DDBAC-induced, resistance-conferring mutant genes were highly enriched in globally collected E. coli strains from wastewater outflow (n = 537) than soil/sediments (n = 714, p < 0.05). Considering the strong adsorption and persistence of QACs, their coexistence with antibiotics poses elevated antimicrobial resistance risks, particularly in wastewater treatment systems with long solid retention time and sewage sludge applied farmland.},
}
@article {pmid39880121,
year = {2025},
author = {Almeida-Santos, AC and Novais, C and Peixe, L and Freitas, AR},
title = {Vancomycin-resistant Enterococcus faecium: A current perspective on resilience, adaptation, and the urgent need for novel strategies.},
journal = {Journal of global antimicrobial resistance},
volume = {41},
number = {},
pages = {233-252},
doi = {10.1016/j.jgar.2025.01.016},
pmid = {39880121},
issn = {2213-7173},
mesh = {Humans ; *Enterococcus faecium/drug effects/genetics/physiology/pathogenicity ; *Vancomycin-Resistant Enterococci/genetics/drug effects/physiology ; *Gram-Positive Bacterial Infections/microbiology/epidemiology/drug therapy ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; *Adaptation, Physiological ; Virulence Factors/genetics ; Plasmids/genetics ; Animals ; Bacteriocins/genetics ; },
abstract = {Vancomycin-resistant Enterococcus faecium (VREfm) has become a critical opportunistic pathogen, urgently requiring new antimicrobial strategies due to its rising prevalence and significant impact on patient safety and healthcare costs. VREfm continues to evolve through mutations and the acquisition of new genes via horizontal gene transfer, contributing to resistance against several last-resort antibiotics. Although primarily hospital-associated, VREfm are also detected in the community, food chain, livestock, and environmental sources like wastewater, indicating diverse transmission pathways and the need for a One Health approach. Advances in genomics have shed light on VREfm's persistence in hospital settings, particularly its adaptation to the gastrointestinal tract of hospitalized patients, recent clonal shifts, and the dominance of specific clonal lineages. Despite extensive research, significant gaps remain in understanding the molecular mechanisms behind VREfm's unique adaptation to clinical environments. In this review, we aim to present an overview of VREfm current prevalence, mechanisms of resistance, and unveil the adaptive traits that have facilitated VREfm's rise and global success. A particular focus is given to key plasmids, namely linear plasmids, virulence factors, and bacteriocins as potential drivers in the global emergence of the ST78 clonal lineage. We also address diagnostic challenges and the limited treatment options available for VREfm, as well as emerging antibiotic alternatives aimed at restoring gut microbiota balance and curbing VREfm proliferation. A multifaceted approach combining research, clinical practices, and public health policies is crucial to mitigate the impact of this superbug and preserve antimicrobial effectiveness for future generations.},
}
@article {pmid39879767,
year = {2025},
author = {Li, S and Bai, Y and Li, Z and Wang, A and Ren, NQ and Ho, SH},
title = {Overlooked role of extracellular polymeric substances in antibiotic-resistance gene transfer within microalgae-bacteria system.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137206},
doi = {10.1016/j.jhazmat.2025.137206},
pmid = {39879767},
issn = {1873-3336},
mesh = {*Microalgae/genetics/metabolism ; *Extracellular Polymeric Substance Matrix/metabolism ; *Drug Resistance, Microbial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; Genes, Bacterial ; *Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; Wastewater/microbiology ; },
abstract = {Controlling the spread of antibiotic-resistance genes (ARGs) under antibiotic stress has become an increasingly urgent issue. Microalgae possess the capability to remove antibiotics while concurrently inhibiting ARGs. Microalgae-bacteria systems can produce significant quantities of extracellular polymeric substances (EPS). However, the roles of EPS in the spread of ARGs have not been sufficiently explored, resulting in an insufficient understanding of the contribution of each EPS component and a lack of analysis on the complex interactions between EPS and ARGs. This study systematically explored the overlooked role of EPS in the transmission of ARGs within microalgae-bacteria systems. The current results showed that the potential of the microalgae-bacteria system for treating antibiotic wastewater. The tightly bound-EPS (TB-EPS) can acquire the higher absolute abundances of ARGs compared with the loosely bound-EPS (LB-EPS). The correlation coefficient between polysaccharides and TB-EPS ARGs was higher than that between polysaccharides and LB-EPS ARGs. The gene patterns of LB-EPS closely clustered with those of TB-EPS, while intracellular ARG gene patterns differed from both TB-EPS and LB-EPS. Metagenomic analyses indicated that the relative abundances of sul1 and sul2 were considerably higher at the beginning stage compared to the end stage. The abundance of Achromobacter, increased by the end stage, aligning with its potential to produce exopolysaccharide. Additionally, the absolute abundance of genes encoding exopolysaccharides (nagB and galE) and conjugative transfer transcription regulator (traF), increased over time. These findings enhanced our comprehension of the significance of EPS on the fate of ARGs in microalgae-bacteria systems during the treatment of antibiotic-contaminated wastewater.},
}
@article {pmid39878503,
year = {2025},
author = {Ndovie, W and Havránek, J and Leconte, J and Koszucki, J and Chindelevitch, L and Adriaenssens, EM and Mostowy, RJ},
title = {Exploration of the genetic landscape of bacterial dsDNA viruses reveals an ANI gap amid extensive mosaicism.},
journal = {mSystems},
volume = {10},
number = {2},
pages = {e0166124},
pmid = {39878503},
issn = {2379-5077},
support = {2020/37/B/NZ8/03492//Narodowe Centrum Nauki (NCN)/ ; PPN/PPO/2018/1/00021//Narodowa Agencja Wymiany Akademickiej (NAWA)/ ; 2020/38/E/NZ8/00432//Narodowe Centrum Nauki (NCN)/ ; MR/X020258/1//UKRI | Medical Research Council (MRC)/ ; BB/X011011/1, BBS/E/F/000PR13634, BBS/E/F/000PR13635, BB/X011054/1, BBS/E/F/000PR13631//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Installation Grant to Rafal Mostowy//European Molecular Biology Organization (EMBO)/ ; //International Visegrad Fund (IVF)/ ; },
mesh = {*Genome, Viral ; *DNA Viruses/genetics/classification ; *Mosaicism ; *Bacteria/virology ; Phylogeny ; Computational Biology/methods ; },
abstract = {Average nucleotide identity (ANI) is a widely used metric to estimate genetic relatedness, especially in microbial species delineation. While ANI calculation has been well optimized for bacteria and closely related viral genomes, accurate estimation of ANI below 80%, particularly in large reference data sets, has been challenging due to a lack of accurate and scalable methods. To bridge this gap, we introduce MANIAC, an efficient computational pipeline optimized for estimating ANI and alignment fraction (AF) in viral genomes with divergence around ANI of 70%. Using a rigorous simulation framework, we demonstrate MANIAC's accuracy and scalability compared to existing approaches, even to data sets of hundreds of thousands of viral genomes. Applying MANIAC to a curated data set of complete bacterial dsDNA viruses revealed a multimodal ANI distribution, with a distinct gap around 80%, akin to the bacterial ANI gap (~90%) but shifted, likely due to viral-specific evolutionary processes such as recombination dynamics and mosaicism. We then evaluated ANI and AF as predictors of genus-level taxonomy using a logistic regression model. We found that this model has strong predictive power (PR-AUC = 0.981), but that it works much better for virulent (PR-AUC = 0.997) than temperate (PR-AUC = 0.847) bacterial viruses. This highlights the complexity of taxonomic classification in temperate phages, known for their extensive mosaicism, and cautions against over-reliance on ANI in such cases. MANIAC can be accessed at https://github.com/bioinf-mcb/MANIAC.IMPORTANCEWe introduce a novel computational pipeline called MANIAC, designed to accurately assess average nucleotide identity (ANI) and alignment fraction (AF) between diverse viral genomes, scalable to data sets of over 100k genomes. Using computer simulations and real data analyses, we show that MANIAC could accurately estimate genetic relatedness between pairs of viral genomes of around 60%-70% ANI. We applied MANIAC to investigate the question of ANI discontinuity in bacterial dsDNA viruses, finding evidence for an ANI gap, akin to the one seen in bacteria but around ANI of 80%. We then assessed the ability of ANI and AF to predict taxonomic genus boundaries, finding its strong predictive power in virulent, but not in temperate phages. Our results suggest that bacterial dsDNA viruses may exhibit an ANI threshold (on average around 80%) above which recombination helps maintain population cohesiveness, as previously argued in bacteria.},
}
@article {pmid39874786,
year = {2025},
author = {Chen, Y and Liu, Y and Zhao, C and Ma, J and Guo, J},
title = {Antibiotic resistance gene pollution in poultry farming environments and approaches for mitigation: A system review.},
journal = {Poultry science},
volume = {104},
number = {3},
pages = {104858},
pmid = {39874786},
issn = {1525-3171},
mesh = {Animals ; *Animal Husbandry/methods ; *Poultry ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Antibiotic resistance genes (ARG) pollution in poultry farming environments has become increasingly critical, primarily driven by the widespread use of antibiotics in animal husbandry. Prolonged antibiotic use has led to the emergence of ARGs and antibiotic-resistant bacteria, spreading via horizontal and vertical gene transfer. The complexity of ARG pollution in poultry farming arises from the unique farming practices, physiological characteristics of poultry, and manure management methods, with manure, wastewater, and air serving as significant vectors for ARG dissemination. Current research indicates that the spread of ARGs poses a significant threat to ecosystems and public health. In response to this growing concern, this review outlines the sources, distribution characteristics, and transmission mechanisms of ARGs in poultry farming environments. It also evaluates the efficacy of existing waste treatment technologies in mitigating ARG contamination. The review proposes several strategies to control ARG dissemination effectively, including reducing antibiotic usage, improving farming practices, optimizing waste management, and strengthening regulatory oversight. It also highlights the need for further research to address existing knowledge gaps and explore more efficient pollution control technologies and management measures. This review aims to provide theoretical support for protecting the environment and public health in the context of poultry farming.},
}
@article {pmid39874626,
year = {2025},
author = {Li, J and Sun, D and Wu, J and Liu, F and Xu, Y and Wang, Y and Shui, X and Li, Q and Zhao, B},
title = {Lithium enhanced plasmid-mediated conjugative transfer of antimicrobial resistance genes in Escherichia coli: Different concentrations and mechanisms.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {279},
number = {},
pages = {107263},
doi = {10.1016/j.aquatox.2025.107263},
pmid = {39874626},
issn = {1879-1514},
mesh = {*Escherichia coli/drug effects/genetics ; *Plasmids/genetics ; *Drug Resistance, Bacterial/genetics ; *Conjugation, Genetic/drug effects ; *Water Pollutants, Chemical/toxicity ; Gene Expression Regulation, Bacterial/drug effects ; *Lithium/toxicity ; *Gene Transfer, Horizontal/drug effects ; *Lithium Chloride/toxicity ; },
abstract = {Conjugative transfer, a pivotal mechanism in the transmission of antimicrobial resistance genes, is susceptible to various environmental pollutants. As an emerging contaminant, lithium (Li) has garnered much attention due to its extensive applications. This research investigated the effects of Li on conjugative transfer process, examining biochemical and omics perspectives. Results revealed that Li could increase the conjugative transfer frequency of both donor and recipient via different mechanisms at varying concentrations. At 0.1 mg/L LiCl, a notable increase in conjugative transfer frequency occurred without ROS elevation. However, the surge of ROS was identified as a crucial regulator at 100 mg/L LiCl, as eliminating ROS would significantly decrease the conjugative transfer frequency. Besides, comparative transcriptome analysis revealed consistent variations in "SOS response", "quorum sensing" and "oxidative phosphorylation" pathways at both 0.1 mg/L and 100 mg/L LiCl concentrations, suggesting their pivotal roles as targets for Li regulation and is independent of Li concentration. While genes related to "conjugative transfer", "pili", "outer membrane protein" and "antioxidant enzyme" were only significantly regulated by 100 mg/L LiCl, possible to be the specific reasons for High (100 mg/L) LiCl increased conjugative transfer frequency. This study reveals the distinct effects and mechanisms of different concentration of Li on conjugative transfer in E. coli, providing a theoretical basis for the understanding of the environmental effects of Li.},
}
@article {pmid39874387,
year = {2025},
author = {Li, Y and Pulford, CV and Díaz, P and Perez-Sepulveda, BM and Duarte, C and Predeus, AV and Wiesner, M and Heavens, D and Low, R and Schudoma, C and Montaño, A and Hall, N and Moreno, J and Hinton, JCD},
title = {Potential links between human bloodstream infection by Salmonella enterica serovar Typhimurium and international transmission to Colombia.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {1},
pages = {e0012801},
pmid = {39874387},
issn = {1935-2735},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Colombia/epidemiology ; *Salmonella typhimurium/genetics/isolation &amp; purification/drug effects/classification ; *Salmonella Infections/transmission/microbiology/epidemiology ; Phylogeny ; *Bacteremia/microbiology/epidemiology/transmission ; Drug Resistance, Multiple, Bacterial ; Whole Genome Sequencing ; Male ; Female ; Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Adult ; Middle Aged ; Child, Preschool ; Adolescent ; Young Adult ; Child ; Infant ; Aged ; Genome, Bacterial ; },
abstract = {Salmonella enterica serovar Typhimurium is a prevalent food-borne pathogen that is usually associated with gastroenteritis infection. S. Typhimurium is also a major cause of bloodstream infections in sub-Saharan Africa, and is responsible for invasive non-typhoidal Salmonella (iNTS) disease. The pathogen also causes bloodstream infection in Colombia, but there has been a lack of information about the S. Typhimurium isolates that were responsible. Here, we investigated the genomic characteristics of 270 S. Typhimurium isolates from bloodstream infection patients in Colombia, collected between 1997 and 2017. We used whole-genome sequencing to analyse multidrug-resistant (MDR) profiles, plasmid distribution, and to define phylogenetic relationships. The study identified the distinct sequence types and phylogenetic clusters of S. Typhimurium prevalent in Colombia. The majority of isolates (90.8%) were ST19, which is distinct from the iNTS-associated S. Typhimurium in sub-Saharan Africa (ST313). The two prominent clusters of MDR S. Typhimurium were either DT104 or closely related to the LT2 reference strain. We used a phylogenetic approach to associate the Colombian clusters with global S. Typhimurium isolates from public databases. By putting the Colombian S. Typhimurium isolates in the context of the global spread of DT104, ST313 and LT2-related variants, we found that the Colombian clusters were introduced to the country via multiple independent events that were consistent with international transmission. We suggest that the acquisition of quinolone and chloramphenicol resistance by the Colombian S. Typhimurium isolates was driven by horizontal gene transfer. Three ST313 isolates that caused bloodstream infection in Colombia were identified. These ST313 isolates were related to the Malawian ST313 lineage 3 &amp; UK ST313, and shared a similarly high invasiveness index. To our knowledge, this is the first report of ST313 in Colombia.},
}
@article {pmid39873499,
year = {2025},
author = {Liu, CC and Hsiao, WWL},
title = {Machine learning reveals the dynamic importance of accessory sequences for Salmonella outbreak clustering.},
journal = {mBio},
volume = {16},
number = {3},
pages = {e0265024},
pmid = {39873499},
issn = {2150-7511},
support = {286GET//Genome British Columbia (Genome BC)/ ; 286GET//Genome Canada (GC)/ ; R831778//Mitacs (Mitacs Canada)/ ; },
mesh = {*Disease Outbreaks ; *Machine Learning ; *Salmonella Infections/epidemiology/microbiology ; Genome, Bacterial ; *Salmonella enterica/genetics/classification/isolation &amp; purification ; Humans ; Animals ; Cluster Analysis ; Interspersed Repetitive Sequences ; Whole Genome Sequencing ; Molecular Epidemiology/methods ; },
abstract = {UNLABELLED: Bacterial typing at whole-genome scales is now feasible owing to decreasing costs in high-throughput sequencing and the recent advances in computation. The unprecedented resolution of whole-genome typing is achieved by genotyping the variable segments of bacterial genomes that can fluctuate significantly in gene content. However, due to the transient and hypervariable nature of many accessory elements, the value of the added resolution in outbreak investigations remains disputed. To assess the analytical value of bacterial accessory genomes in clustering epidemiologically related cases, we trained classifiers on a set of genomes collected from 24 Salmonella enterica outbreaks of food, animal, or environmental origin. The models demonstrated high precision and recall on unseen test data with near-perfect accuracy in classifying clonal and short-term outbreaks. Annotating the genomic features important for cluster classification revealed functional enrichment of molecular fingerprints in genes involved in membrane transportation, trafficking, and carbohydrate metabolism. Importantly, we discovered polymorphisms in mobile genetic elements (MGEs) and gain/loss of MGEs to be informative in defining outbreak clusters. To quantify the ability of MGE variations to cluster outbreak clones, we devised a reference-free tree-building algorithm inspired by colored de Bruijn graphs, which enabled topological comparisons between MGE and standard typing methods. Systematic evaluation of clustering MGEs on an unseen dataset of 34 Salmonella outbreaks yielded mixed results that exemplified the power of accessory sequence variations when core genomes of unrelated cases are insufficiently discriminatory, as well as the distortion of outbreak signals by microevolution events or the incomplete assembly of MGEs.<br><br>IMPORTANCE: Gene-by-gene typing is widely used to detect clusters of foodborne illnesses that share a common origin. It remains actively debated whether the inclusion of accessory sequences in bacterial typing schema is informative or deleterious for cluster definitions in outbreak investigations due to the potential confounding effects of horizontal gene transfer. By training machine learning models on a curated set of historical Salmonella outbreaks, we revealed an enriched presence of outbreak distinguishing features in a wide range of mobile genetic elements. Systematic comparison of the efficacy of clustering different accessory elements against standard sequence typing methods led to our cataloging of scenarios where accessory sequence variations were beneficial and uninformative to resolving outbreak clusters. The presented work underscores the complexity of the molecular trends in enteric outbreaks and seeks to inspire novel computational ways to exploit whole-genome sequencing data in enteric disease surveillance and management.},
}
@article {pmid39871141,
year = {2025},
author = {Nichio, BTL and Chaves, RBR and Pedrosa, FO and Raittz, RT},
title = {Exploring diazotrophic diversity: unveiling Nif core distribution and evolutionary patterns in nitrogen-fixing organisms.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {81},
pmid = {39871141},
issn = {1471-2164},
mesh = {*Nitrogen Fixation/genetics ; *Evolution, Molecular ; Phylogeny ; Nitrogenase/genetics/metabolism ; *Bacterial Proteins/genetics ; Gene Transfer, Horizontal ; },
abstract = {BACKGROUND: Diazotrophs carry out biological nitrogen fixation (BNF) using the nitrogenase enzyme complex (NEC), which relies on nitrogenase encoded by nif genes. Horizontal gene transfer (HGT) and gene duplications have created significant diversity among these genes, making it challenging to identify potential diazotrophs. Previous studies have established a minimal set of Nif proteins, known as the Nif core, which includes NifH, NifD, NifK, NifE, NifN, and NifB. This study aimed to identify potential diazotroph groups based on the Nif core and to analyze the inheritance patterns of accessory Nif proteins related to Mo-nitrogenase, along with their impact on N2 fixation maintenance.<br><br>RESULTS: In a systematic study, 118 diazotrophs were identified, resulting in a database of 2,156 Nif protein sequences obtained with RAFTS&#xb3;G. Using this Nif database and a data mining strategy, we extended our analysis to 711 species and found that 544 contain the Nif core. A partial Nif core set was observed in eight species in this study. Finally, we cataloged 662 species with Nif core, of which 52 were novel. Our analysis generated 10,076 Nif proteins from these species and revealed some Nif core duplications. Additionally, we determined the optimal cluster value (k&#x2009;=&#x2009;10) for analyzing diazotrophic diversity. Combining synteny and phylogenetic analyses revealed distinct syntenies in the nif gene composition across ten groups.<br><br>CONCLUSIONS: This study advances our understanding of the distribution of nif genes, aiding in the prediction and classification of N&#x2082;-fixing organisms. Furthermore, we present a comprehensive overview of the diversity, distribution, and evolutionary relationships among diazotrophic organisms associated with the Nif core. The analysis revealed the phylogenetic and functional organization of different groups, identifying synteny patterns and new nif gene arrangements across various bacterial and archaeal species.The identified groups serve as a valuable framework for further exploration of the molecular mechanisms underlying biological nitrogen fixation and its evolutionary significance across different bacterial lineages.},
}
@article {pmid39870251,
year = {2025},
author = {Oubohssaine, M and Rabeh, K and Hnini, M},
title = {Symbiosis vs pathogenesis in plants: Reflections and perspectives.},
journal = {Microbial pathogenesis},
volume = {200},
number = {},
pages = {107333},
doi = {10.1016/j.micpath.2025.107333},
pmid = {39870251},
issn = {1096-1208},
mesh = {*Symbiosis/physiology ; *Plants/microbiology ; *Plant Diseases/microbiology ; Quorum Sensing ; *Host-Pathogen Interactions ; Plant Growth Regulators/metabolism ; Volatile Organic Compounds/metabolism ; Ecosystem ; },
abstract = {Plant-microbe partnerships constitute a complex and intricately woven network of connections that have evolved over countless centuries, involving both cooperation and antagonism. In various contexts, plants and microorganisms engage in mutually beneficial partnerships that enhance crop health and maintain balance in ecosystems. However, these associations also render plants susceptible to a range of pathogens. Understanding the fundamental molecular mechanisms governing these associations is crucial, given the notable susceptibility of plants to external environmental influences. Based on quorum sensing signals, phytohormone, and volatile organic carbon (VOC) production and others molecules, microorganisms influence plant growth, health, and defense responses. This review explores the multifaceted relationships between plants and their associated microorganisms, encompassing mutualism, commensalism, and antagonism. The molecular mechanisms of symbiotic and pathogenic interactions share similarities but lead to different outcomes. While symbiosis benefits both parties, pathogenesis harms the host. Genetic adaptations optimize these interactions, involving coevolution driving process. Environmental factors influence outcomes, emphasizing the need for understanding and manipulation of microbial communities for beneficial results. Research directions include employing multi-omics techniques, functional studies, investigating environmental factors, understanding evolutionary trajectories, and harnessing knowledge to engineer synthetic microbial consortia for sustainable agriculture and disease management.},
}
@article {pmid39869787,
year = {2025},
author = {Lin, C and Li, LJ and Yang, K and Xu, JY and Fan, XT and Chen, QL and Zhu, YG},
title = {Protozoa-enhanced conjugation frequency alters the dissemination of soil antibiotic resistance.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {39869787},
issn = {1751-7370},
support = {2021-DST-004//Ningbo S&amp;T project/ ; 2022S117//Ningbo Public Welfare project/ ; 42090063//National Natural Science Foundation of China/ ; },
mesh = {*Soil Microbiology ; *Conjugation, Genetic ; Plasmids/genetics ; Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Acanthamoeba castellanii/physiology/genetics ; Animals ; Soil/parasitology ; Bacteria/genetics/drug effects ; Metagenomics ; },
abstract = {Protozoa, as primary predators of soil bacteria, represent an overlooked natural driver in the dissemination of antibiotic resistance genes (ARGs). However, the effects of protozoan predation on ARGs dissemination at the community level, along with the underlying mechanisms, remain unclear. Here we used fluorescence-activated cell sorting, qPCR, combined with metagenomics and reverse transcription quantitative PCR, to unveil how protozoa (Colpoda steinii and Acanthamoeba castellanii) influence the plasmid-mediated transfer of ARGs to soil microbial communities. Protozoan predation reduced the absolute abundance of plasmids but promoted the expression of conjugation-associated genes, leading to a 5-fold and 4.5-fold increase in conjugation frequency in the presence of C. steinii and A. castellanii, respectively. Excessive oxidative stress, increased membrane permeability, and the provoked SOS response closely associated with the increased conjugative transfer. Protozoan predation also altered the plasmid host range and selected for specific transconjugant taxa along with ARGs and virulence factors carried by transconjugant communities. This study underscores the role of protozoa in the plasmid-mediated conjugative transfer of ARGs, providing new insights into microbial mechanisms that drive the dissemination of environmental antibiotic resistance.},
}
@article {pmid39867821,
year = {2025},
author = {Yan, Z and Wang, H and Zhu, Y and Wang, X and Wu, Y and Wang, Y and Zhang, R},
title = {Molecular Epidemiology of Type F Clostridium perfringens Among Diarrheal Patients and Virulence-Resistance Dynamics - 11 Provinces, China, 2024.},
journal = {China CDC weekly},
volume = {7},
number = {3},
pages = {69-76},
pmid = {39867821},
issn = {2096-7071},
abstract = {INTRODUCTION: Type F Clostridium perfringens (C. perfringens) represents a significant pathogen in human gastrointestinal diseases, primarily through its cpe gene encoding C. perfringens enterotoxin (CPE). This investigation examined the prevalence, antimicrobial resistance patterns, and genetic characteristics of Type F C. perfringens within the Chinese population.<br><br>METHODS: The study analyzed 2,068 stool samples collected from 11 provincial hospitals in 2024. Antimicrobial susceptibility testing was conducted following Clinical &amp; Laboratory Standards Institute (CLSI) guidelines, while whole-genome sequencing provided detailed genetic profiles. Evolutionary relationships and clonal transmission patterns were investigated through phylogenetic and genetic environment analyses.<br><br>RESULTS: The prevalence of Type F C. perfringens was 2.38%, with isolates predominantly identified in human clinical samples and higher detection rates in gastroenterology departments. Notably, 47.1% of isolates demonstrated high resistance to metronidazole, while all exhibited intermediate resistance to erythromycin. Phylogenetic analysis revealed high similarity among isolates from patients within the same province (single-nucleotide polymorphism (SNPs)<100), and genetic environment analysis indicated potential horizontal gene transfer between animal and human strains.<br><br>CONCLUSIONS: This investigation predominantly identified Type F C. perfringens in human clinical cases, with sporadic detection in pets and food products. These findings highlight the emergence of Type F C. perfringens outbreaks among diarrheal patients, emphasizing the necessity for targeted interventions as virulence factors increase.},
}
@article {pmid39865504,
year = {2025},
author = {Sharp, PM and Bibollet-Ruche, F and Hahn, BH},
title = {Plasmodium falciparum CyRPA Glycan Binding Does Not Explain Adaptation to Humans.},
journal = {Genome biology and evolution},
volume = {17},
number = {2},
pages = {},
pmid = {39865504},
issn = {1759-6653},
support = {P30 AI045008/AI/NIAID NIH HHS/United States ; R01 AI120810/NH/NIH HHS/United States ; },
mesh = {*Plasmodium falciparum/genetics/metabolism/pathogenicity ; Humans ; *Polysaccharides/metabolism ; Animals ; *Protozoan Proteins/metabolism/genetics/chemistry ; Binding Sites ; Erythrocytes/parasitology ; Protein Binding ; Gorilla gorilla/parasitology ; Malaria, Falciparum/parasitology ; Adaptation, Physiological ; },
abstract = {The human malaria parasite Plasmodium falciparum evolved from a parasite that infects gorillas, termed Plasmodium praefalciparum. The sialic acids on glycans on the surface of erythrocytes differ between humans and other apes. It has recently been shown that the P. falciparum cysteine-rich protective antigen (PfCyRPA) binds human sialoglycans as an essential step in the erythrocyte invasion pathway, while that of the chimpanzee parasite, Plasmodium reichenowi has affinities matching ape glycans. Two amino acid changes, at sites 154 and 209, were shown to be sufficient to switch glycan binding preferences and inferred to reflect adaptation of P. falciparum to humans. However, we show that sites 154 and 209 are identical in P. falciparum and P. praefalciparum, with no other differences located in or near the CyRPA glycan binding sites. Thus, the gorilla precursor appears to have already been preadapted to bind human sialoglycans.},
}
@article {pmid39862584,
year = {2025},
author = {Zheng, Z and Ji, W and Wang, X and Wang, X and Dai, S and Zhang, Z and Zhang, Y and Wang, X and Cao, S and Chen, M and Xie, B and Feng, J and Wu, D},
title = {Household waste-specific ambient air shows greater inhalable antimicrobial resistance risks in densely populated communities.},
journal = {Waste management (New York, N.Y.)},
volume = {194},
number = {},
pages = {309-317},
doi = {10.1016/j.wasman.2025.01.030},
pmid = {39862584},
issn = {1879-2456},
mesh = {China ; Humans ; *Air Microbiology ; *Particulate Matter/analysis ; *Air Pollutants/analysis ; *Drug Resistance, Microbial/genetics ; Environmental Monitoring ; Bacteria/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Household waste is a hotspot of antibiotic resistance, which can be readily emitted to the ambient airborne inhalable particulate matters (PM10) during the day-long storage in communities. Nevertheless, whether these waste-specific inhalable antibiotic resistance genes (ARGs) are associated with pathogenic bacteria or pose hazards to local residents have yet to be explored. By high-throughput metagenomic sequencing and culture-based antibiotic resistance validation, we analyzed 108 airborne PM10 and nearby environmental samples collected across different types of residential communities in Shanghai, the most populous city in China. Compared to the cold-dry period, the warm-humid season had significantly larger PM10-associated antibiotic resistomes in all types of residential communities (T-test, P < 0.001), most of airborne ARGs in which were estimatedly originated from disposed household waste (∼ 30 %). In addition, the airborne bacteria were assembled in a deterministic approach (iCAMP, P < 0.01), where the waste-specific bacteria taxa including Acinetobacter, Pseudomonas, Rhodococcus, and Kocuria had the predominant niches in the airborne microbial assemblages. Notably, these waste-sourced bacteria were also identified as the primary airborne hosts of ARGs encoding the aminoglycoside resistances. Among them, some antibiotic resistant human pathogens, such as Pseudomonas aeruginosa and Acinetobacter baumannii, not only exhibited higher ARG horizontal gene transfer (HGT) potential across the microbial assemblages, but also imposed direct infection risks on the local residents by 2 min inhalation exposure per day. When the daily exposure duration increased to 11 min, the infection-induced illness burden became unignorably high, especially in densely populated urban communities, being twofold greater than rural areas.},
}
@article {pmid39862048,
year = {2025},
author = {Colinet, D and Haon, M and Drula, E and Boyer, M and Grisel, S and Belliardo, C and Koutsovoulos, GD and Berrin, JG and Danchin, EGJ},
title = {Functional Carbohydrate-Active Enzymes Acquired by Horizontal Gene Transfer from Plants in the Whitefly Bemisia tabaci.},
journal = {Genome biology and evolution},
volume = {17},
number = {2},
pages = {},
pmid = {39862048},
issn = {1759-6653},
mesh = {Animals ; *Gene Transfer, Horizontal ; *Hemiptera/genetics/enzymology ; Phylogeny ; *Glycoside Hydrolases/genetics/metabolism ; *Plants/genetics ; },
abstract = {Carbohydrate-active enzymes involved in the degradation of plant cell walls and/or the assimilation of plant carbohydrates for energy uptake are widely distributed in microorganisms. In contrast, they are less frequent in animals, although there are exceptions, including examples of carbohydrate-active enzymes acquired by horizontal gene transfer from bacteria or fungi in several of phytophagous arthropods and plant-parasitic nematodes. Although the whitefly Bemisia tabaci is a major agricultural pest, knowledge of horizontal gene transfer-acquired carbohydrate-active enzymes in this phloem-feeding insect of the Hemiptera order (subfamily Aleyrodinae) is still lacking. We performed a comprehensive and accurate detection of horizontal gene transfer candidates in B. tabaci and identified 136 horizontal gene transfer events, 14 of which corresponding to carbohydrate-active enzymes. The B. tabaci horizontal gene transfer-acquired carbohydrate-active enzymes were not only of bacterial or fungal origin, but some were also acquired from plants. Biochemical analysis revealed that members of the glycoside hydrolase families 17 and 152 acquired from plants are functional beta-glucanases with different substrate specificities, suggesting distinct roles. These two carbohydrate-active enzymes are the first characterized glycoside hydrolase families 17 and 152 glucanases in an animal. We identified a lower number of horizontal gene transfer events in the related Aleyrodinae Trialeurodes vaporariorum, with only three horizontal gene transfer-acquired carbohydrate-active enzymes, including a glycoside hydrolase family 152 glucanase, with phylogenetic analysis suggesting a unique horizontal gene transfer event in the ancestor of the Aleyrodinae. Another glycoside hydrolase family 152 carbohydrate-active enzyme, most likely independently acquired from plants, was also identified in two plant cell-feeding insects of the Thysanoptera order, highlighting the importance of plant-acquired carbohydrate-active enzymes in the biology of piercing-sucking insects.},
}
@article {pmid39861970,
year = {2025},
author = {Saati-Santamaría, Z and Navarro-Gómez, P and Martínez-Mancebo, JA and Juárez-Mugarza, M and Flores, A and Canosa, I},
title = {Genetic and species rearrangements in microbial consortia impact biodegradation potential.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {39861970},
issn = {1751-7370},
support = {//University of Seville from the Ministry of Universities/ ; CLU-2018-04//Regional Government of Castilla y Le&#xf3;n/ ; //European NextGenerationEU program/ ; //University of Salamanca/ ; 101090267//EU Horizon Europe program/ ; ProyExcel_00358//Programa de Excelencia de la Junta de Andaluc&#xed;a/ ; //V Plan Propio de investigaci&#xf3;n of the University Pablo de Olavide/ ; },
mesh = {*Microbial Consortia/genetics ; Biodegradation, Environmental ; Plasmids/genetics ; *Ibuprofen/metabolism ; *Bacteria/genetics/metabolism/classification ; Gene Transfer, Horizontal ; Wastewater/microbiology ; Phylogeny ; },
abstract = {Genomic reorganisation between species and horizontal gene transfer have been considered the most important mechanism of biological adaptation under selective pressure. Still, the impact of mobile genes in microbial ecology is far from being completely understood. Here we present the collection and characterisation of microbial consortia enriched from environments contaminated with emerging pollutants, such as non-steroidal anti-inflammatory drugs. We have obtained and further enriched two ibuprofen-degrading microbial consortia from two unrelated wastewater treatment plants. We have also studied their ability to degrade the drug and the dynamics of the re-organisations of the genetic information responsible for its biodegradation among the species within the consortium. Our results show that genomic reorganisation within microorganisms and species rearrangements occur rapidly and efficiently during the selection process, which may be facilitated by plasmids and/or transposable elements located within the sequences. We show the evolution of at least two different plasmid backbones on samples from different locations, showing rearrangements of genomic information, including genes encoding activities for IBU degradation. As a result, we found variations in the expression pattern of the consortia after evolution under selective pressure, as an adaptation process to the new conditions. This work provides evidence for changes in the metagenomes of microbial communities that allow adaptation under a selective constraint -ibuprofen as a sole carbon source- and represents a step forward in knowledge that can inspire future biotechnological developments for drug bioremediation.},
}
@article {pmid39861872,
year = {2025},
author = {Yakubovskij, VI and Morozova, VV and Kozlova, YN and Tikunov, AY and Fedorets, VA and Zhirakovskaya, EV and Babkin, IV and Bardasheva, AV and Tikunova, NV},
title = {Phage vB_KlebPS_265 Active Against Resistant/MDR and Hypermucoid K2 Strains of Klebsiella pneumoniae.},
journal = {Viruses},
volume = {17},
number = {1},
pages = {},
pmid = {39861872},
issn = {1999-4915},
support = {grant No 122110700002-2//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Klebsiella pneumoniae/virology/drug effects ; Genome, Viral ; Phylogeny ; *Bacteriophages/genetics/classification/isolation &amp; purification/physiology ; Klebsiella Infections/microbiology/therapy ; Humans ; Drug Resistance, Multiple, Bacterial ; Gene Transfer, Horizontal ; Siphoviridae/genetics/classification/isolation &amp; purification/physiology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Klebsiella pneumoniae is an important opportunistic pathogen often resistant to antibiotics. Specific phages can be useful in eliminating infection caused by K. pneumoniae. Klebsiella phage vB_KlebPS_265 (KlebP_265) and its host strain were isolated from the sputum of a patient with Klebsiella infection. KlebP_265 was specific mainly to K. pneumoniae-type K2 strains including hypermucoid strains. Most of the hypermucoid KlebP_265-susceptible strains were antibiotic-resistant. This siphophage demonstrated good lytic activity and stability. The KlebP_265 genome was 46,962 bp and contained 88 putative genes; functions were predicted for 37 of them. No genes encoding integrases, toxins, or antibiotic resistance were found in the genome. So, KlebP_265 could potentially be a therapeutic phage. Comparative analysis indicated that KlebP_265 with the most relative Klebsiella phage DP01 formed the putative Dipiunovirus genus. Genome analysis revealed a large monophyletic group of phages related to KlebP_265 and DP01. This group is divided into two monophyletic clusters of phages forming new putative subfamilies Skatevirinae and Roufvirinae. Phylogenetic analysis showed extensive gene exchange between phages from the putative subfamilies. Horizontal transfer even involved conservative genes and led to clear genomic mosaicism, indicating multiple recombination events in the ancestral phages during evolution.},
}
@article {pmid39859430,
year = {2025},
author = {Yuan, Z and Zhang, J and Duan, D},
title = {Vanadium-Dependent Haloperoxidase Gene Evolution in Brown Algae: Evidence for Horizontal Gene Transfer.},
journal = {International journal of molecular sciences},
volume = {26},
number = {2},
pages = {},
pmid = {39859430},
issn = {1422-0067},
support = {2022HWYQ-087//Shandong Province/ ; 41806202//National Natural Science Foundation of China/ ; 133137KYSB20210034//Chinese Academy of Sciences/ ; },
mesh = {*Gene Transfer, Horizontal ; *Phaeophyceae/genetics/enzymology ; Phylogeny ; *Evolution, Molecular ; *Peroxidases/genetics/metabolism ; *Vanadium/metabolism ; Multigene Family ; },
abstract = {Compared with green plants, brown algae are characterized by their ability to accumulate iodine, contributing to their ecological adaptability in high-iodide coastal environments. Vanadium-dependent haloperoxidase (V-HPO) is the key enzyme for iodine synthesis. Despite its significance, the evolutionary origin of V-HPO genes remains underexplored. This study investigates the genomic and evolutionary dynamics of V-HPOs in brown algae, focusing on Laminariales species, particularly Saccharina japonica. Genomic analyses revealed the extensive expansion of the V-HPO gene family in brown algae, with 88 V-HPOs identified in S. japonica, surpassing the number in red algae. Phylogenetic analysis demonstrated distinct evolutionary divergence between brown and red algal V-HPOs, with the brown algal clade closely related to bacterial V-HPOs. These findings suggest horizontal gene transfer (HGT) played a key role in acquiring V-HPO genes, particularly from Acidobacteriota, a bacterial phylum known for genomic plasticity. Additionally, enriched active transposable elements were identified around V-HPO genomic clusters, highlighting their role in tandem gene duplications and rapid HGT processes. Expression profiling further revealed dynamic regulation of V-HPOs in response to environmental conditions. This study provides new insights into how HGT has driven kelp genomic adaptations and enhances understanding of marine ecological success and evolutionary processes.},
}
@article {pmid39859334,
year = {2025},
author = {Wang, C and Zhao, R and Yang, W and Jiang, W and Tang, H and Du, S and Chen, X},
title = {Cell-to-Cell Natural Transformation Mediated Efficient Plasmid Transfer Between Bacillus Species.},
journal = {International journal of molecular sciences},
volume = {26},
number = {2},
pages = {},
pmid = {39859334},
issn = {1422-0067},
support = {31970030//National Natural Science Foundation of China/ ; J1103513//National Fund for Fostering Talents of Basic Sciences/ ; None//Research (Innovative) Fund of the Laboratory of Wuhan University./ ; },
mesh = {*Plasmids/genetics ; *Transformation, Bacterial ; *Gene Transfer, Horizontal ; *Bacillus subtilis/genetics ; *Bacillus/genetics ; },
abstract = {Horizontal gene transfer (HGT) plays a pivotal role in bacterial evolution, shaping the genetic diversity of bacterial populations. It can occur through mechanisms such as conjugation, transduction, and natural transformation. Bacillus subtilis, a model Gram-positive bacterium, serves not only as a robust system for studying HGT but also as a versatile organism with established industrial applications, such as producing industrial enzymes, antibiotics, and essential metabolites. In this study, we characterize a novel method of plasmid transfer, termed Cell-to-Cell Natural Transformation for Plasmid Transfer (CTCNT-P), which efficiently facilitates plasmid transfer between naturally competent B. subtilis strains. This method involves co-culturing donor and recipient cells under antibiotic stress and achieves significantly higher efficiency compared to traditional methods such as Spizizen medium or electroporation-mediated transformation. Importantly, we demonstrate that CTCNT-P is applicable for plasmid transformation in wild B. subtilis isolates from natural environments and other Bacillus species, including Bacillus amyloliquefaciens, Bacillus licheniformis, and Bacillus thuringiensis. The simplicity and efficiency of CTCNT-P highlight its strong potential for industrial applications, including genetic modification of wild Bacillus strains for synthetic biology and the development of biocontrol agents.},
}
@article {pmid39859326,
year = {2025},
author = {Kusada, H and Tamaki, H},
title = {Evidence for the Worldwide Distribution of a Bile Salt Hydrolase Gene in Enterococcus faecium Through Horizontal Gene Transfer.},
journal = {International journal of molecular sciences},
volume = {26},
number = {2},
pages = {},
pmid = {39859326},
issn = {1422-0067},
support = {JPMJGX23B2//Japan Science and Technology Agency/ ; 21ae0121047h0001//Japan Agency for Medical Research and Development/ ; },
mesh = {*Enterococcus faecium/genetics/enzymology ; *Gene Transfer, Horizontal ; Phylogeny ; *Amidohydrolases/genetics/metabolism ; Humans ; Plasmids/genetics ; *Bacterial Proteins/genetics/metabolism ; Bile Acids and Salts/metabolism ; },
abstract = {Bile salt hydrolase (BSH), a probiotic-related enzyme with cholesterol-assimilating and anti-hypercholesterolemic abilities, has been isolated from intestinal bacteria; however, BSH activity of bacteria in bile-salt-free (non-intestinal) environments is largely unknown. Here, we aimed to identify BSH from non-intestinal Enterococcus faecium and characterize its enzymatic function. We successfully isolated a plasmid-encoded bsh (efpBSH) from E. faecium, and the recombinant EfpBSH showed BSH activity that preferentially hydrolyzed taurine-conjugated bile salts, unlike the activity of known BSHs. EfpBSH functioned optimally at pH 4.0 and 50 °C. EfpBSH exhibited very low amino acid sequence similarity (48.46%) to EfBSH from E. faecalis T2 isolated from human urine, although 241 sequences with 100% identity to EfpBSH were found in both plasmids and chromosomes of E. faecium strains inhabiting intestinal and non-intestinal environments. Phylogenetically, EfpBSH was not affiliated with any known BSH phylogroup and was clearly distinguished from previously identified BSHs from intestinal lactic acid bacteria. Our genome database analysis demonstrated that horizontal gene transfer causes global efpBSH distribution among E. faecium strains in various environments (soil, water, and intestinal samples) and geographical regions (Asia, Africa, Europe, North America, South America, and Australia/Oceania). Overall, our findings are the first to indicate that BSH is not an intestine-specific enzyme and that hitherto-overlooked probiotic candidates with BSH activity can exist in diverse environments.},
}
@article {pmid39859280,
year = {2025},
author = {Liu, X and Luo, H and Liu, ZJ and Yang, BY},
title = {Mitochondrial Genome Characteristics Reveal Evolution of Danxiaorchis yangii and Phylogenetic Relationships.},
journal = {International journal of molecular sciences},
volume = {26},
number = {2},
pages = {},
pmid = {39859280},
issn = {1422-0067},
mesh = {*Genome, Mitochondrial ; *Phylogeny ; *Evolution, Molecular ; *Orchidaceae/genetics/classification ; RNA, Transfer/genetics ; Codon Usage ; Base Composition ; Gene Transfer, Horizontal ; },
abstract = {Danxiaorchis yangii is a fully mycoheterotrophic orchid that lacks both leaves and roots, belonging to the genus Danxiaorchis in the subtribe Calypsoinae. In this study, we assembled and annotated its mitochondrial genome (397,867 bp, GC content: 42.70%), identifying 55 genes, including 37 protein-coding genes (PCGs), 16 tRNAs, and 2 rRNAs, and conducted analyses of relative synonymous codon usage (RSCU), repeat sequences, horizontal gene transfers (HGTs), and gene selective pressure (dN/dS). Additionally, we sequenced and assembled its plastome, which has a reduced size of 110,364 bp (GC content: 36.60%), comprising 48 PCGs, 26 tRNAs, and 4 rRNAs. We identified 64 potential chloroplast DNA fragments transferred to the mitogenome. Phylogenomic analysis focusing on 33 mitogenomes, with Vitis vinifera as the outgroup, indicated that D. yangii is grouped as follows: D. yangii + ((Dendrobium wilsonii + Dendrobium wilsonii henanense) + Phalaenopsis aphrodite). Phylogenetic analysis based on 83 plastid PCGs from these species showed that D. yangii is grouped as follows: (D. yangii + Pha. aphrodite) + (Den. wilsonii + Den. henanense). Gene selective pressure analysis revealed that most mitochondrial and plastid genes in D. yangii are under purifying selection, ensuring functional stability, and certain genes may have undergone positive selection or adaptive evolution, reflecting the species' adaptation to specific ecological environments. Our study provides valuable data on the plastomes and mitogenomes of D. yangii and lays the groundwork for future research on genetic variation, evolutionary relationships, and the breeding of orchids.},
}
@article {pmid39858976,
year = {2025},
author = {He, Y and Dykes, GE and Kanrar, S and Liu, Y and Gunther, NW and Counihan, KL and Lee, J and Capobianco, JA},
title = {Comparative Genomic Analysis of Campylobacter Plasmids Identified in Food Isolates.},
journal = {Microorganisms},
volume = {13},
number = {1},
pages = {},
pmid = {39858976},
issn = {2076-2607},
support = {Current Research Information System number 8072-42000-093//U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), National Program 108/ ; },
abstract = {Campylobacter is one of the leading bacterial causes of gastroenteritis worldwide. It frequently contaminates poultry and other raw meat products, which are the primary sources of Campylobacter infections in humans. Plasmids, known as important mobile genetic elements, often carry genes for antibiotic resistance, virulence, and self-mobilization. They serve as the main vectors for transferring genetic material and spreading resistance and virulence among bacteria. In this study, we identified 34 new plasmids from 43 C. jejuni and C. coli strains isolated from retail meat using long-read and short-read genome sequencing. Pangenomic analysis of the plasmid assemblies and reference plasmids from GenBank revealed five distinct groups, namely, pTet, pVir, mega plasmids (>80 kb), mid plasmids (~30 kb), and small plasmids (<6 kb). Pangenomic analysis identified the core and accessory genes in each group, indicating a high degree of genetic similarity within groups and substantial diversity between the groups. The pTet plasmids were linked to tetracycline resistance phenotypes in host strains. The mega plasmids carry multiple genes (e.g., aph(3')-III, type IV and VI secretion systems, and type II toxin-antitoxin systems) important for plasmid mobilization, virulence, antibiotic resistance, and the persistence of Campylobacter. Together, the identification and comprehensive genetic characterization of new plasmids from Campylobacter food isolates contributes to understanding the mechanisms of gene transfer, particularly the spread of genetic determinants of virulence and antibiotic resistance in this important pathogen.},
}
@article {pmid39858487,
year = {2025},
author = {Tahmasebi, H and Arjmand, N and Monemi, M and Babaeizad, A and Alibabaei, F and Alibabaei, N and Bahar, A and Oksenych, V and Eslami, M},
title = {From Cure to Crisis: Understanding the Evolution of Antibiotic-Resistant Bacteria in Human Microbiota.},
journal = {Biomolecules},
volume = {15},
number = {1},
pages = {},
pmid = {39858487},
issn = {2218-273X},
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Microbiota/drug effects/genetics ; Methicillin-Resistant Staphylococcus aureus/drug effects/genetics ; *Bacteria/drug effects/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {The growing prevalence of antibiotic-resistant bacteria within the human microbiome has become a pressing global health crisis. While antibiotics have revolutionized medicine by significantly reducing mortality and enabling advanced medical interventions, their misuse and overuse have led to the emergence of resistant bacterial strains. Key resistance mechanisms include genetic mutations, horizontal gene transfer, and biofilm formation, with the human microbiota acting as a reservoir for antibiotic resistance genes (ARGs). Industrialization and environmental factors have exacerbated this issue, contributing to a rise in infections with multidrug-resistant (MDR) bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA) and carbapenem-resistant Enterobacteriaceae. These resistant pathogens compromise the effectiveness of essential treatments like surgical prophylaxis and chemotherapy, increase healthcare costs, and prolong hospital stays. This crisis highlights the need for a global One-Health approach, particularly in regions with weak regulatory frameworks. Innovative strategies, including next-generation sequencing (NGS) technologies, offer promising avenues for mitigating resistance. Addressing this challenge requires coordinated efforts, encompassing research, policymaking, public education, and antibiotic stewardship, to safeguard current antibiotics and foster the development of new therapeutic solutions. An integrated, multidimensional strategy is essential to tackle this escalating problem and ensure the sustainability of effective antimicrobial treatments.},
}
@article {pmid39858396,
year = {2024},
author = {Dobrescu, M&#x218; and Țoc, DA and Pană, AG and Costache, C and Butiuc-Keul, A},
title = {The Difference a Year Can Make: How Antibiotic Resistance Mechanisms in Pseudomonas aeruginosa Have Changed in Northwestern Transylvania.},
journal = {Biomolecules},
volume = {15},
number = {1},
pages = {},
pmid = {39858396},
issn = {2218-273X},
support = {13517/15446/03.10.2022//Babe&#x219;-Bolyai University/ ; },
mesh = {*Pseudomonas aeruginosa/drug effects/genetics/isolation &amp; purification ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Romania/epidemiology ; *Drug Resistance, Multiple, Bacterial/genetics ; Humans ; Integrons ; *Pseudomonas Infections/microbiology/drug therapy/epidemiology ; *Drug Resistance, Bacterial/genetics ; Bacterial Proteins/genetics ; },
abstract = {This study examines the prevalence and the mechanisms of antibiotic resistance in Pseudomonas aeruginosa isolates collected from healthcare units in Northwestern Transylvania, Romania, between 2022 and 2023. Given the alarming rise in antibiotic resistance, the study screened 34 isolates for resistance to 10 antibiotics, 46 ARGs, and integrase genes using PCR analysis. The results reveal a concerning increase in multidrug-resistant (MDR) and extensively drug-resistant (XDR) isolates over the two-year period. Notably, the prevalence of ARGs encoding resistance to sulfonamides and beta-lactams, particularly sul1 and blaOXA-50, has shown a significant rise. Furthermore, the study detected the emergence of new resistance mechanisms in the same time interval. These include target protection and even more specific mechanisms, such as metallo-beta-lactamases or enzymes involved in the methylation of 23S rRNA. Statistical analysis further confirmed the correlation between Class I integrons and several ARGs, underscoring the role of horizontal gene transfer in the dissemination of resistance. These findings emphasize the urgent need for updated treatment strategies and monitoring programs to effectively combat the spread of ARGs in clinical settings.},
}
@article {pmid39858353,
year = {2025},
author = {Kløve, DC and Strube, ML and Heegaard, PMH and Astrup, LB},
title = {Mapping Antimicrobial Resistance in Staphylococcus epidermidis Isolates from Subclinical Mastitis in Danish Dairy Cows.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {1},
pages = {},
pmid = {39858353},
issn = {2079-6382},
abstract = {Background/Objectives: Although Staphylococcus epidermidis is a key cause of subclinical mastitis in Danish dairy cows, its sensitivity to antimicrobials remains unexplored. Here, we analyzed sixty S. epidermidis isolates derived from 42 dairy cows across six conventional dairy herds in Denmark. Methods: Phenotypic resistance was measured by antimicrobial susceptibility testing and minimum inhibitory concentration (MIC) analysis, and genotypic resistance was examined through whole-genome sequencing and identification of antimicrobial resistance genes (ARGs). Correspondence between phenotypic and genotypic resistance was then evaluated by Cohen's kappa statistics. Furthermore, the presence of plasmid replicon genes and the strain diversity among the S. epidermidis isolates was investigated to associate these findings with the observed AMR patterns. Results: Results showed that 30/60 isolates (50.0%) were resistant to penicillin phenotypically, while 35/60 (58.3%) were positive for a corresponding blaZ gene (κ = 0.83, p < 0.01). A fosB gene, encoding fosfomycin resistance, was detected in all 60/60 isolates (100.0%), but fosfomycin resistance was not analyzed phenotypically. Based on MIC analysis, 3/60 isolates (5.0%) were multi-drug resistant, showing resistance towards penicillin, erythromycin, and tetracycline. However, in 11/60 genomes (18.3%), ARGs encoding resistance towards ≥3 antimicrobial classes (e.g., beta-lactams, phosphonic acid, tetracyclines, aminoglycosides, macrolides, lincosamides, and fusidane) were detected. Eleven different ARGs were detected among the 60 isolates in total. No methicillin-resistant Staphylococcus epidermidis (MRSE) were recorded. Results further showed that each herd had one primary sequence type (ST) and resistance profile associated with it, and plasmid-mediated horizontal gene transfer of ARGs was indicated This study underscores the importance of routine resistance surveillance and species-specific diagnoses to improve treatment outcomes and ensure prudent use of antimicrobials.},
}
@article {pmid39856955,
year = {2025},
author = {Zhang, Z and Zhao, H and Shi, C},
title = {Clonal Spread and Genetic Mechanisms Underpinning Ciprofloxacin Resistance in Salmonella enteritidis.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {2},
pages = {},
pmid = {39856955},
issn = {2304-8158},
support = {2024YFE0199000//National Key R&amp;D Program of China/ ; 32202193//National Natural Science Foundation of China/ ; 32472458//National Natural Science Foundation of China/ ; },
abstract = {Salmonella enteritidis is a major cause of foodborne illness worldwide, and the emergence of ciprofloxacin-resistant strains poses a significant threat to food safety and public health. This study aimed to investigate the prevalence, spread, and mechanisms of ciprofloxacin resistance in S. enteritidis isolates from food and patient samples in Shanghai, China. A total of 1625 S. enteritidis isolates were screened, and 34 (2.1%) exhibited resistance to ciprofloxacin. Pulsed-field gel electrophoresis (PFGE) results suggested that clonal spread might have persisted among these 34 isolates in the local area for several years. Multiple plasmid-mediated quinolone resistance (PMQR) genes, GyrA mutations in the quinolone resistance-determining region (QRDR), and overexpression of RND efflux pumps were identified as potential contributors to ciprofloxacin resistance. PMQR genes oqxAB, qnrA, qnrB, and aac(6')-Ib-cr as well as GyrA mutations S83Y, S83R, D87Y, D87G, D87N, and S83Y-D87Y were identified. The co-transfer of the PMQR gene oqxAB with the ESBL gene blaCTX-M-14/55 on an IncHI2 plasmid with a size of ~245 kbp was observed through conjugation, highlighting the role of horizontal gene transfer in the dissemination of antibiotic resistance. Sequencing of the oqxAB-bearing plasmid p12519A revealed a 248,746 bp sequence with a typical IncHI2 backbone. A 53,104 bp multidrug resistance region (MRR) was identified, containing two key antibiotic resistance determinants: IS26-oqxR-oqxAB-IS26 and IS26-ΔISEcp1-blaCTX-M-14-IS903B. The findings of this study indicate that ciprofloxacin-resistant S. Enteritidis poses a significant threat to food safety and public health. The persistence of clonal spread and the horizontal transfer of resistance genes highlight the need for enhanced surveillance and control measures to prevent the further spread of antibiotic resistance.},
}
@article {pmid39855970,
year = {2025},
author = {Wang, D and Zhou, X and Fu, Q and Li, Y and Ni, BJ and Liu, X},
title = {Understanding bacterial ecology to combat antibiotic resistance dissemination.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2024.12.011},
pmid = {39855970},
issn = {1879-3096},
abstract = {The dissemination of antibiotic resistance from environmental sources is a growing concern. Despite the widespread occurrence of antibiotic resistance transmission events, there are actually multiple obstacles in the ecosystem that restrict the flow of bacteria and genes, in particular nonnegligible biological barriers. How these ecological factors help combat the dissemination of antibiotic resistance and relevant antibiotic resistance-diminishing organisms (ARDOs) deserves further exploration. This review summarizes the factors that influence the growth, metabolism, and environmental adaptation of antibiotic-resistant bacteria (ARB) and restrict the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Additionally, this review discusses the achievements in the application of ARDOs to improve biotechnology for wastewater and solid waste remediation while highlighting current challenges limiting their broader implementation.},
}
@article {pmid39854814,
year = {2025},
author = {Xu, Z and Li, S and Ma, Y and Li, C and Lu, H and Xiong, J and He, G and Li, R and Ren, X and Huang, B and Pan, X},
title = {Role of organophosphorus pesticides in facilitating plasmid-mediated conjugative transfer: Efficiency and mechanisms.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137318},
doi = {10.1016/j.jhazmat.2025.137318},
pmid = {39854814},
issn = {1873-3336},
mesh = {*Plasmids/genetics ; *Pesticides/toxicity ; *Gene Transfer, Horizontal/drug effects ; Reactive Oxygen Species/metabolism ; *Malathion/toxicity ; *Dimethoate/toxicity ; *Organophosphorus Compounds/toxicity ; Cell Membrane Permeability/drug effects ; Escherichia coli/genetics/drug effects/metabolism ; *Conjugation, Genetic/drug effects ; Drug Resistance, Microbial/genetics ; },
abstract = {Non-antibiotic conditions, including organophosphorus pesticides (OPPs), have been implicated in the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) to varying degrees. While most studies focus on the toxicity of OPPs to humans and animals, their roles in ARG dissemination remain largely unexplored. In this study, we investigate the effects and involved molecular mechanisms of environmentally relevant concentrations of malathion and dimethoate, two representative OPPs, on plasmid-mediated conjugal transfer. By detecting reactive oxygen species (ROS) production and cell membrane permeability, we gained insights into the underlying processes. Furthermore, we substantiated the role of ROS and cell membrane permeability in plasmid-mediated conjugative transfer through the analysis of relevant antioxidant enzyme activities, cell membrane-related indices, and RNA sequences. Additionally, our examination of proton motive force and adenosine triphosphate content provided evidence that OPPs create conditions conducive to plasmid-mediated conjugative transfer from an energetic perspective. The findings of the present study highlight the potential risk of OPPs in promoting ARG spread, which could ultimately provide new theoretical support and direction for future research on the impacts of pesticides on ARG propagation.},
}
@article {pmid39852676,
year = {2025},
author = {Bukari, Z and Emmanuel, T and Woodward, J and Ferguson, R and Ezughara, M and Darga, N and Lopes, BS},
title = {The Global Challenge of Campylobacter: Antimicrobial Resistance and Emerging Intervention Strategies.},
journal = {Tropical medicine and infectious disease},
volume = {10},
number = {1},
pages = {},
pmid = {39852676},
issn = {2414-6366},
abstract = {Antimicrobial resistance (AMR) in Campylobacter species, particularly C. jejuni and C. coli, poses a significant public health threat. These bacteria, which are commonly found in livestock, poultry, companion animals, and wildlife, are the leading causes of foodborne illnesses, often transmitted through contaminated poultry. Extensive exposure to antibiotics in human and veterinary medicine creates selection pressure, driving resistance through mechanisms such as point mutations, horizontal gene transfer, and efflux pumps. Resistance to fluoroquinolones, macrolides, and tetracyclines complicates treatment and increases the risk of severe infections. Drug-resistant Campylobacter is transmitted to humans via contaminated food, water, and direct contact with animals, highlighting its zoonotic potential. Addressing this challenge requires effective interventions. Pre-harvest strategies like biosecurity and immune-based methods reduce bacterial loads on farms, while post-harvest measures, including carcass decontamination and freezing, limit contamination. Emerging approaches, such as bacteriocins and natural antimicrobials, offer chemical-free alternatives. Integrated, multidisciplinary interventions across the food chain are essential to mitigate AMR transmission and enhance food safety. Sustainable agricultural practices, antimicrobial stewardship, and innovative solutions are critical to curbing Campylobacter resistance and protecting global public health. Our review examines the dynamics of antimicrobial resistance in Campylobacter and presents current strategies to mitigate Campylobacter-related AMR, offering valuable insights for antimicrobial control in the poultry industry.},
}
@article {pmid39847570,
year = {2025},
author = {Al Sium, SM and Goswami, B and Chowdhury, SF and Naser, SR and Sarkar, MK and Faruq, MJ and Habib, MA and Akter, S and Banu, TA and Sarkar, MMH and Khan, MS},
title = {An insight into the genome-wide analysis of bacterial defense mechanisms in a uropathogenic Morganella morganii isolate from Bangladesh.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0313141},
pmid = {39847570},
issn = {1932-6203},
mesh = {Bangladesh ; *Morganella morganii/genetics/isolation &amp; purification/pathogenicity ; Humans ; *Genome, Bacterial ; Phylogeny ; *Urinary Tract Infections/microbiology ; Genomic Islands ; Whole Genome Sequencing ; Virulence Factors/genetics ; },
abstract = {The gram-negative, facultative anaerobic bacterium Morganella morganii is linked to a number of illnesses, including nosocomial infections and urinary tract infections (UTIs). A clinical isolate from a UTI patient in Bangladesh was subjected to high-throughput whole genome sequencing and extensive bioinformatics analysis in order to gather knowledge about the genomic basis of bacterial defenses and pathogenicity in M. morganii. With an average nucleotide identity (ANI) of more than 97% similarity to a reference genome and phylogenetic analysis verified the isolate as M. morganii. Genome annotation identified 3,718 protein-coding sequences, including genes for metabolism, protein processing, stress response, energy, and membrane transport. The presence of biosynthetic gene clusters points to the isolate's ability to create bioactive compounds, including antibiotics. Genomic islands contained genes for metal transporters, stress proteins, toxin proteins, and genes related to horizontal gene transfer. The beta-lactam resistance gene blaDHA was found using antimicrobial resistance (AMR) gene analysis across three databases. The virulence genes kdsA and cheY, which may be involved in chemotaxis and lipopolysaccharide production, were also available in the isolate, suggesting its high pathogenicity. The genome contained mobile genetic components and defense mechanisms, such as restriction modification and CRISPR-Cas systems, indicating the bacterium's ability to defend itself against viral attacks. This thorough investigation sheds important light on M. morganii's pathogenicity and adaptive tactics by revealing its genetic characteristics, AMR, virulence components, and defense mechanisms. For the development of targeted treatments and preventing the onset of resistance in clinical care, it is essential to comprehend these genetic fingerprints.},
}
@article {pmid39846752,
year = {2025},
author = {McKeithen-Mead, S and Anderson, ME and García-Heredia, A and Grossman, AD},
title = {Activation and modulation of the host response to DNA damage by an integrative and conjugative element.},
journal = {Journal of bacteriology},
volume = {207},
number = {2},
pages = {e0046224},
pmid = {39846752},
issn = {1098-5530},
support = {T32 GM007287/GM/NIGMS NIH HHS/United States ; R35 GM122538/GM/NIGMS NIH HHS/United States ; R35 GM148343/GM/NIGMS NIH HHS/United States ; R01 GM050895/GM/NIGMS NIH HHS/United States ; MathWorks Science Fellowship//MathWorks (The MathWorks, Inc.)/ ; },
mesh = {*Bacillus subtilis/genetics/virology/metabolism ; *DNA Damage ; *SOS Response, Genetics ; Bacterial Proteins/genetics/metabolism ; *Interspersed Repetitive Sequences ; Gene Expression Regulation, Bacterial ; Conjugation, Genetic ; Prophages/genetics ; Rec A Recombinases/metabolism/genetics ; },
abstract = {Mobile genetic elements help drive horizontal gene transfer and bacterial evolution. Conjugative elements and temperate bacteriophages can be stably maintained in host cells. They can alter host physiology and regulatory responses and typically carry genes that are beneficial to their hosts. We found that ICEBs1, an integrative and conjugative element (ICE) of Bacillus subtilis, inhibits the host response to DNA damage (the SOS response). Activation of ICEBs1 before DNA damage reduced host cell lysis that was caused by SOS-mediated activation of two resident prophages. Further, activation of ICEBs1 itself activated the SOS response in a subpopulation of cells, and this activation was attenuated by the functions of the ICEBs1 genes ydcT and yddA (now ramT and ramA; ram for RecA modulator). Double-mutant analyses indicated that RamA functions to inhibit and RamT functions to both inhibit and activate the SOS response. Both RamT and RamA caused a reduction in RecA filaments, one of the early steps in activation of the SOS response. We suspect that there are several different mechanisms by which mobile genetic elements that generate single-stranded DNA (ssDNA) during their life cycle inhibit the host SOS response and RecA function, as RamT and RamA differ from the known SOS inhibitors encoded by conjugative elements.IMPORTANCEBacterial genomes typically contain mobile genetic elements, including bacteriophages (viruses) and integrative and conjugative elements, that affect host physiology. ICEs can excise from the chromosome and undergo rolling-circle replication, producing ssDNA, a signal that indicates DNA damage and activates the host SOS response. We found that following excision and replication, ICEBs1 of B. subtilis stimulates the host SOS response and that ICEBs1 encodes two proteins that limit the extent of this response. These proteins also reduce the amount of cell killing caused by resident prophages following their activation by DNA damage. These proteins are different from those previously characterized that inhibit the host SOS response and represent a new way in which ICEs can affect their host cells.},
}
@article {pmid39843582,
year = {2024},
author = {Silva, KPT and Khare, A},
title = {Antibiotic resistance mediated by gene amplifications.},
journal = {npj antimicrobials and resistance},
volume = {2},
number = {1},
pages = {35},
pmid = {39843582},
issn = {2731-8745},
support = {Intramural Research Program//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; Intramural Research Program//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Apart from horizontal gene transfer and sequence-altering mutational events, antibiotic resistance can emerge due to the formation of tandem repeats of genomic regions. This phenomenon, also known as gene amplification, has been implicated in antibiotic resistance in both laboratory and clinical scenarios, where the evolution of resistance via amplifications can affect treatment efficacy. Antibiotic resistance mediated by gene amplifications is unstable and consequently can be difficult to detect, due to amplification loss in the absence of the selective pressure of the antibiotic. Further, due to variable copy numbers in a population, amplifications result in heteroresistance, where only a subpopulation is resistant to an antibiotic. While gene amplifications typically lead to resistance by increasing the expression of resistance determinants due to the higher copy number, the underlying mechanisms of resistance are diverse. In this review article, we describe the various pathways by which gene amplifications cause antibiotic resistance, from efflux and modification of the antibiotic, to target modification and bypass. We also discuss how gene amplifications can engender resistance by alternate mutational outcomes such as altered regulation and protein structure, in addition to just an increase in copy number and expression. Understanding how amplifications contribute to bacterial survival following antibiotic exposure is critical to counter their role in the rise of antimicrobial resistance.},
}
@article {pmid39843314,
year = {2025},
author = {Yang, QE and Gao, JT and Zhou, SG and Walsh, TR},
title = {Cutting-edge tools for unveiling the dynamics of plasmid-host interactions.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2024.12.013},
pmid = {39843314},
issn = {1878-4380},
abstract = {The plasmid-mediated transfer of antibiotic resistance genes (ARGs) in complex microbiomes presents a significant global health challenge. This review examines recent technological advancements that have enabled us to move beyond the limitations of culture-dependent detection of conjugation and have enhanced our ability to track and understand the movement of ARGs in real-world scenarios. We critically assess the applications of single-cell sequencing, fluorescence-based techniques and advanced high-throughput chromatin conformation capture (Hi-C) approaches in elucidating plasmid-host interactions at unprecedented resolution. We also evaluate emerging techniques such as CRISPR-based phage engineering and discuss their potential for developing targeted strategies to curb ARG dissemination. Emerging data derived from these technologies have challenged our previous paradigms on plasmid-host compatibility and an awareness of an emerging uncharted realm for ARGs.},
}
@article {pmid39840972,
year = {2025},
author = {Zavan, L and Hor, L and Johnston, EL and Paxman, J and Heras, B and Kaparakis-Liaskos, M},
title = {Antigen 43 associated with Escherichia coli membrane vesicles contributes to bacterial cell association and biofilm formation.},
journal = {Microbiology spectrum},
volume = {13},
number = {3},
pages = {e0189024},
pmid = {39840972},
issn = {2165-0497},
support = {DP190101655//Department of Education and Training | Australian Research Council (ARC)/ ; DP180102987, DP190101613, DP210100673//Department of Education and Training | Australian Research Council (ARC)/ ; GNT1143638//DHAC | National Health and Medical Research Council (NHMRC)/ ; Inspiring Women Fellowship//Veski/ ; },
mesh = {*Biofilms/growth &amp; development ; *Escherichia coli Proteins/metabolism/genetics ; *Uropathogenic Escherichia coli/physiology/genetics/metabolism ; *Escherichia coli/physiology/metabolism ; *Adhesins, Escherichia coli/metabolism/genetics ; Humans ; *Antigens, Bacterial/metabolism/genetics ; Cell Membrane/metabolism ; Bacterial Adhesion ; *Extracellular Vesicles/metabolism ; },
abstract = {Bacterial membrane vesicles (MVs) are produced by all bacteria and contribute to numerous bacterial functions due to their ability to package and transfer bacterial cargo. In doing so, MVs have been shown to facilitate horizontal gene transfer, mediate antimicrobial activity, and promote biofilm formation. Uropathogenic Escherichia coli is a pathogenic Gram-negative organism that persists in the urinary tract of its host due to its ability to form persistent, antibiotic-resistant biofilms. The formation of these biofilms is dependent upon proteins such as Antigen 43 (Ag43), which belongs to the widespread Autotransporter group of bacterial surface proteins. In E. coli, the autotransporter Ag43 has been shown to contribute to bacterial cell aggregation and biofilm formation via self-association of Ag43 between neighboring Ag43-expressing bacteria. As MVs package bacterial proteins, we investigated whether MVs produced by E. coli contained Ag43, and the ability of Ag43-expressing MVs to facilitate cell aggregation and biofilm formation. We showed that Ag43 expressing E. coli produced MVs that contained Ag43 on their surface and had an enhanced ability to bind to E. coli bacteria. Furthermore, we demonstrated that the addition of Ag43-containing MVs to Ag43-expressing E. coli significantly enhanced biofilm formation. These findings reveal the contribution of MVs harboring autotransporters in promoting bacterial aggregation and enhancing biofilm formation, highlighting the impact of MVs and their specific composition to bacterial adaptation and pathogenesis.IMPORTANCEAutotransporter proteins are the largest family of outer membrane and secreted proteins in Gram-negative bacteria which contribute to pathogenesis by promoting aggregation, biofilm formation, persistence, and cytotoxicity. Although the roles of bacterial autotransporters are well known, the ability of bacterial membrane vesicles (MVs) naturally released from the surface of bacteria to contain autotransporters and their role in promoting virulence remains less investigated. Our findings reveal that MVs produced by E. coli contain the autotransporter protein Ag43. Furthermore, we show that Ag43-containing MVs function to enhance bacterial cell interactions and biofilm formation. By demonstrating the ability of MVs to carry functional autotransporter adhesins, this work highlights the importance of MVs in disseminating autotransporters beyond the bacterial cell membrane to ultimately promote cellular interactions and enhance biofilm development. Overall, these findings have significant implications in furthering our understanding of the numerous ways in which MVs can facilitate bacterial persistence and pathogenesis.},
}
@article {pmid39837262,
year = {2025},
author = {Wang, Y and Liu, T and Sida, Y and Zhu, Y},
title = {Diversity and Evolution of the Mobilome Associated with Antibiotic Resistance Genes in Streptococcus anginosus.},
journal = {Microbial drug resistance (Larchmont, N.Y.)},
volume = {31},
number = {2},
pages = {52-63},
doi = {10.1089/mdr.2024.0229},
pmid = {39837262},
issn = {1931-8448},
mesh = {*Streptococcus anginosus/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Drug Resistance, Bacterial/genetics ; *Interspersed Repetitive Sequences/genetics ; Genes, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; DNA Transposable Elements/genetics ; Microbial Sensitivity Tests ; },
abstract = {Streptococcus anginosus is an important cause of pyogenic infections, bacteremia, and chronic maxillary sinusitis. Mobile genetic elements (MGEs) play a key role in lateral gene transfer, resulting in broad transfer of antibiotic resistance genes (ARGs). However, studies on ARG-associated MGEs in S. anginosus are still rare. To fill this gap, we used sequencing data from 11 clinical S. anginosus to characterize their mobilome diversity through comparative analysis. We found 47 well-characterized MGEs, including 23 putative integrative and conjugative elements (ICEs), 16 prophages/integrative mobilizable elements, and 8 composites. They were inserted into 16 positions, 4 of which were hot spots. A comprehensive analysis revealed that ARG-associated ICEs belong to four groups as follows: single serine integrases (ICESan49.2), tyrosine integrases (ICESan26.2), triple serine integrase ICEs (ICESan195.1), and a putative transposon integrase (ICESan49.1), all of which were similar to ICEs/transposons widely distributed among other streptococci. The eight composites were composed of multiple ICEs or transposons through successive accretion events (tandem or/and internal integration). In conclusion, we found that S. anginosus accumulates a variety of ARG-associated ICE/composites that may enable S. anginosus to serve as an ARG-associated MGE repository for other streptococci. The analysis of composites here provides a paradigm to further study mobilome evolution.},
}
@article {pmid39837038,
year = {2025},
author = {Zhao, M and Huang, K and Wen, F and Xia, H and Song, B},
title = {Biochar reduces plasmid-mediated antibiotic resistance gene transfer in earthworm ecological filters for rural sewage treatment.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137230},
doi = {10.1016/j.jhazmat.2025.137230},
pmid = {39837038},
issn = {1873-3336},
mesh = {Animals ; *Charcoal/chemistry ; *Plasmids/genetics ; *Sewage/microbiology ; *Oligochaeta/genetics ; *Drug Resistance, Microbial/genetics ; *Gene Transfer, Horizontal ; Filtration ; Waste Disposal, Fluid/methods ; },
abstract = {The spread of antibiotic resistance genes (ARGs) in rural wastewater threatens both ecological environment and human health. Earthworm ecological filters (EEFs) represent a green technology for rural sewage treatment. However, their effectiveness in removing ARGs remains a significant challenge. This study aims to investigate the role and underlying mechanisms of biochar addition in enhancing ARGs removal in rural sewage using EEFs. To achieve this, the fate of chromosome- and plasmid-carried ARGs was quantified in constructed EEFs, both with and without biochar addition. The results showed that the biochar could effectively remove ARGs from rural sewage, with a better removal efficiency for plasmid-carried ARGs. The absolute abundance of plasmid-carried ARGs in the effluent was reduced by 0.4-11 times compared to chromosomal ones, showing removal stability improved by 13.11-74.51 %. Additionally, the functional microbial community attached on the high porosity of biochar surface promoted ARGs retention, increasing diffusion limitation in microbial assembly mechanisms by 4.61-29.44 %, which played a key role in plasmid-mediated horizontal gene transfer (HGT). Partial least squares structural equation modeling (PLS-SEM) revealed that biochar-mediated environmental changes and the HGT of mobile genetic elements (MGEs) were critical factors in reducing plasmid-carried ARGs in EEFs.},
}
@article {pmid39836086,
year = {2025},
author = {Xia, R and Yin, X and Balcazar, JL and Huang, D and Liao, J and Wang, D and Alvarez, PJJ and Yu, P},
title = {Bacterium-Phage Symbiosis Facilitates the Enrichment of Bacterial Pathogens and Antibiotic-Resistant Bacteria in the Plastisphere.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {6},
pages = {2948-2960},
doi = {10.1021/acs.est.4c08265},
pmid = {39836086},
issn = {1520-5851},
mesh = {*Bacteriophages ; *Symbiosis ; *Bacteria ; Plastics ; Anti-Bacterial Agents ; },
abstract = {The plastisphere, defined as the ecological niche for microbial colonization of plastic debris, has been recognized as a hotspot of pathogenic and antibiotic-resistant bacteria. However, the interactions between bacteria and phages facilitated by the plastisphere, as well as their impact on microbial risks to public health, remain unclear. Here, we analyzed public metagenomic data from 180 plastisphere and environmental samples, stemming from four different habitats and two plastic types (biodegradable and nonbiodegradable plastics) and obtained 611 nonredundant metagenome-assembled genomes (MAGs) and 4061 nonredundant phage contigs. The plastisphere phage community exhibited decreased diversity and virulent proportion compared to those found in environments. Indexes of phage-host interaction networks indicated significant associations of phages with pathogenic and antibiotic-resistant bacteria (ARB), particularly for biodegradable plastics. Known phage-encoded auxiliary metabolic genes (AMGs) were involved in nutrient metabolism, antibiotic production, quorum sensing, and biofilm formation in the plastisphere, which contributed to enhanced competition and survival of pathogens and ARB hosts. Phages also carried transcriptionally active virulence factor genes (VFGs) and antibiotic resistance genes (ARGs), and could mediate their horizontal transfer in microbial communities. Overall, these discoveries suggest that plastisphere phages form symbiotic relationships with their hosts, and that phages encoding AMGs and mediating horizontal gene transfer (HGT) could increase the source of pathogens and antibiotic resistance from the plastisphere.},
}
@article {pmid39833926,
year = {2025},
author = {Li, Z and Zhao, C and Mao, Z and Zhang, F and Dong, L and Song, C and Chen, Y and Fu, X and Ao, Z and Xiong, Y and Hui, Q and Song, W and Penttinen, P and Zhang, S},
title = {Structure and metabolic function of spatiotemporal pit mud microbiome.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {10},
pmid = {39833926},
issn = {2524-6372},
support = {2022HX04//Youth Fund of Postdoctor/ ; 2021JDJQ0038//Youth Fund of Sichuan Province/ ; },
abstract = {BACKGROUND: Pit mud (PM) hosts diverse microbial communities, which serve as a medium to impart flavor and quality to Baijiu and exhibit long-term tolerance to ethanol and acids, resulting in a unique ecosystem. However, the ecology and metabolic functions of PM remain poorly understood, as many taxa in PM represent largely novel lineages. In this study, we used a combination of metagenomic analysis and chemical derivatization LC-MS analysis to provide a comprehensive overview of microbial community structure, metabolic function, phylogeny, horizontal gene transfer, and the relationship with carboxyl compounds in spatiotemporal PM samples.<br><br>RESULTS: Our findings revealed three distinct stages in the spatiotemporal changes of prokaryotic communities in PM: an initial phase dominated by Lactobacillus, a transitional phase, and a final state of equilibrium. Significant variations in &#x3b1;- and &#x3b2;-diversity were observed across different spatial and temporal PM samples. We identified 178 medium- and high-quality non-redundant metagenome-assembled genomes (MAGs), and constructed their phylogenetic tree, depicting their roles in the carbon, nitrogen, and sulfur cycles. The Wood-Ljungdahl pathway and reverse TCA cycle were identified as the main carbon fixation mechanisms, with both hydrogenotrophic and aceticlastic methanogens playing a major role in methane production, and methylotrophic pathway observed in older PM. Furthermore, we identified relationships between prokaryotes and 29 carboxyl metabolites, including medium- and long-chain fatty acids. Horizontal gene transfer (HGT) was widespread in PM, particularly among clostridia, Bacteroidota, Bacilli, and Euryarchaeota, and was shown to play critical roles in fermentation dynamics, carbon fixation, methane production, and nitrogen and sulfur metabolism.<br><br>CONCLUSION: Our study provides new insights into the evolution and function of spatiotemporal PM, as well as its interactions with carboxyl metabolites. Lactobacillus dominated in new PM, while methanogens and clostridia were predominant in older or deeper PM layers. The three distinct stages of prokaryotic community development in PM and HGT played critical roles in metabolic function of spatiotemporal PM. Furthermore, this study highlights the importance of &#x3b1;-diversity, &#x3b2;-diversity, methanogens, and Clostridium as useful indicators for assessing PM quality in the production of high-quality Baijiu.},
}
@article {pmid39829789,
year = {2025},
author = {Robinson, LR and McDevitt, CJ and Regan, MR and Quail, SL and Swartz, M and Wadsworth, CB},
title = {Re-visiting the potential impact of doxycycline post-exposure prophylaxis (doxy-PEP) on the selection of doxycycline resistance in Neisseria commensals.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39829789},
issn = {2692-8205},
support = {R15 AI174182/AI/NIAID NIH HHS/United States ; },
abstract = {Doxycycline post-exposure prophylaxis (doxy-PEP) is a preventative strategy demonstrated to reduce bacterial sexually transmitted infections in high-risk populations. However, the impact of doxy-PEP on antibiotic resistance acquisition in key members of our microbiomes, is as of yet unclear. For example, commensal Neisseria are known reservoirs of resistance for gonococci through horizontal gene transfer (HGT), and are more likely to experience bystander selection due to doxy-PEP as they are universally carried. Thus, the consequences of doxycycline selection on commensal Neisseria will be critical to investigate to understand possible resistance mechanisms that may be transferred to an important human pathogen. Here, we use in vitro antibiotic gradients to evolve four Neisseria commensals (N. cinerea, N. canis, N. elongata, and N. subflava, n=4 per species) across a 20-day time course; and use whole genome sequencing to nominate derived mutations. After selection, 12 of 16 replicates evolved doxycycline resistance (> 1 μg/mL). Across resistant lineages: An A46T substitution in the repressor of the Mtr efflux pump (MtrR) and a V57M substitution in the 30 ribosomal protein S10 were clearly associated with elevated MICs. Additional mutations in ribosomal components also emerged in strains with high MICs (i.e., 16S rRNA G1057C, RplX A14T). We find the MtrR 46T, RpsJ 57M, and RplX 14T circulating in natural commensal populations. Furthermore, in vitro co-evolution of N. gonorrhoeae with Neisseria commensals demonstrated rapid transfer of the pConj plasmid to N. subflava and N. cinerea, and pbla to N. cinerea. Finally, collection of novel commensals from human hosts reveals 46% of isolates carrying doxycycline resistance; and doxycycline resistance was significantly greater in participants self-reporting doxycycline use in the past 6 months. High-level doxycycline resistance (> 8 μg/mL) was always associated with carriage of the ribosomal protection protein (tetM) and pConj. Ultimately, characterizing the contemporary prevalence of doxycycline resistance, and underlying resistance mechanisms, in commensal communities may help us to predict the long-term impact of doxy-PEP on Neisseria, and the likelihood of transferring particular genotypes across species' boundaries.},
}
@article {pmid39827804,
year = {2025},
author = {Ye, T and Li, Y and Zhou, X and Ye, Y and Liu, X and Xiong, W},
title = {Hormesis-like effects of black phosphorus nanosheets on the spread of multiple antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137207},
doi = {10.1016/j.jhazmat.2025.137207},
pmid = {39827804},
issn = {1873-3336},
mesh = {*Phosphorus/toxicity/chemistry ; Hormesis ; *Nanostructures/toxicity/chemistry ; Plasmids/genetics ; Reactive Oxygen Species/metabolism ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Gene Transfer, Horizontal/drug effects ; Escherichia coli/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic/drug effects ; },
abstract = {The production scalability and increasing demand for black phosphorus nanosheets (BPNSs) inevitably lead to environmental leakage. Although BPNSs' ecotoxicological effects have been demonstrated, their indirect health risks, such as inducing increased resistance in pathogenic bacteria, are often overlooked. This study explores the influence of BPNSs on the horizontal gene transfer of antibiotic resistance genes (ARGs) facilitated by the RP4 plasmid, which carries multiple resistance genes. The results indicated that BPNSs exhibited concentration-dependent hormesis-like effects on bacterial conjugation gene transfer. Specifically, at sub-inhibitory concentrations (0.0001-1 mg/L), BPNSs promoted both intra- and intergeneric conjugative transfer, demonstrating an initial increase followed by a decline, with transfer rates rising by 1.5-3.1-fold and 1.5-3.3-fold, respectively. BPNSs were found to induce reactive oxygen species (ROS) production, increase malondialdehyde levels, and trigger the SOS response, enhancing plasmid uptake. Additionally, BPNSs increased membrane permeability by forming pores and upregulating outer membrane porins (OMPs) genes. At higher BPNSs concentrations (0.1-1 mg/L), conjugative frequency was inhibited due to the disruption of the cellular antioxidant system and changes in the adsorption process. These findings underscore the influence of BPNSs on the conjugative transfer of ARGs, complementing current knowledge of the biotoxicity and potential ecological risks associated with BPNSs.},
}
@article {pmid39826759,
year = {2025},
author = {Wang, C and Yin, X and Xu, X and Wang, D and Wang, Y and Zhang, T},
title = {Antibiotic resistance genes in anaerobic digestion: Unresolved challenges and potential solutions.},
journal = {Bioresource technology},
volume = {419},
number = {},
pages = {132075},
doi = {10.1016/j.biortech.2025.132075},
pmid = {39826759},
issn = {1873-2976},
mesh = {Anaerobiosis ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial/genetics ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects ; },
abstract = {Antimicrobial resistance (AMR) threatens public health, necessitating urgent efforts to mitigate the global impact of antibiotic resistance genes (ARGs). Anaerobic digestion (AD), known for volatile solid reduction and energy generation, also presents a feasible approach for the removal of ARGs. This review encapsulates the existing understanding of ARGs and antibiotic-resistant bacteria (ARB) during the AD process, highlighting unresolved challenges pertaining to their detection and quantification. The questions raised and discussed include: Do current ARGs detection methods meet qualitative and quantitative requirements? How can we conduct risk assessments of ARGs? What happens to ARGs when they come into co-exposure with other emerging pollutants? How can the application of internal standards bolster the reliability of the AD resistome study? What are the potential future research directions that could enhance ARG elimination? Investigating these subjects will assist in shaping more efficient management strategies that employ AD for effective ARG control.},
}
@article {pmid39826720,
year = {2025},
author = {Akhoon, BA and Qiao, Q and Stewart, A and Chen, J and Rodriguez Lopez, CM and Corbin, KR},
title = {Pangenomic analysis of the bacterial cellulose-producing genera Komagataeibacter and Novacetimonas.},
journal = {International journal of biological macromolecules},
volume = {298},
number = {},
pages = {139980},
doi = {10.1016/j.ijbiomac.2025.139980},
pmid = {39826720},
issn = {1879-0003},
mesh = {*Cellulose/biosynthesis ; Phylogeny ; *Genome, Bacterial ; *Genomics/methods ; *Acetobacteraceae/genetics/metabolism ; Multigene Family ; Genetic Variation ; },
abstract = {Bacterial cellulose holds significant commercial potential due to its unique structural and chemical properties, making it suitable for applications in electronics, medicine, and pharmaceuticals. However, large-scale BC production remains limited by challenges related to bacterial performance. In this study, we compared 79 microbial genomes from three genera-Komagataeibacter, Novacetimonas, and Gluconacetobacter-to investigate their pangenomes, genetic diversity, and evolutionary relationships. Through comparative genomic and phylogenetic analyses, we identified distinct genome compositions and evolutionary patterns that differ from previous reports. The role of horizontal gene transfer in shaping the genetic diversity and adaptability of these bacteria was also explored. Key determinants in BC production, such as variations in the bacterial cellulose biosynthesis (bcs) operon, carbohydrate uptake genes, and carbohydrate-active enzymes, were examined. Additionally, several biosynthetic gene clusters, including Linocin M18 and sactipeptides, which encode for antimicrobial peptides known as bacteriocins, were identified. These findings reveal new aspects of the genetic diversity in cellulose-producing bacteria and present a comprehensive genomic toolkit that will support future efforts to optimize BC production and improve microbial performance for commercial applications.},
}
@article {pmid39826686,
year = {2025},
author = {Fu, Y and Morris, FC and Pereira, SC and Kostoulias, X and Jiang, Y and Vidor, C and Williams, G and Srikhanta, Y and Macesic, N and Yu, Y and Lyras, D and Peleg, AY},
title = {Mechanisms of blaIMP-4 dissemination across diverse carbapenem-resistant clinical isolates.},
journal = {Journal of global antimicrobial resistance},
volume = {41},
number = {},
pages = {189-194},
doi = {10.1016/j.jgar.2025.01.003},
pmid = {39826686},
issn = {2213-7173},
mesh = {Humans ; Plasmids/genetics ; *beta-Lactamases/genetics ; Microbial Sensitivity Tests ; *Carbapenems/pharmacology ; Australia ; *Bacterial Proteins/genetics ; Anti-Bacterial Agents/pharmacology ; Acinetobacter/genetics/drug effects ; *Carbapenem-Resistant Enterobacteriaceae/genetics/isolation &amp; purification/drug effects ; Gene Transfer, Horizontal ; Conjugation, Genetic ; Klebsiella pneumoniae/genetics ; Enterobacter/genetics/drug effects ; Klebsiella/genetics/drug effects ; },
abstract = {OBJECTIVE: The IMP-4 carbapenemase is an endemic cause of carbapenem resistance in the Asia-Pacific region. Our aim was to determine the dissemination mechanism of the blaIMP-4 gene.<br><br>METHODS: Twelve representative Australian IMP-4 clinical isolates from The Alfred Hospital (Victoria, Australia) were characterised using antimicrobial susceptibility testing, with their genome and plasmid assemblies analysed. The conjugation efficiencies of different plasmids were investigated using filter mating with four recipient strains across two species.<br><br>RESULTS: Selected IMP-4 isolates included six species and four genera (Enterobacter, Klebsiella, Serratia, and Acinetobacter), whereby isolates of the same species belonged to the same sequence type and were closely related. Four IMP-4 plasmid types were noted: IncHI2A types 1 and 2 (Klebsiella spp. and Enterobacter hormaechei, respectively), IncC (Serratia marcescens and Klebsiella pneumoniae), and a novel type in Acinetobacter pittii. Sequence homology was observed across all plasmids at the blaIMP-4 location, termed Region I, with IS26 on IncHI2A, and IS5075 and Tn3 resistance gene cassettes present on IncC plasmids. Genomic rearrangements mediated by IS26 or Tn3 and IS5075 were identified in Region I of plasmids from the same Inc type. The plasmids of each Inc type were capable of conjugative transfer with varying efficiency. IncH12A plasmids and K. pneumoniae IncC displayed higher transfer efficiencies than other plasmids examined in this study when using the recipient E. coli strain J53 (with conjugation efficiencies of 1.17&#xd7;10[-2] to 5.02&#xd7;10[-5], P < 0.001).<br><br>CONCLUSIONS: Clonal spread, Inc type, homologous region, and insertion sequences are important mobility factors in the dissemination and evolution of blaIMP-4 plasmids.},
}
@article {pmid39826554,
year = {2025},
author = {Kirsch, R and Okamura, Y and García-Lozano, M and Weiss, B and Keller, J and Vogel, H and Fukumori, K and Fukatsu, T and Konstantinov, AS and Montagna, M and Moseyko, AG and Riley, EG and Slipinski, A and Vencl, FV and Windsor, DM and Salem, H and Kaltenpoth, M and Pauchet, Y},
title = {Symbiosis and horizontal gene transfer promote herbivory in the megadiverse leaf beetles.},
journal = {Current biology : CB},
volume = {35},
number = {3},
pages = {640-654.e7},
doi = {10.1016/j.cub.2024.12.028},
pmid = {39826554},
issn = {1879-0445},
mesh = {Animals ; *Coleoptera/genetics/physiology/microbiology ; *Gene Transfer, Horizontal ; *Symbiosis/genetics ; *Herbivory ; Biological Evolution ; Phylogeny ; },
abstract = {Beetles that feed on the nutritionally depauperate and recalcitrant tissues provided by the leaves, stems, and roots of living plants comprise one-quarter of herbivorous insect species. Among the key adaptations for herbivory are plant cell wall-degrading enzymes (PCWDEs) that break down the fastidious polymers in the cell wall and grant access to the nutritious cell content. While largely absent from the non-herbivorous ancestors of beetles, such PCWDEs were occasionally acquired via horizontal gene transfer (HGT) or by the uptake of digestive symbionts. However, the macroevolutionary dynamics of PCWDEs and their impact on evolutionary transitions in herbivorous insects remained poorly understood. Through genomic and transcriptomic analyses of 74 leaf beetle species and 50 symbionts, we show that multiple independent events of microbe-to-beetle HGT and specialized symbioses drove convergent evolutionary innovations in approximately 21,000 and 13,500 leaf beetle species, respectively. Enzymatic assays indicate that these events significantly expanded the beetles' digestive repertoires and thereby contributed to their adaptation and diversification. Our results exemplify how recurring HGT and symbiont acquisition catalyzed digestive and nutritional adaptations to herbivory and thereby contributed to the evolutionary success of a megadiverse insect taxon.},
}
@article {pmid39824780,
year = {2025},
author = {Wu, X and Peng, J and Malik, AA and Peng, Z and Luo, Y and Fan, F and Lu, Y and Wei, G and Delgado-Baquerizo, M and Liesack, W and Jiao, S},
title = {A Global Relationship Between Genome Size and Encoded Carbon Metabolic Strategies of Soil Bacteria.},
journal = {Ecology letters},
volume = {28},
number = {1},
pages = {e70064},
doi = {10.1111/ele.70064},
pmid = {39824780},
issn = {1461-0248},
support = {42122050//National Science Foundation for Excellent Young Scholars of China/ ; 42277307 &amp; 41977038//National Natural Science Foundation of China/ ; 2021YFD1900500//National Key Research and Development Program of China/ ; },
mesh = {*Soil Microbiology ; *Carbon/metabolism ; *Genome Size ; *Bacteria/genetics/metabolism ; *Genome, Bacterial ; Gene Transfer, Horizontal ; Microbiota ; Biomass ; },
abstract = {Microbial traits are critical for carbon sequestration and degradation in terrestrial ecosystems. Yet, our understanding of the relationship between carbon metabolic strategies and genomic traits like genome size remains limited. To address this knowledge gap, we conducted a global-scale meta-analysis of 2650 genomes, integrated whole-genome sequencing data, and performed a continental-scale metagenomic field study. We found that genome size was tightly associated with an increase in the ratio between genes encoding for polysaccharide decomposition and biomass synthesis that we defined as the carbon acquisition-to-biomass yield ratio (A/Y). We also show that horizontal gene transfer played a major evolutionary role in the expanded bacterial capacities in carbon acquisition. Our continental-scale field study further revealed a significantly negative relationship between the A/Y ratio and soil organic carbon stocks. Our work demonstrates a global relationship between genome size and the encoded carbon metabolic strategies of soil bacteria across terrestrial microbiomes.},
}
@article {pmid39824112,
year = {2025},
author = {Farooq, A and Rafique, A and Han, E and Park, SM},
title = {Global dissemination of the beta-lactam resistance gene blaTEM-1 among pathogenic bacteria.},
journal = {The Science of the total environment},
volume = {963},
number = {},
pages = {178521},
doi = {10.1016/j.scitotenv.2025.178521},
pmid = {39824112},
issn = {1879-1026},
mesh = {*Bacteria/genetics ; *beta-Lactam Resistance/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Phylogeny ; Genome, Bacterial ; Gene Transfer, Horizontal ; beta-Lactams ; },
abstract = {Antibiotic resistance presents a burgeoning global health crisis, with over 70 % of pathogenic bacteria now exhibiting resistance to at least one antibiotic. This study leverages a vast dataset of 618,853 pathogenic bacterial genomes from the NCBI pathogen detection database, offering comprehensive insights into antibiotic resistance patterns, species-specific profiles, and transmission dynamics of resistant pathogens. We centered our investigation on the beta-lactam resistance gene blaTEM-1, found in 43,339 genomes, revealing its extensive distribution across diverse species and isolation sources. The study unveiled the prevalence of 15 prominent antibiotic resistance genes (ARGs), including those conferring resistance to beta-lactam, aminoglycoside, and tetracycline antibiotics. Distinct resistance patterns were observed between Gram-positive and Gram-negative bacteria, indicating the influence of phylogeny on resistance dissemination. Notably, the blaTEM-1 gene demonstrated substantial prevalence across a wide array of bacterial species (8) and a high number of isolation sources (11). Genetic context analysis revealed associations between blaTEM-1 and mobile genetic elements (MGEs) like transposons and insertion sequences. Additionally, we observed recent horizontal transfer events involving clusters of blaTEM-1 genes and MGEs underscore the potential of MGEs in facilitating the mobilization of ARGs. Our findings underscore the importance of adopting a One Health approach to global genomic pathogen surveillance, aiming to uncover the transmission routes of ARGs and formulate strategies to address the escalating antibiotic resistance crisis.},
}
@article {pmid39824023,
year = {2025},
author = {Guo, X and Yu, P and Guo, J and Zhao, HP and Lai, CY},
title = {Viral auxiliary roles in hydrolytic and biosynthetic metabolism regulate prokaryotic microbial interactions in anaerobic digestion.},
journal = {Water research},
volume = {274},
number = {},
pages = {123140},
doi = {10.1016/j.watres.2025.123140},
pmid = {39824023},
issn = {1879-2448},
mesh = {Anaerobiosis ; Hydrolysis ; *Microbial Interactions ; },
abstract = {Anaerobic digestion (AD) viruses have gained recognition as significant regulators of microbial interactions within AD communities, yet their ecological roles remain largely unexplored. In this study, we investigated the ecological roles of AD viruses in regulating microbial interactions among syntrophic hosts. We recovered 3921 diverse viral sequences from four full-scale anaerobic digesters and confirmed their widespread presence across 127 global metagenomic sampling sites (with >95 % sequence similarity), underscoring the ubiquity of prokaryotic viruses in AD-related systems. Through the construction of virus-prokaryote interactions (66.8 % validated at the transcriptional level) and analysis of viral-host transcriptional abundances, we identified significant associations between AD viruses and key processes, including hydrolysis, acidogenesis, and methanogenesis. Notably, polyvalent viruses were found to interact with both hydrolytic and fermentative communities. We further characterized viral auxiliary metabolism, hydrolytic substrate spectra, and microbial auxotrophy, showing that viruses not only could enhance the breakdown of complex substrates (e.g., cellulose, chitin, peptidoglycan) but also potentially supported the biosynthesis of essential nutrients (e.g., cysteine, methionine, heme, and cobalamin). These activities were proposed to regulate resource fluxes through alternating lysogenic and lytic cycles. Phylogenetic analysis of viral gene and horizontal gene transfer (HGT) identification suggest that AD viruses employ promiscuous infection on syntrophic hosts, potentially as an adaptive evolutionary strategy in the AD ecosystem. This study provides new insights into the ecological roles of AD viruses, highlighting their potential impact on the stability and functionality of AD systems.},
}
@article {pmid39823837,
year = {2025},
author = {Zhang, S and Ye, Q and Wang, M and Zhu, D and Jia, R and Chen, S and Liu, M and Yang, Q and Zhao, X and Wu, Y and Huang, J and Ou, X and Sun, D and Tian, B and He, Y and Wu, Z and Cheng, A},
title = {Isolation and characterization of a broad-spectrum bacteriophage against multi-drug resistant Escherichia coli from waterfowl field.},
journal = {Poultry science},
volume = {104},
number = {2},
pages = {104787},
pmid = {39823837},
issn = {1525-3171},
mesh = {Animals ; *Escherichia coli/virology/drug effects/physiology ; *Drug Resistance, Multiple, Bacterial ; *Poultry Diseases/microbiology/prevention &amp; control ; *Escherichia coli Infections/veterinary/microbiology/prevention &amp; control ; *Ducks ; *Coliphages/physiology/isolation &amp; purification ; China ; Microbial Sensitivity Tests/veterinary ; *Myoviridae/isolation &amp; purification/physiology ; Feces/microbiology/virology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Escherichia coli (E. coli) is a significant pathogen responsible for intestinal infections and foodborne diseases. The rise of antibiotic resistance poses a significant challenge to global public health. Traditional antibiotic therapy is becoming increasingly ineffective, highlighting the urgent need for innovative control strategies. This study explores the potential of bacteriophages as a sustainable alternative to traditional antibiotics. From 2021 to 2022, a total of 183 non-repetitive duck source fecal samples were collected from Mianyang City, Sichuan Province, and 126 strains of E. coli were isolated. The minimum inhibitory concentration (MIC) test showed that these strains exhibited high resistance to piperacillin (96.8%), tetracycline (88.9%), and chloramphenicol (86.5%). It is concerning that 93.7% of the isolates are classified as multidrug-resistant (MDR), posing a significant threat to existing treatment options. 20 bacteriophages were isolated from fecal and soil samples, among which 5 bacteriophages were selected for further analysis. Bacteriophage YP6 showed excellent lytic effects on MDR strains, especially strain MY104, as well as representative serotypes O1 (E. coli MY51) and O18 (E. coli MY106). The identification of YP6 as a member of the Myoviridae family was conducted using transmission electron microscopy, and it was found to have an optimal infection factor of 0.1. Bacteriophages exhibit significant thermal and pH stability, maintaining survival at temperatures up to 60 °C and pH ranges of 4 to 10. Whole genome sequencing confirmed that YP6 has a double stranded DNA genome of 139,323 base pairs (bp), and no antibiotic resistance or virulence genes were found, indicating a low possibility of horizontal gene transfer. In addition, YP6 effectively inhibits the formation of E. coli biofilm, which is a key factor in chronic infections. The in vivo experiments using Galleria mellonella (G. mellonella) larvae have shown that it has a significant protective effect against MDR E. coli infection. In summary, bacteriophage YP6 is expected to become a therapeutic agent against MDR E. coli infection due to its broad host range, environmental stability, and biofilm inhibition properties. Future research should optimize bacteriophage preparations, evaluate the safety and efficacy of animal models, and establish clinical application plans in the field of food safety.},
}
@article {pmid39818750,
year = {2025},
author = {Shao, D and Ju, X and Wu, Y and Zhang, Y and Yan, Z and Li, Y and Wang, L and Parkhill, J and Walsh, TR and Wu, C and Shen, J and Wang, Y and Zhang, R and Shen, Y},
title = {Quaternary Ammonium Compounds: A New Driver and Hidden Threat for mcr-1 Prevalence in Hospital Wastewater and Human Feces.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {3},
pages = {1565-1576},
doi = {10.1021/acs.est.4c11368},
pmid = {39818750},
issn = {1520-5851},
mesh = {*Wastewater/microbiology ; Humans ; Feces/microbiology ; *Quaternary Ammonium Compounds ; Hospitals ; Escherichia coli/genetics ; Plasmids ; Escherichia coli Proteins/genetics ; Colistin ; Drug Resistance, Bacterial/genetics ; },
abstract = {The emergence of mobile colistin resistance gene mcr-1 has attracted global attention. The prevalence of mcr-1-positive Escherichia coli (MCRPEC) in humans largely decreased following the ban of colistin as an animal growth promoter in China. However, the prevalence of MCRPEC in the hospital environment and the relationship between disinfectants and mcr-1 remain unclear. We found that MCRPEC prevalence was low in the feces of healthy humans attending physical examinations in six hospitals (4.6%, 71/1532) but high in hospital wastewater (50.0%, 27/54). mcr-1 was mainly located on IncI2 (63.0% in wastewater and 62.0% in feces) and IncHI2 plasmids (18.5% in wastewater and 21.1% in feces). High similarity of the mcr-1 context and its carrying plasmids was observed in human and wastewater MCRPEC, with several isolates clustering together. The coexistence of the ESBL gene blaCTX-M with mcr-1 occurred in 19.7% of IncI2 plasmids. Notably, 60.0% of IncHI2 plasmids exhibited co-occurrence of mcr-1 with the disinfectant resistance gene (DRG) qacEΔ1, conferring resistance to quaternary ammonium compounds (QACs). We revealed that QACs, rather than the other two types of disinfectants─ortho-phthalaldehyde (OPA) and povidone-iodine (PVP-I)─select for plasmids carrying both qacEΔ1 and mcr-1 and elevate their conjugative transfer frequency. Monitoring of DRGs in MCRPEC and managing disinfectant use are urgently needed in healthcare settings to mitigate the spread of colistin resistance from hospital environments to inpatients.},
}
@article {pmid39817515,
year = {2025},
author = {Djordjevic, M and Zivkovic, L and Ou, HY and Djordjevic, M},
title = {Nonlinear regulatory dynamics of bacterial restriction-modification systems modulates horizontal gene transfer susceptibility.},
journal = {Nucleic acids research},
volume = {53},
number = {2},
pages = {},
pmid = {39817515},
issn = {1362-4962},
support = {7750294//Science Fund of the Republic of Serbia/ ; //Ministry of Science and Technological Development of the Republic of Serbia/ ; 32370186//National Natural Science Foundation of China/ ; },
mesh = {*Gene Transfer, Horizontal ; *DNA Restriction-Modification Enzymes/metabolism/genetics ; Gene Expression Regulation, Bacterial ; *Bacteria/genetics ; Nonlinear Dynamics ; Bacterial Proteins/metabolism/genetics ; Plasmids/genetics ; Models, Genetic ; },
abstract = {Type II restriction-modification (R-M) systems play a pivotal role in bacterial defense against invading DNA, influencing the spread of pathogenic traits. These systems often involve coordinated expression of a regulatory protein (C) with restriction (R) enzymes, employing complex feedback loops for regulation. Recent studies highlight the crucial balance between R and M enzymes in controlling horizontal gene transfer (HGT). This manuscript introduces a mathematical model reflecting R-M system dynamics, informed by biophysical evidence, to minimize reliance on arbitrary parameters. Our analysis clarifies the observed variations in M-to-R ratios, emphasizing the regulatory role of the C protein. We analytically derived a stability diagram for C-regulated R-M systems, offering a more straightforward analysis method over traditional numerical approaches. Our findings reveal conditions leading to both monostability and bistability, linking changes in the M-to-R ratio to factors like cell division timing and plasmid replication rates. These variations may link adjusting defense against phage infection, or the acquisition of new genes such as antibiotic resistance determinants, to changing physiological conditions. We also performed stochastic simulations to show that system regulation may significantly increase M-to-R ratio variability, providing an additional mechanism to generate heterogeneity in bacterial population.},
}
@article {pmid39813956,
year = {2025},
author = {Yang, QE and Lin, Z and Gan, D and Li, M and Liu, X and Zhou, S and Walsh, TR},
title = {Microplastics mediates the spread of antimicrobial resistance plasmids via modulating conjugal gene expression.},
journal = {Environment international},
volume = {195},
number = {},
pages = {109261},
doi = {10.1016/j.envint.2025.109261},
pmid = {39813956},
issn = {1873-6750},
mesh = {*Plasmids/genetics ; *Microplastics/toxicity ; *Conjugation, Genetic/drug effects ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects ; },
abstract = {Antimicrobial resistance (AMR) and environmental degradation are existential global public health threats. Linking microplastics (MPs) and AMR is particularly concerning as MPs pollution would have significant ramifications on controlling of AMR; however, the effects of MPs on the spread and genetic mechanisms of AMR bacteria remain unclear. Herein, we performed Simonsen end-point conjugation to investigate the impact of four commonly used MPs on transfer of clinically relevant plasmids. The transfer breadth of a representative pA/C_MCR-8 plasmid across bacterial communities was confirmed by the cell sorting and 16S rRNA gene amplicon sequencing. Our study shows that exposure to four commonly found MPs promotes the conjugation rates of four clinically relevant AMR plasmids by up to 200-fold, when compared to the non-exposed group and that the transfer rates are MP concentrations demonstrate a positive correlation with higher transfer rates. Furthermore, we show that MPs induce the expression of plasmid-borne conjugal genes and SOS-linked genes such as recA, lexA, dinB and dinD. High-throughput sequencing of the broad transmission of plasmid pA/C_MCR-8, shows distribution over two main phyla, Pseudomonadota (50.0 %-95.0 %) and Bacillota (0.4 %-2.0 %). These findings definitively link two global health emergencies - AMR and environmental degradation via MPs, and to tackle global AMR, we must also now consider plastic utilisation and waste management.},
}
@article {pmid39812022,
year = {2025},
author = {Gamblin, J and Lambert, A and Blanquart, F},
title = {Persistent, Private, and Mobile Genes: A Model for Gene Dynamics in Evolving Pangenomes.},
journal = {Molecular biology and evolution},
volume = {42},
number = {1},
pages = {},
pmid = {39812022},
issn = {1537-1719},
support = {FDT202304016561//Fondation pour la Recherche M&#xe9;dicale/ ; },
mesh = {*Evolution, Molecular ; *Models, Genetic ; *Genome, Bacterial ; Phylogeny ; Gene Transfer, Horizontal ; Salmonella enterica/genetics ; Algorithms ; Genes, Bacterial ; },
abstract = {The pangenome of a species is the set of all genes carried by at least one member of the species. In bacteria, pangenomes can be much larger than the set of genes carried by a single organism. Many questions remain unanswered regarding the evolutionary forces shaping the patterns of the presence/absence of genes in pangenomes of a given species. We introduce a new model for bacterial pangenome evolution along a species phylogeny that explicitly describes the timing of appearance of each gene in the species and accounts for three generic types of gene evolutionary dynamics: persistent genes that are present in the ancestral genome, private genes that are specific to a given clade, and mobile genes that are imported once into the gene pool and then undergo frequent horizontal gene transfers. We call this model the Persistent-Private-Mobile (PPM) model. We develop an algorithm fitting the PPM model and apply it to a dataset of 902 Salmonella enterica genomes. We show that the best fitting model is able to reproduce the global pattern of some multivariate statistics like the gene frequency spectrum and the parsimony vs. frequency plot. Moreover, the gene classification induced by the PPM model allows us to study the position of accessory genes on the chromosome depending on their category, as well as the gene functions that are most present in each category. This work paves the way for a mechanistic understanding of pangenome evolution, and the PPM model developed here could be used for dynamics-aware gene classification.},
}
@article {pmid39809568,
year = {2025},
author = {Simões de Oliveira, G and Lentz, SAM and Müller, CZ and Guerra, RR and Dalmolin, TV and Volpato, FCZ and de Lima-Morales, D and Lamb Wink, P and Barth, AL and Rabinowitz, P and Martins, AF},
title = {Resistome and plasmidome genomic features of mcr-1.1-harboring Escherichia coli: a One Health approach.},
journal = {Journal of applied microbiology},
volume = {136},
number = {1},
pages = {},
doi = {10.1093/jambio/lxaf019},
pmid = {39809568},
issn = {1365-2672},
support = {//INPRA/ ; 465718/2014-0//CNPq/ ; 17/2551-0000514-7//FAPERGS/ ; 2022-0283//FIPE/ ; //HCPA/ ; },
mesh = {*Escherichia coli/genetics/drug effects/isolation &amp; purification ; *Plasmids/genetics ; Swine/microbiology ; Animals ; Brazil ; *Escherichia coli Proteins/genetics ; Chickens/microbiology ; Humans ; Anti-Bacterial Agents/pharmacology ; *Escherichia coli Infections/microbiology/veterinary ; Colistin/pharmacology ; Microbial Sensitivity Tests ; Drug Resistance, Multiple, Bacterial/genetics ; One Health ; Whole Genome Sequencing ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; },
abstract = {AIMS: This study evaluated the phenotypic and genotypic traits of mcr-1.1-harboring Escherichia coli isolates from chickens, pigs, humans, and farm environments. The resistome and the mobile genetic elements associated with the spread of mcr-1.1 in Southern Brazil were also characterized.<br><br>METHODS AND RESULTS: The 22 mcr-1.1-harboring E. coli isolates from different origins were selected for antimicrobial susceptibility testing and whole genome sequencing for characterization of the resistome, plasmids, and sequence types. All isolates presented several resistance genes and harbored the mcr-1.1 gene in a highly similar IncX4 plasmid. Furthermore, the mcr-1.1 gene co-occurred with the mcr-3.12 gene in a multidrug-resistant isolate from the farm environment.<br><br>CONCLUSIONS: These findings demonstrate that the mcr-1.1 gene in E. coli isolates from Brazil is spreading mainly by horizontal transfer of the IncX4 plasmid. The co-occurrence of mcr-1.1 and mcr-3.12 highlights pig farming as an important reservoir of colistin resistance.},
}
@article {pmid39807864,
year = {2025},
author = {Nakatsu, G and Ko, D and Michaud, M and Franzosa, EA and Morgan, XC and Huttenhower, C and Garrett, WS},
title = {Virulence factor discovery identifies associations between the Fic gene family and Fap2[+] fusobacteria in colorectal cancer microbiomes.},
journal = {mBio},
volume = {16},
number = {2},
pages = {e0373224},
pmid = {39807864},
issn = {2150-7511},
support = {R01 CA154426/CA/NCI NIH HHS/United States ; //Cancer Research UK (CRUK)/ ; R01CA154426//HHS | NIH | National Cancer Institute (NCI)/ ; },
mesh = {Humans ; *Virulence Factors/genetics ; *Colorectal Neoplasms/microbiology ; *Fusobacterium/genetics/pathogenicity/isolation &amp; purification ; *Gastrointestinal Microbiome ; *Lectins/genetics/metabolism ; Genome, Bacterial ; Multigene Family ; *Fusobacteria/genetics/pathogenicity ; Feces/microbiology ; *Bacterial Proteins/genetics/metabolism ; },
abstract = {Fusobacterium is a bacterium associated with colorectal cancer (CRC) tumorigenesis, progression, and metastasis. Fap2 is a fusobacteria-specific outer membrane galactose-binding lectin that mediates Fusobacterium adherence to and invasion of CRC tumors. Advances in omics analyses provide an opportunity to profile and identify microbial genomic features that correlate with the cancer-associated bacterial virulence factor Fap2. Here, we analyze genomes of Fusobacterium colon tumor isolates and find that a family of post-translational modification enzymes containing Fic domains is associated with Fap2 positivity in these strains. We demonstrate that Fic family genes expand with the presence of Fap2 in the fusobacterial pangenome. Through comparative genomic analysis, we find that Fap2[+] Fusobacteriota are highly enriched with Fic gene families compared to other cancer-associated and human gut microbiome bacterial taxa. Using a global data set of CRC shotgun metagenomes, we show that fusobacterial Fic and Fap2 genes frequently co-occur in the fecal microbiomes of individuals with late-stage CRC. We further characterize specific Fic gene families harbored by Fap2[+] Fusobacterium animalis genomes and detect recombination events and elements of horizontal gene transfer via synteny analysis of Fic gene loci. Exposure of a F. animalis strain to a colon adenocarcinoma cell line increases gene expression of fusobacterial Fic and virulence-associated adhesins. Finally, we demonstrate that Fic proteins are synthesized by F. animalis as Fic peptides are detectable in F. animalis monoculture supernatants. Taken together, our study uncovers Fic genes as potential virulence factors in Fap2[+] fusobacterial genomes.IMPORTANCEAccumulating data support that bacterial members of the intra-tumoral microbiota critically influence colorectal cancer progression. Yet, relatively little is known about non-adhesin fusobacterial virulence factors that may influence carcinogenesis. Our genomic analysis and expression assays in fusobacteria identify Fic domain-containing genes, well-studied virulence factors in pathogenic bacteria, as potential fusobacterial virulence features. The Fic family proteins that we find are encoded by fusobacteria and expressed by Fusobacterium animalis merit future investigation to assess their roles in colorectal cancer development and progression.},
}
@article {pmid39805347,
year = {2025},
author = {Sasikumar, J and Shaikh, HA and Naik, B and Laha, S and Das, SP},
title = {Emergence of fungal hybrids - Potential threat to humans.},
journal = {Microbial pathogenesis},
volume = {200},
number = {},
pages = {107278},
doi = {10.1016/j.micpath.2025.107278},
pmid = {39805347},
issn = {1096-1208},
mesh = {Humans ; *Fungi/genetics/pathogenicity ; *Hybridization, Genetic ; Genome, Fungal ; *Mycoses/microbiology ; Genetic Variation ; Virulence ; Epigenesis, Genetic ; Aspergillus/genetics/pathogenicity ; Gene Transfer, Horizontal ; Candida/genetics/pathogenicity ; },
abstract = {Fungal hybrids arise through the interbreeding of distinct species. This hybridization process fosters increased genetic diversity and the emergence of new traits. Mechanisms driving hybridization include the loss of heterozygosity, copy number variations, and horizontal gene transfer. Genetic mating barriers, changes in ploidy, chromosomal instability, and genomic diversity influence hybridization. These factors directly impact the fitness and adaptation of hybrid offspring. Epigenetic factors, including DNA methylation, histone modifications, non-coding RNAs, and chromatin remodelling, play a role in post-mating isolation in hybrids. In addition to all these mechanisms, successful hybridization in fungi is ensured by cellular mechanisms like mitochondrial inheritance, transposable elements, and other genome conversion mechanisms. These mechanisms support hybrid life and enhance the virulence and pathogenicity of fungal hybrids, which provoke diseases in host organisms. Recent advancements in sequencing have uncovered fungal hybrids in pathogens like Aspergillus, Candida, and Cryptococcus. Examples of these hybrids, such as Aspergillus latus, Candida metapsilosis, and Cryptococcus neoformans, induce severe human infections. Identifying fungal hybrids is challenging due to their altered genome traits. ITS sequencing has emerged as a promising method for diagnosing these hybrids. To prevent the emergence of novel hybrid fungal pathogens, it is crucial to develop effective diagnostic techniques and closely monitor pathogenic fungal populations for signs of hybridization. This comprehensive review delves into various facts about fungal hybridization, including its causes, genetic outcomes, barriers, diagnostic strategies, and examples of emerging fungal hybrids. The review emphasises the potential threat that fungal hybrids pose to human health and highlights their clinical significance.},
}
@article {pmid39803089,
year = {2024},
author = {Yadav, KS and Pawar, S and Datkhile, K and Patil, SR},
title = {Study on the Mobile Colistin Resistance (mcr-1) Gene in Gram-Negative Bacilli in a Rural Tertiary Care Hospital in Western Maharashtra.},
journal = {Cureus},
volume = {16},
number = {12},
pages = {e75569},
pmid = {39803089},
issn = {2168-8184},
abstract = {BACKGROUND: Colistin, a last-resort antibiotic for treating multidrug-resistant Gram-negative bacterial infections, has increased resistance as a result of the emergence of the mcr-1 gene. The mcr-1gene, which confers colistin resistance, is often carried on plasmids, facilitating its spread by horizontal gene transfer among bacterial populations. The rising prevalence of mcr-1-mediated resistance poses significant challenges for infection control and treatment efficacy. This study aimed to detect and investigate the prevalence of the mcr-1 gene among Gram-negative bacilli isolated from clinical specimens in a rural tertiary care hospital and to analyze the plasmid-mediated mechanisms of colistin resistance.<br><br>MATERIALS AND METHODS: A cross-sectional study was conducted over two years at Krishna Institute of Medical Sciences, Karad. Gram-negative bacilli were isolated from clinical specimens and identified using standard methodology. Antimicrobial susceptibility testing was performed by using the Vitek-2 Compact (bioMerieux, Marcy-l'&#xc9;toile, France) method and the colistin-resistance broth microdilution method (BMD). Polymerase chain reaction (PCR) was done for the presence of mcr-1 gene in colistin-resistant isolates.<br><br>RESULTS: Out of 359 Gram-negative bacilli isolates, 93 (25.90%) demonstrated resistance to colistin. Among these resistant strains, the mcr-1 gene was identified in 13 (13.97%) of the isolates. The gene was predominantly found in Pseudomonas aeruginosa (8, 61.53%), followed by Klebsiella pneumoniae (3, 23.07%), Acinetobacter baumannii (2, 15.38%) among the 13 isolates. Out of the various specimens received, mcr-1 gene was found in endotracheal tube (4, 30.76%), urine (4, 30.76%), pus (3, 23.07%), sputum (1, 7.69%), and blood (1, 7.69%). Colistin minimum inhibitory concentration (MIC) value for these resistant isolates ranged from 4 to 16 &#xb5;g/ml.<br><br>CONCLUSION: The study highlights a significant prevalence of mcr-1 plasmid-mediated colistin resistance gene among Gram-negative bacilli in the hospital. This possibly highlights the frequent misuse of colistin in animal husbandry from this rural area. The findings underscore the importance of monitoring resistance patterns and implementing stringent infection control measures.},
}
@article {pmid39801834,
year = {2025},
author = {Bustamante, M and Mei, S and Daras, IM and van Doorn, GS and Falcao Salles, J and de Vos, MGJ},
title = {An eco-evolutionary perspective on antimicrobial resistance in the context of One Health.},
journal = {iScience},
volume = {28},
number = {1},
pages = {111534},
pmid = {39801834},
issn = {2589-0042},
abstract = {The One Health approach musters growing concerns about antimicrobial resistance due to the increased use of antibiotics in healthcare and agriculture, with all of its consequences for human, livestock, and environmental health. In this perspective, we explore the current knowledge on how interactions at different levels of biological organization, from genetic to ecological interactions, affect the evolution of antimicrobial resistance. We discuss their role in different contexts, from natural systems with weak selection, to human-influenced environments that impose a strong pressure toward antimicrobial resistance evolution. We emphasize the need for an eco-evolutionary approach within the One Health framework and highlight the importance of horizontal gene transfer and microbiome interactions for increased understanding of the emergence and spread of antimicrobial resistance.},
}
@article {pmid39801293,
year = {2025},
author = {Marquiegui-Alvaro, A and Kottara, A and Chacón, M and Cliffe, L and Brockhurst, M and Dixon, N},
title = {Genetic Bioaugmentation-Mediated Bioremediation of Terephthalate in Soil Microcosms Using an Engineered Environmental Plasmid.},
journal = {Microbial biotechnology},
volume = {18},
number = {1},
pages = {e70071},
pmid = {39801293},
issn = {1751-7915},
support = {BB/P01738X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T005742/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/W012723/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; EP/S022856/1//Engineering and Physical Sciences Research Council/ ; },
mesh = {*Plasmids/genetics ; *Soil Microbiology ; Biodegradation, Environmental ; *Pseudomonas putida/genetics/metabolism ; *Soil Pollutants/metabolism ; *Phthalic Acids/metabolism ; Gene Transfer, Horizontal ; Metabolic Engineering ; },
abstract = {Harnessing in situ microbial communities to clean-up polluted natural environments is a potentially efficient means of bioremediation, but often the necessary genes to breakdown pollutants are missing. Genetic bioaugmentation, whereby the required genes are delivered to resident bacteria via horizontal gene transfer, offers a promising solution to this problem. Here, we engineered a conjugative plasmid previously isolated from soil, pQBR57, to carry a synthetic set of genes allowing bacteria to consume terephthalate, a chemical component of plastics commonly released during their manufacture and breakdown. Our engineered plasmid caused a low fitness cost and was stably maintained in terephthalate-contaminated soil by the bacterium P. putida. Plasmid carriers efficiently bioremediated contaminated soil in model soil microcosms, achieving complete breakdown of 3.2 mg/g of terephthalate within 8 days. The engineered plasmid horizontally transferred the synthetic operon to P. fluorescens in situ, and the resulting transconjugants degraded 10 mM terephthalate during a 180-h incubation. Our findings show that environmental plasmids carrying synthetic catabolic operons can be useful tools for in situ engineering of microbial communities to perform clean-up even of complex environments like soil.},
}
@article {pmid39799916,
year = {2025},
author = {Li, Y and Liu, X and Guo, S and Wang, L and Tang, J},
title = {The combination of polystyrene microplastics and di (2-ethylhexyl) phthalate promotes the conjugative transfer of antibiotic resistance genes between bacteria.},
journal = {Ecotoxicology and environmental safety},
volume = {289},
number = {},
pages = {117681},
doi = {10.1016/j.ecoenv.2025.117681},
pmid = {39799916},
issn = {1090-2414},
mesh = {*Diethylhexyl Phthalate/toxicity ; *Polystyrenes/toxicity ; *Microplastics/toxicity ; *Plasticizers/toxicity ; *Drug Resistance, Bacterial/genetics ; *Bacteria/drug effects/genetics ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Gene Transfer, Horizontal/drug effects ; *Water Pollutants, Chemical/toxicity ; },
abstract = {Plastic pollution has become a common phenomenon. The process of plastic degradation is accompanied by the release of microplastics and plasticizers. However, the coexistence of microplastics and plasticizers on the transfer of antibiotic resistance genes (ARGs) has not been reported until now. Here, polystyrene (PS) microplastics and plasticizer di (2-ethylhexyl) phthalate (DEHP) were used for combined treatment experiment and their effects and mechanisms on the transfer of ARGs between bacteria were explored. By increasing cell membrane permeability and the expression of correlated genes, the combined treatment group showed promoting effects on the transfer of ARGs than that of control, with the highest promoting effects observed at 1 mg/L PS and 0.1 mg/L DEHP, which was 3.0 times higher in ARGs transfer rate than that of control. It was found that PS and DEHP treatment alone also led to a higher conjugative transfer frequency, and the frequency of the combined treatment was lower than that of the corresponding single treatment group. This indicated that the effects of DEHP and microplastics on ARGs transfer might be antagonistic. Transcriptome analysis indicated that the transfer of ARGs affects bacterial ion binding, oxidative stress, and energy metabolism processes, while the expression of genes related to cell membrane permeability, DNA repair, bacterial drug resistance, and quorum sensing also increase. This study may provide new insights for explaining the combined effects of various pollutants in the environment on the spread of ARGs.},
}
@article {pmid39799674,
year = {2025},
author = {Li, Y and Qin, W and Xin, X and Tang, C and Huang, Y and He, X and Chen, L and Yu, G and Yu, F},
title = {Dynamic impact of polyethylene terephthalate nanoplastics on antibiotic resistance and microplastics degradation genes in the rhizosphere of Oryza sativa L.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137173},
doi = {10.1016/j.jhazmat.2025.137173},
pmid = {39799674},
issn = {1873-3336},
mesh = {*Polyethylene Terephthalates/toxicity ; *Oryza/microbiology/drug effects/genetics/metabolism ; *Rhizosphere ; *Microplastics/toxicity/metabolism ; *Soil Pollutants/toxicity/metabolism ; Soil Microbiology ; *Drug Resistance, Microbial/genetics/drug effects ; Biodegradation, Environmental ; Genes, Bacterial ; },
abstract = {This study examined the effects of polyethylene terephthalate (PET) nanoplastics on the rhizosphere of Oryza sativa L., focusing on dynamic changes and interactions among microbial communities, antibiotic resistance genes (ARGs) and microplastic degradation genes (MDGs). PET exposure altered the structure and function of soil microbial, enabling specific microbial groups to thrive in polluted environments. High-dose PET treatments markedly increased the abundance and dissemination of ARGs, primarily via resistance mechanisms such as antibiotic efflux and target alteration. By providing additional carbon sources and surfaces for microbial attachment, PET stimulated the growth of microorganisms harboring MDGs, resulting in an increase in MDGs abundance. The elevated expression of MDGs facilitated the propagation of ARGs, with overlapping host microorganisms suggesting that certain microbial groups exhibit dual metabolic capabilities, enabling them to endure both antibiotic and microplastic pressures. Toxic byproducts of microplastic degradation, such as mono-ethylhexyl phthalate, further promoted ARGs dissemination by increasing horizontal gene transfer frequency. Structural equation modeling revealed that PET indirectly influenced ARGs and MDGs expression by altering soil C/N ratio, available phosphorus, and enzyme activities. Thus, nanoscale PET exacerbates ecological risks to soil microbial communities by driving co-propagation of ARGs and MDGs, highlighting the persistent threat of composite pollution to agroecosystems.},
}
@article {pmid39798650,
year = {2025},
author = {Zhang, X and Guo, W and Zhang, Z and Gao, P and Tang, P and Liu, T and Yao, X and Li, J},
title = {Insights into the mobility and bacterial hosts of antibiotic resistance genes under dinotefuran selection pressure in aerobic granular sludge based on metagenomic binning and functional modules.},
journal = {Environmental research},
volume = {268},
number = {},
pages = {120807},
doi = {10.1016/j.envres.2025.120807},
pmid = {39798650},
issn = {1096-0953},
mesh = {*Sewage/microbiology ; *Guanidines/toxicity ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents ; Selection, Genetic ; Aerobiosis ; },
abstract = {Dinotefuran (DIN) is toxic to non-target organisms and accelerates the evolution of antibiotic resistance, which poses a problem for the stable operation of the activated sludge process in wastewater treatment plants (WWTPs). However, the emergence and the transfer mechanism of antibiotic resistance genes (ARGs) in activated sludge systems under DIN stress remains unclear. Thus, in the study, the potential impact of DIN on ARGs and virulence factor genes (VFGs) in aerobic granular sludge (AGS) was investigated in depth using metagenomic binning and functional modules. It was found that DIN stress increased the total abundance of ARGs, mobile genetic elements (MGEs), and VFGs in the AGS system, with the highest abundance of fabG (4.6%), tnpA (55.6%) and LPS (39.0%), respectively. The proliferation of the enteric pathogens Salmonella enterica and Escherichia coli in the system indicates that DIN induces exposure of harmless bacteria to the infected environment. The genera Nitrospira (1169 ARG subtypes) and Dechloromonas (663 ARG subtypes) were identified as the potentially antibiotic-resistant bacteria carrying the most ARGs and MGEs in the metagenome-assembled genomes. Co-localization patterns of some ARGs, MGEs, and the SOS response-related gene lexA were observed on metagenome-assembled contigs under high levels of DIN exposure, suggesting DIN stimulated ROS production (101.8% increase over control), altered cell membrane permeability, and increased the potential for horizontal gene transfer (HGT). Furthermore, the DNA damage caused by DIN in AGS led to the activation of the antioxidant system and the SOS repair response, which in turn promoted the expression of the type IV secretion system and HGT through the flagellar channel. This study extends the previously unappreciated DIN understanding of the spread and associated risks of ARGs and VFGs in the AGS system of WWTPs. It elucidates how DIN facilitates HGT, offering a scientific basis for controlling emerging contaminant-induced resistance.},
}
@article {pmid39797530,
year = {2025},
author = {Liu, Y and Gong, C and Hu, Y and Han, H and Tian, T and Luo, Y and Yang, X and Xie, W and Wu, Q and Wang, S and Guo, Z and Zhang, Y},
title = {Silencing of the plant-derived horizontally transferred gene BtSC5DL effectively controls Bemisia tabaci MED.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.8638},
pmid = {39797530},
issn = {1526-4998},
support = {2021YFD1400600//National Key R&amp;D Program of China/ ; 32221004//National Natural Science Foundation of China/ ; CARS-23//Earmarked Fund for CARS/ ; Y2023XK15//Central Public-Interest Scientific Institution Basal Research Fund of the Chinese Academy of Agricultural Sciences./ ; Y2024XK01//Central Public-Interest Scientific Institution Basal Research Fund of the Chinese Academy of Agricultural Sciences./ ; //Beijing Key Laboratory for Pest Control and Sustainable Cultivation of Vegetables/ ; CAAS-ASTIP-IVFCAAS//Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences/ ; },
abstract = {BACKGROUND: The whitefly Bemisia tabaci is a notorious agricultural pest known for its ability to cause significant crop damage through direct feeding and virus transmission. Its remarkable adaptability and reproductive capacity are linked to its ability to acquire and integrate horizontally transferred genes (HTGs) into its genome. These HTGs increase the physiological and metabolic capacities of this pest, including cholesterol synthesis, which is critical for its survival and reproductive success. Among these genes, we identified a plant-derived B. tabaci Δ7-sterol C5-desaturase-like gene (BtSC5DL), which plays a pivotal role in B. tabaci cholesterol metabolism and reproductive biology.<br><br>RESULTS: In this study, we cloned and identified the BtSC5DL gene from B. tabaci Mediterranean (MED). Bioinformatics and molecular analyses revealed that BtSC5DL was transferred from plants to B. tabaci millions of years ago and is now stably expressed in this species. Silencing BtSC5DL through dsRNA feeding resulted in significant reductions in egg production and cholesterol content in B. tabaci MED. Furthermore, virus-induced gene silencing (VIGS) experiments confirmed that long-term suppression of BtSC5DL had a notable ability to control whitefly populations.<br><br>CONCLUSION: Our results demonstrate the crucial role of BtSC5DL in cholesterol biosynthesis in B. tabaci MED and suggest that the acquisition of this gene significantly enhances the reproductive capacity of this species. These findings provide a theoretical basis for the development of RNA interference (RNAi)-based pest control strategies targeting BtSC5DL, offering a potential new approach for the effective management of whitefly populations in agricultural settings. &#xa9; 2025 Society of Chemical Industry.},
}
@article {pmid39794121,
year = {2025},
author = {Liu, Y and Botelho, J and Iranzo, J},
title = {Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer.},
journal = {Genome research},
volume = {35},
number = {2},
pages = {268-278},
pmid = {39794121},
issn = {1549-5469},
mesh = {*Gene Transfer, Horizontal ; Evolution, Molecular ; Phylogeny ; *Genetic Linkage ; *Archaea/genetics ; *Bacteria/genetics ; *Interspersed Repetitive Sequences/genetics ; Genome, Bacterial ; Genomics ; },
abstract = {Prokaryotes have evolved a wide repertoire of defense systems to prevent invasion by mobile genetic elements (MGEs). However, because MGEs are vehicles for the exchange of beneficial accessory genes, defense systems could consequently impede rapid adaptation in microbial populations. Here, we study how defense systems impact horizontal gene transfer (HGT) in the short term and long term. By combining comparative genomics and phylogeny-aware statistical methods, we quantify the association between the presence of seven widespread defense systems and the abundance of MGEs in the genomes of 196 bacterial and one archaeal species. We also calculate the differences in the rates of gene gain and loss between lineages that possess and lack each defense system. Our results show that the impact of defense systems on HGT is highly taxon and system dependent and, in most cases, not statistically significant. Timescale analysis reveals that defense systems must persist in a lineage for a relatively long time to exert an appreciable negative impact on HGT. In contrast, for shorter evolutionary timescales, frequent coacquisition of MGEs and defense systems results in a net positive association of the latter with HGT. Given the high turnover rates experienced by defense systems, we propose that the inhibitory effect of most defense systems on HGT is masked by their strong linkage with MGEs. These findings help explain the contradictory conclusions of previous research by pointing at mobility and within-host retention times as key factors that determine the impact of defense systems on genome plasticity.},
}
@article {pmid39793087,
year = {2025},
author = {Zhang, Y and Tu, C and Bai, J and Li, X and Sun, Z and Xu, L},
title = {Metabolic enhancement contributed by horizontal gene transfer is essential for dietary specialization in leaf beetles.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {1},
pages = {e2415717122},
pmid = {39793087},
issn = {1091-6490},
support = {32370523//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Animals ; *Coleoptera/genetics/metabolism ; *Gene Transfer, Horizontal ; *Plant Leaves/parasitology/metabolism/genetics ; *Larva/metabolism/genetics/growth &amp; development ; *Cellulose/metabolism ; Diet ; },
abstract = {Horizontal gene transfer (HGT) from bacteria to insects is widely reported and often associated with the adaptation and diversification of insects. However, compelling evidence demonstrating how HGT-conferred metabolic adjustments enable species to adapt to surrounding environment remains scarce. Dietary specialization is an important ecological strategy adopted by animals to reduce inter- and intraspecific competition for limited resources. Adults of the leaf beetle Plagiodera versicolora (Coleoptera) preferentially consume new leaves; nevertheless, we found that they selectively oviposit on mature leaves, thereby establishing a distinct dietary niche separation between adults and larvae. Based on the de novo assembled chromosome-level genome, we identified two horizontally transferred genes with cellulose degradation potential, belonging to the glycosyl hydrolase 48 family (GH48-1 and GH48-2). Prokaryotic expression of the HGTs confirmed the cellulose degradation capability of the two genes. Knockdown of GH48 significantly hampered the growth and survival rate of larvae feeding on mature leaves compared to wild-type larvae, with no similar effect observed in adults. Replenishing the GH48-expressing bacteria compensated for the knockdown of these two genes and recurred larval adaptability to mature leaves. Taken together, our results highlight the advantage and metabolic enhancement conferred by the two cellulose-degrading HGTs in P. versicolora larvae, enabling their development on cellulose-enriched mature leaves and underscoring the indispensable role of HGTs in facilitating the adaptation of leaf beetles to plants.},
}
@article {pmid39791879,
year = {2025},
author = {Kohlmeier, MG and O'Hara, GW and Ramsay, JP and Terpolilli, JJ},
title = {Closed genomes of commercial inoculant rhizobia provide a blueprint for management of legume inoculation.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {2},
pages = {e0221324},
pmid = {39791879},
issn = {1098-5336},
support = {UMU1810-001RTX, UMU1901-002RTX//Grains Research and Development Corporation (GRDC)/ ; FT170100235//Australian Research Council Future Fellowship/ ; },
mesh = {*Genome, Bacterial ; *Fabaceae/microbiology ; Australia ; Symbiosis ; Phylogeny ; *Agricultural Inoculants/genetics ; *Rhizobium/genetics ; *Rhizobiaceae/genetics ; Soil Microbiology ; Root Nodules, Plant/microbiology ; },
abstract = {UNLABELLED: Rhizobia are soil bacteria capable of establishing symbiosis within legume root nodules, where they reduce atmospheric N2 into ammonia and supply it to the plant for growth. Australian soils often lack rhizobia compatible with introduced agricultural legumes, so inoculation with exotic strains has become a common practice for over 50 years. While extensive research has assessed the N2-fixing capabilities of these inoculants, their genomics, taxonomy, and core and accessory gene phylogeny are poorly characterized. Furthermore, in some cases, inoculant strains have been developed from isolations made in Australia. It is unknown whether these strains represent naturalized exotic organisms, native rhizobia with a capacity to nodulate introduced legumes, or recombinant strains arising from horizontal transfer between introduced and native bacteria. Here, we describe the complete, closed genome sequences of 42 Australian commercial rhizobia. These strains span the genera, Bradyrhizobium, Mesorhizobium, Methylobacterium, Rhizobium, and Sinorhizobium, and only 23 strains were identified to species level. Within inoculant strain genomes, replicon structure and location of symbiosis genes were consistent with those of model strains for each genus, except for Rhizobium sp. SRDI969, where the symbiosis genes are chromosomally encoded. Genomic analysis of the strains isolated from Australia showed they were related to exotic strains, suggesting that they may have colonized Australian soils following undocumented introductions. These genome sequences provide the basis for accurate strain identification to manage inoculation and identify the prevalence and impact of horizontal gene transfer (HGT) on legume productivity.<br><br>IMPORTANCE: Inoculation of cultivated legumes with exotic rhizobia is integral to Australian agriculture in soils lacking compatible rhizobia. The Australian inoculant program supplies phenotypically characterized high-performing strains for farmers but in most cases, little is known about the genomes of these rhizobia. Horizontal gene transfer (HGT) of symbiosis genes from inoculant strains to native non-symbiotic rhizobia frequently occurs in Australian soils and can impact the long-term stability and efficacy of legume inoculation. Here, we present the analysis of reference-quality genomes for 42 Australian commercial rhizobial inoculants. We verify and classify the genetics, genome architecture, and taxonomy of these organisms. Importantly, these genome sequences will facilitate the accurate strain identification and monitoring of inoculants in soils and plant nodules, as well as enable detection of horizontal gene transfer to native rhizobia, thus ensuring the efficacy and integrity of Australia's legume inoculation program.},
}
@article {pmid39789078,
year = {2025},
author = {Lee, D and Muir, P and Lundberg, S and Lundholm, A and Sandegren, L and Koskiniemi, S},
title = {A CRISPR-Cas9 system protecting E. coli against acquisition of antibiotic resistance genes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1545},
pmid = {39789078},
issn = {2045-2322},
mesh = {*CRISPR-Cas Systems ; *Escherichia coli/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; },
abstract = {Antimicrobial resistance (AMR) is an increasing problem worldwide, and new treatment options for bacterial infections are direly needed. Engineered probiotics show strong potential in treating or preventing bacterial infections. However, one concern with the use of live bacteria is the risk of the bacteria acquiring genes encoding for AMR or virulence factors through horizontal gene transfer (HGT), and the transformation of the probiotic into a superbug. Therefore, we developed an engineered CRISPR-Cas9 system that protects bacteria from horizontal gene transfer. We synthesized a CRISPR locus targeting eight AMR genes and cloned this with the Cas9 and transacting tracrRNA on a medium copy plasmid. We next evaluated the efficiency of the system to block HGT through transformation, transduction, and conjugation. Our results show that expression of the CRISPR-Cas9 system successfully protects E. coli MG1655 from acquiring the targeted resistance genes by transformation or transduction with 2-3 logs of protection depending on the system for transfer and the target gene. Furthermore, we show that the system blocks conjugation of a set of clinical plasmids, and that the system is also able to protect the probiotic bacterium E. coli Nissle 1917 from acquiring AMR genes.},
}
@article {pmid39788974,
year = {2025},
author = {Scarpa, A and Pianezza, R and Gellert, HR and Haider, A and Kim, BY and Lai, EC and Kofler, R and Signor, S},
title = {Double trouble: two retrotransposons triggered a cascade of invasions in Drosophila species within the last 50 years.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {516},
pmid = {39788974},
issn = {2041-1723},
support = {P35093//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; P30 CA008748/CA/NCI NIH HHS/United States ; P34965//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; R01 HD108914/HD/NICHD NIH HHS/United States ; NSF-EPSCoR-2032756//National Science Foundation (NSF)/ ; R01 GM083300/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Retroelements/genetics ; *Gene Transfer, Horizontal ; *Phylogeny ; *Evolution, Molecular ; Drosophila/genetics ; Genome, Insect ; Drosophila melanogaster/genetics ; Introduced Species ; },
abstract = {Horizontal transfer of genetic material in eukaryotes has rarely been documented over short evolutionary timescales. Here, we show that two retrotransposons, Shellder and Spoink, invaded the genomes of multiple species of the melanogaster subgroup within the last 50 years. Through horizontal transfer, Spoink spread in D. melanogaster during the 1980s, while both Shellder and Spoink invaded D. simulans in the 1990s. Possibly following hybridization, D. simulans infected the island endemic species D. mauritiana (Mauritius) and D. sechellia (Seychelles) with both TEs after 1995. In the same approximate time-frame, Shellder also invaded D. teissieri, a species confined to sub-Saharan Africa. We find that the donors of Shellder and Spoink are likely American Drosophila species from the willistoni, cardini, and repleta groups. Thus, the described cascade of TE invasions could only become feasible after D. melanogaster and D. simulans extended their distributions into the Americas 200 years ago, likely aided by human activity. Our work reveals that cascades of TE invasions, likely initiated by human-mediated range expansions, could have an impact on the genomic and phenotypic evolution of geographically dispersed species. Within a few decades, TEs could invade many species, including island endemics, with distributions very distant from the donor of the TE.},
}
@article {pmid39788725,
year = {2025},
author = {Robinson, LR and McDevitt, CJ and Regan, MR and Quail, SL and Wadsworth, CB},
title = {In vitro evolution of ciprofloxacin resistance in Neisseria commensals and derived mutation population dynamics in natural Neisseria populations.},
journal = {FEMS microbiology letters},
volume = {372},
number = {},
pages = {},
pmid = {39788725},
issn = {1574-6968},
support = {R15 AI174182/AI/NIAID NIH HHS/United States ; /GM/NIGMS NIH HHS/United States ; R15AI174182/NH/NIH HHS/United States ; SAMN41424178//SRA/ ; },
mesh = {*Ciprofloxacin/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Mutation ; *Neisseria/genetics/drug effects ; Humans ; Microbial Sensitivity Tests ; DNA Gyrase/genetics ; Evolution, Molecular ; DNA Topoisomerase IV/genetics ; Bacterial Proteins/genetics ; },
abstract = {Commensal Neisseria are members of a healthy human oropharyngeal microbiome; however, they also serve as a reservoir of antimicrobial resistance for their pathogenic relatives. Despite their known importance as sources of novel genetic variation for pathogens, we still do not understand the full suite of resistance mutations commensal species can harbor. Here, we use in vitro selection to assess the mutations that emerge in response to ciprofloxacin selection in commensal Neisseria by passaging four replicates of four different species in the presence of a selective antibiotic gradient for 20 days; then categorized derived mutations with whole genome sequencing. Ten out of sixteen selected cells lines across the four species evolved ciprofloxacin resistance (≥1 ug/ml); with resistance-contributing mutations primarily emerging in DNA gyrase subunit A and B (gyrA and gyrB), topoisomerase IV subunits C and E (parC and parE), and the multiple transferable efflux pump repressor (mtrR). Of note, these derived mutations appeared in the same loci responsible for ciprofloxacin-reduced susceptibility in the pathogenic Neisseria, suggesting conserved mechanisms of resistance across the genus. Additionally, we tested for zoliflodacin cross-resistance in evolved strain lines and found 6 lineages with elevated zoliflodacin minimum inhibitory concentrations. Finally, to interrogate the likelihood of experimentally derived mutations emerging and contributing to resistance in natural Neisseria, we used a population-based approach and identified GyrA 91I as a substitution circulating within commensal Neisseria populations and ParC 85C in a single gonococcal isolate. A small cluster of gonococcal isolates shared commensal alleles at parE, suggesting recent cross-species recombination events.},
}
@article {pmid39787839,
year = {2025},
author = {Zhao, W and Hou, Y and Wei, L and Wei, W and Zhang, K and Duan, H and Ni, BJ},
title = {Chlorination-induced spread of antibiotic resistance genes in drinking water systems.},
journal = {Water research},
volume = {274},
number = {},
pages = {123092},
doi = {10.1016/j.watres.2025.123092},
pmid = {39787839},
issn = {1879-2448},
mesh = {*Drinking Water/microbiology ; *Halogenation ; *Drug Resistance, Microbial/genetics ; Water Purification ; Disinfection ; Chlorine ; },
abstract = {Chlorine, the most widely utilized disinfectant for drinking water globally, has recently been implicated in facilitating the spread of antibiotic resistance genes (ARGs), raising concerns about its underestimated environmental and ecological risks. However, given the current fragmented research focus and results, a comprehensive understanding of the potential mechanisms and influencing factors behind chlorination-promoted ARGs transmission in drinking water systems is crucial. This work is the first to systematically review the variations in abundance, transmission mechanisms, influencing factors, and mitigation strategies related to ARGs during the chlorination process. The results indicated that chlorination could induce genetic mutations and promote horizontal gene transfer through multiple pathways, including increased reactive oxygen species, enhanced membrane permeability, stimulation of the SOS response, and activation of efflux pumps. In addition, this work delves into significant discoveries regarding the factors affecting ARG transmission in drinking water, such as chlorine concentration, reaction time, disinfection byproducts, pipe materials, biofilms, and the water matrix. A series of effective strategies from water source to point-of-use were proposed aimed at mitigating ARGs transmission risks in the drinking water system. Finally, we address existing challenges and outline future research directions to overcome these bottlenecks. Overall, this review aims to advance our understanding of the role of chlorination in the dissemination of ARGs and to inspire innovative research ideas for optimizing disinfection techniques, minimizing the risks of antibiotic resistance transmission, and enhancing the safety of drinking water.},
}
@article {pmid39786570,
year = {2025},
author = {Chen, J and Garfinkel, DJ and Bergman, CM},
title = {Horizontal Transfer and Recombination Fuel Ty4 Retrotransposon Evolution in Saccharomyces.},
journal = {Genome biology and evolution},
volume = {17},
number = {1},
pages = {},
pmid = {39786570},
issn = {1759-6653},
support = {R01 GM124216/GM/NIGMS NIH HHS/United States ; R01GM124216/NH/NIH HHS/United States ; //University of Georgia Research Foundation/ ; },
mesh = {*Retroelements ; *Gene Transfer, Horizontal ; *Saccharomyces/genetics ; *Evolution, Molecular ; *Recombination, Genetic ; Phylogeny ; Genome, Fungal ; Saccharomyces cerevisiae/genetics ; },
abstract = {Horizontal transposon transfer (HTT) plays an important role in the evolution of eukaryotic genomes; however, the detailed evolutionary history and impact of most HTT events remain to be elucidated. To better understand the process of HTT in closely related microbial eukaryotes, we studied Ty4 retrotransposon subfamily content and sequence evolution across the genus Saccharomyces using short- and long-read whole genome sequence data, including new PacBio genome assemblies for two Saccharomyces mikatae strains. We find evidence for multiple independent HTT events introducing the Tsu4 subfamily into specific lineages of Saccharomyces paradoxus, Saccharomyces cerevisiae, Saccharomyces eubayanus, Saccharomyces kudriavzevii and the ancestor of the S. mikatae/Saccharomyces jurei species pair. In both S. mikatae and S. kudriavzevii, we identified novel Ty4 clades that were independently generated through recombination between resident and horizontally transferred subfamilies. Our results reveal that recurrent HTT and lineage-specific extinction events lead to a complex pattern of Ty4 subfamily content across the genus Saccharomyces. Moreover, our results demonstrate how HTT can lead to coexistence of related retrotransposon subfamilies in the same genome that can fuel evolution of new retrotransposon clades via recombination.},
}
@article {pmid39780077,
year = {2025},
author = {Lv, C and Abdullah, M and Su, CL and Chen, W and Zhou, N and Cheng, Z and Chen, Y and Li, M and Simpson, KW and Elsaadi, A and Zhu, Y and Lipkin, SM and Chang, YF},
title = {Genomic characterization of Escherichia coli with a polyketide synthase (pks) island isolated from ulcerative colitis patients.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {19},
pmid = {39780077},
issn = {1471-2164},
mesh = {Humans ; *Polyketide Synthases/genetics ; *Colitis, Ulcerative/microbiology/genetics ; *Escherichia coli/genetics/isolation &amp; purification ; *Phylogeny ; *Genomic Islands ; Genome, Bacterial ; Genomics ; Gene Transfer, Horizontal ; Virulence Factors/genetics ; Escherichia coli Infections/microbiology ; Peptides ; Polyketides ; },
abstract = {The E. coli strains harboring the polyketide synthase (pks) island encode the genotoxin colibactin, a secondary metabolite reported to have severe implications for human health and for the progression of colorectal cancer. The present study involves whole-genome-wide comparison and phylogenetic analysis of pks harboring E. coli isolates to gain insight into the distribution and evolution of these organisms. Fifteen E. coli strains isolated from patients with ulcerative colitis (UC) were sequenced, 13 of which harbored pks islands. In addition, 2,654 genomes from the public database were also screened for pks harboring E. coli genomes, 158 of which were pks-positive (pks[+]) isolates. Whole-genome-wide comparison and phylogenetic analysis revealed that 171 (158 + 13) pks[+] isolates belonged to phylogroup B2, and most of the isolates belong to sequence types ST73 and ST95. One isolate from a UC patient was of the sequence type ST8303. The maximum likelihood tree based on the core genome of pks[+] isolates revealed horizontal gene transfer across sequence types and serotypes. Virulome and resistome analyses revealed the0020preponderance of virulence genes and a reduced number of antimicrobial genes in pks[+] isolates. This study significantly contributes to understanding the evolution of pks islands in E. coli.},
}
@article {pmid39778056,
year = {2025},
author = {Silva, JK and Hervé, V and Mies, US and Platt, K and Brune, A},
title = {A Novel Lineage of Endosymbiotic Actinomycetales: Genome Reduction and Acquisition of New Functions in Bifidobacteriaceae Associated With Termite Gut Flagellates.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70010},
pmid = {39778056},
issn = {1462-2920},
support = {//Max-Planck-Gesellschaft/ ; },
mesh = {*Symbiosis ; Animals ; *Isoptera/microbiology ; *Genome, Bacterial ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Actinomycetales/genetics/metabolism ; Gene Transfer, Horizontal ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/parasitology ; Metagenome ; },
abstract = {Cellulolytic flagellates are essential for the symbiotic digestion of lignocellulose in the gut of lower termites. Most species are associated with host-specific consortia of bacterial symbionts from various phyla. 16S rRNA-based diversity studies and taxon-specific fluorescence in situ hybridization revealed a termite-specific clade of Actinomycetales that colonise the cytoplasm of Trichonympha spp. and other gut flagellates, representing the only known case of intracellular Actinomycetota in protists. Comparative analysis of eleven metagenome-assembled genomes from lower termites allowed us to describe them as new genera of Bifidobacteriaceae. Like the previously investigated Candidatus Ancillula trichonymphae, they ferment sugars via the bifidobacterium shunt but, unlike their free-living relatives, experienced significant genome erosion. Additionally, they acquired new functions by horizontal gene transfer from other gut bacteria, including the capacity to produce hydrogen. Members of the genus Ancillula (average genome size 1.56 ± 0.2 Mbp) retained most pathways for the synthesis of amino acids, including a threonine/serine exporter, providing concrete evidence for the basis of the mutualistic relationship with their host. By contrast, Opitulatrix species (1.23 ± 0.1 Mbp) lost most of their biosynthetic capacities, indicating that an originally mutualistic symbiosis is on the decline.},
}
@article {pmid39777960,
year = {2025},
author = {Perez, MF and Angelov, A and Übelacker, M and Torres Tejerizo, GA and Farias, ME and Liebl, W and Dib, JR},
title = {Linear Plasmids in Micrococcus: Insights Into a Common Ancestor and Transfer by Conjugation.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70020},
pmid = {39777960},
issn = {1462-2920},
support = {PICT 2018 N&#xb0; 2545 PRESTAMO BID//Agencia Nacional de Promoci&#xf3;n de la Investigaci&#xf3;n, el Desarrollo Tecnol&#xf3;gico y la Innovaci&#xf3;n/ ; PIUNT A618/2//Universidad Nacional de Tucum&#xe1;n/ ; },
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Micrococcus/genetics ; *Conjugation, Genetic ; Evolution, Molecular ; Phylogeny ; Open Reading Frames ; DNA, Bacterial/genetics ; Base Composition ; },
abstract = {Actinobacteria have frequently been reported in the Andean Puna, including strains of the genus Micrococcus. These strains demonstrate resistance to high levels of UV radiation, arsenic, and multiple antibiotics, and possess large linear plasmids. A comparative analysis of the sequences and putative functions of these plasmids was conducted. The presence of large regions with high sequence identity (exceeding 30 kb in total) in all three studied Micrococcus megaplasmids indicates a clear evolutionary link among these elements. Genes related to essential plasmid functions were primarily found within these conserved regions, while genes associated with resistance to metals and antibiotics resided in accessory regions. Moreover, the abundance of open reading frames related to transposition and recombination, along with local deviations from the average GC content, provides evidence for the mosaic nature and considerable genetic plasticity of these plasmids. This study presents evidence of a common ancestor for linear plasmids in Micrococcus and suggests that horizontal gene transfer likely occurs frequently within Andean lakes, providing the native microbial community with a beneficial gene pool to withstand extreme conditions. Additionally, the successful transfer of the linear plasmid pLMA1 by a DNase-insensitive, conjugation-type mechanism and its potential use as a genetic vector is demonstrated.},
}
@article {pmid39777461,
year = {2025},
author = {Blanchais, C and Pages, C and Campos, M and Boubekeur, K and Contarin, R and Orlando, M and Siguier, P and Laaberki, MH and Cornet, F and Charpentier, X and Rousseau, P},
title = {Interplay between the Xer recombination system and the dissemination of antibioresistance in Acinetobacter baumannii.},
journal = {Nucleic acids research},
volume = {53},
number = {1},
pages = {},
pmid = {39777461},
issn = {1362-4962},
support = {//University of Toulouse III Paul Sabatier/ ; ANR-AAPG2021-InXS//Agence Nationale de la Recherche/ ; ANR-11-LABX-0048//LabEx Ecofect/ ; ANR-11-IDEX-0007//Universit&#xe9; de Lyon/ ; EQU202303016268//Fondation pour la Recherche M&#xe9;dicale/ ; ANR-AAPG2021-InXS//Agence Nationale de la Recherche/ ; },
mesh = {*Acinetobacter baumannii/genetics/drug effects ; *Plasmids/genetics ; *Recombination, Genetic ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Recombinases/metabolism/genetics ; Escherichia coli/genetics/drug effects ; },
abstract = {Antibiotic-resistant infections are a pressing clinical challenge. Plasmids are known to accelerate the emergence of resistance by facilitating horizontal gene transfer of antibiotic resistance genes between bacteria. We explore this question in Acinetobacter baumannii, a globally emerging nosocomial pathogen responsible for a wide range of infections with a worrying accumulation of resistance, particularly involving plasmids. In this species, plasmids of the Rep_3 family harbor antibiotic resistance genes within variable regions flanked by potential site-specific recombination sites recognized by the XerCD recombinase. We first show that the Xer system of A. baumannii functions as described in Escherichia coli, resolving chromosome dimers at the dif site and recombining plasmid-carried sites. However, the multiple Xer recombination sites found in Rep_3 plasmids do not allow excision of plasmid fragments. Rather, they recombine to cointegrate plasmids, which could then evolve to exchange genes. Cointegrates represent a significant fraction of the plasmid population and their formation is controlled by the sequence of recombination sites, which determines the compatibility between recombination sites. We conclude that plasmids in A. baumannii frequently recombine by Xer recombination, allowing a high level of yet controlled plasticity in the acquisition and combination of antibiotic resistance genes.},
}
@article {pmid39776180,
year = {2025},
author = {Shimuta, K and Ohama, Y and Ito, S and Hoshina, S and Takahashi, H and Igawa, G and Dorin Yamamoto, M and Akeda, Y and Ohnishi, M},
title = {Emergence of ceftriaxone-resistant Neisseria gonorrhoeae through horizontal gene transfer among Neisseria spp.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf008},
pmid = {39776180},
issn = {1537-6613},
abstract = {OBJECTIVES: It has been suggested that the emergence of ceftriaxone-resistant strains of Neisseria gonorrhoeae involves the incorporation of the penA gene from commensal Neisseria spp. that are resistant to ceftriaxone. However, the mechanism of this mosaic penA generation is unknown.<br><br>METHODS: We obtained 10 strains of commensal Neisseria spp. showing ceftriaxone MIC >0.5 mg/L. The similarity of the penA gene region of these commensal Neisseria spp. strains and some ceftriaxone-resistant N. gonorrhoeae strains was investigated. To obtain transformants, commensal Neisseria spp., Neisseria lactamica, gDNA was used as donor DNA and a N. gonorrhoeae strain as the recipient.<br><br>RESULTS: The sequence similarity in certain regions of penA-murE between some of the commensal Neisseria spp. strains and the N. gonorrhoeae FC428 strain was very high. The sequence of these regions was very similar among some ceftriaxone-resistant strains of Neisseria spp. The PenA of the transformants matched the full PenA 60 of the original FC428 strain. Furthermore, our findings indicated that the source of resistance could have been a penA fragment derived from Neisseria spp. that originally carried the same sequence.<br><br>CONCLUSIONS: We suggest that FC428 developed ceftriaxone resistance by acquiring part of the penA-murE gene region from N. lactamica through horizontal gene transfer. The ceftriaxone-resistant N. lactamica shown here may also have emerged by acquiring part of penA from other Neisseria spp. From this work, our data provide insights into the understanding of the mechanism underlying the evolution of drug-resistant gonorrhea-causing strains.},
}
@article {pmid39772912,
year = {2025},
author = {Figueroa, D and Ruiz, D and Tellini, N and De Chiara, M and Kessi-Pérez, EI and Martínez, C and Liti, G and Querol, A and Guillamón, JM and Salinas, F},
title = {Optogenetic control of horizontally acquired genes prevent stuck fermentations in yeast.},
journal = {Microbiology spectrum},
volume = {13},
number = {2},
pages = {e0179424},
pmid = {39772912},
issn = {2165-0497},
support = {1210955//ANID | Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico (FONDECYT)/ ; 11220533//ANID | Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico (FONDECYT)/ ; 1201104//ANID | Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico (FONDECYT)/ ; ID24I10027//ANID | Fondo de Fomento al Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico (FONDEF)/ ; ID21I10198//ANID | Fondo de Fomento al Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico (FONDEF)/ ; ICN17_022//Agencia Nacional de Investigaci&#xf3;n y Desarrollo (ANID)/ ; 21200745//Agencia Nacional de Investigaci&#xf3;n y Desarrollo (ANID)/ ; },
mesh = {*Fermentation/genetics ; *Saccharomyces cerevisiae/genetics/metabolism ; Wine/microbiology ; *Optogenetics/methods ; Nitrogen/metabolism ; *Gene Transfer, Horizontal ; Gene Expression Regulation, Fungal ; Vitis/microbiology ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; },
abstract = {Nitrogen limitations in the grape must be the main cause of stuck fermentations during the winemaking process. In Saccharomyces cerevisiae, a genetic segment known as region A, which harbors 12 protein-coding genes, was acquired horizontally from a phylogenetically distant yeast species. This region is mainly present in the genome of wine yeast strains, carrying genes that have been associated with nitrogen utilization. Despite the putative importance of region A in yeast fermentation, its contribution to the fermentative process is largely unknown. In this work, we used a wine yeast strain to evaluate the contribution of region A to the fermentation process. To do this, we first sequenced the genome of the wine yeast strain using long-read sequencing and determined that region A is present in a single copy. We then implemented an optogenetic system in this wine yeast strain to precisely regulate the expression of each gene, generating a collection of 12 strains that allow for light-activated gene expression. To evaluate the role of these genes during fermentation, we assayed this collection using microculture and fermentation experiments in synthetic must with varying amounts of nitrogen concentration. Our results show that changes in gene expression for genes within this region can impact growth parameters and fermentation rate. We additionally found that the expression of various genes in region A is necessary to complete the fermentation process and prevent stuck fermentations under low nitrogen conditions. Altogether, our optogenetics-based approach demonstrates the importance of region A in completing fermentation under nitrogen-limited conditions.IMPORTANCEStuck fermentations due to limited nitrogen availability in grape must represent one of the main problems in the winemaking industry. Nitrogen limitation in grape must reduces yeast biomass and fermentation rate, resulting in incomplete fermentations with high levels of residual sugar, undesired by-products, and microbiological instability. Here, we used an optogenetic approach to demonstrate that expression of genes within region A is necessary to complete fermentations under low nitrogen availability. Overall, our results suggest that region A is a genetic signature for adaptation to low nitrogen conditions.},
}
@article {pmid39771135,
year = {2024},
author = {Li, Z and Yuan, D},
title = {Metagenomic Analysis Reveals the Effects of Microplastics on Antibiotic Resistance Genes in Sludge Anaerobic Digestion.},
journal = {Toxics},
volume = {12},
number = {12},
pages = {},
pmid = {39771135},
issn = {2305-6304},
support = {No. 52170097//the National Natural Science Foundation of China/ ; },
abstract = {Sewage sludge is recognized as both a source and a reservoir for antibiotic resistance genes (ARGs). Within an anaerobic digestion (AD) system, the presence of microplastics (MPs) has been observed to potentially facilitate the proliferation of these ARGs. Understanding the influence of MPs on microbial behavior and horizontal gene transfer (HGT) within the AD system is crucial for effectively managing the dissemination of ARGs in the environment. This study utilized metagenomic approaches to analyze the dynamics of various types of ARGs and potential microbial mechanisms under exposure to MPs during the AD process. The findings indicated that MPs in the AD process can enhance the proliferation of ARGs, with the extent of this enhancement increasing with the dosage of MPs: polyethylene (PE), polyethylene terephthalate (PET), and polylactic acid (PLA) MPs increased the abundance of ARGs in the anaerobic digestion system by up to 29.90%, 18.64%, and 14.15%, respectively. Additionally, the presence of MPs increased the relative abundance of mobile genetic elements (MGEs) during the AD process. Network correlation analysis further revealed that plasmids represent the predominant category of MGEs involved in the HGT of ARGs. Propionibacterium and Alicycliphilus were identified as the primary potential hosts for these ARGs. The results of gene function annotation indicated that exposure to MPs led to an increased the relative abundance of genes related to the production of reactive oxygen species (ROS), alterations in membrane permeability, ATP synthesis, and the secretion of extracellular polymeric substances (EPS). These genes play crucial roles in influencing the HGT of ARGs.},
}
@article {pmid39770765,
year = {2024},
author = {Cangioli, L and Tabacchioni, S and Visca, A and Fiore, A and Aprea, G and Ambrosino, P and Ercole, E and Sørensen, S and Mengoni, A and Bevivino, A},
title = {Genome Insights into Beneficial Microbial Strains Composing SIMBA Microbial Consortia Applied as Biofertilizers for Maize, Wheat and Tomato.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770765},
issn = {2076-2607},
support = {862695//European Union's Horizon 2020/ ; },
abstract = {For the safe use of microbiome-based solutions in agriculture, the genome sequencing of strains composing the inoculum is mandatory to avoid the spread of virulence and multidrug resistance genes carried by them through horizontal gene transfer to other bacteria in the environment. Moreover, the annotated genomes can enable the design of specific primers to trace the inoculum into the soil and provide insights into the molecular and genetic mechanisms of plant growth promotion and biocontrol activity. In the present work, the genome sequences of some members of beneficial microbial consortia that have previously been tested in greenhouse and field trials as promising biofertilizers for maize, tomato and wheat crops have been determined. Strains belong to well-known plant-growth-promoting bacterial genera such as Bacillus, Burkholderia, Pseudomonas and Rahnella. The genome size of strains ranged from 4.5 to 7.5 Mbp, carrying many genes spanning from 4402 to 6697, and a GC content of 0.04% to 3.3%. The annotation of the genomes revealed the presence of genes that are implicated in functions related to antagonism, pathogenesis and other secondary metabolites possibly involved in plant growth promotion and gene clusters for protection against oxidative damage, confirming the plant-growth-promoting (PGP) activity of selected strains. All the target genomes were found to possess at least 3000 different PGP traits, belonging to the categories of nitrogen acquisition, colonization for plant-derived substrate usage, quorum sensing response for biofilm formation and, to a lesser extent, bacterial fitness and root colonization. No genes putatively involved in pathogenesis were identified. Overall, our study suggests the safe application of selected strains as "plant probiotics" for sustainable agriculture.},
}
@article {pmid39770663,
year = {2024},
author = {Ben Natan, M and Masasa, M and Shashar, N and Guttman, L},
title = {Antibiotic Resistance in Vibrio Bacteria Associated with Red Spotting Disease in Sea Urchin Tripneustes gratilla (Echinodermata).},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
pmid = {39770663},
issn = {2076-2607},
support = {3-0000-17701//The Israeli Ministry of Health/ ; },
abstract = {The red spotting disease harms sea urchins to the extent of mass mortality in the ocean and echinocultures, accompanied by environmental damage and economic losses. The current study emphasizes the antimicrobial resistance of three isolated bacteria, closely related to Vibrio harveyi, Vibrio owensii, and Vibrio fortis, associated with red spotting in the cultured sea urchin Tripneustes gratilla. In vitro trials examined the susceptibility of these bacterial isolates to various antibiotics. In addition, using an in silico examination, we revealed the arsenal of antimicrobial resistance genes in available genomes of various pathogenic Vibrio associated with diseases in sea urchins, fish, shellfish, and corals. These two approaches enabled the discussion of the similarities and differences between aquatic pathogenic Vibrio and their antibiotic resistance. Among them, we revealed a core resistance to tetracyclines and penams by the in vitro examined strains. At the same time, the in silico study also supported this core resistance by the presence of the adeF and CRP genes in the bacterial genomes. Nevertheless, variability and specific resistance were evident at the species and strain levels in the Vibrio bacteria and genomes. The in vitro trials highlighted the diverse resistance of the Vibrio harveyi-like isolate to all examined antibiotics, while the other two isolates were found susceptible to nitrofurantoin and sulfamethoxazole. The resistance of the Vibrio harveyi-like isolate could not have been obtained in the genome of the proposed relative of Vibrio harveyi VHJR7 that lacks the oqxA and oqxB genes, which enables such a resistance. A unique sensitivity of the Vibrio fortis-like isolate to erythromycin is proposed when compared to other isolated Vibrio and Vibrio genomes that seem capable of resisting this drug. According to the results, we propose nitrofurantoin or sulfamethoxazole for treating two of the red-spotting-associated isolates (Vibrio fortis and Vibrio owensii-like), but not Vibrio harveyi-like. We assume that a shared resistance to some antibiotics by Vibrios is gained by a horizontal gene transfer while previous exposures of a bacterial strain to a specific drug may induce the development of a unique resistance. Finally, we discuss the novel knowledge on antibiotic resistance in Vibrio from the current research in light of the potential risks when using drugs for disease control in aquaculture.},
}
@article {pmid39770308,
year = {2024},
author = {Islam, MM and Jung, DE and Shin, WS and Oh, MH},
title = {Colistin Resistance Mechanism and Management Strategies of Colistin-Resistant Acinetobacter baumannii Infections.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
pmid = {39770308},
issn = {2076-0817},
support = {Grant Nos. 2022R1F1A1071415 and NRF-RS-2023-00275307 and Grant No. 2019R1A6C1010033//National Research Foundation of Korea (NRF) funded by the Ministry of Education &amp; Basic Science Research Capacity Enhancement Project through Korea Basic Science Institute (National research Facilities and Equipment Center) grant funded by the Ministry o/ ; },
mesh = {*Acinetobacter baumannii/drug effects/genetics ; *Colistin/pharmacology/therapeutic use ; Humans ; *Acinetobacter Infections/drug therapy ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics/drug effects ; Drug Resistance, Bacterial/genetics/drug effects ; Animals ; },
abstract = {The emergence of antibiotic-resistant Acinetobacter baumannii (A. baumannii) is a pressing threat in clinical settings. Colistin is currently a widely used treatment for multidrug-resistant A. baumannii, serving as the last line of defense. However, reports of colistin-resistant strains of A. baumannii have emerged, underscoring the urgent need to develop alternative medications to combat these serious pathogens. To resist colistin, A. baumannii has developed several mechanisms. These include the loss of outer membrane lipopolysaccharides (LPSs) due to mutation of LPS biosynthetic genes, modification of lipid A (a constituent of LPSs) structure through the addition of phosphoethanolamine (PEtN) moieties to the lipid A component by overexpression of chromosomal pmrCAB operon genes and eptA gene, or acquisition of plasmid-encoded mcr genes through horizontal gene transfer. Other resistance mechanisms involve alterations of outer membrane permeability through porins, the expulsion of colistin by efflux pumps, and heteroresistance. In response to the rising threat of colistin-resistant A. baumannii, researchers have developed various treatment strategies, including antibiotic combination therapy, adjuvants to potentiate antibiotic activity, repurposing existing drugs, antimicrobial peptides, nanotechnology, photodynamic therapy, CRISPR/Cas, and phage therapy. While many of these strategies have shown promise in vitro and in vivo, further clinical trials are necessary to ensure their efficacy and widen their clinical applications. Ongoing research is essential for identifying the most effective therapeutic strategies to manage colistin-resistant A. baumannii. This review explores the genetic mechanisms underlying colistin resistance and assesses potential treatment options for this challenging pathogen.},
}
@article {pmid39766551,
year = {2024},
author = {Li, R and Dai, H and Wang, W and Peng, R and Yu, S and Zhang, X and Huo, ZY and Yuan, Q and Luo, Y},
title = {Local Electric Field-Incorporated In-Situ Copper Ions Eliminating Pathogens and Antibiotic Resistance Genes in Drinking Water.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
pmid = {39766551},
issn = {2079-6382},
support = {2022YFC3205400//National Key R&amp;D Program of China/ ; 42377436 &amp; 52200079//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND/OBJECTIVES: Pathogen inactivation and harmful gene destruction from water just before drinking is the last line of defense to protect people from waterborne diseases. However, commonly used disinfection methods, such as chlorination, ultraviolet irradiation, and membrane filtration, experience several challenges such as continuous chemical dosing, the spread of antibiotic resistance genes (ARGs), and intensive energy consumption.<br><br>METHODS: Here, we perform a simultaneous elimination of pathogens and ARGs in drinking water using local electric fields and in-situ generated trace copper ions (LEF-Cu) without external chemical dosing. A 100-&#x3bc;m thin copper wire placed in the center of a household water pipe can generate local electric fields and trace copper ions near its surface after an external low voltage is applied.<br><br>RESULTS: The local electric field rapidly damages the outer structure of microorganisms through electroporation, and the trace copper ions can effectively permeate the electroporated microorganisms, successfully damaging their nucleic acids. The LEF-Cu disinfection system achieved complete inactivation (>6 log removal) of Escherichia coli O157:H7, Pseudomonas aeruginosa PAO1, and bacteriophage MS2 in drinking water at 2 V for 2 min, with low energy consumption (10[-2] kWh/m[3]). Meanwhile, the system effectively damages both intracellular (0.54~0.64 log) and extracellular (0.5~1.09 log) ARGs and blocks horizontal gene transfer.<br><br>CONCLUSIONS: LEF-Cu disinfection holds promise for preventing horizontal gene transfer and providing safe drinking water for household applications.},
}
@article {pmid39766521,
year = {2024},
author = {de Andrade, FCC and Carvalho, MF and Figueiredo, AMS},
title = {Survival Strategies of Staphylococcus aureus: Adaptive Regulation of the Anti-Restriction Gene ardA-H1 Under Stress Conditions.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
pmid = {39766521},
issn = {2079-6382},
support = {443804/2018-4 and 307672/2019-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e tecnol&#xf3;gico (CNPq)/ ; E-26/210.875/2016, E-26/211.554/2019, E-26.200.952/2020, and E-26/203.941/2024//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa (FAPERJ)/ ; 001//Funda&#xe7;&#xe3;o Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; INV-007641/GATES/Bill &amp; Melinda Gates Foundation/United States ; },
abstract = {Background/Objective: The anti-restriction protein ArdA-H1, found in multiresistant Staphylococcus aureus (MRSA) strains from the ST239-SCCmecIII lineage, inhibits restriction-modification systems, fostering horizontal gene transfer (HGT) and supporting genetic adaptability and resistance. This study investigates the regulatory mechanisms controlling ardA-H1 expression in S. aureus under various stress conditions, including acidic pH, iron limitation, and vancomycin exposure, and explores the roles of the Agr quorum sensing system. Methods: The expression of ardA-H1 was analyzed in S. aureus strains exposed to environmental stressors using real-time quantitative reverse transcription PCR. Comparisons were made between Agr-functional and Agr-deficient strains. In addition, Agr inhibition was achieved using a heterologous Agr autoinducing peptide. Results: The Agr system upregulated ardA-H1 expression in acidic and iron-limited conditions. However, vancomycin induced ardA-H1 activation specifically in the Agr-deficient strain GV69, indicating that an alternative regulatory pathway controls ardA-H1 expression in the absence of agr. The vancomycin response in GV69 suggests that diminished quorum sensing may offer a survival advantage by promoting persistence and HGT-related adaptability. Conclusion: Overall, our findings provide new insights into the intricate relationships between quorum-sensing, stress responses, bacterial virulence, and genetic plasticity, enhancing our understanding of S. aureus adaptability in challenging environments.},
}
@article {pmid39765217,
year = {2025},
author = {Niault, T and van Houte, S and Westra, E and Swarts, DC},
title = {Evolution and ecology of anti-defence systems in phages and plasmids.},
journal = {Current biology : CB},
volume = {35},
number = {1},
pages = {R32-R44},
doi = {10.1016/j.cub.2024.11.033},
pmid = {39765217},
issn = {1879-0445},
mesh = {*Plasmids/genetics ; *Bacteriophages/genetics/physiology ; *Bacteria/virology/genetics ; Archaea/genetics/virology ; Evolution, Molecular ; Biological Evolution ; Interspersed Repetitive Sequences ; },
abstract = {Prokaryotes (Bacteria and Archaea) encode a highly diversified arsenal of defence systems that protect them against mobile genetic elements, such as phages and plasmids. In turn, mobile genetic elements encode anti-defence systems that allow them to escape the activity of these defence systems. This has resulted in an evolutionary arms race in which defence systems and anti-defence systems evolve and adapt continuously, driving intriguing innovation and enormous diversification on both sides. Over 150 prokaryotic defence systems have been identified to date. Anti-defence systems are known for only a subset of these, but more are being discovered at a steady rate. Despite an increasing understanding of the highly diverse molecular mechanisms of anti-defence systems, their diverse evolutionary origins, the selective pressures they are subjected to, and their ecological importance and implications often remain obscure. In this review, we describe the diverse strategies that phage and plasmid anti-defence systems employ to escape host defence systems. We explore the evolutionary origins of anti-defence systems and describe different factors that exert selective pressure, affecting their maintenance and diversification. We describe how, in turn, defence systems themselves evolved to act upon anti-defence mechanisms, thereby adding a new layer to the co-evolutionary battle between prokaryotes and their mobile genetic elements. We discuss how the continuous selective pressures found in dynamic microbial communities promote the retention and diversification of these anti-defence systems. Finally, we consider the ecological implications for both hosts and their mobile genetic elements, noting how the balance of defence and anti-defence strategies can shape microbial community composition, influence horizontal gene transfer, and impact ecosystem stability.},
}
@article {pmid39763003,
year = {2025},
author = {Feng, Y and Lu, X and Zhao, J and Li, H and Xu, J and Li, Z and Wang, M and Peng, Y and Tian, T and Yuan, G and Zhang, Y and Liu, J and Zhang, M and Zhu La, AT and Qu, G and Mu, Y and Guo, W and Wu, Y and Zhang, Y and Wang, D and Hu, Y and Kan, B},
title = {Regional antimicrobial resistance gene flow among the One Health sectors in China.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {3},
pmid = {39763003},
issn = {2049-2618},
support = {2022YFC2303900//National Key Research and Development Program of China/ ; 22193064//major projects of the National Natural Science Foundation of China/ ; },
mesh = {Humans ; China ; *Gene Transfer, Horizontal ; *One Health ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; *Anti-Bacterial Agents/pharmacology ; *Gene Flow ; Feces/microbiology ; Drug Resistance, Bacterial/genetics ; Food Microbiology ; Metagenomics/methods ; Genes, Bacterial/genetics ; },
abstract = {BACKGROUND: Antimicrobial resistance poses a significant threat to global health, with its spread intricately linked across human, animal, and environmental sectors. Revealing the antimicrobial resistance gene (ARG) flow among the One Health sectors is essential for better control of antimicrobial resistance.<br><br>RESULTS: In this study, we investigated regional ARG transmission among humans, food, and the environment in Dengfeng, Henan Province, China by combining large-scale metagenomic sequencing with culturing of resistant bacterial isolates in 592 samples. A total of 40 ARG types and 743 ARG subtypes were identified, with a predominance of multidrug resistance genes. Compared with microbes from human fecal samples, those from food and environmental samples showed a significantly higher load of ARGs. We revealed that dietary habits and occupational exposure significantly affect ARG abundance. Pseudomonadota, particularly Enterobacteriaceae, were identified as the main ARG carriers shaping the resistome. The resistome in food samples was found more affected by mobile genetic elements (MGEs), whereas in environmental samples, it was more associated with the microbial composition. We evidenced that horizontal gene transfer (HGT) mediated by plasmids and phages, together with strain transmission, particularly those associated with the Enterobacteriaceae members, drive regional ARG flow. Lifestyle, dietary habits, and occupational exposure are all correlated with ARG dissemination and flies and food are important potential sources of ARGs to humans. The widespread mobile carbapenemase gene, OXA-347, carried by non-Enterobacteriaceae bacteria in the human gut microbiota, requires particular attention. Finally, we showed that machine learning models based on microbiome profiles were effective in predicting the presence of carbapenem-resistant strains, suggesting a valuable approach for AMR surveillance.<br><br>CONCLUSIONS: Our study provides a full picture of regional ARG transmission among the One Health sectors in a county-level city in China, which facilitates a better understanding of the complex routes of ARG transmission and highlights new points of focus for AMR surveillance and control. Video Abstract.},
}
@article {pmid39760498,
year = {2025},
author = {Peirano, G and Pitout, JDD},
title = {Rapidly spreading Enterobacterales with OXA-48-like carbapenemases.},
journal = {Journal of clinical microbiology},
volume = {63},
number = {2},
pages = {e0151524},
pmid = {39760498},
issn = {1098-660X},
mesh = {*beta-Lactamases/genetics/metabolism ; Humans ; *Bacterial Proteins/genetics/metabolism ; *Enterobacteriaceae Infections/epidemiology/microbiology/transmission ; *Enterobacteriaceae/enzymology/genetics/isolation &amp; purification/drug effects ; Anti-Bacterial Agents/pharmacology ; Klebsiella pneumoniae/enzymology/genetics ; Escherichia coli/enzymology/genetics ; Plasmids ; Gene Transfer, Horizontal ; },
abstract = {Enterobacterales (mostly Klebsiella pneumoniae, Escherichia coli) with OXA-48-like carbapenemases (e.g., OXA-48, -181, -232, -244) are undermining the global efficiency of carbapenem therapy. In the Middle East, North Africa, and some European countries, OXA-48-like carbapenemases are the most common types of carbapenemases among Enterobacterales. Currently, OXA-48 is endemic in the Middle East, North Africa, Spain, France, and Belgium; OXA-181 is endemic in Sub-Saharan Africa and the Indian Subcontinent, while OXA-232 has been increasing in the Indian Subcontinent. European countries (e.g., Germany, Denmark, Switzerland, France) are experiencing community outbreaks with E. coli ST38 that produce OXA-244, and these strains have been introduced into Norwegian, Polish, and Czech hospitals. The global ascendancy of OXA-48-like genes is due to the combination of carbapenemases with horizontal spread through promiscuous plasmids (e.g., IncL, IncX3, ColE2) and vertical spread with certain high-risk multidrug-resistant clones (e.g., K. pneumoniae ST14, ST15, ST147, ST307; E. coli ST38, ST410). This is a powerful "gene survival strategy" that has assisted with the survival of OXA-48-like genes in different environments including the community setting. The laboratory diagnosis is complex; therefore, bacteria with "difficult to detect" variants (e.g., OXA-244, OXA-484) are likely underreported and are spreading silently "beneath the radar" in hospital and community settings. K. pneumoniae and E. coli with OXA-48-like carbapenemases are forces to be reckoned with.},
}
@article {pmid39756571,
year = {2025},
author = {Heneghan, PG and Salzberg, LI and Wolfe, KH},
title = {Zymocin-like killer toxin gene clusters in the nuclear genomes of filamentous fungi.},
journal = {Fungal genetics and biology : FG &amp; B},
volume = {176},
number = {},
pages = {103957},
doi = {10.1016/j.fgb.2024.103957},
pmid = {39756571},
issn = {1096-0937},
mesh = {*Multigene Family ; Phylogeny ; *Genome, Fungal ; *Mycotoxins/genetics ; Chitinases/genetics ; Fusarium/genetics ; *Ribonucleases/genetics ; Saccharomyces cerevisiae/genetics ; *Fungi/genetics ; Colletotrichum/genetics ; Killer Factors, Yeast ; },
abstract = {Zymocin-like killer toxins are anticodon nucleases secreted by some budding yeast species, which kill competitor yeasts by cleaving tRNA molecules. They are encoded by virus-like elements (VLEs), cytosolic linear DNA molecules that are also called killer plasmids. To date, toxins of this type have been found only in budding yeast species (Saccharomycotina). Here, we show that the nuclear genomes of many filamentous fungi (Pezizomycotina) contain small clusters of genes coding for a zymocin-like ribonuclease (γ-toxin), a chitinase (toxin α/β-subunit), and in some cases an immunity protein. The γ-toxins from Fusarium oxysporum and Colletotrichum siamense abolished growth when expressed intracellularly in S. cerevisiae. Phylogenetic analysis of glycoside hydrolase 18 (GH18) domains shows that the chitinase genes in the gene clusters are members of the previously described C-II subgroup of Pezizomycotina chitinases. We propose that the Pezizomycotina gene clusters originated by integration of a yeast-like VLE into the nuclear genome, but this event must have been ancient because (1) phylogenetically, the Pezizomycotina C-II chitinases and the Saccharomycotina VLE-encoded toxin α/β subunit chitinases are sister clades with neither of them nested inside the other, and (2) many of the Pezizomycotina toxin cluster genes contain introns, whereas VLEs do not. One of the toxin gene clusters in Fusarium graminearum is a locus that has previously been shown to be under diversifying selection in North American populations of this plant pathogen. We also show that two genera of agaric mushrooms (Basidiomycota) have acquired toxin gene clusters by horizontal transfers from different Pezizomycotina donors.},
}
@article {pmid39754881,
year = {2025},
author = {Li, X and Zhang, Z and Liu, H and Wen, H and Wang, Q},
title = {The fate of intracellular and extracellular antibiotic resistance genes during ultrafiltration-ultraviolet-chlorination in a full-scale wastewater treatment plant.},
journal = {Journal of hazardous materials},
volume = {486},
number = {},
pages = {137088},
doi = {10.1016/j.jhazmat.2024.137088},
pmid = {39754881},
issn = {1873-3336},
mesh = {*Ultraviolet Rays ; Halogenation ; Ultrafiltration ; *Wastewater/microbiology ; Disinfection/methods ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; *Water Purification/methods ; Waste Disposal, Fluid/methods ; },
abstract = {Effluent from wastewater treatment plants (WWTPs) is recognized as a significant source of antibiotic resistance genes (ARGs) in the environment. Advanced treatment processes such as ultrafiltration (UF), ultraviolet (UV) light disinfection, and chlorination have emerged as promising approaches for ARG removal. However, the efficacy of sequential disinfection processes, such as UF-UV-chlorination on intracellular (iARGs) and extracellular ARGs (eARGs), remains largely unknown. This study investigates the impact of this sequential disinfection process on the fate of iARGs, eARGs, and a crucial mobile genetic element (intI1) within a full-scale WWTP. Our findings revealed that the UF-UV-chlorination process effectively reduced the overall absolute abundance of detected ARGs in the effluent by 1.93 log, and intI1 by 0.86 log, compared to secondary effluent. The majority of these removals was achieved due to the UF and UV disinfection, while chlorination showed negligible impact on the absolute abundance of ARGs in the final effluent. Notably, five genera were identified as potential hosts for intI1 and eight iARGs, including aac(6')-Ib-cr, drfA1, sul1, sul2, ermB, mefA, tetA, and tetX, suggesting a high potential for horizontal gene transfer involving these ARGs. Overall, this study demonstrated that UF-UV-chlorination is a highly effective method for reducing ARGs in effluent from WWTPs.},
}
@article {pmid39752084,
year = {2025},
author = {Heiss, J and Huson, DH and Steel, M},
title = {Transformations to Simplify Phylogenetic Networks.},
journal = {Bulletin of mathematical biology},
volume = {87},
number = {2},
pages = {20},
pmid = {39752084},
issn = {1522-9602},
support = {23-UOC-003//Marsden Fund/ ; },
mesh = {*Phylogeny ; *Mathematical Concepts ; *Models, Genetic ; Biological Evolution ; Evolution, Molecular ; },
abstract = {The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or lateral gene transfer events between lineages, and so the history of life is more accurately described by a rooted phylogenetic network. Nevertheless, phylogenetic networks may be complex and difficult to interpret, so biologists sometimes prefer a tree that summarises the central tree-like trend of evolution. In this paper, we formally investigate methods for transforming an arbitrary phylogenetic network into a tree (on the same set of leaves) and ask which ones (if any) satisfy a simple consistency condition. This consistency condition states that if we add additional species into a phylogenetic network (without otherwise changing this original network) then transforming this enlarged network into a rooted phylogenetic tree induces the same tree on the original set of species as transforming the original network. We show that the LSA (lowest stable ancestor) tree method satisfies this consistency property, whereas several other commonly used methods (and a new one we introduce) do not. We also briefly consider transformations that convert arbitrary phylogenetic networks to another simpler class, namely normal networks.},
}
@article {pmid39750749,
year = {2025},
author = {Molari, M and Shaw, LP and Neher, RA},
title = {Quantifying the Evolutionary Dynamics of Structure and Content in Closely Related E. coli Genomes.},
journal = {Molecular biology and evolution},
volume = {42},
number = {1},
pages = {},
pmid = {39750749},
issn = {1537-1719},
support = {/WT_/Wellcome Trust/United Kingdom ; //Sir Henry Wellcome Postdoctoral Fellow/ ; 220422/Z/20/Z//Wellcome/ ; //University of Basel/ ; },
mesh = {*Escherichia coli/genetics ; *Evolution, Molecular ; *Genome, Bacterial ; Phylogeny ; Synteny ; },
abstract = {Bacterial genomes primarily diversify via gain, loss, and rearrangement of genetic material in their flexible accessory genome. Yet the dynamics of accessory genome evolution are very poorly understood, in contrast to the core genome where diversification is readily described by mutations and homologous recombination. Here, we tackle this problem for the case of very closely related genomes. We comprehensively describe genome evolution within n=222 genomes of Escherichia coli ST131, which likely shared a common ancestor around 100 years ago. After removing putative recombinant diversity, the total length of the phylogeny is 6,000 core genome substitutions. Within this diversity, we find 22 modifications to core genome synteny and estimate around 2,000 structural changes within the accessory genome, i.e. one structural change for every three core genome substitutions. Sixty-three percent of loci with structural diversity could be resolved into individual gain and loss events with 10-fold more gains than losses, demonstrating a dominance of gains due to insertion sequences and prophage integration. Our results suggest the majority of synteny changes and insertions in our dataset are likely deleterious and only persist for a short time before being removed by purifying selection.},
}
@article {pmid39749146,
year = {2024},
author = {Chaves, CRS and Salamandane, A and Vieira, EJF and Salamandane, C},
title = {Antibiotic Resistance in Fermented Foods Chain: Evaluating the Risks of Emergence of Enterococci as an Emerging Pathogen in Raw Milk Cheese.},
journal = {International journal of microbiology},
volume = {2024},
number = {},
pages = {2409270},
pmid = {39749146},
issn = {1687-918X},
abstract = {Fermented foods, particularly fermented dairy products, offer significant health benefits but also present serious concerns. Probiotic bacteria, such as lactic acid bacteria (LAB), found in these foods have been strongly linked to the selection and dissemination of antibiotic resistance genes (ARGs). This study aims to examine the potential risks associated with fermented foods, despite their importance in human nutrition, by analyzing the entire production chain from raw material acquisition to storage. Focusing on cheese production as a key fermented food, the study will investigate various aspects, including dairy farm management, milk acquisition, milk handling, and the application of good manufacturing practices (GMP) and good hygiene practices (GHP) in cheese production. The findings of this review highlight that ARGs found in LAB are similar to those observed in hygiene indicator bacteria like E. coli and pathogens like S. aureus. The deliberate use of antibiotics in dairy farms and the incorrect use of disinfectants in cheese factories contribute to the prevalence of antibiotic-resistant bacteria in cheeses. Cheese factories, with their high frequency of horizontal gene transfer, are environments where the microbiological diversity of raw milk can enhance ARG transfer. The interaction between the raw milk microbiota and other environmental microbiotas, facilitated by cross-contamination, increases metabolic communication between bacteria, further promoting ARG transfer. Understanding these bacterial and ARG interactions is crucial to ensure food safety for consumers.},
}
@article {pmid39747694,
year = {2025},
author = {Hsu, TY and Nzabarushimana, E and Wong, D and Luo, C and Beiko, RG and Langille, M and Huttenhower, C and Nguyen, LH and Franzosa, EA},
title = {Profiling lateral gene transfer events in the human microbiome using WAAFLE.},
journal = {Nature microbiology},
volume = {10},
number = {1},
pages = {94-111},
pmid = {39747694},
issn = {2058-5276},
support = {R24DK110499//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; K23DK125838//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; T32CA009001//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; Career Development Award//Crohn's and Colitis Foundation (Crohn's &amp; Colitis Foundation)/ ; T32 CA009001/CA/NCI NIH HHS/United States ; U54DE023798//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; Research Scholars Award//American Gastroenterological Association (AGA)/ ; },
mesh = {Humans ; *Gene Transfer, Horizontal ; *Microbiota/genetics ; Phylogeny ; Metagenome/genetics ; Algorithms ; *Bacteria/genetics/classification ; Metagenomics/methods ; *Computational Biology/methods ; },
abstract = {Lateral gene transfer (LGT), also known as horizontal gene transfer, facilitates genomic diversification in microbial populations. While previous work has surveyed LGT in human-associated microbial isolate genomes, the landscape of LGT arising in personal microbiomes is not well understood, as there are no widely adopted methods to characterize LGT from complex communities. Here we developed, benchmarked and validated a computational algorithm (WAAFLE or Workflow to Annotate Assemblies and Find LGT Events) to profile LGT from assembled metagenomes. WAAFLE prioritizes specificity while maintaining high sensitivity for intergenus LGT. Applying WAAFLE to >2,000 human metagenomes from diverse body sites, we identified >100,000 high-confidence previously uncharacterized LGT (~2 per microbial genome-equivalent). These were enriched for mobile elements, as well as restriction-modification functions associated with the destruction of foreign DNA. LGT frequency was influenced by biogeography, phylogenetic similarity of involved pairs (for example, Fusobacterium periodonticum and F. nucleatum) and donor abundance. These forces manifest as networks in which hub taxa donate unequally with phylogenetic neighbours. Our findings suggest that human microbiome LGT may be more ubiquitous than previously described.},
}
@article {pmid39742307,
year = {2024},
author = {Lian, ZH and Salam, N and Tan, S and Yuan, Y and Li, MM and Li, YX and Liu, ZT and Hu, CJ and Lv, AP and OuYang, YT and Lu, CY and Zhang, JY and Chen, Y and Chen, LB and Luo, ZH and Ma, B and Hua, ZS and Jiao, JY and Li, WJ and Liu, L},
title = {Metagenomic analysis sheds light on the mixotrophic lifestyle of bacterial phylum Zhuqueibacterota.},
journal = {iMeta},
volume = {3},
number = {6},
pages = {e249},
pmid = {39742307},
issn = {2770-596X},
abstract = {Zhuqueibacterota is a novel bacterial phylum proposed based on hot spring metagenomes and public metagenome-assembled genomes, classified within the Fibrobacterota-Chlorobiota-Bacteroidota superphylum. This globally distributed phylum consists of one class and five orders, with the majority of its members being facultative anaerobes. Notably, the order Zhuqueibacterales utilizes hydrogen as an electron donor for carbon fixation through the Calvin Benson Bassham cycle. Phylogenetic and metabolic analyses reveal the phylum's key role in the carbon cycle, with frequent horizontal gene transfer events influencing its evolutionary trajectory.},
}
@article {pmid39740178,
year = {2024},
author = {Zahir, A and Okorie, PA and Nwobasi, VN and David, EI and Nwankwegu, RO and Azi, F},
title = {Harnessing Microbial Signal Transduction Systems in Natural and Synthetic Consortia for Biotechnological Applications.},
journal = {Biotechnology and applied biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1002/bab.2707},
pmid = {39740178},
issn = {1470-8744},
abstract = {Signal transduction is crucial for communication and cellular response in microbial communities. Consortia rely on it for effective communication, responding to changing environmental conditions, establishing community structures, and performing collective behaviors. Microbial signal transduction can be through quorum sensing (QS), two-component signal transduction systems, biofilm formation, nutrient sensing, chemotaxis, horizontal gene transfer stress response, and so forth. The consortium uses small signaling molecules in QS to regulate gene expression and coordinate intercellular communication and behaviors. Biofilm formation allows cells to adhere and aggregate, promoting species interactions and environmental stress resistance. Chemotaxis enables directional movement toward or away from chemical gradients, promoting efficient resource utilization and community organization within the consortium. In recent years, synthetic microbial consortia have gained attention for their potential applications in biotechnology and bioremediation. Understanding signal transduction in natural and synthetic microbial consortia is important for gaining insights into community dynamics, evolution, and ecological function. It can provide strategies for biotechnological innovation for enhancing biosensors, biodegradation, bioenergy efficiency, and waste reduction. This review provides compelling insight that will advance our understanding of microbial signal transduction dynamics and its role in orchestrating microbial interactions, which facilitate coordination, cooperation, gene expression, resource allocation, and trigger specific responses that determine community success.},
}
@article {pmid39737801,
year = {2024},
author = {Singh, S and Selvakumar, S and Swaminathan, P},
title = {In silico targeting of AmpC beta-lactamases in Enterobacter cloacae: unveiling Piperenol B as a potent antimicrobial lead.},
journal = {Journal of biomolecular structure &amp; dynamics},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/07391102.2024.2446661},
pmid = {39737801},
issn = {1538-0254},
abstract = {Antimicrobial Resistance poses a major threat to human health worldwide. Microorganisms develop multi-drug resistance due to intrinsic factors, evolutionary chromosomal alterations, and horizontal gene transfer. Enterobacter cloacae, a common nosocomial bacterium, can cause various infections and is classified as multidrug-resistant. This species produces AmpC enzymes, serine beta-lactamases that hydrolyze beta-lactam antibiotics by cleaving their beta-lactam ring, contributing to its resistance. Traditionally, many phytoconstituents have been used for their antibacterial properties against microorganisms. This study explores phytocompounds to mitigate the effects of beta-lactamase enzymes. In this study, we selected 12592 phytoconstituents with antibacterial properties from Dr. Duke's Ethnobotanical and Phytochemical Database for the virtual screening process. Initial hits were selected based on highest docking scores and then filtered using the ADMET property. Among these, a promising compound Piperenol B showed the highest docking score of -9.1 kcal/mol. A 240 ns molecular dynamics simulation showed that Piperenol B maintained stable conformation and showed consistent results in multiple runs with AmpC protein. Piperenol B complex had a binding free energy score of -61.75 ± 8.0 kJ/mol, whereas the known AmpC inhibitor Clavulanic acid showed -46.64 ± 3.2 kJ/mol. Non-covalent contacts in protein-ligand interactions and specific subunit interfaces were examined using the Protein Contacts Atlas. The STRING database was used to construct the Protein-Protein interaction for AmpC and its interacting proteins. The findings of this study suggested that Piperenol B could be an effective inhibitor of the targeted AmpC protein in Enterobacter cloacae which requires validation in in vitro studies.},
}
@article {pmid39736215,
year = {2025},
author = {Wang, Y and Ge, J and Xian, W and Tang, Z and Xue, B and Yu, J and Yao, YF and Liu, H and Qiu, J and Liu, X},
title = {Phosphorylation of the prokaryotic histone-like protein H-NS modulates bacterial virulence in Salmonella Typhimurium.},
journal = {Microbiological research},
volume = {292},
number = {},
pages = {128041},
doi = {10.1016/j.micres.2024.128041},
pmid = {39736215},
issn = {1618-0623},
mesh = {*Salmonella typhimurium/pathogenicity/genetics/metabolism ; Phosphorylation ; *Bacterial Proteins/metabolism/genetics ; Virulence/genetics ; Gene Expression Regulation, Bacterial ; *DNA-Binding Proteins/metabolism/genetics ; *Histones/metabolism ; Type III Secretion Systems/metabolism/genetics ; Humans ; Protein Processing, Post-Translational ; Salmonella Infections/microbiology ; },
abstract = {H-NS is a prokaryotic histone-like protein that binds to bacterial chromosomal DNA with important regulatory roles in gene expression. Unlike histone proteins, hitherto post-translational modifications of H-NS are still largely uncharacterized, especially in bacterial pathogens. Salmonella Typhimurium is a primary enteric pathogen and its virulence is mainly dependent on specialized type III secretion systems (T3SSs), which were evolutionarily acquired via horizontal gene transfer. Previous studies have shown that H-NS plays a critical role in silencing foreign T3SS genes. Here, we found that H-NS is phosphorylated at multiple residues in S. Typhimurium, including S45, Y61, S78, S84, T86, and T106. Notably, we demonstrated that phosphorylation of H-NS S78 promotes its dissociation from DNA via a mechanism dependent on dimer formation, thereby leading to transcriptional activation of target genes. Functionally, phosphoryl-H-NS contributes to the expression of T3SS-associated proteins and hence increases bacterial virulence during infection. Therefore, our study reveals a novel mechanism by which covalent modifications of prokaryotic histone-like proteins regulate bacterial virulence of an important human pathogen.},
}
@article {pmid39733752,
year = {2025},
author = {Feng, B and Chen, J and Wang, C and Wang, P and You, G and Lin, J and Gao, H},
title = {Removal of ofloxacin and inhibition of antibiotic resistance gene spread during the aerobic biofilm treatment of rural domestic sewage through the micro-nano aeration technology.},
journal = {Journal of hazardous materials},
volume = {486},
number = {},
pages = {137020},
doi = {10.1016/j.jhazmat.2024.137020},
pmid = {39733752},
issn = {1873-3336},
mesh = {*Biofilms ; *Ofloxacin/isolation &amp; purification/metabolism ; *Anti-Bacterial Agents ; *Sewage/microbiology ; *Water Pollutants, Chemical/metabolism ; Aerobiosis ; Biodegradation, Environmental ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; },
abstract = {Micro-nano aeration (MNA) has great potential for emerging contaminant removal. However, the mechanism of antibiotic removal and antibiotic resistance gene (ARG) spread, and the impact of the different aeration conditions remain unclear. This study investigated the adsorption and biodegradation of ofloxacin (OFL) and the spread of ARGs in aerobic biofilm systems under MNA and conventional aeration (CVA) conditions. Results showed that the MNA increased OFL removal by 17.27 %-40.54 % and decreased total ARG abundance by 36.37 %-54.98 %, compared with CVA. MNA-induced biofilm rough morphology, high zeta potential, and reduced extracellular polymeric substance (EPS) secretion enhanced OFL adsorption. High dissolved oxygen and temperature, induced by MNA-enriched aerobic bacteria and their carrying OFL-degrading genes, enhanced OFL biodegradation. MNA inhibited the enrichment of ARG host bacteria, which acquired ARGs possibly via horizontal gene transfer (HGT). Functional profiles involved in the HGT process, including reactive oxygen species production, membrane permeability, mobile genetic elements (MGEs), adenosine triphosphate synthesis, and EPS secretion, were down-regulated by MNA, inhibiting ARG spread. Partial least-squares path modeling revealed that MGEs might be the main factor inhibiting ARG spread. This study provides insights into the mechanisms by which MNA enhances antibiotic removal and inhibits ARG spread in aerobic biofilm systems.},
}
@article {pmid39733355,
year = {2024},
author = {Kumar, G and Balakrishna, K and Mukhopadhyay, C and Kalwaje Eshwara, V},
title = {Characterization and comparative analysis of antimicrobial resistance in Escherichia coli from hospital and municipal wastewater treatment plants.},
journal = {Journal of water and health},
volume = {22},
number = {12},
pages = {2276-2288},
pmid = {39733355},
issn = {1477-8920},
support = {Intramural Fund//Manipal Academy of Higher Education/ ; },
mesh = {*Escherichia coli/drug effects/genetics/isolation &amp; purification ; *Wastewater/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Integrons ; Hospitals ; Drug Resistance, Bacterial ; Waste Disposal, Fluid ; },
abstract = {The spread of antimicrobial resistance (AMR) poses global health threats, with wastewater treatment plants (WWTPs) as hotspots for its development. Horizontal gene transfer facilitates acquisition of resistance genes, particularly through integrons in Escherichia coli. Our study investigates E. coli isolates from hospital and municipal WWTPs, focusing on integrons, their temporal correlation and phenotypic and molecular characterization of AMR. Samples from hospital and municipal WWTPs were collected over two seasons, pre-monsoon (March-May) and post-monsoon (December-February). From the hospital (hWWTP) and municipal (mWWTP) influents, 45 and 172 E. coli isolates were obtained, respectively. E. coli from hWWTP exhibited significantly higher resistance rates than mWWTP to most tested antimicrobials except tetracycline. The hWWTP isolates showed a higher prevalence (86.7%) of multidrug resistance (MDR) compared with mWWTP (48.3%). The proportion of MDR isolates from mWWTP nearly doubled in the post-monsoon season. Integron positivity was 17.7% (hWWTP) and 19.7% (mWWTP) with common gene cassettes conferring resistance to trimethoprim and aminoglycosides. Phylogroup analysis showed a predominance of group A in hWWTP and group B1 in mWWTP. The study highlights the role of hospital and municipal wastewater in disseminating AMR, with high rates of MDR E. coli and class 1 integrons detected.},
}
@article {pmid39731890,
year = {2025},
author = {Zhang, Y and Zhu, D and Zhou, S and Gong, H and Dai, X},
title = {Antibiotic resistome during two-stage partial nitritation/anammox process for sludge anaerobic digestion reject water treatment.},
journal = {Journal of hazardous materials},
volume = {486},
number = {},
pages = {136967},
doi = {10.1016/j.jhazmat.2024.136967},
pmid = {39731890},
issn = {1873-3336},
mesh = {*Sewage/microbiology ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; *Water Purification/methods ; *Waste Disposal, Fluid/methods ; Genes, Bacterial ; Bioreactors ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Anaerobic digestion (AD) reject water serves as a significant reservoir for antibiotic resistance genes (ARGs), underscoring the importance of understanding ARGs dynamics during treatment processes. Partial nitritation /anammox (PN/A) has become an increasingly adopted process, while comprehensive investigation on ARG behavior within this system, especially in full-scale, remains limited. This study explores the distribution of ARGs in a full-scale two-stage PN/A system, with an anaerobic/anoxic/oxic (AAO) system for comparison. The sludge in partial nitritation (PN) stage exhibited higher ARG abundance (0.82 copy/cell) compared to that in anammox stage (0.21-0.26 copy/cell). In anammox sludge samples, 95.8-99.1 % of the mobile genetic elements (MGEs) were identified as tnpA, while the PN stage showing greater diversity. Some ARGs co-occur in the same contigs, and some of these ARGs belong to different ARGs types, which is related to multi-antibiotic resistance, with the highest frequency observed in the PN stage. The abundance of contigs with ARG-MGE co-occurrence, suggesting the possibility of horizontal gene transfer (HGT), was most prevalent in the AAO system. Potential ARG hosts were identified by metagenomic binning, and some functional bacteria, like Nitrosomonas, were regarded as ARGs host. This study offers a comprehensive analysis of the complexities of ARGs distribution within full-scale two-stage PN/A systems treating AD reject water.},
}
@article {pmid39731837,
year = {2025},
author = {Yang, R and Tang, J and Niu, J and Hou, B and Zhang, L},
title = {Dissemination mechanisms of unique antibiotic resistance genes from flowback water to soil revealed by combined Illumina and Nanopore sequencing.},
journal = {Water research},
volume = {273},
number = {},
pages = {123030},
doi = {10.1016/j.watres.2024.123030},
pmid = {39731837},
issn = {1879-2448},
mesh = {*Soil Microbiology ; *Drug Resistance, Microbial/genetics ; Soil/chemistry ; Nanopore Sequencing ; },
abstract = {As a byproduct of shale gas extraction, flowback water (FW) is produced in large quantities globally. Due to the unique interactions between pollutants and microorganisms, FW always harbor multiple antibiotic resistance genes (ARGs) that have been confirmed in our previous findings, potentially serving as a point source for ARGs released into the environment. However, whether ARGs in FW can disseminate or integrate into the environmental resistome remains unclear. In this study, unique ARGs from FW were identified, and the ARG profiles in soil and FW-spiked soil were compared using a combination of Illumina and Nanopore sequencing. The results indicated that the total abundance of the soil resistome increased by 30.8 % in soil contaminated with FW. Of this increase, 11.1 % was attributable to the integration of exogenous ARGs from FW into the soil resistome. Sequence alignment at the gene level further confirmed the successful integration of 20 unique ARG sequences classified as multidrug and vancomycin resistance genes into the soil resistome. These 20 ARG sequences were detected only in the FW. Multiple lines of evidence indicated that horizontal gene transfer dominated ARG dissemination in soil contaminated by FW. This conclusion is supported by the discrepancy between changes in mobile ARGs and host abundance, the upregulation of oxidative stress-related genes (SOD1 and SOD2) and the SOS response (lexA and recA), as well as the upregulation of genes related to quorum sensing (virD4, virB9, and virB3) and naked DNA uptake (pilD, pilT, and pilQ).},
}
@article {pmid39731060,
year = {2024},
author = {Shen, SP and Lin, HC and Chen, JF and Wang, HS and Huang, YY and Hsia, KC and Lin, JH and Kuo, YW and Li, CM and Hsu, YC and Tsai, SY and Ho, HH},
title = {Assessment of the safety and gut microbiota modulation ability of an infant formula containing Bifidobacterium animalis ssp. lactis CP-9 or Lactobacillus salivarius AP-32 and the effects of the formula on infant growth outcomes: insights from a four-month clinical study in infants under two months old.},
journal = {BMC pediatrics},
volume = {24},
number = {1},
pages = {840},
pmid = {39731060},
issn = {1471-2431},
mesh = {Humans ; *Infant Formula ; *Gastrointestinal Microbiome ; *Probiotics ; Infant ; Male ; Female ; *Bifidobacterium animalis ; *Ligilactobacillus salivarius ; Infant, Newborn ; Child Development ; Milk, Human/microbiology ; },
abstract = {BACKGROUND: Breast milk is a natural treasure for infants, and its microbiota contains a rich array of bacterial species. When breastfeeding is not possible, infant formula with probiotics can be used as a sole source or as a breast milk supplement. The main aim of this study was to evaluate the growth outcomes and tolerance of infants consuming an infant formula containing Bifidobacterium animalis ssp. lactis CP-9 (B. animalis CP-9) or Lactobacillus salivarius AP-32 (L. salivarius AP-32), which were isolated from breast milk and the guts of healthy infants. The safety of these strains in terms of antibiotic resistance and their ability to modulate the gut microbiota were also evaluated.<br><br>METHODS: One hundred eighty healthy infants were included in this study and separated into three groups: the control group, the L. salivarius AP-32 group, and the B. animalis CP-9 group. In this clinical study, adverse events, growth effects, and the incidence of allergies and gastrointestinal disorders in infants consuming infant formula containing B. animalis CP-9 or L. salivarius AP-32 were evaluated. Finally, the impact of the probiotic infant formula on the gut microbiota was elucidated via next-generation sequencing (NGS) analysis.<br><br>RESULTS: The 4-month interventional study revealed that body weight, recumbent length, and head circumference were similar among the three groups. No adverse events related to the intervention were observed. The microbiota composition was more diverse on day 0 and became more uniform by month 4. B. animalis CP-9 and L. salivarius AP-32 were found to be susceptible to streptomycin, tetracycline, erythromycin, clindamycin, chloramphenicol, and ampicillin.<br><br>CONCLUSIONS: The use of infant formula containing B. animalis CP-9 and L. salivarius AP-32 was considered safe and well tolerated, with no adverse events observed during the study. While these strains showed low antibiotic resistance and no immediate concerns related to antibiotic resistance genes, further research is needed to comprehensively assess their long-term safety and efficacy and the potential risk of horizontal gene transfer in broader contexts.<br><br>TRIAL REGISTRATION: The trial was registered with the US Library of Medicine (clinicaltrials.gov) with the number NCT03993301 on 20/06/2019.},
}
@article {pmid39730778,
year = {2025},
author = {Cotta, SR and Dias, ACF and Mendes, R and Andreote, FD},
title = {Role of horizontal gene transfer and cooperation in rhizosphere microbiome assembly.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {56},
number = {1},
pages = {225-236},
pmid = {39730778},
issn = {1678-4405},
support = {2018/24049-2//Fapesp/ ; 485116/2013-8//CNPq/ ; 405163/2018-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {*Gene Transfer, Horizontal ; *Rhizosphere ; *Microbiota/genetics ; *Soil Microbiology ; *Bacteria/genetics/metabolism/classification ; },
abstract = {Microbes employ a variety of mechanisms, encompassing chemical signaling (e.g., quorum-sensing molecules) and genetic processes like horizontal gene transfer (HGT), to engage in interactions. HGT, in particular, holds a pivotal role as it facilitates the generation of metabolic diversity, thus directly or indirectly influencing microorganisms' interactions and functioning within their habitat. In this study, we investigate the correlations between enhanced metabolic diversity through HGT and cooperative behavior in the rhizosphere. Despite the potential drawbacks of cooperative behavior, which renders it susceptible to exploitation by cheaters based on evolutionary theory, HGT emerges as a mitigating factor. It serves as a valuable and adaptive tool for survival in competitive environments, notably the rhizosphere. By initiating a comprehensive discussion on these processes combined, we anticipate achieving a profound understanding of the rhizosphere microbiome, ultimately enhancing soil microbiology management and the exploitation of this ecological niche.},
}
@article {pmid39729844,
year = {2025},
author = {Ku, H and Kelk, D and Bauer, DC and Sidhu, JPS},
title = {Phage-plasmid hybrids as vectors for antibiotic resistance in environmental Escherichia coli.},
journal = {The Science of the total environment},
volume = {959},
number = {},
pages = {178157},
doi = {10.1016/j.scitotenv.2024.178157},
pmid = {39729844},
issn = {1879-1026},
mesh = {*Escherichia coli/genetics/virology/drug effects ; *Plasmids/genetics ; *Bacteriophages/genetics ; Anti-Bacterial Agents ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Virulence Factors/genetics ; },
abstract = {This study investigated the potential role of phages in the dissemination of antimicrobial resistance genes (ARGs) and virulence factor genes (VFGs) in Escherichia coli (E. coli). A comprehensive in silico analysis of 18,410 phage sequences retrieved from the National Center for Biotechnology Information database (NCBI) revealed distinct carriage patterns for ARGs and VFGs between lytic, temperate, and chronic phage types. Notably, 57 temperate phages carried ARGs, particularly associated with multidrug and aminoglycoside resistance. Temperate phages (8.97 %, 635/7081) and chronic phages (8.09 %, 14/173) exhibited a significantly higher prevalence of VFGs (Chi-Square, p ≤ 0.05), particularly associated with exotoxin-related genes, compared to lytic phages (0.05 %, 6/11,156). This underscores the role phages play as reservoirs and potential vectors for the dissemination of ARGs and VFGs in bacteria. Our environmental E. coli isolates (n = 60) were found to carry 179 intact prophages containing polymyxin, macrolide, tetracycline, and multidrug resistance genes as well as various VFGs. This study documents the presence of phage-plasmids (P-Ps) in environmental E. coli isolates, offering new insights into horizontal gene transfer (HGT) mechanisms. Notably, the blaCTX-M-15 gene, associated with beta-lactam resistance, was identified in two P-Ps, suggesting a potentially novel route for the dissemination of beta-lactam resistance. The diverse replicon types observed in P-Ps suggest a broader integration capacity compared to traditional plasmids, potentially enabling the blaCTX-M-15 gene dissemination across diverse bacterial species. This study provides valuable insights into the multifaceted role of phages in shaping the antimicrobial resistance landscape. Further research is necessary to fully understand the intricate mechanisms underlying phage-mediated ARG and VFG dissemination.},
}
@article {pmid39729729,
year = {2025},
author = {Wang, M and Yao, Y and Yang, Y and Zhu, D and Wang, M and Jia, R and Chen, S and Zhao, X and Yang, Q and Wu, Y and Zhang, S and Huang, J and Ou, X and Tian, B and Sun, D and Zhang, L and Yu, Y and He, Y and Wu, Z and Cheng, A and Liu, M},
title = {The characterization of outer membrane vesicles (OMVs) and their role in mediating antibiotic-resistance gene transfer through natural transformation in Riemerella anatipestifer.},
journal = {Poultry science},
volume = {104},
number = {2},
pages = {104730},
pmid = {39729729},
issn = {1525-3171},
mesh = {*Riemerella/genetics/drug effects/physiology ; *Gene Transfer, Horizontal ; Poultry Diseases/microbiology ; Animals ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Ducks ; Flavobacteriaceae Infections/veterinary/microbiology ; },
abstract = {Riemerella anatipestifer (R. anatipestifer, RA) is the etiological agent of duck serositis, an acute multisystemic disease in ducks that is globally distributed and causes serious economic losses in the duck industry. Despite exhibiting multidrug resistance, the transmission mechanism of its antibiotic resistance genes (ARGs) remains incompletely identified. To contribute to addressing this gap, in this study, outer membrane vesicles (OMVs) from the RA strain CH-1 were isolated and characterized to investigate their involvement in ARG transfer in RA. Sequencing and data analysis revealed that RA CH-1 OMVs had ∼2.04 Mb genomic size, representing 88.3 % of the RA CH-1 genomic length. Proteomic analysis showed that OMVs contained 577 proteins, representing 27.2 % of the bacterial proteins. Subsequent investigations demonstrated that OMVs from antibiotic-resistant strains transferred ARG fragments and plasmids to the sensitive strain RA ATCC11845, relying on the natural transformation system, and the transformants exhibited corresponding resistance. Overall, OMV-mediated horizontal transfer of ARGs serving as a significant mechanism for acquiring multiple resistance genes in R. anatipestifer.},
}
@article {pmid39729001,
year = {2024},
author = {Elbir, H},
title = {Updating the Relationship Between the Threshold Value of Average Nucleotide Identity and Digital DNA-DNA Hybridization for Reliable Taxonomy of Corynebacterium.},
journal = {Veterinary sciences},
volume = {11},
number = {12},
pages = {},
pmid = {39729001},
issn = {2306-7381},
abstract = {Currently, bacterial classification at the species level relies on the 95-96% average nucleotide identity (ANI) value that is known to be equivalent to a 70% digital DNA-DNA hybridization (dDDH) value. However, during the routine identification of bacteria in the uteri of camels with a history of conception failure, we found that four out of the seven strains (2298A, 2569A, 2652, 2571B, 1103A, 2571A, and 335C) could not be assigned to any valid Corynebacterium species. Furthermore, a 70% dDDH value did not correspond to a 95-96% ANI value in strain 2569A. Thus, we aimed to classify these strains and explain the mechanisms underlying gene repertoire diversity and the disagreement we found between the ANI and dDDH cutoff values. For this study, we extracted information from the genomes of 150 Corynebacterium-type species and seven sequenced genomes of uterine Corynebacterium isolates. We found that the 96.67% OrthoANI value should be used in place of the generally accepted 95-96% ANI threshold in order to obtain an equivalent 70% dDDH value. Phylogenomic analysis determined the evolutionary position of each uterine strain. Then, strains 2652 and 2571B were classified as C. camporealensis based on the ANI value (98.44% and 98.72%) and dDDH value (85.8% and 88.5%). Strain 2569A had a 96.58% ANI and a 69.4% dDDH value and was classified as C. urogenitale. The strains 335C, 1103A, 2571A, and 2298A were classified as novel Corynebacterium based on the ANI value (77.12, 94.01%, 94.26%, and 94.03%) and dDDH value (21.3%, 54.1%, 54.9%, and 51.3%), respectively. Genes for menaquinone biosynthesis and the saturation of chains were detected in uterine strains and their closely related type strains. Gene gain predominates as a source of variation in the gene repertoire. Most of these genes are gained by horizontal gene transfer, driven by genomic islands and prophage. In summary, we refined the ANI cutoff value for an accurate diagnosis of Corynebacterium. Moreover, we clarified the mechanism underlying the diversity of the gene repertoire and expanded the number of Corynebacterium species isolated from the camel uterus.},
}
@article {pmid39727166,
year = {2025},
author = {},
title = {Correction to 'GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome'.},
journal = {Nucleic acids research},
volume = {53},
number = {1},
pages = {},
doi = {10.1093/nar/gkae1307},
pmid = {39727166},
issn = {1362-4962},
}
@article {pmid39727139,
year = {2024},
author = {Wang, Q and Qiu, JH and Sun, Y and Ni, N and Sun, SJ and Li, XL and Yang, SJ and Liu, YR and Cui, YY},
title = {[Research progress on the effect of estuary microplastics on antibiotic resistance genes].},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {35},
number = {10},
pages = {2916-2924},
doi = {10.13287/j.1001-9332.202410.028},
pmid = {39727139},
issn = {1001-9332},
mesh = {*Microplastics ; *Water Pollutants, Chemical/analysis ; *Estuaries ; Biofilms/drug effects/growth &amp; development ; Drug Resistance, Microbial/genetics ; Environmental Monitoring ; Gene Transfer, Horizontal ; },
abstract = {Estuaries are transitional zones between rivers and marine environments, with intensive human activities. Pollutants pose a threat to the ecological systems of estuaries. Among these pollutants, microplastics and antibiotic resistant genes have gained significant attention due to their potential impacts on estuarine organisms and human health. Microplastics can form unique biofilms, adsorb pollutants from the surrounding environment, and provide potential hosts for antibiotic resistant genes, with positive consequence on horizontal gene transfer of antibiotic resistance. We provided an overview of the pollution status of microplastics and antibiotic resistant genes in estua-rine areas, with a particular emphasis on the influence of biofilms formed on microplastics on the enrichment, transport, and transfer of antibiotic resistant genes. We also highlighted the limitations in current research, regarding microplastic sampling, analysis methods, and inconsistent reporting units. Furthermore, we proposed prospects for the biodegradation of microplastics and potential risk assessment of microplastic biofilms.},
}
@article {pmid39725890,
year = {2024},
author = {Javier-López, R and Geliashvili, N and Birkeland, NK},
title = {Comparative genomics of Fervidobacterium: a new phylogenomic landscape of these wide-spread thermophilic anaerobes.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1248},
pmid = {39725890},
issn = {1471-2164},
support = {328955//Norges Forskningsr&#xe5;d/ ; 328955//Norges Forskningsr&#xe5;d/ ; 862555//ERA-NET Cofund on Food Systems and Climate (FOSC)/ ; 862555//ERA-NET Cofund on Food Systems and Climate (FOSC)/ ; 862555//ERA-NET Cofund on Food Systems and Climate (FOSC)/ ; CPEA-LT-2017/10061//Norwegian Directorate for Higher Education and Skills/ ; CPEA-LT-2017/10061//Norwegian Directorate for Higher Education and Skills/ ; },
mesh = {*Phylogeny ; *Genome, Bacterial ; *Genomics ; RNA, Ribosomal, 16S/genetics ; Base Composition ; },
abstract = {BACKGROUND: Fervidobacterium is a genus of thermophilic anaerobic Gram-negative rod-shaped bacteria belonging to the phylum Thermotogota. They can grow through fermentation on a wide range of sugars and protein-rich substrates. Some can also break down feather keratin, which has significant biotechnological potential. Fervidobacteria genomes have undergone several horizontal gene transfer events, sharing DNA with unrelated microbial taxa. Despite increasing biotechnological and evolutionary interest in this genus, only seven species have been described to date. Here, we present and describe six new and complete Fervidobacterium genomes, including the type strains Fervidobacterium gondwanense CBS-1[ T], F. islandicum H-21[ T] and F. thailandense FC2004[T], one novel isolate from Georgia (strain GSH) and two strains (DSM 21710 and DSM 13770) that have not been previously described along with an evolutionary and phylogenomic analysis of the genus.<br><br>RESULTS: The complete genomes were around 2&#xa0;Mb with approximately 2,000 CDS identified and annotated in each of them and a G&#x2009;+&#x2009;C content ranging from 38.9&#xa0;mol% to 45.8&#xa0;mol%. Phylogenomic comparisons of all currently available Fervidobacterium genomes, including OrthoANI and TYGS analyses, as well as a phylogenetic analysis based on the 16S rRNA gene, identified six species and nine subspecies clusters across the genus, with a consistent topology and a distant and separately branching species, Fervidobacterium thailandense. F. thailandense harbored the highest number of transposases, CRISPR clusters, pseudo genes and horizontally transferred regions The pan genome of the genus showed that 44% of the genes belong to the cloud pangenome, with most of the singletons found also in F. thailandense.<br><br>CONCLUSIONS: The additional genome sequences described in this work and the comparison with all available Fervidobacterium genome sequences provided new insights into the evolutionary history of this genus and supported a phylogenetic reclassification. The phylogenomic results from OrthoANI and TYGS analyses revealed that F. riparium and F. gondwanense belong to the same genome species, and includes Fervidobacterium sp. 13770, while "F. pennivorans" strain DYC belongs to a separate genome species, whereas Fervidobacterium sp. 21710 and Fervidobacterium sp. GSH within the Fervidobacterium pennivorans clade represent two subspecies. F. changbaicum is reclassified as F. islandicum.},
}
@article {pmid39725200,
year = {2025},
author = {Song, M and Wang, K and Xie, Y and Wen, X and Tu, Y and Teng, T and Luo, C and Zhang, D},
title = {Impacts of anthropogenic disturbances on antibiotic resistomes in biological soil crusts on the Qinghai-Tibetan Plateau.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {367},
number = {},
pages = {125582},
doi = {10.1016/j.envpol.2024.125582},
pmid = {39725200},
issn = {1873-6424},
mesh = {*Soil Microbiology ; Tibet ; *Environmental Monitoring ; *Anti-Bacterial Agents ; *Drug Resistance, Microbial/genetics ; *Anthropogenic Effects ; Soil/chemistry ; China ; Humans ; },
abstract = {Biological soil crusts (BSCs) are the main landscape on the Qinghai-Tibetan Plateau and an ecological indicator of human disturbance. Information about antibiotic resistomes in BSCs on the Qinghai-Tibetan Plateau can provide baseline for the risk assessment and management of resistomes and yet to be explored. This work investigated the profiles and geographic patterns of antibiotic resistomes in BSCs along the Lhasa River and their response to anthropogenic activities for the first time. Various antibiotic resistance genes (ARGs) were widely distributed in BSCs, but had relatively lower detection frequency and abundance comparing to soils from human disturbed sites. ARGs profiles in BSCs were separated by altitude from 3860 to 3880 m, possibly attributing to the difference in anthropogenic activities. Above 3860 m, resistomes exhibited lower abundance including total ARGs, aadA, blaSFO and tnpA-04 owing to the rare human activities; at human disturbed sites with altitude <3860 m, the detection frequency and relative abundance of tetG02, oprJ, qacEdelta1-01, and ARGs with the mechanism of efflux pump were higher and viewed as potential indicators of human activities. Anthropogenic activities potentially promoted the horizontal gene transfer of ARGs in BSCs at human disturbed sites from co-occurrence network analysis. Our findings provided fundamental information of antibiotic resistomes in BSCs on the Qinghai-Tibetan Plateau, and unraveled possible mechanisms of human disturbance in shaping antibiotic resistomes.},
}
@article {pmid39724227,
year = {2024},
author = {Shahid, U and Hooi, SL and Lim, SY and Mohd Aris, A and Khor, BC and Ayub, Q and Tan, HS},
title = {Metagenomic surveillance of microbial community and antibiotic resistant genes associated with Malaysian wastewater during the COVID-19 pandemic.},
journal = {Current genetics},
volume = {71},
number = {1},
pages = {1},
pmid = {39724227},
issn = {1432-0983},
mesh = {*Wastewater/microbiology ; *COVID-19/epidemiology ; Malaysia/epidemiology ; *Metagenomics/methods ; *SARS-CoV-2/genetics ; Humans ; Drug Resistance, Microbial/genetics ; Pandemics ; Microbiota/genetics ; Metagenome ; Bacteria/genetics/classification/drug effects ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; },
abstract = {Wastewater is a reservoir of pathogens and hotspots for disseminating antibiotic resistance genes across species. The metagenomic surveillance of wastewater provides insight into the native microbial community, antibiotic-resistance genes (ARGs) and mobile genetic elements. t. The COVID-19 pandemic has caused wider dissemination of ARGs and resistant bacteria in wastewater. Although immensely significant, no research has been performed on the Malaysian wastewater microbial community and ARGs or their correlation with COVID-19 infections. This study utilised a 16S metagenomics approach to characterise the microbial community in Malaysian wastewater during high and low-case phases of the pandemic. Bacteria belonging to Bacteriodales, Bacillales, Actinomycetales and opportunistic pathogens-Arcobacters, Flavobacteria, and Campylobacterales, Neisseriales, were enriched during higher COVID-19 pandemic (active cases). Additionally, copy number profiling of ARGs in water samples showed the prevalence of elements conferring resistance to antibiotics like sulphonamides, cephalosporins, and colistin. The high prevalence of intI1 and other ion-based transporters in samples highlights an extensive risk of horizontal gene transfer to previously susceptible species. Our study emphasises the importance of wastewater surveillance in understanding microbial community dynamics and ARG dissemination, particularly during public health crises like the COVID-19 pandemic.},
}
@article {pmid39724170,
year = {2025},
author = {Farrell, AA and Nesbø, CL and Zhaxybayeva, O},
title = {Bacterial Growth Temperature as a Horizontally Acquired Polygenic Trait.},
journal = {Genome biology and evolution},
volume = {17},
number = {1},
pages = {},
pmid = {39724170},
issn = {1759-6653},
support = {//Dartmouth Fellowship/ ; },
mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/classification ; *Temperature ; *Multifactorial Inheritance ; Phylogeny ; Evolution, Molecular ; Genome, Bacterial ; Adaptation, Physiological/genetics ; },
abstract = {Evolutionary events leading to organismal preference for a specific growth temperature, as well as genes whose products are needed for a proper function at that temperature, are poorly understood. Using 64 bacteria from phylum Thermotogota as a model system, we examined how optimal growth temperature changed throughout Thermotogota history. We inferred that Thermotogota's last common ancestor was a thermophile and that some Thermotogota evolved the mesophilic and hyperthermophilic lifestyles secondarily. By modeling gain and loss of genes throughout Thermotogota history and by reconstructing their phylogenies, we demonstrated that adaptations to lower and higher growth temperature involve both the acquisition of necessary genes and loss of unnecessary genes. Via a pangenome-wide association study, we correlated presence/absence of 68 genes with specific optimal growth temperature intervals. While some of these genes are poorly characterized, most are involved in metabolism of amino acids, nucleotides, carbohydrates, and lipids, as well as in signal transduction and regulation of transcription. Most of the 68 genes have a history of horizontal gene transfer with other bacteria and archaea that often grow at similar temperatures, suggesting that parallel acquisitions of genes likely promote independent adaptations of different Thermotogota species to specific growth temperatures.},
}
@article {pmid39723821,
year = {2025},
author = {Sanchez, VA and Renner, T and Baker, LJ and Hendry, TA},
title = {Genome evolution following an ecological shift in nectar-dwelling Acinetobacter.},
journal = {mSphere},
volume = {10},
number = {1},
pages = {e0101024},
pmid = {39723821},
issn = {2379-5042},
mesh = {*Acinetobacter/genetics/classification ; *Genome, Bacterial ; *Plant Nectar/metabolism ; Phylogeny ; *Evolution, Molecular ; Ecosystem ; Gene Transfer, Horizontal ; },
abstract = {UNLABELLED: The bacterial genus Acinetobacter includes species found in environmental habitats like soil and water, as well as taxa adapted to be host-associated or pathogenic. High genetic diversity may allow for this habitat flexibility, but the specific genes underlying switches between habitats are poorly understood. One lineage of Acinetobacter has undergone a substantial habitat change by evolving from a presumed soil-dwelling ancestral state to thrive in floral nectar. Here, we compared the genomes of floral-dwelling and pollinator-associated Acinetobacter, including newly described species, with genomes from relatives found in other environments to determine the genomic changes associated with this ecological shift. Following one evolutionary origin of floral nectar adaptation, nectar-dwelling Acinetobacter taxa have undergone reduction in genome size compared with relatives and have experienced dynamic gene gains and losses as they diversified. Gene content changes suggest a shift to metabolism of monosaccharides rather than diverse carbohydrates, and scavenging of nitrogen sources, which we predict to be beneficial in nectar environments. Gene gains appear to result from duplication events, evolutionary divergence, and horizontal gene transfer. Most notably, nectar-dwelling Acinetobacter acquired the ability to degrade pectin from plant pathogens, and the genes underlying this ability have duplicated and are under selection within the clade. We hypothesize that this ability was a key trait for adaptation to floral nectar, as it could improve access to nutrients in the nutritionally unbalanced habitat of nectar. These results identify the genomic changes and traits coinciding with a dramatic habitat switch from soil to floral nectar.<br><br>IMPORTANCE: Many bacteria, including the genus Acinetobacter, commonly evolve to exploit new habitats. However, the genetic changes that underlie habitat switches are often unknown. Floral nectar is home to specialized microbes that can grow in this nutritionally unbalanced habitat. Several specialized Acinetobacter species evolved from soil-dwelling relatives to become common and abundant in floral nectar. Here, we investigate the genomic adaptations required to successfully colonize a novel habitat like floral nectar. We performed comparative genomics analyses between nectar-dwelling Acinetobacter and Acinetobacter species from other environments, like soil and water. We find that although gene loss coincided with the switch to living in nectar, gains of specific genes from other bacteria may have been particularly important for this ecological change. Acinetobacter living in nectar gained genes for degrading pectin, a plant polysaccharide, which may improve access to nutrients in their environment. These findings shed light on how evolutionary novelty evolves in bacteria.},
}
@article {pmid39721637,
year = {2025},
author = {Zhou, JZ and Sun, QN and Li, A and Wang, XJ and Zhao, JF},
title = {[Simultaneous Removal of Antibiotic-resistant Bacteria, Genes, and Inhibition of Horizontal Transfer using Vis-rGO-CNCF-enhanced Peroxymonosulfate Activation Process].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {1},
pages = {305-317},
doi = {10.13227/j.hjkx.202401171},
pmid = {39721637},
issn = {0250-3301},
mesh = {*Graphite/chemistry ; *Drug Resistance, Bacterial/genetics ; Peroxides/chemistry ; Copper/chemistry ; Gene Transfer, Horizontal ; Ferric Compounds/chemistry ; Anti-Bacterial Agents/pharmacology/chemistry ; Water Purification/methods ; Bacteria/genetics/drug effects ; Oxidation-Reduction ; Drug Resistance, Microbial/genetics ; },
abstract = {As emerging contaminants, antibiotic-resistant bacteria （ARBs） and antibiotic-resistant genes （ARGs） pose a serious threat to human health and ecological security. Here, a reduced graphene oxide and g-C3N4 co-doped copper ferrite （rGO-CNCF） were synthesized. The composite material was characterized using XRD, FTIR, XPS, SEM-EDS, TEM, and DRS analysis methods, and a visible-light-assisted rGO-CNCF-activated PMS system was constructed for the removal of ARB and ARGs in water. The results showed that the complete inactivation of 8.01 log SA-ARB could be achieved within 30 min when the catalyst dosage was 0.2 g·L[-1], The PMS dosage was 0.3 g·L[-1], and the initial pH value of the solution was 7.0. The Vis-rGO-CNCF/PMS system was able to effectively reduce the horizontal transfer of SA-ARGs, and this system had a good destructive ability for intracellular and extracellular SA-ARGs. The destruction ability of the advanced oxidation process for the two pollutants together, SMT and SA-ARB, was maintained at a high level. This system could destroy the cell membrane structure of resistant bacteria, causing cell fragmentation, and quenching experiments showed that singlet oxygen （[1]O2） played a major role in the system. This study can provide a promising method for controlling ARB and ARG pollution in water and controlling the horizontal transfer of ARGs.},
}
@article {pmid39719706,
year = {2025},
author = {Zhang, AN and Gaston, JM and Cárdenas, P and Zhao, S and Gu, X and Alm, EJ},
title = {CRISPR-Cas spacer acquisition is a rare event in human gut microbiome.},
journal = {Cell genomics},
volume = {5},
number = {1},
pages = {100725},
pmid = {39719706},
issn = {2666-979X},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *CRISPR-Cas Systems/genetics ; Gene Transfer, Horizontal/genetics ; Bacteriophages/genetics ; Bifidobacterium longum/genetics ; Metagenome/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Genome, Bacterial/genetics ; },
abstract = {Host-parasite relationships drive the evolution of both parties. In microbe-phage dynamics, CRISPR functions as an adaptive defense mechanism, updating immunity via spacer acquisition. Here, we investigated these interactions within the human gut microbiome, uncovering low frequencies of spacer acquisition at an average rate of one spacer every ∼2.9 point mutations using isolates' whole genomes and ∼2.7 years using metagenome time series. We identified a highly prevalent CRISPR array in Bifidobacterium longum spreading via horizontal gene transfer (HGT), with six spacers found in various genomic regions in 15 persons from the United States and Europe. These spacers, targeting two prominent Bifidobacterium phages, comprised 76% of spacer occurrence of all spacers targeting these phages in all B. longum populations. This result suggests that HGT of an entire CRISPR-Cas system introduced three times more spacers than local CRISPR-Cas acquisition in B. longum. Overall, our findings identified key ecological and evolutionary factors in prokaryote adaptive immunity.},
}
@article {pmid39718247,
year = {2025},
author = {Santos, PKF and de Souza Araujo, N and Françoso, E and Werren, JH and Kapheim, KM and Arias, MC},
title = {The genome of the solitary bee Tetrapedia diversipes (Hymenoptera, Apidae).},
journal = {G3 (Bethesda, Md.)},
volume = {15},
number = {2},
pages = {},
pmid = {39718247},
issn = {2160-1836},
support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 306932/2016-4//CNPq - Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2013/12530-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; DEB1257053//USNSF/ ; },
mesh = {Animals ; Bees/genetics/microbiology ; *Genome, Insect ; Genomics/methods ; Molecular Sequence Annotation ; Phylogeny ; Gene Transfer, Horizontal ; Wolbachia/genetics ; DNA Transposable Elements ; },
abstract = {Tetrapedia diversipes is a Neotropical solitary bee commonly found in trap-nests, known for its morphological adaptations for floral oil collection and prepupal diapause during the cold and dry season. Here, we present the genome assembly of T. diversipes (332 Mbp), comprising 2,575 scaffolds, with 15,028 predicted protein-coding genes. Repetitive elements constitute 38.68% of the genome, notably Class II transposable elements. An investigation into lateral gene transfers identified a low frequency (0.037%) of nuclear copies of mitochondrial DNA and 18 candidate regions from bacterial origins. Furthermore, the annotation of 3 scaffolds reveals the presence of the Wolbachia endosymbiont genome, confirming the infection by 2 strains in T. diversipes populations. This genome contributes valuable insights into Neotropical bee genomics, offering a resource for comparative studies and enhancing our understanding of the molecular basis of solitary bee adaptations and interactions.},
}
@article {pmid39717269,
year = {2024},
author = {Zhang, S and Shu, Y and Yang, Z and Zhong, Z and Wang, M and Jia, R and Chen, S and Liu, M and Zhu, D and Zhao, X and Wu, Y and Yang, Q and Huang, J and Ou, X and Sun, D and Tian, B and Wu, Z and He, Y and Cheng, A},
title = {Decoding the enigma: unveiling the transmission characteristics of waterfowl-associated bla NDM-5-positive Escherichia coli in select regions of China.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1501594},
pmid = {39717269},
issn = {1664-302X},
abstract = {Escherichia coli (E. coli) serves as a critical indicator microorganism for assessing the prevalence and dissemination of antibiotic resistance, notably harboring various antibiotic-resistant genes (ARGs). Among these, the emergence of the bla NDM gene represents a significant threat to public health, especially since carbapenem antibiotics are vital for treating severe infections caused by Gram-negative bacteria. This study aimed to characterize the antibiotic resistance features of bla NDM-5-positive E. coli strains isolated from waterfowl in several regions of China and elucidate the dissemination patterns of the bla NDM-5 gene. We successfully isolated 103 bla NDM-5-positive E. coli strains from 431 intestinal fecal samples obtained from waterfowl across five provincial-level units in China, with all strains exhibiting multidrug resistance (MDR). Notably, the bla NDM-5 gene was identified on plasmids, which facilitate efficient and stable horizontal gene transfer (HGT). Our adaptability assays indicated that while the bla NDM-5-positive plasmid imposed a fitness cost on the host bacteria, the NDM-5 protein was successfully induced and purified, exhibiting significant enzymatic activity. One strain, designated DY51, exhibited a minimum inhibitory concentration (MIC) for imipenem of 4 mg/L, which escalated to 512 mg/L following exposure to increasing imipenem doses. This altered strain demonstrated stable resistance to imipenem alongside improved adaptability, correlating with elevated relative expression levels of the bla NDM-5 and overexpression of efflux pumps. Collectively, this study highlights the horizontal dissemination of the bla NDM-5 plasmid among E. coli strains, confirms the associated fitness costs, and provides insights into the mechanisms underlying the stable increase in antibiotic resistance to imipenem. These findings offer a theoretical framework for understanding the dissemination dynamics of bla NDM-5 in E. coli, which is essential for developing effective strategies to combat carbapenem antibiotic resistance.},
}
@article {pmid39716502,
year = {2025},
author = {Zheng, J and Li, YY and Lu, YS and Wang, D and Liu, C and Peng, HL and Shi, CH and Xie, KZ and Zhang, K and Sun, LL and Zhou, CM and Gu, WJ},
title = {Impact of different continuous fertilizations on the antibiotic resistome associated with a subtropical triple-cropping system over one decade.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {367},
number = {},
pages = {125564},
doi = {10.1016/j.envpol.2024.125564},
pmid = {39716502},
issn = {1873-6424},
mesh = {*Fertilizers ; *Soil Microbiology ; *Agriculture/methods ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents ; Soil/chemistry ; Manure ; Chickens ; Animals ; Zea mays ; Crops, Agricultural ; },
abstract = {The prevalence of antibiotic resistance genes (ARGs) in agricultural soils has garnered significant attention. However, the long-term impacts of various nitroge (N)-substitution fertilization regimes on the distribution of soil ARGs and their dominant drivers in a subtropical triple-cropping system remain largely unexplored. This study employed a metagenomic approach to analyze soil ARGs, microbial communities, mobile genetic elements (MGEs), and viruses from a maize-maize-cabbage rotation field experiment with five different fertilization regimes. Soil samples were collected in 2012 and 2021. A total of 615 unique ARG subtypes were identified, with multidrug, bacitracin, and rifamycin resistance genes being the most abundant. Notably, ARG types. the continuous application of fresh chicken manure (CM) over 10 years significantly increased both the count of unique ARG subtypes and the total ARG abundance compared to other fertilization regimes, such as inorganic fertilizer and composted chicken manure. Specifically, the abundance of genes associated with antibiotic target replacement (e.g., sul1 and sul2) in the CM-treated soil rose by 8.83-fold from 2021 to 2012. Our random forest analysis revealed that the abundance of three MGEs (QacEdelta, plasmids, and IstB), two viral families (Myoviridae and Podoviridae), two bacterial phyla (Chloroflexi and Planctomycetes), and two environmental factors (pH and soil organic matter (SOM)) significantly influenced the distribution of ARGs. Furthermore, variance decomposition analysis underscored the critical roles of the three MGEs and the two viral families in the dissemination of ARGs, suggesting that horizontal gene transfer (HGT) may play a key role in ARG spread. These findings enhance our understanding of how different fertilization practices influence ARG dissemination in subtropical triple-cropping agroecosystems over the long term and provide valuable insights for optimizing fertilization management strategies.},
}
@article {pmid39710145,
year = {2025},
author = {Tavares, RDS and Tacão, M and Henriques, I},
title = {Integrons are key players in the spread of beta-lactamase-encoding genes.},
journal = {International journal of antimicrobial agents},
volume = {65},
number = {3},
pages = {107421},
doi = {10.1016/j.ijantimicag.2024.107421},
pmid = {39710145},
issn = {1872-7913},
mesh = {*Integrons/genetics ; *beta-Lactamases/genetics ; Humans ; *Bacteria/genetics/drug effects/enzymology ; Anti-Bacterial Agents/pharmacology ; beta-Lactam Resistance/genetics ; *Gene Transfer, Horizontal ; },
abstract = {Integrons mediate the acquisition and expression of gene cassettes (GCs). The production of beta-lactamases (BLs) is the most relevant mechanism of beta-lactams resistance. To explore the role of integrons in BL genes dissemination, sequences and metadata were retrieved from the INTEGRALL database and a literature review performed. Integrons (mostly class 1) carrying ≥1 BL-encoding genes (n = 1981) were detected in 37 bacterial genera and encoded BLs from 18 families. A total of 159 BL-encoding gene cassettes (BLGCs) were identified, representing all Ambler classes, with blaOXA-, blaVIM- and blaIMP-carrying integrons the most prevalent. blaGES, blaBEL and most metallo-BLs were exclusively associated with integrons. BL genes from 13 families were identified as genes captured by ISCR1 in complex integrons (n = 234), namely blaNDM, blaCTX-M and blaTEM. Frequently co-detected GCs encoded resistance to all major classes of antibiotics, namely aminoglycosides, phenicols and trimethoprim. Most BLGCs encoded resistance to carbapenems (n = 90) and Pseudomonas aeruginosa was the most frequent host. Most bla-carrying integrons were from clinical contexts and wastewater was the richest environmental compartment. The frequent association of BLs and integrons indicates a significant role in dissemination of beta-lactams resistance. Considering that integrons are (i) low-cost structures often associated with other mobile elements, and (ii) often carry multiple GCs (interchangeable according to environmental stimuli), the association of BL genes with integrons should always be considered a risk factor for the spread of beta-lactam resistance when performing surveillance and epidemiological studies. Further studies monitoring prevalence and diversity of integrons, particularly across non-clinical environments, will draw a more comprehensive picture of integron-associated dissemination of beta-lactams resistance.},
}
@article {pmid39708795,
year = {2025},
author = {Tarnopol, RL and Tamsil, JA and Cinege, G and Ha, JH and Verster, KI and Ábrahám, E and Magyar, LB and Kim, BY and Bernstein, SL and Lipinszki, Z and Andó, I and Whiteman, NK},
title = {Experimental horizontal transfer of phage-derived genes to Drosophila confers innate immunity to parasitoids.},
journal = {Current biology : CB},
volume = {35},
number = {3},
pages = {514-529.e7},
pmid = {39708795},
issn = {1879-0445},
support = {R35 GM119816/GM/NIGMS NIH HHS/United States ; T32 GM132022/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Gene Transfer, Horizontal ; *Immunity, Innate/genetics ; *Wasps/physiology ; *Drosophila melanogaster/genetics/immunology/parasitology ; *Bacteriophages/genetics ; },
abstract = {Metazoan parasites have played a major role in shaping innate immunity in animals. Insect hosts and parasitoid wasps are excellent models for illuminating how animal innate immune systems have evolved to neutralize these enemies. One such strategy relies on symbioses between insects and intracellular bacteria that express phage-encoded toxins. In some cases, the genes that encode these toxins have been horizontally transferred to the genomes of the insects. Here, we used genome editing in Drosophila melanogaster to recapitulate the evolution of two toxin genes-cytolethal distending toxin B (cdtB) and apoptosis inducing protein of 56kDa (aip56)-that were horizontally transferred likely from phages of endosymbiotic bacteria to insects millions of years ago. We found that a cdtB::aip56 fusion gene (fusionB), which is conserved in D. ananassae subgroup species, dramatically promoted fly survival and suppressed parasitoid wasp development when heterologously expressed in D. melanogaster immune tissues. We found that FusionB was a functional nuclease and was secreted into the host hemolymph where it targeted the parasitoid embryo's serosal tissue. Although the mechanism of toxicity remains unknown, when expressed ubiquitously, fusionB resulted in delayed development of late-stage fly larvae and eventually killed pupating flies. These results point to the salience of regulatory constraint in mitigating autoimmunity during the domestication process following horizontal transfer. Our findings demonstrate how horizontal gene transfer can instantly provide new, potent innate immune modules in animals.},
}
@article {pmid39708598,
year = {2025},
author = {Sun, D and Shi, X and Shen, Y and Liu, Y and Luo, S and Jin, Y and Zhai, W and Liu, L and Deng, Z and Sun, C and Liu, D and Yang, X and Xie, Y and Krüger-Haker, H and Wu, C and Schwarz, S and Shen, J and Chen, Y and Ma, S and Wang, Y},
title = {Comparative efficacy of anaerobic digestion systems in removing antimicrobial resistance genes from swine wastewater.},
journal = {Journal of hazardous materials},
volume = {485},
number = {},
pages = {136868},
doi = {10.1016/j.jhazmat.2024.136868},
pmid = {39708598},
issn = {1873-3336},
mesh = {Animals ; *Wastewater/microbiology ; Swine ; Anaerobiosis ; *Waste Disposal, Fluid/methods ; Bioreactors ; *Genes, Bacterial ; Anti-Bacterial Agents ; *Drug Resistance, Microbial/genetics ; Sewage/microbiology ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Swine farm wastewater is a major reservoir of antimicrobial resistance genes (ARGs). Anaerobic digestion (AD), widely implemented in farms, has been extensively studied for ARG removal. However, a comparative study on ARG removal efficiency across the four principal AD systems - up-flow anaerobic sludge blanket (UASB), continuous stirred tank reactor (CSTR), buried biogas digester (BBD), and septic tank (SPT) - is lacking. Herein, we employed metagenomic sequencing, ultra-performance liquid chromatography-tandem mass spectrometry, as well as atomic absorption spectrometry/atomic fluorescence spectrophotometry, and revealed that UASB and CSTR achieved higher removal efficiencies for both ARGs (67% and 57%) and antibiotic residues (100% and 90%) compared to BBD and SPT. Acinetobacter, Escherichia, Pseudomonas and Streptococcus were the primary ARG hosts, comprising over 65% of the total abundance in influent samples. UASB and CSTR systems demonstrated superior removal efficiencies for both mobile genetic elements (MGEs) and antibiotic residues, both of which had essential impacts on ARG profiles. In addition, heavy metals might contribute to variation in ARGs through horizontal gene transfer. Collectively, the variation in microbial communities and better removal of both MGEs and antibiotic residues contribute to the remarkable ARG removal efficiency of UASB and CSTR, therefore, advocating for the widespread adoption of these two AD systems in swine farms.},
}
@article {pmid39706477,
year = {2025},
author = {Bientz, L and Guyet, U and Guiraud, J and Metifiot, M and Moulieras, M and Aillerie, S and Coulange-Mayonnove, L and Boureima-Abdou, B and Groppi, A and Nikolski, M and Bébéar, C and Pereyre, S and Dubois, V},
title = {Mobilization of an ICEclc-Like Element as a Potential Mechanism for the Spread of IMP-13 Carbapenemase in Pseudomonas aeruginosa.},
journal = {Journal of global antimicrobial resistance},
volume = {41},
number = {},
pages = {44-51},
doi = {10.1016/j.jgar.2024.12.006},
pmid = {39706477},
issn = {2213-7173},
mesh = {*Pseudomonas aeruginosa/genetics/drug effects/enzymology/isolation &amp; purification ; *beta-Lactamases/genetics ; *Bacterial Proteins/genetics ; Humans ; Anti-Bacterial Agents/pharmacology ; Pseudomonas Infections/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Retrospective Studies ; *Interspersed Repetitive Sequences ; Carbapenems/pharmacology ; },
abstract = {Carbapenem-resistant Pseudomonas aeruginosa is a global public health concern. IMP-13 is a carbapenemase that was described for the first time in 2001 but is often underestimated due to poor hydrolysis of carbapenems and a lack of molecular detection. The aim of this study was to characterize the genetic support of blaIMP-13 in P. aeruginosa and to assess the ability of mobile genetic elements to disseminate this resistance. A retrospective analysis conducted between 2010 and 2020 revealed eight multiresistant P. aeruginosa isolates by their production of the carbapenemase IMP-13 in Bordeaux. Additionally, three of the studied isolates exhibited high-level resistance to imipenem and imipenem-relebactam that was linked to an insertion sequence in the oprD gene. Successful mating was achieved, and transconjugants and parental clinical isolate genomes were sequenced. All clinical isolates were found to be ST621 strains. The data revealed that blaIMP-13 was carried on an Integrative and Conjugative Element (ICEclc-like) of 88,589 bp with a 62% GC content harboring 85 CDSs, and was inserted at the tRNA[Gly] locus PA0729.1. The ICE was identical in the eight studied clinical isolates and in all the ST621 strains found in the databases. The conjugation rate was low, at approximately 10[-8] transconjugants per donor and ICE transfer appeared to mobilize some adjacent parental genes located immediately downstream of the ICE. In conclusion, these results suggest that even if the spread of blaIMP-13 is mainly due to an epidemic ST621 clone, the mobilization of a blaIMP-13-carrying ICEclc-like element is possible and should not be underestimated.},
}
@article {pmid39706021,
year = {2025},
author = {Dinesh, R and Sreena, CP and Sheeja, TE and Srinivasan, V and Subila, KP and Sona, C and Kumar, IPV and Anusree, M and Alagupalamuthirsolai, M and Jayarajan, K and Sajith, V},
title = {Co-resistance is the dominant mechanism of co-selection and dissemination of antibiotic resistome in nano zinc oxide polluted soil.},
journal = {Journal of hazardous materials},
volume = {485},
number = {},
pages = {136885},
doi = {10.1016/j.jhazmat.2024.136885},
pmid = {39706021},
issn = {1873-3336},
mesh = {*Zinc Oxide/toxicity ; *Soil Pollutants/toxicity ; Soil Microbiology ; *Anti-Bacterial Agents/pharmacology ; *Metal Nanoparticles/toxicity ; Genes, Bacterial ; Bacteria/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; Microbiota/drug effects ; Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; },
abstract = {The broader soil bacterial community responses at ecotoxicologically relevant levels of nano ZnO (nZnO) focussing on co-selection of antibiotic resistance (AR) were investigated. nZnO imposed a stronger influence than the bulk counterpart (bZnO) on antibiotic resistance genes (ARGs) with multidrug resistance (MDR) systems being predominant (63 % of total ARGs). Proliferation of biomarker ARGs especially for last resort antibiotic like vancomycin was observed and Streptomyces hosted multiple ARGs. nZnO was the major driver of the resistome with efflux systems dominating the AR mechanism. Environmental risk associated with nZnO was mediated through metal driven co-selection of ARGs and their probable transfer to eukaryotic hosts through horizontal gene transfer (HGT) via mobile genetic elements (MGEs). Novel resistance genes tetA, mdtA, int and tnpA validated in our study can be used as biomarkers for rapid detection of nZnO toxicity in soils. qRT-PCR validation of resistome in the rhizosphere soil microbiome of turmeric indicated that Zn levels decreased by 16 % compared to bulk soil with 80 % bioaccumulation in rhizomes at 1000 mg Zn kg[-1] and subsequent down regulation of ARGs. Expression of key biosynthetic genes for curcumin in turmeric rhizomes showed an increase up to 500 mg Zn kg[-1] as nZnO. Validation of co-selection phenomenon in microcosm with 10 mg kg[-1] tetracycline without added Zn indicated 20 % upregulation of Zn resistance genes (ZRGs) like czcA, yiip and zntA.},
}
@article {pmid39699696,
year = {2024},
author = {Yagisawa, F and Fujiwara, T and Yamashita, S and Hirooka, S and Tamashiro, K and Izumi, J and Kanesaki, Y and Onuma, R and Misumi, O and Nakamura, S and Yoshikawa, H and Kuroiwa, H and Kuroiwa, T and Miyagishima, SY},
title = {A fusion protein of polyphosphate kinase 1 (PPK1) and a Nudix hydrolase is involved in inorganic polyphosphate accumulation in the unicellular red alga Cyanidioschyzon merolae.},
journal = {Plant molecular biology},
volume = {115},
number = {1},
pages = {9},
pmid = {39699696},
issn = {1573-5028},
support = {22K06299//Japan Society for the Promotion of Science/ ; 22K06396//Japan Society for the Promotion of Science/ ; 22K15166//Japan Society for the Promotion of Science/ ; 22H02657//Japan Society for the Promotion of Science/ ; 24H00579//Japan Society for the Promotion of Science/ ; JPMJMI22E1//JST-Mirai Program/ ; NIG-JOINT 68A2024//National Institute of Genetics/ ; S1311017//Ministry of Education, Culture, Sports, Science and Technology/ ; Spatiotemporal Genomics Project//University of the Ryukyus/ ; Researcher exchange promotion program//Research Organization of Information and Systems/ ; },
mesh = {*Rhodophyta/genetics/enzymology/metabolism ; *Polyphosphates/metabolism ; *Phosphotransferases (Phosphate Group Acceptor)/metabolism/genetics ; *Phylogeny ; *Nudix Hydrolases ; Pyrophosphatases/metabolism/genetics ; Recombinant Fusion Proteins/metabolism/genetics ; },
abstract = {Inorganic polyphosphate (polyP) is a linear polymer of phosphate that plays various roles in cells, including in phosphate and metal homeostasis. Homologs of the vacuolar transporter chaperone 4 (VTC4), catalyzing polyP synthesis in many eukaryotes, are absent in red algae, which are among the earliest divergent plant lineages. We identified homologs of polyphosphate kinase 1 (PPK1), a conserved polyP synthase in bacteria, in 42 eukaryotic genomes, including 31 species detected in this study and 12 species of red algae. Phylogenetic analysis suggested that most eukaryotic PPK1 homologs originated from horizontal gene transfer from a prokaryote to a plant before the divergence of red algae and Viridiplantae. In red algae, the homologs were fused to a nucleoside diphosphate-linked moiety X (Nudix) hydrolase of the diphosphoinositol polyphosphate phosphohydrolase (DIPP) family. We characterized the fusion protein CmPPK1 in the unicellular red alga Cyanidioschyzon merolae, which has been used in studies on basic features of eukaryotes. In the knockout strain ∆CmPPK1, polyP was undetectable, suggesting a primary role for CmPPK1 in polyP synthesis. In addition, ∆CmPPK1 showed altered metal balance. Mutations in the catalytically important residues of the Nudix hydrolase domain (NHD) either increased or decreased polyP contents. Both high and low polyP NHD mutants were susceptible to phosphate deprivation, indicating that adequate NHD function is necessary for normal phosphate starvation responses. The results reveal the unique features of PPK1 in red algae and promote further investigation of polyP metabolism and functions in red algae and eukaryotic evolution.},
}
@article {pmid39696916,
year = {2025},
author = {Prabhu, C and Satyaprasad, AU and Deekshit, VK},
title = {Understanding Bacterial Resistance to Heavy Metals and Nanoparticles: Mechanisms, Implications, and Challenges.},
journal = {Journal of basic microbiology},
volume = {65},
number = {2},
pages = {e2400596},
doi = {10.1002/jobm.202400596},
pmid = {39696916},
issn = {1521-4028},
support = {//This work was funded by the Indian Council of Medical Research (grant no. AMR/DHR/GIA/3/ECD-II/2020)./ ; },
mesh = {*Metals, Heavy/pharmacology ; *Nanoparticles ; *Bacteria/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Drug Resistance, Bacterial ; Drug Resistance, Multiple, Bacterial ; },
abstract = {Antimicrobial resistance is a global health problem as it contributes to high mortality rates in several infectious diseases. To address this issue, engineered nanoparticles/nano-formulations of antibiotics have emerged as a promising strategy. Nanoparticles are typically defined as materials with dimensions up to 100 nm and are made of different materials such as inorganic particles, lipids, polymers, etc. They are widely dispersed in the environment through various consumer products, and their clinical applications are diverse, ranging from contrast agents in imaging to carriers for gene and drug delivery. Nanoparticles can also act as antimicrobial agents either on their own or in combination with traditional antibiotics to produce synergistic effects, earning them the label of "next-generation therapeutics." They have also shown great effectiveness against multidrug-resistant pathogens responsible for nosocomial infections. However, overexposure or prolonged exposure to sublethal doses of nanoparticles can promote the development of resistance in human pathogens. The resistance can arise from various factors such as genetic mutation, horizontal gene transfer, production of reactive oxygen species, changes in the outer membrane of bacteria, efflux-induced resistance, cross-resistance from intrinsic antibiotic resistance determinants, plasmid-mediated resistance, and many more. Continuous exposure to nanoparticles can also transform an antibiotic-susceptible bacterial pathogen into multidrug resistance. Considering all these, the current review focuses on the mode of action of different heavy metals and nanoparticles and possible mechanisms through which bacteria attain resistance towards these heavy metals and nanoparticles.},
}
@article {pmid39696539,
year = {2024},
author = {Pianezza, R and Haider, A and Kofler, R},
title = {GenomeDelta: detecting recent transposable element invasions without repeat library.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {315},
pmid = {39696539},
issn = {1474-760X},
support = {P35093//Austrian Science Fund (FWF)/ ; },
mesh = {*DNA Transposable Elements ; Animals ; *Drosophila melanogaster/genetics ; Software ; Ascomycota/genetics ; Gene Library ; },
abstract = {We present GenomeDelta, a novel tool for identifying sample-specific sequences, such as recent transposable element (TE) invasions, without requiring a repeat library. GenomeDelta compares high-quality assemblies with short-read data to detect sequences absent from the short reads. It is applicable to both model and non-model organisms and can identify recent TE invasions, spatially heterogeneous sequences, viral insertions, and hotizontal gene transfers. GenomeDelta was validated with simulated and real data and used to discover three recent TE invasions in Drosophila melanogaster and a novel TE with geographic variation in Zymoseptoria tritici.},
}
@article {pmid39695425,
year = {2024},
author = {Yu, L and Zhao, Y and Zhang, S and Ni, W and Zhang, L and Xue, C and Wang, P and Zhang, X},
title = {Antimicrobial resistance and virulence factors analysis of a multidrug-resistant Acinetobacter baumannii isolated from chickens using whole-genome sequencing.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {526},
pmid = {39695425},
issn = {1471-2180},
support = {32202810//National Natural Science Foundation of China/ ; ZR2022QC115//Natural Science Foundation of Shandong Province/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Acinetobacter baumannii/genetics/drug effects/pathogenicity/isolation &amp; purification ; *Virulence Factors/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; *Whole Genome Sequencing ; *Acinetobacter Infections/microbiology/veterinary ; *Genome, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Poultry Diseases/microbiology ; Microbial Sensitivity Tests ; Virulence/genetics ; Plasmids/genetics ; },
abstract = {Multidrug-resistant (MDR) Acinetobacter baumannii (A. baumannii) is currently recognized not only as a significant nosocomial pathogen but also is an emerging bacterial infection in food-producing animals, posing a critical threat to global health. However, this is a hindrance to detailed bioinformatic studies of MDR A. baumannii of chicken origin due to the lack of its complete genome sequence. Here, we report whole-genome sequencing analysis of MDR A. baumannii Y03 isolated from chickens. The Y03 genome consists of 1 circular chromosome and 4 circular plasmids, The Y03 chromosome harbors 41 antimicrobial resistance genes conferring resistance to major classes of antibiotics, including β-lactams, phenicols, macrolides, lincosamides, aminoglycosides, and nitrofurans, as well as 135 virulence factors involved in effector delivery system, immune modulation, adherence, stress survival, biofilm, exotoxin, and nutritional/metabolic factor. The in vivo infection experiments certificated that Y03 was virulent to chickens. Meanwhile, we used PCR amplification method to detect 10 antimicrobial resistance genes including abeM, adeB, adeH, adeK, blaapmC, blaOXA-90, catB9, macB, folP, and parE, as well as 14 virulence genes including lpxC, pilO, fimT, ompA, basA, bauA, gspL, csu, pgaC, plc2, tssA, tviB, bap, and vgrG. Whole-genome sequencing analysis revealed that Y03 contained 46 horizontal gene transfer elements, including 11 genomic islands, 30 transposons, and 5 prophages, as well as 518 mutations associated with reduced virulence and 44 mutations resulting in loss of pathogenicity. Furthermore, there were 22 antibiotic targets and 28 lethal mutations on the Y03 chromosome that could be used as potential targets to prevent, control, and treat infections caused by MDR A. baumannii Y03. Therefore, this study contributes to the development of strategies for the prevention, control, and treatment of A. baumannii infections and their spread in chickens.},
}
@article {pmid39694196,
year = {2025},
author = {Panigrahi, M and Rajawat, D and Nayak, SS and Jain, K and Nayak, A and Rajput, AS and Sharma, A and Dutt, T},
title = {A comprehensive review on genomic insights and advanced technologies for mastitis prevention in dairy animals.},
journal = {Microbial pathogenesis},
volume = {199},
number = {},
pages = {107233},
doi = {10.1016/j.micpath.2024.107233},
pmid = {39694196},
issn = {1096-1208},
mesh = {Animals ; *Mastitis, Bovine/prevention &amp; control/genetics ; *Genomics/methods ; Female ; Cattle ; *Dairying/methods ; Milk ; Proteomics ; },
abstract = {Mastitis is a multi-etiological disease that significantly impacts milk production and reproductive efficiency. It is highly prevalent in dairy populations subjected to intensive selection for higher milk yield and where inbreeding is common. The issue is amplified by climate change and poor hygiene management, making disease control challenging. Key obstacles include antibiotic resistance, maximum residue levels, horizontal gene transfer, and limited success in breeding for resistance. Predictive genomics offers a promising solution for mastitis prevention by identifying genetic traits linked with susceptibility to mastitis. This review compiles the research and findings on genomics and its allied approaches, such as pan-genomics, epigenetics, proteomics, and transcriptomics, for diagnosing, understanding, and treating mastitis. In dairy production, artificial intelligence (AI), particularly deep learning (DL) techniques like convolutional neural networks (CNNs), has demonstrated significant potential to enhance milk production and improve farm profitability. It highlights the integration of advanced technologies like machine learning (ML), CRISPR, and pan-genomics to improve our knowledge of mastitis epidemiology, pathogen evolution, and the development of more effective diagnostic, preventive and therapeutic strategies for dairy herds. Genomic advancements provide critical insights into the complexities of mastitis, offering new avenues for understanding its dynamics. Integrating these findings with key predisposing factors can drive targeted prevention and more effective disease management.},
}
@article {pmid39693608,
year = {2025},
author = {Laidlaw, A and Blondin-Brosseau, M and Shay, J and Dussault, F and Rao, M and Petronella, N and Tamber, S},
title = {Variation in plasmid conjugation among nontyphoidal Salmonella enterica serovars.},
journal = {Canadian journal of microbiology},
volume = {71},
number = {},
pages = {1-14},
doi = {10.1139/cjm-2024-0164},
pmid = {39693608},
issn = {1480-3275},
mesh = {*Plasmids/genetics ; *Salmonella enterica/genetics/drug effects/classification ; *Conjugation, Genetic ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Humans ; Serogroup ; Animals ; Salmonella Infections/microbiology ; },
abstract = {Conjugation is a complex phenomenon involving multiple plasmid, bacterial, and environmental factors. Here we describe an IncI1 plasmid encoding multidrug antibiotic resistance to aminoglycosides, sulfonamides, and third-generation cephalosporins. This plasmid is widespread geographically among animal, human, and environmental sectors. We present data on the transmissibility of this plasmid from Salmonella enterica ser. Kentucky into 40 strains of S. enterica (10 strains each from serovars Enteritidis, Heidelberg, Infantis, and Typhimurium). Thirty seven out of 40 strains were able to take up the plasmid. Rates of conjugation were variable between strains ranging from 10[-8] to 10[-4]. Overall, serovars Enteritidis and Typhimurium demonstrated the highest rates of conjugation, followed by Heidelberg, and then Infantis. No relationships were observed between the recipient cell surface and rate of conjugation. Recipient cell numbers correlated positively with conjugation rate and strains with high conjugation rates had marginally but significantly higher growth parameters compared to strains that took up the plasmid at lower frequencies. Environmental conditions known to impact cell growth, such as temperature, nutrient availability, and the presence of antibiotics, had a modulating effect on conjugation. Collectively, these results will further understanding of plasmid transmission dynamics in Salmonella, which is a critical first step towards the development of mitigation strategies.},
}
@article {pmid39692564,
year = {2024},
author = {Sloan, DB and Broz, AK and Kuster, SA and Muthye, V and Peñafiel-Ayala, A and Marron, JR and Lavrov, DV and Brieba, LG},
title = {Expansion of the MutS gene family in plants.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koae277},
pmid = {39692564},
issn = {1532-298X},
support = {R35 GM148134/GM/NIGMS NIH HHS/United States ; },
abstract = {The widely distributed MutS gene family functions in recombination, DNA repair, and protein translation. Multiple evolutionary processes have expanded this gene family in plants relative to other eukaryotes. Here, we investigate the origins and functions of these plant-specific genes. Cyanobacterial-like MutS1 and MutS2 genes were ancestrally gained via plastid endosymbiotic gene transfer. MutS1 was subsequently lost in seed plants, whereas MutS2 was duplicated in Viridiplantae (i.e., land plants and green algae). Viridiplantae also have two anciently duplicated copies of the eukaryotic MSH6 gene and acquired MSH1 via horizontal gene transfer - potentially from a nucleocytovirus. Despite sharing a name, "plant MSH1" is not directly related to the MSH1 gene in some fungi and animals, which may be an ancestral eukaryotic gene acquired via mitochondrial endosymbiosis and subsequently lost in most eukaryotes. There has been substantial progress in understanding the functions of plant MSH1 and MSH6 genes, but the cyanobacterial-like MutS1 and MutS2 genes remain uncharacterized. Known functions of bacterial homologs and predicted protein structures, including fusions to diverse nuclease domains, provide hypotheses about potential molecular mechanisms. Because most plant-specific MutS proteins are mitochondrial and/or plastid-targeted, the expansion of this family has played a large role in shaping plant organelle genetics.},
}
@article {pmid39690351,
year = {2024},
author = {Ullah, H and Hassan, SHA and Yang, Q and Salama, ES and Liu, P and Li, X},
title = {Dynamic interaction of antibiotic resistance between plant microbiome and organic fertilizers: sources, dissemination, and health risks.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {1},
pages = {4},
pmid = {39690351},
issn = {1573-0972},
support = {lzujbky-2024-ey12//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Animals ; Humans ; Agriculture/methods ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/genetics/classification ; Drug Resistance, Bacterial/drug effects/genetics ; *Fertilizers/analysis ; Gene Transfer, Horizontal ; *Manure/microbiology ; *Microbiota/drug effects ; *Plants/microbiology ; Sewage/microbiology ; Soil/chemistry ; *Soil Microbiology ; Wastewater/chemistry/microbiology ; },
abstract = {Antibiotic resistance is a global health problem driven by the irrational use of antibiotics in different areas (such as agriculture, animal farming, and human healthcare). Sub-lethal concentrations of antibiotic residues impose selective pressure on environmental, plant-associated, and human microbiome leading to the emergence of antibiotic-resistant bacteria (ARB). This review summarizes all sources of antibiotic resistance in agricultural soils (including manure, sewage sludge, wastewater, hospitals/pharmaceutical industry, and bioinoculants). The factors (such as the physicochemical properties of soil, root exudates, concentration of antibiotic exposure, and heavy metals) that facilitate the transmission of resistance in plant microbiomes are discussed. Potential solutions for effective measures and control of antibiotic resistance in the environment are also hypothesized. Manure exhibits the highest antibiotics load, followed by hospital and municipal WW. Chlortetracycline, tetracycline, and sulfadiazine have the highest concentrations in the manure. Antibiotic resistance from organic fertilizers is transmitted to the plant microbiome via horizontal gene transfer (HGT). Plant microbiomes serve as transmission routes of ARB and ARGS to humans. The ingestion of ARB leads to human health risks (such as ineffectiveness of medication, increased morbidity, and mortality).},
}
@article {pmid39689477,
year = {2025},
author = {Li, S and Wang, K and Wang, D and Wang, H and Zhao, H and Pu, J and Wang, K and Li, C},
title = {Distribution and environmental dissemination of antibiotic resistance genes in poultry farms and surrounding ecosystems.},
journal = {Poultry science},
volume = {104},
number = {1},
pages = {104665},
pmid = {39689477},
issn = {1525-3171},
mesh = {Animals ; RNA, Ribosomal, 16S/analysis/genetics ; *Bacteria/genetics/drug effects/isolation &amp; purification ; Farms ; Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Ecosystem ; Anti-Bacterial Agents/pharmacology ; *Chickens ; Animal Husbandry ; Microbiota ; *Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; Cloaca/microbiology ; },
abstract = {Antibiotic resistance poses a significant threat to human and animal health worldwide, with farms serving as crucial reservoirs of Antibiotic Resistance Genes (ARGs) and Antibiotic-resistant bacteria. However, the distribution of ARGs in poultry farms and their transmission patterns in the environment remain poorly understood. This study collected samples of aerosol microorganisms, cloacal matter, soil, and vegetables from poultry farms and surrounding environments at three different distances. We used 16S rRNA gene sequencing and HT-qPCR to analyze the characteristics of aerosol microbial communities and the abundance of ARGs. At the phylum level, Proteobacteria, Firmicutes, and Bacteroidetes were dominant in cloacal samples, aerosol samples, and vegetable samples, while Proteobacteria Actinobacteriota and Acidobacteria dominated soil. Pseudomonas was dominant in cloacal samples at the genus level, whereas Fusobacterium was prevalent in soil. The diversity and richness of bacterial communities were more similar between cloacal samples than those observed between either sample type compared with soil. Our results showed that tetracycline and aminoglycoside ARG relative abundance was high across all sample types but significantly increased within feces/air compared to soils/vegetables. Association analysis revealed five potential host genera for ARG/MGE presence among various microbiota populations studied here. Our findings confirm that farms are important sources for the environmental dissemination of pathogens and ARGs.},
}
@article {pmid39688393,
year = {2025},
author = {Lurie-Weinberger, MN and Bychenko-Banyas, D and Mor, M and Laviad-Shitrit, S and Kaplan, E and Rakovitsky, N and Keren-Paz, A and Ben-Zvi, C and Carmeli, Y},
title = {In vivo interspecies dissemination of IncM2-type blaNDM-1 carrying plasmid.},
journal = {Microbiology spectrum},
volume = {13},
number = {2},
pages = {e0039924},
pmid = {39688393},
issn = {2165-0497},
mesh = {*beta-Lactamases/genetics/metabolism ; *Plasmids/genetics ; *Klebsiella pneumoniae/genetics/drug effects/enzymology/isolation &amp; purification ; Humans ; *Escherichia coli/genetics/drug effects/enzymology/isolation &amp; purification ; Drug Resistance, Multiple, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Male ; Klebsiella Infections/microbiology ; Gene Transfer, Horizontal ; Female ; Microbial Sensitivity Tests ; Enterobacteriaceae Infections/microbiology ; Bacterial Proteins/genetics ; Middle Aged ; Aged ; },
abstract = {The gastrointestinal tract is a unique ecological niche with a high abundance of various Enterobacterales in close proximity. This allows the exchange of mobile genetic elements that carry resistance determinants. In the hospital setting, resistant organisms are prevalent and selective antibiotic pressure is high, providing a supportive platform for interspecies dissemination of resistance. Seven New Delhi metallo-beta-lactamase(NDM) positive and one NDM-negative bacteria were sent for WGS followed by bioinformatics analysis. Here, we describe three separate cases of patients simultaneously colonized by two NDM producing-species (Escherichia coli and Klebsiella pneumoniae), in which we documented interspecies dissemination of the blaNDM-1 by an 87,450 bp IncM2 type multi-drug resistance plasmid (here named pNCICAN_NDM-01_21-il). This plasmid was found to be highly conjugative. Our results underline the risk of interspecies horizontal plasmid dissemination. Such events may cause the emergence of high-risk clones, as well as lead to under-recognized multi-species outbreaks.IMPORTANCEConjugative, carbapenemase-carrying multidrug-resistant plasmids that can move between species of clinically relevant Enterobacterales pose a great risk to patients' health, especially when they spread inside a medical institution. Yet, most institutions monitor bacteria according to species and are at risk of missing plasmid-driven outbreaks. Thus, this work indicates that plasmid surveillance is an important tool for infection control.},
}
@article {pmid39686544,
year = {2024},
author = {Stott, C and Diop, A and Raymann, K and Bobay, LM},
title = {Co-evolution and Gene Transfers Drive Speciation Patterns in Host-Associated Bacteria.},
journal = {Molecular biology and evolution},
volume = {41},
number = {12},
pages = {},
pmid = {39686544},
issn = {1537-1719},
support = {R01 GM132137/GM/NIGMS NIH HHS/United States ; DEB-2344788//National Science Foundation/ ; R01GM132137/NH/NIH HHS/United States ; DEB-1831730//National Science Foundation NSF/ ; },
mesh = {*Gene Transfer, Horizontal ; Animals ; Bees/microbiology/genetics ; *Genetic Speciation ; Bacteria/genetics ; Gastrointestinal Microbiome ; Host Microbial Interactions/genetics ; Symbiosis ; Homologous Recombination ; Evolution, Molecular ; },
abstract = {Microbial communities that maintain symbiotic relationships with animals evolve by adapting to the specific environmental niche provided by their host, yet understanding their patterns of speciation remains challenging. Whether bacterial speciation occurs primarily through allopatric or sympatric processes remains an open question. In addition, patterns of DNA transfers, which are pervasive in bacteria, are more constrained in a closed host-gut system. Eusocial bees have co-evolved with their specialized microbiota for over 85 million years, constituting a simple and valuable system to study the complex dynamics of host-associated microbial interactions. Here, we studied the patterns of speciation and evolution of seven specialized gut bacteria from three clades of eusocial bee species: western honey bees, eastern honey bees, and bumblebees. We conducted genomic analyses to infer species delineation relative to the patterns of homologous recombination (HR), and horizontal gene transfer (HGT). The studied bacteria presented various modes of evolution and speciation relative to their hosts, but some trends were consistent across all of them. We observed a clear interruption of HR between bacteria inhabiting different bee hosts, which is consistent with a mechanism of allopatric speciation, but we also identified interruptions of HR within hosts, suggesting recent or ongoing sympatric speciation. In contrast to HR, we observed that HGT events were not constrained by species borders. Overall, our findings show that in host-associated bacterial populations, patterns of HR and HGT have different impacts on speciation patterns, which are driven by both allopatric and sympatric speciation processes.},
}
@article {pmid39684674,
year = {2024},
author = {Wiśniewski, P and Chajęcka-Wierzchowska, W and Zadernowska, A},
title = {High-Pressure Processing Influences Antibiotic Resistance Gene Transfer in Listeria monocytogenes Isolated from Food and Processing Environments.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684674},
issn = {1422-0067},
support = {2018/29/B/NZ9/00645 (OPUS-15)//National Science Center/ ; },
mesh = {*Listeria monocytogenes/genetics/drug effects ; *Food Microbiology ; *Anti-Bacterial Agents/pharmacology ; Food Handling/methods ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Pressure ; Daucus carota/microbiology/genetics ; },
abstract = {The study aimed to assess the high-pressure processing (HPP) impact on antibiotic resistance gene transfer in L. monocytogenes from food and food processing environments, both in vitro (in microbiological medium) and in situ (in carrot juice), using the membrane filter method. Survival, recovery, and frequency of antibiotic resistance gene transfer analyses were performed by treating samples with HPP at different pressures (200 MPa and 400 MPa). The results showed that the higher pressure (400 MPa) had a significant effect on increasing the transfer frequency of genes such as fosX, encoding fosfomycin resistance, and tet_A1, tet_A3, tetC, responsible for tetracycline resistance, both in vitro and in situ. In contrast, the Lde gene (the gene encoding ciprofloxacin resistance) was not transferred under any conditions. In the food matrix (carrot juice), greater variability in results was observed, suggesting that food matrices may have a protective effect on bacteria and modify HPP efficacy. In general, an increase in MIC values for antibiotics was noted in transconjugants compared to donors. Genotypic analysis of transconjugants showed differences in genetic structure, especially after exposure to 400 MPa pressure, indicating genotypic changes induced by pressure stress. The study confirms the possibility of antibiotic resistance genes transfer in the food environment, even from strains showing initial susceptibility to antibiotics carrying so-called silent antibiotic resistance genes, highlighting the public health risk of the potential spread of antibiotic-resistant strains through the food chain. The findings suggest that high-pressure processing can increase and decrease the frequency of resistance gene transfer depending on the strain, antibiotic combination, and processing conditions.},
}
@article {pmid39671179,
year = {2024},
author = {Chen, X and Urban, JM and Wurlitzer, J and Wei, X and Han, J and E O'Connor, S and Rudolf, JD and Köllner, TG and Chen, F},
title = {Canonical terpene synthases in arthropods: Intraphylum gene transfer.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {51},
pages = {e2413007121},
pmid = {39671179},
issn = {1091-6490},
mesh = {Animals ; *Alkyl and Aryl Transferases/genetics/metabolism ; *Gene Transfer, Horizontal ; *Arthropods/genetics/enzymology ; *Phylogeny ; Male ; Female ; Evolution, Molecular ; Terpenes/metabolism ; },
abstract = {Insects employ terpenoids for communication both within and between species. While terpene synthases derived from isoprenyl diphosphate synthase have been shown to catalyze terpenoid biosynthesis in some insects, canonical terpene synthases (TPS) commonly found in plants, fungi, and bacteria were previously unidentified in insects. This study reveals the presence of TPS genes in insects, likely originating via horizontal gene transfer from noninsect arthropods. By examining 361 insect genomes, we identified TPS genes in five species of the Sciaridae family (fungus gnats). Additionally, TPS genes were found in Collembola (springtails) and Acariformes (mites) among diverse noninsect arthropods. Selected TPS enzymes from Sciaridae, Collembola, and Acariformes display monoterpene, sesquiterpene, and/or diterpene synthase activities. Through comprehensive protein database search and phylogenetic analysis, the TPS genes in Sciaridae were found to be most closely related to those in Acariformes, suggesting transfer of TPS genes from Acariformes to Sciaridae. In the model Sciaridae Bradysia coprophila, all five TPS genes are most highly expressed in adult males, suggesting a sex- and developmental stage-specific role of their terpenoid products. The finding of TPS genes in insects and their possible evolutionary origin through intraphylum gene transfer within arthropods sheds light on metabolic innovation in insects.},
}
@article {pmid39670763,
year = {2025},
author = {Dalia, TN and Dalia, AB},
title = {SbcB facilitates natural transformation in Vibrio cholerae in an exonuclease-independent manner.},
journal = {Journal of bacteriology},
volume = {207},
number = {1},
pages = {e0041924},
pmid = {39670763},
issn = {1098-5530},
support = {R35 GM128674/GM/NIGMS NIH HHS/United States ; R35GM128674//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*Vibrio cholerae/genetics/enzymology/metabolism ; *Bacterial Proteins/metabolism/genetics ; *Gene Transfer, Horizontal ; *Transformation, Bacterial ; *Exonucleases/metabolism/genetics ; Rec A Recombinases/metabolism/genetics ; },
abstract = {UNLABELLED: Natural transformation (NT) is a conserved mechanism of horizontal gene transfer in bacterial species. During this process, DNA is taken up into the cytoplasm where it can be integrated into the host genome by homologous recombination. We have previously shown that some cytoplasmic exonucleases inhibit NT by degrading ingested DNA prior to its successful recombination. However, one exonuclease, SbcB, counterintuitively promotes NT in Vibrio cholerae. Here, through a systematic analysis of the distinct steps of NT, we show that SbcB acts downstream of DNA uptake into the cytoplasm, but upstream of recombinational branch migration. Through mutational analysis, we show that SbcB promotes NT in a manner that does not rely on its exonuclease activity. Finally, we provide genetic evidence that SbcB directly interacts with the primary bacterial recombinase, RecA. Together, these data advance our molecular understanding of horizontal gene transfer in V. cholerae and reveal that SbcB promotes homologous recombination during NT in a manner that does not rely on its canonical exonuclease activity.<br><br>IMPORTANCE: Horizontal gene transfer by natural transformation contributes to the spread of antibiotic resistance and virulence factors in bacterial species. Here, we study how one protein, SbcB, helps facilitate this process in the facultative bacterial pathogen Vibrio cholerae. SbcB is a well-known for its exonuclease activity (i.e., the ability to degrade the ends of linear DNA). Through this study, we uncover that while SbcB is important for natural transformation, it does not facilitate this process using its exonuclease activity. Thus, this work helps further our understanding of the molecular events required for this conserved evolutionary process and uncovers a function for SbcB beyond its canonical exonuclease activity.},
}
@article {pmid39668116,
year = {2025},
author = {Fagerquist, CK and Shi, Y and Park, J},
title = {Colicin Immunity Proteins of Pathogenic Bacteria Detected by Antibiotic-Induced SOS Response, Plasmid Sequencing, MALDI-TOF-TOF Mass Spectrometry, and Top-Down Proteomic Analysis.},
journal = {Rapid communications in mass spectrometry : RCM},
volume = {39},
number = {5},
pages = {e9964},
doi = {10.1002/rcm.9964},
pmid = {39668116},
issn = {1097-0231},
support = {ARS project number 0500-00093-001-00-D//USDA-ARS/ ; USDA-ARS project numbers: 2030-42000-055-000-D//USDA-ARS/ ; 0500-00093-001-00-D//USDA-ARS/ ; 2030-42000-055-000-D//USDA-ARS/ ; },
mesh = {*Colicins/genetics/chemistry ; *Proteomics/methods ; *Plasmids/genetics ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; *Anti-Bacterial Agents/pharmacology ; *SOS Response, Genetics ; Escherichia coli Proteins/genetics ; Shiga-Toxigenic Escherichia coli/genetics ; Sequence Analysis, DNA ; },
abstract = {RATIONALE: Plasmids can play a major role in the survival of pathogenic bacteria. Plasmids are acquired through horizontal gene transfer resulting in their spread across various strains, species and genera of bacteria. Colicins are bacterial protein toxins expressed by plasmid genes and released against co-located bacterial competitors.<br><br>METHODS: Three Shiga toxin-producing E.&#x2009;coli (STEC), whose genomes were sequenced previously, were analyzed using a combination of antibiotic induction, MALDI-TOF-TOF mass spectrometry, top-down proteomic analysis, and small plasmid sequencing. Protein biomarkers were identified using in-house software that matches protein mass and fragment ions of backbone cleavage by the aspartic acid effect. Predicted in silico protein structures assisted in the interpretation of protein ion fragmentation.<br><br>RESULTS: In addition to proteomic identification of phage-encoded Shiga toxin, we were able to identify plasmid-encoded immunity proteins for colicin D and E3. The genes for these plasmid-encoded proteins were not found in the previous genomic sequencing. However, resequencing of these strains for small plasmids revealed the genes to be present on 7-8&#x2009;kb sized plasmids. Upstream of the colicin/immunity genes was an inverted repeat of the SOS/LexA box that represses gene expression until antibiotic challenge.<br><br>CONCLUSIONS: Our top-down proteomic method demonstrates that it is possible to screen putative pathogenic bacteria (whose genomes have been sequenced in full, in part or not at all) for the presence of phage- and plasmid-encoded toxin and colicin genes under SOS control. Small plasmid sequencing confirmed the presence of colicin/immunity genes (and their regulatory control) suggested from induction and top-down proteomic analysis.},
}
@article {pmid39667859,
year = {2025},
author = {Pham, VD and Gerlinsky, M and Lettrari, S and Gänzle, MG},
title = {Evolution and ecology of C30 carotenoid synthesis in Lactobacillaceae and application of pigmented lactobacilli in pasta production.},
journal = {Food microbiology},
volume = {127},
number = {},
pages = {104688},
doi = {10.1016/j.fm.2024.104688},
pmid = {39667859},
issn = {1095-9998},
mesh = {*Carotenoids/metabolism ; *Fermentation ; *Phylogeny ; *Flour/microbiology/analysis ; Lactobacillaceae/metabolism/genetics/classification/isolation &amp; purification ; Triticum/microbiology ; Food Microbiology ; Pigmentation ; Bacterial Proteins/genetics/metabolism ; Color ; },
abstract = {Pasta is a staple food in many parts of the world. A bright yellow colour of pasta is preferred by consumers. However, the colour is easily degraded during pasta processing. In a sourdough used for pasta production, we identified the pigmented Fructilactobacillus spp. FUA 3913, which represents a novel species that remains to be described ,and carries genes for the carotenoid-producing enzymes CrtM and CrtN in its genome. HPLC and spectral analysis identified the carotenoid as 4,4'-diaponeurosporene which is also produced by other lactobacilli expressing CrtM and CrtN. The topology of the CrtM/N trees does not match the phylogeny of the organisms, indicating that the enzymes were acquired by horizontal gene transfer. Pigmentation is frequent in insect-associated lactobacilli and lactobacilli that are part of the phyllosphere. Pigmented heterofermentative lactobacilli may enhance the yellow colour of durum semolina pasta by two mechanisms, first, by producing carotenoids and second, by preventing lipoxygenase-mediated degradation of durum carotenoids during dough mixing and extrusion. The comparison of the influence of fermentation with the non-pigmented, homofermentative Lactiplantibacillus plantarum, the non-pigmented heterofermentative Fructilactobacillus sanfranciscensis and the pigmented, heterofermentative Fructilactobacillus spp. FUA3913 indicated that inhibition of lipid oxidation is more relevant for the colour of pasta. In summary, our study provides novel insights into the evolution of C30 carotenoid and ecology of lactobacilli, and documents the use of pigmented lactobacilli to enhance the yellow colour of fermented foods.},
}
@article {pmid39667662,
year = {2025},
author = {Sandmann, G},
title = {Origin and evolution of yeast carotenoid pathways.},
journal = {Biochimica et biophysica acta. Molecular and cell biology of lipids},
volume = {1870},
number = {2},
pages = {159586},
doi = {10.1016/j.bbalip.2024.159586},
pmid = {39667662},
issn = {1879-2618},
mesh = {*Carotenoids/metabolism ; *Evolution, Molecular ; *Yeasts/metabolism/genetics ; },
abstract = {Carotenoid pathways exist in nature in all domains. Comparison of the genes involved and their distribution allowed the elucidation of the origin and evolution of carotenoid biosynthesis from an early common ancestor of prokaryotes to Bacteria and Archaea. From the latter domain, carotenogenic genes are inherited by fungi as the only phylum of Eukarya. Carotenoid biosynthesis in the algal-plant lineage emerged independently by endosymbiotic gene transfer from an engulfed carotenogenic cyanobacterium. The early set of carotenogenic genes included crtB of phytoene synthase, the desaturase gene crtI, and the lycopene cyclase gene crtYcd for the synthesis of β-carotene. This carotenoid is further metabolised either to zeaxanthin and retinal due to the presence of crtZ and ccd or elongated to a C50 carotenoids by the crtEb gene product. The diversified pathways, especially in bacteria and fungi, result from gene modifications altering the substrate and product specificities of the corresponding enzymes or from the acquisition of novel genes. This was highlighted in more detail for the carotenoid pathways in the red yeasts of Basidiomycota leading to torularhodin, 2'-plectaniaxanthin, and astaxanthin.},
}
@article {pmid39660924,
year = {2025},
author = {Christel, S and Carrell, AA and Hochanadel, LH and Villalobos Solis, MI and Abraham, PE and Jawdy, SS and Chaves, JE and Engle, NL and Berhane, T-K and Yao, T and Chen, J-G and Muchero, W and Tschaplinski, TJ and Cregger, MA and Michener, JK},
title = {Catabolic pathway acquisition by rhizosphere bacteria readily enables growth with a root exudate component but does not affect root colonization.},
journal = {mBio},
volume = {16},
number = {1},
pages = {e0301624},
pmid = {39660924},
issn = {2150-7511},
support = {//U.S. Department of Energy (DOE)/ ; },
mesh = {*Rhizosphere ; *Plant Roots/microbiology ; *Gene Transfer, Horizontal ; *Pseudomonas/metabolism/genetics ; *Soil Microbiology ; Metabolic Networks and Pathways/genetics ; Benzyl Alcohols/metabolism ; Plant Exudates/metabolism ; },
abstract = {Horizontal gene transfer (HGT) is a fundamental evolutionary process that plays a key role in bacterial evolution. The likelihood of a successful transfer event is expected to depend on the precise balance of costs and benefits resulting from pathway acquisition. Most experimental analyses of HGT have focused on phenotypes that have large fitness benefits under appropriate selective conditions, such as antibiotic resistance. However, many examples of HGT involve phenotypes that are predicted to provide smaller benefits, such as the ability to catabolize additional carbon sources. We have experimentally simulated the consequences of one such HGT event in the laboratory, studying the effects of transferring a pathway for catabolism of the plant-derived aromatic compound salicyl alcohol between rhizosphere isolates from the Pseudomonas genus. We find that pathway acquisition enables rapid catabolism of salicyl alcohol with only minor disruptions to the existing metabolic and regulatory networks of the new host. However, this new catabolic potential does not confer a measurable fitness advantage during competitive growth in the rhizosphere. We conclude that the phenotype of salicyl alcohol catabolism is readily transferable but is selectively neutral under environmentally relevant conditions. We propose that this condition is common and that HGT of many pathways will be self-limiting because the selective benefits are small.IMPORTANCEHorizontal gene transfer (HGT) is a key process in microbial evolution, but the factors limiting HGT are poorly understood. Aside from the rather unique scenario of antibiotic resistance, the evolutionary benefits of pathway acquisition are still unclear. To experimentally test the effects of pathway acquisition, we transferred a pathway for catabolism of a plant-derived aromatic compound between soil bacteria isolated from the roots of poplar trees and determined the resulting phenotypic and fitness effects. We found that pathway acquisition allowed bacteria to grow using the plant-derived compound in the laboratory, but that this new phenotype did not provide an advantage when the bacteria were reinoculated onto plant roots. These results suggest that the benefits of pathway acquisition may be small when measured under ecologically-relevant conditions. From an engineering perspective, efforts to alter microbial community composition in situ by manipulating catabolic pathways or nutrient availability will be challenging when gaining access to a new niche does not provide a benefit.},
}
@article {pmid39660283,
year = {2024},
author = {Fang, L and Chen, R and Li, C and Sun, J and Liu, R and Shen, Y and Guo, X},
title = {The association between the genetic structures of commonly incompatible plasmids in Gram-negative bacteria, their distribution and the resistance genes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1472876},
pmid = {39660283},
issn = {2235-2988},
mesh = {*Plasmids/genetics ; *Gram-Negative Bacteria/genetics/drug effects ; *Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Incompatible plasmids play a crucial role in the horizontal transfer of antibiotic resistance in bacteria, particularly in Gram-negative bacteria, and have thus attracted considerable attention in the field of microbiological research. In the 1970s, these plasmids, housing an array of resistance genes and genetic elements, were predominantly discovered. They exhibit a broad presence in diverse host bacteria, showcasing diversity in geographic distribution and the spectrum of antibiotic resistance genes. The complex genetic structure of plasmids further accelerates the accumulation of resistance genes in Gram-negative bacteria. This article offers a comprehensive review encompassing the discovery process, host distribution, geographic prevalence, carried resistance genes, and the genetic structure of different types incompatible plasmids, including IncA, IncC, IncF, IncL, IncM, IncH, and IncP. It serves as a valuable reference for enhancing our understanding of the role of these different types of plasmids in bacterial evolution and the dissemination of antibiotic resistance.},
}
@article {pmid39655960,
year = {2025},
author = {Tian, Q and Ye, H and Zhou, X and Wang, J and Zhang, L and Sun, W and Duan, C and Fan, M and Zhou, W and Bi, C and Ye, Q and Wong, A},
title = {Evaluating the health risk of probiotic supplements from the perspective of antimicrobial resistance.},
journal = {Microbiology spectrum},
volume = {13},
number = {1},
pages = {e0001924},
pmid = {39655960},
issn = {2165-0497},
support = {SpF2021002//Wenzhou-Kean University Student Partnering with Faculty (SpF) research program/ ; SpF2021029//Wenzhou-Kean University Student Partnering with Faculty (SpF) research program/ ; },
mesh = {*Probiotics/administration &amp; dosage/pharmacology ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Dietary Supplements ; Drug Resistance, Bacterial/genetics ; Streptomycin/pharmacology ; Caco-2 Cells ; Escherichia coli/drug effects/genetics ; Enterococcus faecalis/drug effects/genetics ; Microbial Sensitivity Tests ; Staphylococcus aureus/drug effects/genetics ; Erythromycin/pharmacology ; },
abstract = {UNLABELLED: Antimicrobial resistance remains a public health threat. Probiotics harboring antimicrobial resistant genes (ARGs) have, in recent years, been considered a potential health risk. Studies conducted on probiotics from increasingly popular health supplements have raised the possibility of transmitting ARGs to commensals in the human gut, concomitantly establishing a reservoir of ARGs and risking acquisition by opportunistic pathogens. Building on our previous study that reported multiple antibiotic resistance in probiotics of health supplements, in this research, we have attempted to detect their ARGs that may account for resistant phenotypes. ARGs responsible for tetracycline, macrolide, aminoglycoside, and glycopeptide resistance were prevalent in probiotics. Through laboratory adaptive evolution studies, we also show that streptomycin-adapted probiotics gained resistance to erythromycin, tetracycline, and doxycycline more effectively than non-adapted ones. When co-incubated with Enterococcus faecalis, Escherichia coli, or Staphylococcus aureus on Caco-2 and/or HCT-116 cells, streptomycin resistance was transferred from the adapted probiotics to generate transconjugants at frequencies comparable to or higher than that of other studies conducted through filter mating. Consistently, ARGs conferring resistance to streptomycin (aadA) and erythromycin [erm(B)-1] were detected in E. coli and S. aureus transconjugants, respectively, after co-incubation with streptomycin-adapted probiotics on Caco-2 cells. aadA and erm(B)-1 were both detected in E. faecalis transconjugant after the same co-incubation on HCT-116 cells. Our data and future comparative genomics and metagenomics studies conducted on animal models and in healthy, immunocompromised, and/or antibiotic-treated human cohorts will contribute to a more comprehensive understanding of probiotic consumption, application, and safety.<br><br>IMPORTANCE: Probiotics are becoming increasingly popular, with promising applications in food and medicine, but the risk of transferring ARGs to disease-causing bacteria has raised concerns. Our study detected ARGs in probiotics of health supplements conferring resistance to tetracycline, macrolide, aminoglycoside, and glycopeptide drugs. Streptomycin-adapted probiotics also gained resistance to other antibiotics more effectively than non-adapted ones. Importantly, we showed that streptomycin resistance could be transferred to other bacteria after co-incubation with probiotics on human intestinal cells. ARGs responsible for erythromycin and streptomycin resistance, which were initially absent in the recipient bacteria, were also detected in the transconjugants. Our data build the foundation for future studies that will be conducted on animal models and in humans and leveraging advanced metagenomics approaches to clarify the long-term health risk of probiotic consumption.},
}
@article {pmid39653497,
year = {2024},
author = {St Leger, RJ},
title = {The evolution of complex Metarhizium-insect-plant interactions.},
journal = {Fungal biology},
volume = {128},
number = {8 Pt B},
pages = {2513-2528},
doi = {10.1016/j.funbio.2024.01.001},
pmid = {39653497},
issn = {1878-6146},
mesh = {*Metarhizium/genetics/pathogenicity/physiology ; Animals ; *Insecta/microbiology ; *Plants/microbiology ; Gene Transfer, Horizontal ; Symbiosis ; Biological Evolution ; Host Specificity ; Host-Pathogen Interactions ; },
abstract = {Metarhizium species interact with plants, insects, and microbes within a diffuse coevolutionary framework that benefits soil health, biodiversity, and plant growth. The insect host ranges of these fungi vary greatly. Specialization to a narrow host range usually occurs in the tropics with its stable insect populations, and is characterized by the rapid evolution of existing protein sequences, sexual recombination, and small genomes. Host-generalists are associated with temperate regions and ephemeral insect populations. Their mutualistic plant-colonizing lifestyle increases survival when insects are rare, while facultative entomopathogenicity feeds both the fungi and plants when insects are common. Generalists have lost meiosis and associated genome defense mechanisms, enabling gene duplications to diversify functions related to plant colonization and host exploitation. Horizontal gene transfer events via transposons have also contributed to host range changes, while parasexuality combines beneficial mutations within individual clones of generalists. There is also a lot of genetic variation in insect populations and both pathogen virulence and insect immunity are linked with variations in stress responses. Thus, susceptibility to generalists can vary due to non-specific resistance to multiple stressors, multipurpose physical and chemical barriers, and heterogeneity in physiological and behavioral factors, such as sleep.},
}
@article {pmid39647412,
year = {2024},
author = {He, T and Xie, J and Jin, L and Zhao, J and Zhang, X and Liu, H and Li, XD},
title = {Seasonal dynamics of the phage-bacterium linkage and associated antibiotic resistome in airborne PM2.5 of urban areas.},
journal = {Environment international},
volume = {194},
number = {},
pages = {109155},
doi = {10.1016/j.envint.2024.109155},
pmid = {39647412},
issn = {1873-6750},
mesh = {*Bacteriophages/genetics ; *Particulate Matter ; China ; *Bacteria/genetics/drug effects ; *Seasons ; Humans ; Air Microbiology ; Cities ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Air Pollutants/analysis ; Metagenomics ; Drug Resistance, Bacterial/genetics ; Microbiota ; },
abstract = {Inhalable microorganisms in airborne fine particulate matter (PM2.5), including bacteria and phages, are major carriers of antibiotic resistance genes (ARGs) with strong ecological linkages and potential health implications for urban populations. A full-spectrum study on ARG carriers and phage-bacterium linkages will shed light on the environmental processes of antibiotic resistance from airborne dissemination to the human lung microbiome. Our metagenomic study reveals the seasonal dynamics of phage communities in PM2.5, their impacts on clinically important ARGs, and potential implications for the human respiratory microbiome in selected cities of China. Gene-sharing network comparisons show that air harbours a distinct phage community connected to human- and water-associated viromes, with 57 % of the predicted hosts being potential bacterial pathogens. The ARGs of common antibiotics, e.g., peptide and tetracycline, dominate both the antibiotic resistome associated with bacteria and phages in PM2.5. Over 60 % of the predicted hosts of vARG-carrying phages are potential bacterial pathogens, and about 67 % of these hosts have not been discovered as direct carriers of the same ARGs. The profiles of ARG-carrying phages are distinct among urban sites, but show a significant enrichment in abundance, diversity, temperate lifestyle, and matches of CRISPR (short for 'clustered regularly interspaced short palindromic repeats') to identified bacterial genomes in winter and spring. Moreover, phages putatively carry 52 % of the total mobile genetic element (MGE)-ARG pairs with a unique 'flu season' pattern in urban areas. This study highlights the role that phages play in the airborne dissemination of ARGs and their delivery of ARGs to specific opportunistic pathogens in human lungs, independent of other pathways of horizontal gene transfer. Natural and anthropogenic stressors, particularly wind speed, UV index, and level of ozone, potentially explained over 80 % of the seasonal dynamics of phage-bacterial pathogen linkages on antibiotic resistance. Therefore, understanding the phage-host linkages in airborne PM2.5, the full-spectrum of antibiotic resistomes, and the potential human pathogens involved, will be of benefit to protect human health in urban areas.},
}
@article {pmid39644844,
year = {2025},
author = {Liu, X and Fan, Q and Li, F and Wu, C and Yi, S and Lu, H and Wu, Y and Liu, Y and Tian, J},
title = {Assessing foodborne health risks from dietary exposure to antibiotic resistance genes and opportunistic pathogens in three types of vegetables: An in vitro simulation of gastrointestinal digestion.},
journal = {Journal of hazardous materials},
volume = {484},
number = {},
pages = {136731},
doi = {10.1016/j.jhazmat.2024.136731},
pmid = {39644844},
issn = {1873-3336},
mesh = {*Vegetables/microbiology ; Risk Assessment ; Humans ; *Dietary Exposure ; Genes, Bacterial ; Digestion ; Bacteria/genetics ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Foodborne health risks posed by antibiotic resistant genes (ARGs) and pathogenic bacteria have garnered increasing global attention. However, the patterns of their propagation and reduction, as well as the resulting health risks in the human gastrointestinal tract, remain unknown. We employed leafy vegetables (water spinach), solanaceous vegetables (pepper), and root vegetables (radish) to investigate the propagation and reduction patterns of ARGs and pathogenic bacteria within an in vitro simulated digestion system. This system mimicked the soil-vegetable-stomach-small intestine (SVSTI) transmission chain. We found that kan, oqxA, and multidrug resistance genes were enriched by 1.10-fold, 11.2-fold, and 2.21-fold, respectively, along the transmission chain. The succession of bacterial communities and horizontal gene transfer mediated by intl1 were identified as the primary drivers of ARG accumulation. Notably, certain pathogenic bacteria (Bacillus cereus, Klebsiella pneumoniae) accumulated in the intestinal environment. According to our proposed health risk assessment system, Bacillus species, as potential ARG hosts, and multidrug ARGs are at a higher risk of exposure to intestinal environment through the transmission chain. Our findings highlight the significant health risks associated with the intake of ARGs and pathogenic bacteria carried by vegetables, emphasizing an urgent need to implement effective biological control measures in vegetable production and consumption.},
}
@article {pmid39642748,
year = {2025},
author = {Lin, H and Diarra, MS and Jia, G and Zhao, X},
title = {Detection of plasmids in Salmonella from poultry and investigating the potential horizontal transfer of antimicrobial resistance and virulence genes: PLASMID TRANSFER OF RESISTANCE AND VIRULENCE.},
journal = {Poultry science},
volume = {104},
number = {1},
pages = {104591},
pmid = {39642748},
issn = {1525-3171},
mesh = {*Plasmids/genetics ; Animals ; *Salmonella/genetics/pathogenicity/drug effects ; *Gene Transfer, Horizontal ; *Poultry Diseases/microbiology ; Virulence/genetics ; *Salmonella Infections, Animal/microbiology ; *Drug Resistance, Bacterial/genetics ; Chickens ; Anti-Bacterial Agents/pharmacology ; Poultry ; },
abstract = {Antimicrobial resistance genes (ARGs) and virulence genes (VGs) have been widely reported in Salmonella which are major foodborne pathogens from poultry. This study assessed the replicon typing and conjugative ability of plasmids from poultry-derived Salmonella as well as ARGs and VGs carried by these plasmids using an in silico approach. Both PlasmidFinder 2.1 and VRprofile2 were employed to detect plasmids in Salmonella sequences downloaded from the National Center for Biotechnology Information (NCBI) Reference Sequences (RefSeq) database, and then oriTfinder was used to determine the conjugative ability of plasmids. The ARGs and VGs on plasmids were identified by both VRprofile2 and oriTfinder. The phenotypes of ARGs were predicted by ResFinder 4.1 and oriTfinder, while the phenotypes of virulence were predicted by oriTfinder and VRprofile2. We identified 183 plasmid sequences from 309 downloaded sequences. Among them, 77 (42.1 %) plasmids were conjugative, 25 (13.7 %) mobilizable, and 81 (44.3 %) non-mobilizable. Fifty-one plasmids (27.9 %) contained multi-replicons. One hundred and five plasmids carried 58 ARGs, belonging to 12 classes. The most prevalent ARG groups in plasmids were the aminoglycoside, β-lactam, sulfonamide, and tetracycline groups. In addition, 49 plasmids carried 36 different VGs belonging to 13 gene classes. The most prevalent VG groups were the adhesin, type III secretion system, and resistance to complement killing groups. The detected high percentage of conjugative plasmids and existence of many multiple replicons suggest possible high rates of plasmid-mediated horizontal gene transfer (HGT) events. Detection of previously unreported plasmid-borne VG (fdeC) from Salmonella in poultry calls for more vigilant monitoring.},
}
@article {pmid39642232,
year = {2024},
author = {Urquhart, AS and Gluck-Thaler, E and Vogan, AA},
title = {Gene acquisition by giant transposons primes eukaryotes for rapid evolution via horizontal gene transfer.},
journal = {Science advances},
volume = {10},
number = {49},
pages = {eadp8738},
pmid = {39642232},
issn = {2375-2548},
mesh = {*Gene Transfer, Horizontal ; *DNA Transposable Elements/genetics ; *Evolution, Molecular ; Phylogeny ; Eukaryota/genetics ; Fungi/genetics ; Multigene Family ; Genome, Fungal ; },
abstract = {Horizontal gene transfer (HGT) disseminates genetic information between species and is a powerful mechanism of adaptation. Yet, we know little about its underlying drivers in eukaryotes. Giant Starship transposons have been implicated as agents of fungal HGT, providing an unprecedented opportunity to reveal the evolutionary parameters behind this process. Here, we characterize the ssf gene cluster, which contributes to formaldehyde resistance, and use it to demonstrate how mobile element evolution shapes fungal adaptation. We found that ssf clusters have been acquired by various distantly related Starships, which each exhibit multiple instances of horizontal transfer across fungal species (at least nine events, including between different taxonomic orders). Many ssf clusters have subsequently integrated into their host's genome, illustrating how Starships shape the evolutionary trajectory of fungal hosts beyond any single transfer. Our results demonstrate the key role Starships play in mediating rapid and repeated adaptation via HGT, elevating the importance of mobile element evolution in eukaryotic biology.},
}
@article {pmid39642107,
year = {2024},
author = {Wingfield, BD and Wingfield, MJ},
title = {Gene transfer between fungal species triggers repeated coffee wilt disease outbreaks.},
journal = {PLoS biology},
volume = {22},
number = {12},
pages = {e3002901},
pmid = {39642107},
issn = {1545-7885},
mesh = {*Plant Diseases/microbiology ; *Gene Transfer, Horizontal ; *Disease Outbreaks ; Coffea/microbiology ; Coffee/microbiology ; DNA Transposable Elements/genetics ; },
abstract = {Two outbreaks of coffee wilt disease have devastated African coffee production. A PLOS Biology study suggests that horizontal gene transfer via large Starship transposons between 2 fungal species played a key role in the repeated emergence of the disease.},
}
@article {pmid39642000,
year = {2024},
author = {Villavicencio, F and Albán, V and Satán, C and Quintana, H and Enríquez, W and Jaramillo, K and Flores, F and Arisqueta, L},
title = {Salmonella enterica Serovar Infantis KPC-2 Producer: First Isolate Reported in Ecuador.},
journal = {Microbial drug resistance (Larchmont, N.Y.)},
volume = {30},
number = {12},
pages = {502-508},
doi = {10.1089/mdr.2024.0072},
pmid = {39642000},
issn = {1931-8448},
mesh = {Ecuador ; *Anti-Bacterial Agents/pharmacology ; *beta-Lactamases/genetics ; *Salmonella enterica/drug effects/genetics ; Humans ; *Microbial Sensitivity Tests ; *Plasmids ; *Whole Genome Sequencing ; Serogroup ; Salmonella Infections/microbiology/drug therapy ; Gene Transfer, Horizontal ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {Antimicrobial resistance is currently considered a public health threat. Carbapenems are antimicrobials for hospital use, and Enterobacterales resistant to these β-lactams have spread alarmingly in recent years, especially those that cause health care-associated infections. The blaKPC gene is considered one of the most important genetic determinants disseminated by plasmids, promoting horizontal gene transfer. This study describes, for the first time in Ecuador, and worldwide, the presence of a blaKPC-2 gene in an isolate of Salmonella enterica serovar Infantis from a clinical sample. Through whole-genome sequencing, we characterized the genetic determinants of antimicrobial resistance in this Salmonella ST-32 strain. Our results showed the presence of several resistance genes, including blaCTX-M-65, and a conjugative plasmid Kpn-WC17-007-03 that may be responsible for the horizontal transference of these resistance mechanisms.},
}
@article {pmid39640918,
year = {2024},
author = {Baede, VO and Jlassi, O and Lesiczka, PM and Younsi, H and Jansen, HJ and Dachraoui, K and Segobola, J and Ben Said, M and Veneman, WJ and Dirks, RP and Sprong, H and Zhioua, E},
title = {Similarities between Ixodes ricinus and Ixodes inopinatus genomes and horizontal gene transfer from their endosymbionts.},
journal = {Current research in parasitology &amp; vector-borne diseases},
volume = {6},
number = {},
pages = {100229},
pmid = {39640918},
issn = {2667-114X},
abstract = {The taxa Ixodes ricinus and Ixodes inopinatus are sympatric in Tunisia. The genetics underlying their morphological differences are unresolved. In this study, ticks collected in Jouza-Amdoun, Tunisia, were morphologically identified and sequenced using Oxford Nanopore Technologies. Three complete genome assemblies of I. inopinatus and three of I. ricinus with BUSCO scores of ∼98% were generated, including the reconstruction of mitochondrial genomes and separation of both alleles of the TRPA1, TROSPA and calreticulin genes. Deep sequencing allowed the first descriptions of complete bacterial genomes for "Candidatus Midichloria mitochondrii", Rickettsia helvetica and R. monacensis from North Africa, and the discovery of extensive integration of parts of the Spiroplasma ixodetis and "Ca. M. mitochondrii" into the nuclear genome of these ticks. Phylogenetic analyses of the mitochondrial genome, the nuclear genes, and symbionts showed differentiation between Tunisian and Dutch ticks, but high genetic similarities between Tunisian I. ricinus and I. inopinatus. Subtraction of the genome assemblies identified the presence of some unique sequences, which could not be confirmed when screening a larger batch of I. ricinus and I. inopinatus ticks using PCR. Our findings yield compelling evidence that I. inopinatus is genetically highly similar, if not identical, to sympatric I. ricinus. Defined morphological differences might be caused by extrinsic factors such as micro-climatic conditions or bloodmeal composition. Our findings support the existence of different lineages of I. ricinus as well of its symbionts/pathogens from geographically dispersed locations.},
}
@article {pmid39637834,
year = {2024},
author = {Peck, LD and Llewellyn, T and Bennetot, B and O'Donnell, S and Nowell, RW and Ryan, MJ and Flood, J and Rodríguez de la Vega, RC and Ropars, J and Giraud, T and Spanu, PD and Barraclough, TG},
title = {Horizontal transfers between fungal Fusarium species contributed to successive outbreaks of coffee wilt disease.},
journal = {PLoS biology},
volume = {22},
number = {12},
pages = {e3002480},
pmid = {39637834},
issn = {1545-7885},
mesh = {*Plant Diseases/microbiology ; *Fusarium/genetics/pathogenicity/isolation &amp; purification ; *Gene Transfer, Horizontal ; *Coffea/microbiology/genetics ; *Genome, Fungal/genetics ; Phylogeny ; Disease Outbreaks ; Host Specificity ; },
abstract = {Outbreaks of fungal diseases have devastated plants and animals throughout history. Over the past century, the repeated emergence of coffee wilt disease caused by the fungal pathogen Fusarium xylarioides severely impacted coffee production across sub-Saharan Africa. To improve the disease management of such pathogens, it is crucial to understand their genetic structure and evolutionary potential. We compared the genomes of 13 historic strains spanning 6 decades and multiple disease outbreaks to investigate population structure and host specialisation. We found that F. xylarioides comprised at least 4 distinct lineages: 1 host-specific to Coffea arabica, 1 to C. canephora var. robusta, and 2 historic lineages isolated from various Coffea species. The presence/absence of large genomic regions across populations, the higher genetic similarities of these regions between species than expected based on genome-wide divergence and their locations in different loci in genomes across populations showed that horizontal transfers of effector genes from members of the F. oxysporum species complex contributed to host specificity. Multiple transfers into F. xylarioides populations matched different parts of the F. oxysporum mobile pathogenicity chromosome and were enriched in effector genes and transposons. Effector genes in this region and other carbohydrate-active enzymes important in the breakdown of plant cell walls were shown by transcriptomics to be highly expressed during infection of C. arabica by the fungal arabica strains. Widespread sharing of specific transposons between F. xylarioides and F. oxysporum, and the correspondence of a putative horizontally transferred regions to a Starship (large mobile element involved in horizontal gene transfers in fungi), reinforce the inference of horizontal transfers and suggest that mobile elements were involved. Our results support the hypothesis that horizontal gene transfers contributed to the repeated emergence of coffee wilt disease.},
}
@article {pmid39637801,
year = {2025},
author = {Zhang, S and Zheng, S and Gong, Y and Wang, Y and Wei, Q and Zhu, Y and Liu, L and Wu, R and Du, S},
title = {Does the herbicide napropamide exhibit enantioselective effects across genus plasmid transfer from Escherichia coli to Bacillus subtilis?.},
journal = {Journal of hazardous materials},
volume = {484},
number = {},
pages = {136704},
doi = {10.1016/j.jhazmat.2024.136704},
pmid = {39637801},
issn = {1873-3336},
mesh = {*Herbicides/chemistry/pharmacology/toxicity ; *Escherichia coli/genetics/drug effects ; *Bacillus subtilis/genetics/drug effects ; *Plasmids/genetics ; Stereoisomerism ; Molecular Docking Simulation ; Conjugation, Genetic/drug effects ; Gene Transfer, Horizontal/drug effects ; },
abstract = {The dissemination of plasmid-borne antibiotic resistance genes (ARGs) into the environment is an urgent concern. However, the enantioselective effects of herbicides on plasmid conjugation among bacterial genera and their underlying mechanisms remain unclear. This study demonstrates for the first time that the herbicide napropamide (NAP), commonly used in vegetable fields, exhibits a concentration-dependent effect on the transfer efficiency of the pBE2R plasmid from Escherichia coli to Bacillus subtilis. Notably, at a concentration of 5 mg L[-1], R-NAP increased transfer efficiency by threefold compared to the S-enantiomer. Scanning electron microscopy revealed that R-NAP caused less structural damage to bacteria than S-NAP but more effectively reduced cell wall components (lipopolysaccharides and peptidoglycan) in donor and recipient bacteria, increasing reactive oxygen species levels and membrane permeability. Transcriptomic analysis indicated that NAP enantiomers altered the expression of genes related to membrane transport activity and transposons. Cross-domain network analysis identified yieK, ygeH, and ydbL as key genes mediating conjugation transfer. Molecular docking results showed that NAP likely interacts hydrophobically with the active sites of the proteins encoded by these genes. In conclusion, herbicides like R-NAP should be carefully managed in fields irrigated with livestock manure to mitigate the risk of ARG transfer and accumulation in crops.},
}
@article {pmid39637780,
year = {2025},
author = {Huang, C and Cui, M and Li, T and Zheng, C and Qiu, M and Shan, M and Li, B and Zhang, L and Yu, Y and Fang, H},
title = {Migration of fungicides, antibiotics and resistome in the soil-lettuce system.},
journal = {Journal of hazardous materials},
volume = {484},
number = {},
pages = {136725},
doi = {10.1016/j.jhazmat.2024.136725},
pmid = {39637780},
issn = {1873-3336},
mesh = {*Fungicides, Industrial/analysis ; *Anti-Bacterial Agents/pharmacology/analysis ; *Soil Microbiology ; *Lactuca/microbiology ; *Soil Pollutants/analysis ; Bacteria/genetics/drug effects ; Gene Transfer, Horizontal ; Genes, Bacterial ; },
abstract = {The emergence and spread of antibiotic resistance genes (ARGs) have become a serious issue in global agricultural production. However, understanding how these ARGs spread across different spatial scales, especially when exposed to both pesticides and antibiotics, has remained a challenge. Here, metagenomic assembly and binning methodologies were used to determine the spread pathway of ARGs in the soil-lettuce system under individual and combined exposure of fungicides (carbendazim and pyraclostrobin) and antibiotics (chlortetracycline and ciprofloxacin). These agrochemicals not only facilitated the spread of ARGs from soil to lettuce but also significantly elevated the risk of developing multi-antibiotic resistance among bacteria, especially to some antibiotic types (i.e. sulfonamide, aminoglycoside, quinolone, and tetracycline). ARGs could be migrated through distinct pathways, including both vertical and horizontal gene transfer, with plasmids playing a crucial role in facilitating the horizontal gene transfer. These transfer pathways have enabled key pathogenic bacteria belonging to the genera Acinetobacter, Pseudomonas, and Pantoea to acquire resistance and remain recalcitrant, posing the potential risk to crop health and food safety. In summary, our findings highlighted that fungicide and antibiotic could drive upward migration of ARGs in the soil-lettuce system and reduced the quality safety of agricultural products.},
}
@article {pmid39636264,
year = {2024},
author = {Romanov, KA and O'Connor, TJ},
title = {Legionella pneumophila, a Rosetta stone to understanding bacterial pathogenesis.},
journal = {Journal of bacteriology},
volume = {206},
number = {12},
pages = {e0032424},
pmid = {39636264},
issn = {1098-5530},
support = {R21 AI119580/AI/NIAID NIH HHS/United States ; 1R21AI166238//HHS | National Institutes of Health (NIH)/ ; 1R01A1163273//HHS | National Institutes of Health (NIH)/ ; 1R01AI125402//HHS | National Institutes of Health (NIH)/ ; 1R21AI119580//HHS | National Institutes of Health (NIH)/ ; R01 AI125402/AI/NIAID NIH HHS/United States ; },
mesh = {*Legionella pneumophila/pathogenicity/genetics/physiology ; Humans ; *Host-Pathogen Interactions ; *Legionnaires' Disease/microbiology ; *Virulence Factors/genetics/metabolism ; Amoeba/microbiology ; Animals ; Host Specificity ; Virulence ; },
abstract = {Legionella pneumophila is an environmentally acquired pathogen that causes respiratory disease in humans. While the discovery of L. pneumophila is relatively recent compared to other bacterial pathogens, over the past 50 years, L. pneumophila has emerged as a powerhouse for studying host-pathogen interactions. In its natural habitat of fresh water, L. pneumophila interacts with a diverse array of protozoan hosts and readily evolve to expand their host range. This has led to the accumulation of the most extensive arsenal of secreted virulence factors described for a bacterial pathogen and their ability to infect humans. Within amoebae and human alveolar macrophages, the bacteria replicate within specialized membrane-bound compartments, establishing L. pneumophila as a model for studying intracellular vacuolar pathogens. In contrast, the virulence factors required for intracellular replication are specifically tailored to individual host cells types, allowing the pathogen to adapt to variation between disparate niches. The broad host range of this pathogen, combined with the extensive diversity and genome plasticity across the Legionella genus, has thus established this bacterium as an archetype to interrogate pathogen evolution, functional genomics, and ecology. In this review, we highlight the features of Legionella that establish them as a versatile model organism, new paradigms in bacteriology and bacterial pathogenesis resulting from the study of Legionella, as well as current and future questions that will undoubtedly expand our understanding of the complex and intricate biology of the microbial world.},
}
@article {pmid39631624,
year = {2025},
author = {Chen, W and Li, Z and Zheng, J and Wang, D and Gao, S and Zhou, W and Shen, H and Zhang, Y and Cao, X},
title = {A comprehensive analysis of the epidemiological and genomic characteristics of global Serratia Marcescens.},
journal = {Journal of global antimicrobial resistance},
volume = {40},
number = {},
pages = {81-89},
doi = {10.1016/j.jgar.2024.11.013},
pmid = {39631624},
issn = {2213-7173},
mesh = {*Serratia marcescens/genetics/drug effects/classification/isolation &amp; purification ; Humans ; *Serratia Infections/epidemiology/microbiology ; Phylogeny ; *Genome, Bacterial ; Genomics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; beta-Lactamases/genetics ; Bacterial Proteins/genetics ; Drug Resistance, Bacterial/genetics ; Global Health ; },
abstract = {BACKGROUND: Serratia marcescens outbreaks present significant challenges in clinical treatment, necessitating a deeper understanding of its epidemiological and genomic traits.<br><br>OBJECTIVE: To analyse the epidemiological and genomic characteristics of S. marcescens at a global scale.<br><br>METHODS: High-quality genomes of S. marcescens were retrieved from NCBI and annotated using Prodigal. Antibiotic resistance genes (ARGs) were identified via Blastn, sequence types (STs) were determined with a proprietary tool, and phylogenetic analysis was conducted to explore evolutionary relationships.<br><br>RESULTS: The study analysed genomes from 33 countries, with major contributions from the USA (27.8%), UK (15.3%), Italy (14.7%), and Japan (10.7%). Human clinical samples accounted for 73.5% of the isolates, primarily from blood (44.8%) and sputum (19.3%). Eleven ARGs were identified, with sde being the most prevalent. Carbapenemase genes included blaSME, blaKPC, and blaNDM-1, though co-occurrence in individual strains was absent. Novel ARGs, including armA, rmtC, and fosA7.2, were reported. Among 855 genomes with identified STs, ST366, ST367, ST365, and ST423 were most common. Phylogenetic analysis highlighted significant genetic diversity and distinct evolutionary lineages.<br><br>CONCLUSION: Temporal analysis showed a genome peak in 2019, underscoring the global prevalence and adaptability of S. marcescens. The distribution of ARGs across diverse STs emphasizes horizontal gene transfer as a key driver of resistance. Judicious antibiotic use is essential to mitigate further resistance.},
}
@article {pmid39631390,
year = {2025},
author = {Feyissa, BA and de Becker, EM and Salesse-Smith, CE and Shu, M and Zhang, J and Yates, TB and Xie, M and De, K and Gotarkar, D and Chen, MSS and Jawdy, SS and Carper, DL and Barry, K and Schmutz, J and Weston, DJ and Abraham, PE and Tsai, CJ and Morrell-Falvey, JL and Taylor, G and Chen, JG and Tuskan, GA and Long, SP and Burgess, SJ and Muchero, W},
title = {An orphan gene BOOSTER enhances photosynthetic efficiency and plant productivity.},
journal = {Developmental cell},
volume = {60},
number = {5},
pages = {723-734.e7},
doi = {10.1016/j.devcel.2024.11.002},
pmid = {39631390},
issn = {1878-1551},
mesh = {*Photosynthesis/genetics ; *Populus/genetics/growth &amp; development/metabolism ; Arabidopsis/genetics/metabolism/growth &amp; development ; Gene Expression Regulation, Plant ; Genome-Wide Association Study ; Ribulose-Bisphosphate Carboxylase/genetics/metabolism ; Plants, Genetically Modified ; *Genes, Plant ; Biomass ; *Plant Proteins/genetics/metabolism ; Plastids/metabolism/genetics ; },
abstract = {Organelle-to-nucleus DNA transfer is an ongoing process playing an important role in the evolution of eukaryotic life. Here, genome-wide association studies (GWAS) of non-photochemical quenching parameters in 743 Populus trichocarpa accessions identified a nuclear-encoded genomic region associated with variation in photosynthesis under fluctuating light. The identified gene, BOOSTER (BSTR), comprises three exons, two with apparent endophytic origin and the third containing a large fragment of plastid-encoded Rubisco large subunit. Higher expression of BSTR facilitated anterograde signaling between nucleus and plastid, which corresponded to enhanced expression of Rubisco, increased photosynthesis, and up to 35% greater plant height and 88% biomass in poplar accessions under field conditions. Overexpression of BSTR in Populus tremula × P. alba achieved up to a 200% in plant height. Similarly, Arabidopsis plants heterologously expressing BSTR gained up to 200% in biomass and up to 50% increase in seed.},
}
@article {pmid39631158,
year = {2025},
author = {Wang, Y and Liu, X and Huang, C and Han, W and Gu, P and Jing, R and Yang, Q},
title = {Antibiotic resistance genes and virulence factors in the plastisphere in wastewater treatment plant effluent: Health risk quantification and driving mechanism interpretation.},
journal = {Water research},
volume = {271},
number = {},
pages = {122896},
doi = {10.1016/j.watres.2024.122896},
pmid = {39631158},
issn = {1879-2448},
mesh = {*Wastewater/microbiology ; *Drug Resistance, Microbial/genetics ; *Virulence Factors ; Waste Disposal, Fluid ; Biofilms ; Water Pollutants, Chemical ; Risk Assessment ; },
abstract = {Microplastics (MPs) are ubiquitous in wastewater treatment plants (WWTPs) and provide a unique niche for the spread of pollutants. To date, risk assessments and driving mechanisms of pathogens, antibiotic resistance genes (ARGs), and virulence factors (VFs) in the plastisphere are still lacking. Here, the microbiota, ARGs, VFs, their potential health risks, and biologically driving mechanisms on polythene (PE), polyethylene terephthalate (PET), poly (butyleneadipate-co-terephthalate) and polylactic acid blends (PBAT/PLA), PLA MPs, and gravel in WWTP effluent were investigated. The results showed that plastisphere and gravel biofilm harbored more distinctive microorganisms, promoting the uniqueness of pathogens, ARGs, and VFs compared to WWTP effluent. The abundance of major pathogens, ARGs, and VFs in the plastisphere was 1.01-1.35 times higher than that in the effluent. The high health risk of ARGs (HRA) calculated by fully considering the abundance, clinical relevance, pathogenicity, accessibility and mobility, and the high proportion of resistance contigs with mobile genetic elements confirmed that the plastisphere posed the highest potential health risk. Candidatus Microthrix and Candidatus Promineifilum were the essential hosts of ARGs and VFs in the plastisphere and gravel biofilm, respectively. High metabolic activity such as amino acid metabolism and biosynthesis of secondary metabolites, and highly expressed key genes increased the synthesis of ARGs and VFs. The primary mechanisms driving ARG enrichment in the plastisphere were enhanced microbial metabolic activity, increased frequency of horizontal gene transfer, heightened antibiotic inactivation and efflux, and reduced cell permeability. This study provided new insights into the ARGs, VFs, and health risks of the plastisphere and emphasized the importance of strict control of wastewater discharge.},
}
@article {pmid39630207,
year = {2025},
author = {Markert, EX and Severe, L and Severe, K and Twing, KI and Ward, LM},
title = {Genomes of novel Serratia strains from suburban soil.},
journal = {Microbiology resource announcements},
volume = {14},
number = {1},
pages = {e0086624},
pmid = {39630207},
issn = {2576-098X},
abstract = {Here, we present genomes of three strains of Serratia initially isolated from suburban soil-one strain of S. ureilytica and two strains of S. quinivorans-resistant to multiple classes of antibiotics. This expands the genomic sampling of a group relevant to the ecosystem and human health.},
}
@article {pmid39628168,
year = {2024},
author = {Gu, JY and Li, WY and Zhou, Y and Zhang, GS},
title = {[Environmental Pollution and Extraction Methods of Extracellular Antibiotic Resistance Genes in Water].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {45},
number = {12},
pages = {7041-7048},
doi = {10.13227/j.hjkx.202401087},
pmid = {39628168},
issn = {0250-3301},
mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/isolation &amp; purification/drug effects ; China ; *Drug Resistance, Bacterial/genetics ; Environmental Monitoring ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Water Microbiology ; },
abstract = {Antibiotics are widely used to treat diseases such as bacterial infections. However, the abuse of antibiotics has led to the spread of antibiotic resistant bacteria and intracellular and extracellular antibiotic resistance genes, making China one of the countries with the highest incidence of antibiotic resistance and thus threatening public health. Extracellular antibiotic resistance genes, as one of the novel environmental pollutants, could exist in water for a long time and could be transmitted between different bacteria through horizontal gene transfer, resulting in the spread of antibiotic resistance. At present, due to the limitation of enrichment and recovery methods, the in-depth studies of extracellular antibiotic resistance genes in water have been rarely reported. Thus, it is impossible to carry out effective supervision and risk assessments. Based on literature analysis and investigation, the pollution sources, current situations, and characteristics of extracellular antibiotic resistance genes in water are expounded. Meanwhile, the advantages and disadvantages of their enrichment and recovery methods are compared and analyzed and the enrichment and recovery methods are verified and discussed through practical cases. These provide theoretical reference for studies such as examining extracellular antibiotic resistance genes in water on their transmission and provide a technical basis for antibiotic resistance control and health risk assessments of extracellular antibiotic resistance genes.},
}
@article {pmid39626640,
year = {2025},
author = {Magyar, LB and Ábrahám, E and Lipinszki, Z and Tarnopol, RL and Whiteman, NK and Varga, V and Hultmark, D and Andó, I and Cinege, G},
title = {Pore-Forming Toxin-Like Proteins in the Anti-Parasitoid Immune Response of Drosophila.},
journal = {Journal of innate immunity},
volume = {17},
number = {1},
pages = {10-28},
pmid = {39626640},
issn = {1662-8128},
support = {R35 GM119816/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Pore Forming Cytotoxic Proteins/genetics/metabolism ; *Wasps/immunology ; *Drosophila/immunology/parasitology/genetics ; *Drosophila Proteins/genetics/metabolism ; *Hemolysin Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Phylogeny ; Immunity, Innate ; Hemocytes/immunology ; Hemolymph/metabolism ; Bacterial Toxins/genetics ; },
abstract = {INTRODUCTION: Species of the ananassae subgroup of Drosophilidae are highly resistant to parasitoid wasp infections. We have previously shown that the genes encoding cytolethal distending toxin B (CdtB) and the apoptosis inducing protein of 56 kDa (AIP56) were horizontally transferred to these fly species from prokaryotes and are now instrumental in the anti-parasitoid immune defense of Drosophila ananassae. Here we describe a new family of genes, which encode proteins with hemolysin E domains, heretofore only identified in prokaryotes. Hemolysin E proteins are pore-forming toxins, important virulence factors of bacteria.<br><br>METHODS: Bioinformatical, transcriptional, and protein expressional studies were used.<br><br>RESULTS: The hemolysin E-like genes have a scattered distribution among the genomes of species belonging to several different monophyletic lineages in the family Drosophilidae. We detected structural homology with the bacterial Hemolysin E toxins and showed that the origin of the D. ananassae hemolysin E-like genes (hl1-38) is consistent with prokaryotic horizontal gene transfer. These genes encode humoral factors, secreted into the hemolymph by the fat body and hemocytes. Their expression is induced solely by parasitoid infection and the proteins bind to the developing parasitoids.<br><br>CONCLUSIONS: Hemolysin E-like proteins acquired by horizontal gene transfer and expressed by the primary immune organs may contribute to the elimination of parasitoids, as novel humoral factors in Drosophila innate immunity.},
}
@article {pmid39621811,
year = {2024},
author = {Wright, RCT and Wood, AJ and Bottery, MJ and Muddiman, KJ and Paterson, S and Harrison, E and Brockhurst, MA and Hall, JPJ},
title = {A chromosomal mutation is superior to a plasmid-encoded mutation for plasmid fitness cost compensation.},
journal = {PLoS biology},
volume = {22},
number = {12},
pages = {e3002926},
pmid = {39621811},
issn = {1545-7885},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Plasmids/genetics ; *Pseudomonas fluorescens/genetics ; *Mutation ; *Chromosomes, Bacterial/genetics ; *Genetic Fitness ; Gene Transfer, Horizontal ; Evolution, Molecular ; },
abstract = {Plasmids are important vectors of horizontal gene transfer in microbial communities but can impose a burden on the bacteria that carry them. Such plasmid fitness costs are thought to arise principally from conflicts between chromosomal- and plasmid-encoded molecular machineries, and thus can be ameliorated by compensatory mutations (CMs) that reduce or resolve the underlying causes. CMs can arise on plasmids (i.e., plaCM) or on chromosomes (i.e., chrCM), with contrasting predicted effects upon plasmid success and subsequent gene transfer because plaCM can also reduce fitness costs in plasmid recipients, whereas chrCM can potentially ameliorate multiple distinct plasmids. Here, we develop theory and a novel experimental system to directly compare the ecological effects of plaCM and chrCM that arose during evolution experiments between Pseudomonas fluorescens SBW25 and its sympatric mercury resistance megaplasmid pQBR57. We show that while plaCM was predicted to succeed under a broader range of parameters in mathematical models, chrCM dominated in our experiments, including conditions with numerous recipients, due to a more efficacious mechanism of compensation, and advantages arising from transmission of costly plasmids to competitors (plasmid "weaponisation"). We show analytically the presence of a mixed Rock-Paper-Scissors (RPS) regime for CMs, driven by trade-offs with horizontal transmission, that offers one possible explanation for the observed failure of plaCM to dominate even in competition against an uncompensated plasmid. Our results reveal broader implications of plasmid-bacterial evolution for plasmid ecology, demonstrating the importance of specific compensatory mutations for resistance gene spread. One consequence of the superiority of chrCM over plaCM is the likely emergence in microbial communities of compensated bacteria that can act as "hubs" for plasmid accumulation and dissemination.},
}
@article {pmid39621273,
year = {2025},
author = {Hancks, DC},
title = {An Evolutionary Framework Exploiting Virologs and Their Host Origins to Inform Poxvirus Protein Functions.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2860},
number = {},
pages = {257-272},
pmid = {39621273},
issn = {1940-6029},
mesh = {Animals ; Humans ; Evolution, Molecular ; Genome, Viral ; Host Specificity/genetics ; Host-Pathogen Interactions/genetics ; Open Reading Frames/genetics ; *Poxviridae/genetics/physiology ; Poxviridae Infections/virology/veterinary ; *Viral Proteins/genetics/metabolism ; },
abstract = {Poxviruses represent evolutionary successful infectious agents. As a family, poxviruses can infect a wide variety of species including humans, fish, and insects. While many other viruses are species-specific, an individual poxvirus species is often capable of infecting diverse hosts and cell types. For example, the prototypical poxvirus, vaccinia, is well known to infect numerous human cell types but can also infect cells from divergent hosts like frog neurons. Notably, poxvirus infections result in both detrimental human and animal diseases. The most infamous disease linked to a poxvirus is smallpox caused by variola virus. Poxviruses are large double-stranded DNA viruses, which uniquely replicate in the cytoplasm of cells. The model poxvirus genome encodes ~200 nonoverlapping protein-coding open reading frames (ORFs). Poxvirus gene products impact various biological processes like the production of virus particles, the host range of infectivity, and disease pathogenesis. In addition, poxviruses and their gene products have biomedical application with several species commonly engineered for use as vaccines and oncolytic virotherapy. Nevertheless, we still have an incomplete understanding of the functions associated with many poxvirus genes. In this chapter, we outline evolutionary insights that can complement ongoing studies of poxvirus gene functions and biology, which may serve to elucidate new molecular activities linked to this biomedically relevant class of viruses.},
}
@article {pmid39617215,
year = {2025},
author = {Zuccarotto, A and Sollitto, M and Leclère, L and Panzella, L and Gerdol, M and Leone, S and Castellano, I},
title = {Molecular evolution of ovothiol biosynthesis in animal life reveals diversity of the natural antioxidant ovothiols in Cnidaria.},
journal = {Free radical biology &amp; medicine},
volume = {227},
number = {},
pages = {117-128},
doi = {10.1016/j.freeradbiomed.2024.11.037},
pmid = {39617215},
issn = {1873-4596},
mesh = {Animals ; *Antioxidants/metabolism ; *Evolution, Molecular ; *Cnidaria/genetics/metabolism ; Phylogeny ; Transcriptome ; },
abstract = {Sulfoxide synthase OvoA is the key enzyme involved in the biosynthesis of ovothiols (OSHs), secondary metabolites endowed with unique antioxidant properties. Understanding the evolution of such enzymes and the diversity of their metabolites should reveal fundamental mechanisms governing redox signaling and environmental adaptation. "Early-branching" animals such as Cnidaria display unique molecular diversity and symbiotic relationships responsible for the biosynthesis of natural products, however, they have been neglected in previous research on antioxidants and OSHs. In this work, we have integrated genome and transcriptome mining with biochemical analyses to study the evolution and diversification of OSHs biosynthesis in cnidarians. By tracing the history of the ovoA gene, we inferred its loss in the latest common ancestor of Medusozoa, followed by the acquisition of a unique ovoB/ovoA chimaeric gene in Hydrozoa, likely through a horizontal gene transfer from dinoflagellate donors. While Anthozoa (corals and anemones), bearing canonical ovoA genes, produced a striking variety of OSHs (A, B, and C), the multifunctional enzyme in Hydrozoa was related to OSH B biosynthesis, as shown in Clytia hemisphaerica. Surprisingly, the ovoA-lacking jellyfish Aurelia aurita and Pelagia noctiluca also displayed OSHs, and we provided evidence of their incorporation from external sources. Finally, transcriptome mining revealed ovoA conserved expression pattern during larval development from Cnidaria to more evolved organisms and its regulation by external stimuli, such as UV exposure. The results of our study shed light on the origin and diversification of OSH biosynthesis in basal animals and highlight the importance of redox-active molecules from ancient metazoans as cnidarians to vertebrates.},
}
@article {pmid39615392,
year = {2025},
author = {Zhao, C and Suyamud, B and Yuan, Y and Ghosh, S and Xu, X and Hu, J},
title = {Effect of non-antibiotic factors on conjugative transfer of antibiotic resistance genes in aquaculture water.},
journal = {Journal of hazardous materials},
volume = {483},
number = {},
pages = {136701},
doi = {10.1016/j.jhazmat.2024.136701},
pmid = {39615392},
issn = {1873-3336},
mesh = {Aquaculture ; *Conjugation, Genetic/drug effects ; *Gene Transfer, Horizontal/drug effects ; *Drug Resistance, Bacterial/genetics ; Oxolinic Acid/pharmacology ; Genes, Bacterial ; Reactive Oxygen Species/metabolism ; Hydrogen Peroxide/pharmacology ; *Water Microbiology ; Plasmids/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; },
abstract = {Aquaculture water with antibiotic resistance genes (ARGs) is escalating due to the horizontal gene transfer. Non-antibiotic stressors specifically found, including those from fishery feed and disinfectants, are potential co-selectors. However, the mechanisms underlying this process remains unclear. Intragenus and intergenus conjugative transfer systems of the antibiotic-resistant plasmid RP4 were established to examine conjugative transfer frequency under exposure to five widely used non-antibiotic factors in aquaculture water: iodine, oxolinic acid, NO2-N, NO3-N and H2O2 and four different recipient bacteria: E. coli HB101, Citrobacter portucalensis SG1, Vibrio harveyi and Vibrio alginolyticus. The study found that low concentrations of non-antibiotic factors significantly promoted conjugative transfer, whereas high concentrations inhibited it. Moreover, the conjugation transfer efficiencies were significantly different with different bacterial species within (E. coli HB101 ∼ 10[-3] %) or cross genera (C. portucalensis SG1 ∼10[-5] %, V. harveyi ∼1 %). Besides, excessive exposure concentrations inhibited the expression of related genes and the generation of reactive oxygen species (ROS). Regulation of multiple related genes and ROS-induced SOS responses are common primary mechanisms. However, the mechanisms of non-antibiotic factors differ from those of standard antibiotics, with direct changes in cell membrane permeability potentially playing a dominant role. Additionally, variations among non-antibiotic factors and the specific characteristics of bacterial species contribute to differences in conjugation mechanisms. Notably, this study found that non-antibiotic factors could increase the frequency of intergeneric conjugation beyond that of intrageneric conjugation. Furthermore, non-antibiotic factors influenced by multiple transport systems may raise the risk of unintended cross-resistance, significantly amplifying the potential for resistance gene spread. This study underscores the significance of non-antibiotic factors in the propagation of ARGs, highlighting their role in advancing aquaculture development and protecting human health.},
}
@article {pmid39611838,
year = {2025},
author = {Liu, F and Wang, S-H and Cheewangkoon, R and Zhao, R-L},
title = {Uneven distribution of prokaryote-derived horizontal gene transfer in fungi: a lifestyle-dependent phenomenon.},
journal = {mBio},
volume = {16},
number = {1},
pages = {e0285524},
pmid = {39611838},
issn = {2150-7511},
support = {2022YFD1200600//MOST | National Key Research and Development Program of China (NKPs)/ ; KFJ-BRP-009//biological resources programme, chinese academy of sciences/ ; 221111110600//Henan Province key research and development project/ ; },
mesh = {*Gene Transfer, Horizontal ; *Fungi/genetics/classification ; *Phylogeny ; *Genome, Fungal ; *Bacteria/genetics/classification ; Evolution, Molecular ; Symbiosis/genetics ; },
abstract = {UNLABELLED: Horizontal gene transfer (HGT) in fungi is less understood despite its significance in prokaryotes. In this study, we systematically searched for HGT events in 829 representative fungal genomes. Using a combination of sequence similarity and phylogeny-based approaches, we detected 20,093 prokaryotic-derived transferred genes across 750 fungal genomes, via 8,815 distinct HGT events. Notably, our analysis revealed that eight lifestyle-related traits significantly influence HGT diversity in fungi. For instance, parasites exhibited the highest estimated number of HGT-acquired genes, followed by saprotrophs, with symbionts showing the lowest. HGT-acquired genes were predominantly associated with metabolism and cellular functions and underwent purifying selection. Moreover, horizontally transferred genes with introns have significantly higher expression levels compared to intron-lacking genes, suggesting a probable role of intron gains in the adaptation of HGT-acquired genes. Overall, our findings highlight the influence of lifestyle on HGT diversity in fungi and underscore the substantial contribution of HGT to fungal adaptation.<br><br>IMPORTANCE: This study sheds new light on the role of horizontal gene transfer (HGT) in fungi, an area that has remained relatively unexplored compared to its well-established prevalence in bacteria. By analyzing 829 fungal genomes, we identified over 20,000 genes that fungi acquired from prokaryotes, revealing the significant impact of HGT on fungal evolution. Our findings highlight that fungal lifestyle traits, such as being parasitic or saprotrophic, play a key role in determining the extent of HGT, with parasites showing the highest gene acquisition rates. We also uncovered unique patterns of HGT occurrence based on fungal morphology and reproduction. Importantly, genes with introns, which are more highly expressed, appear to play a crucial role in fungal adaptation. This research deepens our understanding of how HGT contributes to the metabolic diversity and ecological success of fungi, and it underscores the broader significance of gene transfer in shaping fungal evolution.},
}
@article {pmid39611587,
year = {2024},
author = {Sayid, R and van den Hurk, AWM and Rothschild-Rodriguez, D and Herrema, H and de Jonge, PA and Nobrega, FL},
title = {Characteristics of phage-plasmids and their impact on microbial communities.},
journal = {Essays in biochemistry},
volume = {68},
number = {5},
pages = {583-592},
pmid = {39611587},
issn = {1744-1358},
support = {AUF 5188//Amsterdam University Fund/ ; PhD fellowship//Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers (ACS)/ ; //Bowel Research UK (BRUK)/ ; Aspasia premium (015.017.050)//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; BB/T008768/1//Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Black Futures Research Studentship//University of Southampton (University of Southampton UK)/ ; },
mesh = {*Bacteriophages/physiology ; *Plasmids/genetics ; *Bacteria/virology/genetics ; *Microbiota ; CRISPR-Cas Systems ; },
abstract = {Bacteria host various foreign genetic elements, most notably plasmids and bacteriophages (or phages). Historically, these two classes were seen as separate, but recent research has shown considerable interplay between them. Phage-plasmids (P-Ps) exhibit characteristics of both phages and plasmids, allowing them to exist extrachromosomally within bacterial hosts as plasmids, but also to infect and lyse bacteria as phages. This dual functionality enables P-Ps to utilize the modes of transmission of both phage and plasmids, facilitating the rapid dissemination of genetic material, including antibiotic resistance and virulence genes, throughout bacterial populations. Additionally, P-Ps have been found to encode toxin-antitoxin and CRISPR-Cas adaptive immune systems, which enhance bacterial survival under stress and provide immunity against other foreign genetic elements. Despite a growing body of literature on P-Ps, large gaps remain in our understanding of their ecological roles and environmental prevalence. This review aims to synthesise existing knowledge and identify research gaps on the impacts of P-Ps on microbial communities.},
}
@article {pmid39611041,
year = {2024},
author = {Liu, L and Lian, ZH and Lv, AP and Salam, N and Zhang, JC and Li, MM and Sun, WM and Tan, S and Luo, ZH and Gao, L and Yuan, Y and Ming, YZ and OuYang, YT and Li, YX and Liu, ZT and Hu, CJ and Chen, Y and Hua, ZS and Shu, WS and Hedlund, BP and Li, WJ and Jiao, JY},
title = {Insights into chemoautotrophic traits of a prevalent bacterial phylum CSP1-3, herein Sysuimicrobiota.},
journal = {National science review},
volume = {11},
number = {11},
pages = {nwae378},
pmid = {39611041},
issn = {2053-714X},
abstract = {Candidate bacterial phylum CSP1-3 has not been cultivated and is poorly understood. Here, we analyzed 112 CSP1-3 metagenome-assembled genomes and showed they are likely facultative anaerobes, with 3 of 5 families encoding autotrophy through the reductive glycine pathway (RGP), Wood-Ljungdahl pathway (WLP) or Calvin-Benson-Bassham (CBB), with hydrogen or sulfide as electron donors. Chemoautotrophic enrichments from hot spring sediments and fluorescence in situ hybridization revealed enrichment of six CSP1-3 genera, and both transcribed genes and DNA-stable isotope probing were consistent with proposed chemoautotrophic metabolisms. Ancestral state reconstructions showed that the ancestors of phylum CSP1-3 may have been acetogens that were autotrophic via the RGP, whereas the WLP and CBB were acquired by horizontal gene transfer. Our results reveal that CSP1-3 is a widely distributed phylum with the potential to contribute to the cycling of carbon, sulfur and nitrogen. The name Sysuimicrobiota phy. nov. is proposed.},
}
@article {pmid39608506,
year = {2025},
author = {Chetri, S},
title = {Escherichia coli: An arduous voyage from commensal to Antibiotic-resistance.},
journal = {Microbial pathogenesis},
volume = {198},
number = {},
pages = {107173},
doi = {10.1016/j.micpath.2024.107173},
pmid = {39608506},
issn = {1096-1208},
mesh = {Humans ; *Virulence Factors/genetics ; *Anti-Bacterial Agents/pharmacology ; *Escherichia coli Infections/microbiology/drug therapy ; *Escherichia coli/genetics/drug effects/pathogenicity ; Animals ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Gastrointestinal Microbiome/drug effects ; Drug Resistance, Multiple, Bacterial/genetics ; Virulence/genetics ; Symbiosis ; },
abstract = {Escherichia coli (E. coli), a normal intestinal microbiota is one of the most common pathogen known for infecting urinary tract, wound, lungs, bone marrow, blood system and brain. Irrational and overuse of commercially available antibiotics is the most imperative reason behind the emergence of the life threatening infections caused due to antibiotic resistant pathogens. The World Health Organization (WHO) identified antimicrobial resistance (AMR) as one of the 10 biggest public health threats of our time. This harmless commensal can acquire a range of mobile genetic elements harbouring genes coding for virulence factors becoming highly versatile human pathogens causing severe intestinal and extra intestinal diseases. Although, E. coli has been the most widely studied micro-organism, it never ceases to astound us with its ability to open up new research avenues and reveal cutting-edge survival mechanisms in diverse environments that impact human and surrounding environment. This review aims to summarize and highlight persistent research gaps in the field, including: (i) the transfer of resistant genes among bacterial species in diverse environments, such as those associated with humans and animals; (ii) the development of resistance mechanisms against various classes of antibiotics, including quinolones, tetracyclines, etc., in addition to β-lactams; and (iii) the relationship between resistance and virulence factors for understanding how virulence factors and resistance interact to gain a better grasp of how resistance mechanisms impact an organism's capacity to spread illness and interact with the host's defences. Moreover, this review aims to offer a thorough overview, exploring the history and factors contributing to antimicrobial resistance (AMR), the different reported pathotypes, and their links to virulence in both humans and animals. It will also examine their prevalence in various contexts, including food, environmental, and clinical settings. The objective is to deliver a more informative and current analysis, highlighting the evolution from microbiota (historical context) to sophisticated diseases caused by highly successful pathogens. Developing more potent tactics to counteract antibiotic resistance in E. coli requires filling in these gaps. By bridging these gaps, we can strengthen our capacity to manage and prevent resistance, which will eventually enhance public health and patient outcomes.},
}
@article {pmid39606649,
year = {2024},
author = {Qing, Y and Zou, Z and Jiang, G and Qin, L and Liu, K and Liu, Z},
title = {A global perspective on the abundance, diversity and mobility of antibiotic resistance genes in Escherichia coli.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1442159},
pmid = {39606649},
issn = {2297-1769},
abstract = {INTRODUCTION: Escherichia coli (E. coli), a ubiquitous opportunistic pathogen, poses a growing threat to human health due to the increasing prevalence of antibiotic resistance. However, a comprehensive understanding of the global distribution, diversity, and transmission of antibiotic resistance genes (ARGs) in E. coli remains lacking, hindering effective strategies to combat resistance.<br><br>METHODS: In this study, we analyzed 94,762 E. coli genome sequences obtained from the NCBI database using advanced bioinformatics tools. ARGs were identified by comparing sequences against a custom ARG database using BLAST. Mobile genetic element (MGE)-associated ARGs were identified by matching with ISfinder databases. Global distribution of ARGs was analyzed by clustering mobile ARG sequences with 99% genetic similarity.<br><br>RESULTS: Our analysis revealed that 50.51% of the E. coli genome sequences contained ARGs, totaling 301,317 identified ARG sequences. These ARGs were categorized into 12 major classes and 229 subtypes. Notably, ARGs associated with multi-drug resistance (MDR), &#x3b2;-lactams, macrolide-lincosamide-streptogramins (MLS), tetracyclines, and aminoglycosides were particularly abundant, with the subtypes mdtK, macB, and ampC being especially prevalent. Additionally, significant differences in ARG abundance and diversity were observed across countries, with higher diversity found in high-income nations. Furthermore, 9.28% of the ARG sequences were linked to MGEs, accounting for 98.25% of all ARG subtypes. Notably, 4.20% of mobile ARGs were identified in over 20 countries, with &#x3b2;-lactam and aminoglycoside ARGs being the most widespread.<br><br>DISCUSSION: This study provides a comprehensive overview of the global distribution and transmission of ARGs in E. coli. The high abundance of MDR and &#x3b2;-lactam-related ARGs, along with their widespread transmission across countries, highlights the urgent need for global surveillance and control measures. Furthermore, the strong association between ARGs and MGEs underscores the role of horizontal gene transfer in the spread of resistance. The observed variations in ARG diversity between countries suggest that socioeconomic factors, such as healthcare infrastructure and antibiotic usage patterns, significantly influence ARG prevalence. These findings are crucial for informing global strategies to mitigate the spread of antibiotic resistance and improve public health outcomes.},
}
@article {pmid39606646,
year = {2024},
author = {Wang, Z and Sun, M and Guo, S and Wang, Y and Meng, L and Shi, J and Geng, C and Han, D and Fu, X and Xue, J and Ma, H and Liu, K},
title = {Detection of drug resistance in Escherichia coli from calves with diarrhea in the Tongliao region: an analysis of multidrug-resistant strains.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1466690},
pmid = {39606646},
issn = {2297-1769},
abstract = {INTRODUCTION: Escherichia coli is a major pathogen responsible for calf diarrhea, which has been exacerbated by the irrational and unscientific use of antimicrobial drugs, leading to significant drug resistance.<br><br>METHODS: This study focused on the isolation and identification of E. coli from calf diarrhea samples in the Tongliao area of China. Isolation was conducted using selective media, Gram staining, and 16S rRNA sequencing. The minimum inhibitory concentration (MIC) of E. coli was determined through the microbroth dilution method. Additionally, the presence of antibiotic-resistant genes was detected, and multidrug-resistant strains were selected for whole-genome sequencing (WGS).<br><br>RESULTS: The results revealed that all 40 isolated strains of E. coli exhibited resistance to sulfadiazine sodium, enrofloxacin, and ciprofloxacin, with 90% of the strains being susceptible to polymyxin B. Notably, strains 11, 23, and 24 demonstrated severe resistance. The detection rates of the antibiotic resistance genes TEM-1, TEM-206, strA, strB, qacH, and blaCTX were 100%, indicating a high prevalence of these genes. Moreover, the majority of strains carried antibiotic resistance genes consistent with their resistance phenotypes. WGS of strains 11, 23, and 24 revealed genome sizes of 4,897,185&#x2009;bp, 4,920,234&#x2009;bp, and 4,912,320&#x2009;bp, respectively. These strains carried two, one, and two plasmids, respectively. The prediction of antibiotic resistance genes showed a substantial number of these genes within the genomes, with strain 24 harboring the highest number, totaling 77 subspecies containing 88 antibiotic resistance genes.<br><br>DISCUSSION: In conclusion, all 40 isolated strains of E. coli from calf diarrhea in this study were multidrug-resistant, exhibiting a broad distribution of antibiotic resistance genes and mobile components. This poses a significant risk of horizontal gene transfer, highlighting the critical situation of antibiotic resistance in this region.},
}
@article {pmid39605964,
year = {2024},
author = {Jia, J and Liu, Q and Zhao, E and Li, X and Xiong, X and Wu, C},
title = {Biofilm formation on microplastics and interactions with antibiotics, antibiotic resistance genes and pathogens in aquatic environment.},
journal = {Eco-Environment &amp; Health},
volume = {3},
number = {4},
pages = {516-528},
pmid = {39605964},
issn = {2772-9850},
abstract = {Microplastics (MPs) in aquatic environments easily support biofilm development, which can interact with other environmental pollutants and act as harbors for microorganisms. Recently, numerous studies have investigated the fate and behavior of MP biofilms in aquatic environments, highlighting their roles in the spread of pathogens and antibiotic resistance genes (ARGs) to aquatic organisms and new habitats. The prevalence and effects of MP biofilms in aquatic environments have been extensively investigated in recent decades, and their behaviors in aquatic environments need to be synthesized systematically with updated information. This review aims to reveal the development of MP biofilm and its interactions with antibiotics, ARGs, and pathogens in aquatic environments. Recent research has shown that the adsorption capabilities of MPs to antibiotics are enhanced after the biofilm formation, and the adsorption of biofilms to antibiotics is biased towards chemisorption. ARGs and microorganisms, especially pathogens, are selectively enriched in biofilms and significantly different from those in surrounding waters. MP biofilm promotes the propagation of ARGs through horizontal gene transfer (HGT) and vertical gene transfer (VGT) and induces the emergence of antibiotic-resistant pathogens, resulting in increased threats to aquatic ecosystems and human health. Some future research needs and strategies in this review are also proposed to better understand the antibiotic resistance induced by MP biofilms in aquatic environments.},
}
@article {pmid39605872,
year = {2024},
author = {Kettlewell, R and Jones, C and Felton, TW and Lagator, M and Gifford, DR},
title = {Insights into durability against resistance from the antibiotic nitrofurantoin.},
journal = {npj antimicrobials and resistance},
volume = {2},
number = {1},
pages = {41},
pmid = {39605872},
issn = {2731-8745},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Nitrofurantoin has shown exceptional durability against resistance over 70 years of use. This longevity stems from factors such as rapid achievement of therapeutic concentrations, multiple physiological targets against bacteria, low risk of horizontal gene transfer, and the need to acquire multiple mutations to achieve resistance. These combined features limit resistance emergence and spread of nitrofurantoin resistance. We propose nitrofurantoin as an exemplar for developing other durable treatments.},
}
@article {pmid39603126,
year = {2025},
author = {Zhao, W and Zhang, B and Zheng, S and Yan, W and Yu, X and Ye, C},
title = {High temperatures promote antibiotic resistance genes conjugative transfer under residual chlorine: Mechanisms and risks.},
journal = {Journal of hazardous materials},
volume = {483},
number = {},
pages = {136675},
doi = {10.1016/j.jhazmat.2024.136675},
pmid = {39603126},
issn = {1873-3336},
mesh = {*Chlorine ; *Hot Temperature ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; *Conjugation, Genetic/drug effects ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; *Gene Transfer, Horizontal ; },
abstract = {The impact of residual chlorine on the dissemination of antibiotic resistance during the distribution and storage of water has become a critical concern. However, the influence of rising temperatures attributed to global warming on this process remains ambiguous, warranting further investigation. This study investigated the effects of different temperatures (17, 27, 37, and 42°C) on the conjugative transfer of antibiotic resistance genes (ARGs) under residual chlorine (0, 0.1, 0.3, and 0.5 mg/L). The results indicated that high temperatures significantly increased the conjugative transfer frequency of ARGs in intra-species under residual chlorine. Compared to 17°C, the transfer frequencies at 27°C, 37°C, and 42°C increased by 1.07-2.43, 1.20-4.80, and 1.24-2.82 times, respectively. The promoting effect of high temperatures was mainly due to the generation of reactive oxygen species, the triggered SOS response, and the formation of pilus channels. Transcriptomic analysis demonstrated that higher temperature stimulates the electron transport chain, thereby enhancing ATP production and facilitating the processes of conjugative, as confirmed by inhibitor validation. Additionally, rising temperatures similarly promoted the frequency of conjugative transfer in inter-species and communities under residual chlorine. These further highlighted the risk of antibiotic resistance spread in extreme and prolonged high-temperature events. The increased risk of antibiotic resistance in the process of drinking water transmission under the background of climate warming is emphasized.},
}
@article {pmid39602248,
year = {2024},
author = {Dai, L and Wu, Z and Sahin, O and Zhao, S and Yu, EW and Zhang, Q},
title = {Mutation-based mechanism and evolution of the potent multidrug efflux pump RE-CmeABC in Campylobacter.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {51},
pages = {e2415823121},
pmid = {39602248},
issn = {1091-6490},
support = {R01 AI140669/AI/NIAID NIH HHS/United States ; R01AI140669//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {*Campylobacter jejuni/genetics/metabolism ; *Evolution, Molecular ; *Drug Resistance, Multiple, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Bacterial Proteins/genetics/metabolism ; *Mutation ; *Membrane Transport Proteins/genetics/metabolism ; Campylobacter/genetics/metabolism ; Humans ; Campylobacter Infections/microbiology ; Promoter Regions, Genetic ; Amino Acid Substitution ; },
abstract = {The resistance-nodulation-cell division (RND) superfamily of multidrug efflux systems are important players in mediating antibiotic resistance in gram-negative pathogens. Campylobacter jejuni, a major enteric pathogen, utilizes an RND-type transporter system, CmeABC, as the primary mechanism for extrusion of various antibiotics. Recently, a functionally potent variant of CmeABC (named RE-CmeABC) emerged in clinical Campylobacter isolates, conferring enhanced resistance to multiple antibiotic classes. Despite the clinical importance of RE-CmeABC, the molecular mechanisms for its functional gain and its evolutionary trajectory remain unknown. Here, we demonstrated that amino acid substitutions in RE-CmeB (inner membrane transporter), but not in RE-CmeA (periplasmic protein) and RE-CmeC (outer membrane protein), in conjunction with a nucleotide mutation in the promoter region of the efflux operon, are responsible for the functional gain of the multidrug efflux system. We also showed that RE-cmeABC is emerging globally and distributed in genetically diverse C. jejuni strains, suggesting its possible spread by horizontal gene transfer. Notably, many of RE-cmeABC harboring isolates were associated with the human host including strains from large disease outbreaks, indicating the clinical relevance and significance of RE-CmeABC. Evolutionary analysis indicated that RE-cmeB likely originated from Campylobacter coli, but its expansion mainly occurred in C. jejuni, possibly driven by antibiotic selection pressure. Additionally, RE-cmeB, but not RE-cmeA and RE-cmeC, experienced a selective sweep and was progressing to be fixed during evolution. Together, these results identify a mutation-based mechanism for functional gain in RE-CmeABC and reveal the key role of RE-CmeB in facilitating Campylobacter adaptation to antibiotic selection.},
}
@article {pmid39599864,
year = {2024},
author = {Richards, VA and Ferrell, BD and Polson, SW and Wommack, KE and Fuhrmann, JJ},
title = {Soybean Bradyrhizobium spp. Spontaneously Produce Abundant and Diverse Temperate Phages in Culture.},
journal = {Viruses},
volume = {16},
number = {11},
pages = {},
pmid = {39599864},
issn = {1999-4915},
support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; S10 OD028725/OD/NIH HHS/United States ; 1736030//National Science Foundation/ ; },
mesh = {*Bradyrhizobium/virology ; *Glycine max/virology/microbiology ; *Bacteriophages/isolation &amp; purification/genetics/classification/physiology/ultrastructure ; Lysogeny ; Genome, Viral ; Symbiosis ; Microscopy, Electron, Transmission ; },
abstract = {Soybean bradyrhizobia (Bradyrhizobium spp.) are symbiotic root-nodulating bacteria that fix atmospheric nitrogen for the host plant. The University of Delaware Bradyrhizobium Culture Collection (UDBCC; 353 accessions) was created to study the diversity and ecology of soybean bradyrhizobia. Some UDBCC accessions produce temperate (lysogenic) bacteriophages spontaneously under routine culture conditions without chemical or other apparent inducing agents. Spontaneous phage production may promote horizontal gene transfer and shape bacterial genomes and associated phenotypes. A diverse subset (n = 98) of the UDBCC was examined for spontaneously produced virus-like particles (VLPs) using epifluorescent microscopy, with a majority (69%) producing detectable VLPs (>1 × 10[7] mL[-1]) in laboratory culture. Phages from the higher-producing accessions (>2.0 × 10[8] VLP mL[-1]; n = 44) were examined using transmission electron microscopy. Diverse morphologies were observed, including various tail types and lengths, capsid sizes and shapes, and the presence of collars or baseplates. In many instances, putative extracellular vesicles of a size similar to virions were also observed. Three of the four species examined (B. japonicum, B. elkanii, and B. diazoefficiens) produced apparently tailless phages. All species except B. ottawaense also produced siphovirus-like phages, while all but B. diazoefficiens additionally produced podovirus-like phages. Myovirus-like phages were restricted to B. japonicum and B. elkanii. At least three strains were polylysogens, producing up to three distinct morphotypes. These observations suggest spontaneously produced phages may play a significant role in the ecology and evolution of soybean bradyrhizobia.},
}
@article {pmid39599778,
year = {2024},
author = {Yoxsimer, AM and Offenberg, EG and Katzer, AW and Bell, MA and Massengill, RL and Kingsley, DM},
title = {Genomic Sequence of the Threespine Stickleback Iridovirus (TSIV) from Wild Gasterosteus aculeatus in Stormy Lake, Alaska.},
journal = {Viruses},
volume = {16},
number = {11},
pages = {},
pmid = {39599778},
issn = {1999-4915},
support = {R01 GM124330/GM/NIGMS NIH HHS/United States ; Investigator/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; *Phylogeny ; Alaska ; *Smegmamorpha/virology ; *Genome, Viral ; *Fish Diseases/virology ; *Open Reading Frames ; *Iridovirus/genetics/classification/isolation &amp; purification ; *Lakes/virology ; DNA Virus Infections/veterinary/virology ; Genomics/methods ; DNA, Viral/genetics ; },
abstract = {The threespine stickleback iridovirus (TSIV), a double-stranded DNA virus, was the first megalocytivirus detected in wild North American fishes. We report a second occurrence of TSIV in threespine stickleback (Gasterosteus aculeatus) from Stormy Lake, Alaska, and assemble a nearly complete genome of TSIV. The 115-kilobase TSIV genome contains 94 open reading frames (ORFs), with 91 that share homology with other known iridoviruses. We identify three ORFs that likely originate from recent lateral gene transfers from a eukaryotic host and one ORF with homology to B22 poxvirus proteins that likely originated from a lateral gene transfer between viruses. Phylogenetic analysis of 24 iridovirus core genes and pairwise sequence identity analysis support TSIV as a divergent sister taxon to other megalocytiviruses and a candidate for a novel species designation. Screening of stickleback collected from Stormy Lake before and after a 2012 rotenone treatment to eliminate invasive fish shows 100% positivity for TSIV in the two years before treatment (95% confidence interval: 89-100% prevalence) and 0% positivity for TSIV in 2024 after treatment (95% confidence interval: 0 to 3.7% prevalence), suggesting that the rotenone treatment and subsequent crash and reestablishment of the stickleback population is associated with loss of TSIV.},
}
@article {pmid39599474,
year = {2024},
author = {McDonald, NL and Wareham, DW and Bean, DC},
title = {Aeromonas and mcr-3: A Critical Juncture for Transferable Polymyxin Resistance in Gram-Negative Bacteria.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
pmid = {39599474},
issn = {2076-0817},
mesh = {Humans ; *Aeromonas/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacterial Proteins/genetics ; *Colistin/pharmacology/therapeutic use ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli Proteins/genetics ; Gene Transfer, Horizontal ; Gram-Negative Bacteria/drug effects/genetics ; *Gram-Negative Bacterial Infections/microbiology/drug therapy ; Microbial Sensitivity Tests ; Phylogeny ; *Polymyxins/pharmacology/therapeutic use ; Transferases (Other Substituted Phosphate Groups) ; },
abstract = {Polymyxin antibiotics B and colistin are considered drugs of last resort for the treatment of multi-drug and carbapenem-resistant Gram-negative bacteria. With the emergence and dissemination of multi-drug resistance, monitoring the use and resistance to polymyxins imparted by mobilised colistin resistance genes (mcr) is becoming increasingly important. The Aeromonas genus is widely disseminated throughout the environment and serves as a reservoir of mcr-3, posing a significant risk for the spread of resistance to polymyxins. Recent phylogenetic studies and the identification of insertion elements associated with mcr-3 support the notion that Aeromonas spp. may be the evolutionary origin of the resistance gene. Furthermore, mcr-3-related genes have been shown to impart resistance in naïve E. coli and can increase the polymyxin MIC by up to 64-fold (with an MIC of 64 mg/L) in members of Aeromonas spp. This review will describe the genetic background of the mcr gene, the epidemiology of mcr-positive isolates, and the relationship between intrinsic and transferable mcr resistance genes, focusing on mcr-3 and mcr-3-related genes.},
}
@article {pmid39597557,
year = {2024},
author = {Shah, Y and Kafaie, S},
title = {Evaluating Sequence Alignment Tools for Antimicrobial Resistance Gene Detection in Assembly Graphs.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
pmid = {39597557},
issn = {2076-2607},
abstract = {Antimicrobial resistance (AMR) is an escalating global health threat, often driven by the horizontal gene transfer (HGT) of resistance genes. Detecting AMR genes and understanding their genomic context within bacterial populations is crucial for mitigating the spread of resistance. In this study, we evaluate the performance of three sequence alignment tools-Bandage, SPAligner, and GraphAligner-in identifying AMR gene sequences from assembly and de Bruijn graphs, which are commonly used in microbial genome assembly. Efficiently identifying these genes allows for the detection of neighboring genetic elements and possible HGT events, contributing to a deeper understanding of AMR dissemination. We compare the performance of the tools both qualitatively and quantitatively, analyzing the precision, computational efficiency, and accuracy in detecting AMR-related sequences. Our analysis reveals that Bandage offers the most precise and efficient identification of AMR gene sequences, followed by GraphAligner and SPAligner. The comparison includes evaluating the similarity of paths returned by each tool and measuring output accuracy using a modified edit distance metric. These results highlight Bandage's potential for contributing to the accurate identification and study of AMR genes in bacterial populations, offering important insights into resistance mechanisms and potential targets for mitigating AMR spread.},
}
@article {pmid39597512,
year = {2024},
author = {Banerji, A and Brinkman, NE and Davis, B and Franklin, A and Jahne, M and Keely, SP},
title = {Food Webs and Feedbacks: The Untold Ecological Relevance of Antimicrobial Resistance as Seen in Harmful Algal Blooms.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
pmid = {39597512},
issn = {2076-2607},
abstract = {Antimicrobial resistance (AMR) has long been framed as an epidemiological and public health concern. Its impacts on the environment are unclear. Yet, the basis for AMR is altered cell physiology. Just as this affects how microbes interact with antimicrobials, it can also affect how they interact with their own species, other species, and their non-living environment. Moreover, if the microbes are globally notorious for causing landscape-level environmental issues, then these effects could alter biodiversity and ecosystem function on a grand scale. To investigate these possibilities, we compiled peer-reviewed literature from the past 20 years regarding AMR in toxic freshwater cyanobacterial harmful algal blooms (HABs). We examined it for evidence of AMR affecting HAB frequency, severity, or persistence. Although no study within our scope was explicitly designed to address the question, multiple studies reported AMR-associated changes in HAB-forming cyanobacteria (and co-occurring microbes) that pertained directly to HAB timing, toxicity, and phase, as well as to the dynamics of HAB-afflicted aquatic food webs. These findings highlight the potential for AMR to have far-reaching environmental impacts (including the loss of biodiversity and ecosystem function) and bring into focus the importance of confronting complex interrelated issues such as AMR and HABs in concert, with interdisciplinary tools and perspectives.},
}
@article {pmid39596782,
year = {2024},
author = {Mendoza-Guido, B and Barrantes, K and Rodríguez, C and Rojas-Jimenez, K and Arias-Andres, M},
title = {The Impact of Urban Pollution on Plasmid-Mediated Resistance Acquisition in Enterobacteria from a Tropical River.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
pmid = {39596782},
issn = {2079-6382},
support = {C1455, C2650, C3509//Vicerrector&#xed;a de Investigaci&#xf3;n of the Universidad de Costa Rica/ ; SIA 0483-21//Universidad Nacional, Costa Rica/ ; Proyecto Plasmidoma//Consejo Nacional de Rectores (CONARE), Costa Rica/ ; },
abstract = {Background: The exposure of environmental bacteria to contaminants in aquatic ecosystems accelerates the dissemination of antibiotic-resistance genes (ARGs) through horizontal gene transfer (HGT). Methods: In this study, we sampled three locations along a contamination gradient of a polluted river, focusing on isolating Enterobacteria from the surface waters to investigate the relationship between urban pollution and antibiotic resistance. The genomes of 15 isolates (5 per site) were sequenced to identify plasmid-borne ARGs and their association with resistance phenotypes. Results: Isolates from the site with the highest contamination (Site 3) showeda larger number of ARGs, plasmids, and resistance phenotypes. Notably, one of the isolates analyzed, E. coli A231-12, exhibited phenotypic resistance to seven antibiotics, presumably conferred by a single plasmid carrying 12 ARGs. Comparative analysis of this plasmid revealed its close evolutionary relationship with another IncH plasmid hosted by Salmonella enterica, underscoring its high ARG burden in the aquatic environment. Other plasmids identified in our isolates carried sul and dfrA genes, conferring resistance to trimethoprim/sulfamethoxazole, a commonly prescribed antibiotic combination in clinical settings. Conclusions: These results highlight the critical need to expand research on the link between pollution and plasmid-mediated antimicrobial resistance in aquatic ecosystems, which can act as reservoirs of ARGs.},
}
@article {pmid39596781,
year = {2024},
author = {Ifedinezi, OV and Nnaji, ND and Anumudu, CK and Ekwueme, CT and Uhegwu, CC and Ihenetu, FC and Obioha, P and Simon, BO and Ezechukwu, PS and Onyeaka, H},
title = {Environmental Antimicrobial Resistance: Implications for Food Safety and Public Health.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
pmid = {39596781},
issn = {2079-6382},
abstract = {Antimicrobial resistance (AMR) is a serious global health issue, aggravated by antibiotic overuse and misuse in human medicine, animal care, and agriculture. This study looks at the different mechanisms that drive AMR, such as environmental contamination, horizontal gene transfer, and selective pressure, as well as the severe implications of AMR for human and animal health. This study demonstrates the need for concerted efforts across the scientific, healthcare, agricultural, and policy sectors to control the emergence of AMR. Some crucial strategies discussed include developing antimicrobial stewardship (AMS) programs, encouraging targeted narrow-spectrum antibiotic use, and emphasizing the significance of strict regulatory frameworks and surveillance systems, like the Global Antimicrobial Resistance and Use Surveillance System (GLASS) and the Access, Watch, and Reserve (AWaRe) classification. This study also emphasizes the need for national and international action plans in combating AMR and promotes the One Health strategy, which unifies environmental, animal, and human health. This study concludes that preventing the spread of AMR and maintaining the effectiveness of antibiotics for future generations requires a comprehensive, multidisciplinary, and internationally coordinated strategy.},
}
@article {pmid39596258,
year = {2024},
author = {Dec, M and Nowak, T and Webster, J and Wódz, K},
title = {Serotypes, Antimicrobial Susceptibility, and Potential Mechanisms of Resistance Gene Transfer in Erysipelothrix rhusiopathiae Strains from Waterfowl in Poland.},
journal = {International journal of molecular sciences},
volume = {25},
number = {22},
pages = {},
pmid = {39596258},
issn = {1422-0067},
mesh = {Animals ; Poland ; *Erysipelothrix/genetics ; *Serogroup ; *Anti-Bacterial Agents/pharmacology ; *Geese/microbiology ; Ducks/microbiology ; Microbial Sensitivity Tests ; Erysipelothrix Infections/microbiology/genetics ; Multilocus Sequence Typing ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {Erysipelas is a significant problem in the waterfowl farming in Poland, and information on the characteristics of the Erysipelothrix rhusiopathiae strains causing this disease is limited. In this study, we determined the serotypes, antimicrobial susceptibility, and potential mechanisms of resistance gene transfer in E. rhusiopathiae isolates (n = 60) from domestic geese and ducks. We also developed a multiplex PCR for the detection of resistance genes. The antimicrobial susceptibility of the isolates was assessed using the broth microdilution method. Resistance genes, integrative conjugative element (ICE)-specific genes, phage-specific genes, and serotype determinants were detected by PCR. Multilocus sequence typing (MLST) was performed for selected resistant strains. The comparative analyses included 260 E. rhusiopathiae strains whose whole genome sequences (WGSs) are publicly available. E. rhusiopathiae isolates represented 7 serotypes, among which serotypes 5 (38.3%) and 1b (28.3%) were the most common. All strains were susceptible to β-lactams, and the vast majority of them were resistant to tetracycline (85%) and enrofloxacin (80%). The percentages of isolates resistant to other antimicrobials used ranged from 3.3% to 16.7%. Ten isolates (16.7%) were found to be multidrug resistant (MDR). The genotypic resistance profiles of the E. rhusiopathiae strains corresponded to their phenotypic resistance, and the amplification patterns obtained using the 10-plex PCR developed in this study were fully consistent with the results of single PCRs. The most prevalent resistance gene was tetM. In enrofloxacin-resistant strains, nonsynonymous mutations in the gyrA and parC genes were identified. The presence of ICE-specific genes was confirmed in resistant strains, and in MDR isolates of serotype 8 that represented sequence type (ST) 113, prophage DNA (Javan630-like) linked to the lsaE gene was additionally detected. The results indicate that β-lactam antibiotics should be the first choice for the treatment of waterfowl erysipelas in Poland. ICEs, including a transposon from the Tn916/Tn1545 family, and bacteriophages are most likely responsible for the transfer of resistance genes in E. rhusiopathiae.},
}
@article {pmid39592962,
year = {2024},
author = {Mane, A and Sanderson, H and White, AP and Zaheer, R and Beiko, R and Chauve, C},
title = {Plaseval: a framework for comparing and evaluating plasmid detection tools.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {365},
pmid = {39592962},
issn = {1471-2105},
mesh = {*Plasmids/genetics/metabolism ; Software ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: Plasmids play a major role in the transfer of antimicrobial resistance (AMR) genes among bacteria via horizontal gene transfer. The identification of plasmids in short-read assemblies is a challenging problem and a very active research area. Plasmid binning aims at detecting, in a draft genome assembly, groups (bins) of contigs likely to originate from the same plasmid. Several methods for plasmid binning have been developed recently, such as PlasBin-flow, HyAsP, gplas, MOB-suite, and plasmidSPAdes. This motivates the problem of evaluating the performances of plasmid binning methods, either against a given ground truth or between them.<br><br>RESULTS: We describe PlasEval, a novel method aimed at comparing the results of plasmid binning tools. PlasEval computes a dissimilarity measure between two sets of plasmid bins, that can originate either from two plasmid binning tools, or from a plasmid binning tool and a ground truth set of plasmid bins. The PlasEval dissimilarity accounts for the contig content of plasmid bins, the length of contigs and is repeat-aware. Moreover, the dissimilarity score computed by PlasEval is broken down into several parts, that allows to understand qualitative differences between the compared sets of plasmid bins. We illustrate the use of PlasEval by benchmarking four recently developed plasmid binning tools-PlasBin-flow, HyAsP, gplas, and MOB-recon-on a data set of 53 E. coli bacterial genomes.<br><br>CONCLUSION: Analysis of the results of plasmid binning methods using PlasEval shows that their behaviour varies significantly. PlasEval can be used to decide which specific plasmid binning method should be used for a specific dataset. The disagreement between different methods also suggests that the problem of plasmid binning on short-read contigs requires further research. We believe that PlasEval can prove to be an effective tool in this regard. PlasEval is publicly available at https://github.com/acme92/PlasEval.},
}
@article {pmid39592922,
year = {2024},
author = {Das, VA and Gautam, B and Yadav, PK and Varadwaj, PK and Wadhwa, G and Singh, S},
title = {Computational approach to identify novel genomic features conferring high fitness in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 associated with plant growth promotion (PGP) in apple.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {1127},
pmid = {39592922},
issn = {1471-2229},
mesh = {*Bacillus/genetics/physiology ; *Malus/microbiology/genetics ; *Genome, Bacterial ; Genetic Fitness ; Genomics/methods ; Genomic Islands ; Computational Biology/methods ; },
abstract = {A comparative genomic analysis approach provides valuable information about genetic variations and evolutionary relationships among microorganisms, aiding not only in the identification of functional genes responsible for traits such as pathogenicity, antibiotic resistance, and metabolic capabilities but also in enhancing our understanding of microbial genomic diversity and their ecological roles, such as supporting plant growth promotion, thereby enabling the development of sustainable strategies for agriculture. We used two strains from different Bacillus species, Bacillus velezensis AK-0 and Bacillus atrophaeus CNY01, which have previously been reported to have PGP activity in apple, and performed comparative genomic analysis to understand their evolutionary process and obtain a mechanistic understanding of their plant growth-promoting activity. We identified genomic features such as mobile genetic elements (MGEs) that encode key proteins involved in the survival, adaptation and growth of these bacterial strains. The presence of genomic islands and intact prophage DNA in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 suggests that horizontal gene transfer has contributed to their diversification and acquisition of adaptive traits, enhancing their evolutionary advantage. We also identified novel DNA motifs that are associated with key physiological processes and metabolic pathways.},
}
@article {pmid39591316,
year = {2024},
author = {Jafari Jozani, R and Khallawi, MFHA and Trott, D and Petrovski, K and Low, WY and Hemmatzadeh, F},
title = {Unravelling Antimicrobial Resistance in Mycoplasma hyopneumoniae: Genetic Mechanisms and Future Directions.},
journal = {Veterinary sciences},
volume = {11},
number = {11},
pages = {},
pmid = {39591316},
issn = {2306-7381},
support = {2021/0025//Australian Pork (APL)/ ; },
abstract = {Antimicrobial resistance (AMR) in Mycoplasma hyopneumoniae, the causative agent of Enzootic Pneumonia in swine, poses a significant challenge to the swine industry. This review focuses on the genetic foundations of AMR in M. hyopneumoniae, highlighting the complexity of resistance mechanisms, including mutations, horizontal gene transfer, and adaptive evolutionary processes. Techniques such as Whole Genome Sequencing (WGS) and multiple-locus variable number tandem repeats analysis (MLVA) have provided insights into the genetic diversity and resistance mechanisms of M. hyopneumoniae. The study underscores the role of selective pressures from antimicrobial use in driving genomic variations that enhance resistance. Additionally, bioinformatic tools utilizing machine learning algorithms, such as CARD and PATRIC, can predict resistance traits, with PATRIC predicting 7 to 12 AMR genes and CARD predicting 0 to 3 AMR genes in 24 whole genome sequences available on NCBI. The review advocates for a multidisciplinary approach integrating genomic, phenotypic, and bioinformatics data to combat AMR effectively. It also elaborates on the need for refining genotyping methods, enhancing resistance prediction accuracy, and developing standardized antimicrobial susceptibility testing procedures specific to M. hyopneumoniae as a fastidious microorganism. By leveraging contemporary genomic technologies and bioinformatics resources, the scientific community can better manage AMR in M. hyopneumoniae, ultimately safeguarding animal health and agricultural productivity. This comprehensive understanding of AMR mechanisms will be beneficial in the adaptation of more effective treatment and management strategies for Enzootic Pneumonia in swine.},
}
@article {pmid39590772,
year = {2024},
author = {Cui, H and Lu, J and Ding, W and Zhang, W},
title = {Genomic Features and Antimicrobial Activity of Phaeobacter inhibens Strains from Marine Biofilms.},
journal = {Marine drugs},
volume = {22},
number = {11},
pages = {},
pmid = {39590772},
issn = {1660-3397},
mesh = {*Biofilms/drug effects ; *Rhodobacteraceae/genetics ; *Phylogeny ; *Genome, Bacterial ; *Anti-Bacterial Agents/pharmacology ; *Tropolone/pharmacology/analogs &amp; derivatives ; Multigene Family ; Aquatic Organisms ; Vibrio/genetics/drug effects ; Genomics/methods ; Animals ; },
abstract = {Members of the genus Phaeobacter are widely distributed in the marine environment and are known for their ability to produce tropodithietic acid (TDA). Studies investigating the genomic and metabolic features of Phaeobacter strains from marine biofilms are sparse. Here, we analyze the complete genomes of 18 Phaeobacter strains isolated from biofilms on subtidal stones, with the aim of determining their potential to synthesize secondary metabolites. Based on whole-genome comparison and average nucleotide identity calculation, the isolated bacteria are classified as novel strains of Phaeobacter inhibens. Further analysis reveals a total of 153 biosynthetic gene clusters, which are assigned to 32 gene cluster families with low similarity to previously published ones. Complete TDA clusters are identified in 14 of the 18 strains, while in the other 4 strains the TDA clusters are rather incomplete and scattered across different chromosome and plasmid locations. Phylogenetic analysis suggests that their presence or absence may be potentially attributed to horizontal gene transfer. High-performance liquid chromatography-mass spectrometry analysis demonstrates the production of TDA in all the examined strains. Furthermore, the Phaeobacter strains have strong antibacterial activity against the pathogenic strain Vibrio owensii ems001, which is associated with acute hepatopancreatic necrosis in South American white shrimp. Altogether, this study ameliorates our knowledge of marine biofilm-associated Phaeobacter and offers new avenues for exploiting marine antimicrobial agents.},
}
@article {pmid39589125,
year = {2024},
author = {Zhang, Z and Tong, M and Ding, W and Liu, S and Jong, M-C and Radwan, AA and Cai, Z and Zhou, J},
title = {Changes in the diversity and functionality of viruses that can bleach healthy coral.},
journal = {mSphere},
volume = {9},
number = {12},
pages = {e0081624},
pmid = {39589125},
issn = {2379-5042},
mesh = {*Anthozoa/virology/microbiology ; Animals ; *Microbiota/genetics ; *Viruses/genetics/classification ; *Metagenomics ; Bacteria/genetics/classification/virology/isolation &amp; purification ; Symbiosis ; Bacteriophages/genetics/physiology/classification/isolation &amp; purification ; },
abstract = {UNLABELLED: Coral microbiomes play a crucial role in maintaining the health and functionality of holobionts. Disruption in the equilibrium of holobionts, including bacteria, fungi, and archaea, can result in the bleaching of coral. However, little is known about the viruses that can infect holobionts in coral, especially bacteriophages. Here, we employed a combination of amplicon and metagenomic analyses on Acropora muricata and Galaxea astreata to investigate the diversity and functionality of viruses in healthy and bleached corals. Analysis showed that the alpha diversity of holobionts (bacteria, eukaryotes, zooxanthellae, and lysogenic and lytic viruses) was higher in bleached corals than that in healthy corals. Meanwhile, bleached corals exhibited a relatively higher abundance of specific viral classes, including Revtraviricetes, Arfiviricetes, Faserviricetes, Caudoviricetes, Herviviricetes, and Tectiliviricetes; moreover, we found that the expression levels of functional genes involved in carbon and sulfur metabolism were enriched. An increase in Vibrio abundance has been reported as a notable factor in coral bleaching; our analysis also revealed an increased abundance of Vibrio in bleached coral. Finally, bleached corals contained a higher abundance of Vibrio phages and encoded more virulence factor genes to increase the competitiveness of Vibrio after coral bleaching. In conclusion, we attempted to understand the causes of coral bleaching from the perspective of phage-bacteria-coral tripartite interaction.<br><br>IMPORTANCE: Viruses, especially bacteriophages, outnumber other microorganisms by approximately 10-fold and represent the most abundant members of coral holobionts. Corals represent a model system for the study of symbiosis, the influence of viruses on organisms inhabiting healthy coral reef, the role of rapid horizontal gene transfer, and the expression of auxiliary metabolic genes. However, the least studied component of coral holobiont are viruses. Therefore, there is a critical need to investigate the viral community of viruses, and their functionality, in healthy and bleached coral. Here, we compared the composition and functionality of viruses in healthy and bleached corals and found that viruses may participate in the induction of coral bleaching by enhancing the expression of virulence genes and other auxiliary metabolic functions.},
}
@article {pmid39587099,
year = {2024},
author = {Sheikh, S and Fu, CJ and Brown, MW and Baldauf, SL},
title = {The Acrasis kona genome and developmental transcriptomes reveal deep origins of eukaryotic multicellular pathways.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10197},
pmid = {39587099},
issn = {2041-1723},
support = {VR 2017-04351//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2100888//National Science Foundation (NSF)/ ; },
mesh = {*Transcriptome ; *Dictyostelium/genetics/growth &amp; development ; Genome, Protozoan ; Amoeba/genetics ; Phylogeny ; Gene Transfer, Horizontal ; Protozoan Proteins/genetics/metabolism ; Proteome/metabolism/genetics ; Genome ; },
abstract = {Acrasids are amoebae with the capacity to form multicellular fruiting bodies in a process known as aggregative multicellularity (AGM). This makes acrasids the only known example of multicellularity among the earliest branches of eukaryotes (the former Excavata). Here, we report the Acrasis kona genome sequence plus transcriptomes from pre-, mid- and post-developmental stages. The genome is rich in novelty and genes with strong signatures of horizontal transfer, and multigene families encode nearly half of the amoeba's predicted proteome. Development in A. kona appears molecularly simple relative to the AGM model, Dictyostelium discoideum. However, the acrasid also differs from the dictyostelid in that it does not appear to be starving during development. Instead, developing A. kona appears to be very metabolically active, does not induce autophagy and does not up-regulate its proteasomal genes. Together, these observations strongly suggest that starvation is not essential for AGM development. Nonetheless, development in the two amoebae appears to employ remarkably similar pathways for signaling, motility and, potentially, construction of an extracellular matrix surrounding the developing cell mass. Much of this similarity is also shared with animal development, suggesting that much of the basic tool kit for multicellular development arose early in eukaryote evolution.},
}
@article {pmid39581358,
year = {2025},
author = {Fischer, K and Jordbræk, SV and Olsen, S and Bockwoldt, M and Schwacke, R and Usadel, B and Krause, K},
title = {Taken to extremes: Loss of plastid rpl32 in Streptophyta and Cuscuta's unconventional solution for its replacement.},
journal = {Molecular phylogenetics and evolution},
volume = {204},
number = {},
pages = {108243},
doi = {10.1016/j.ympev.2024.108243},
pmid = {39581358},
issn = {1095-9513},
mesh = {Phylogeny ; *Plastids/genetics ; Gene Transfer, Horizontal ; *Streptophyta/genetics/classification ; *Cuscuta/genetics/classification ; *Evolution, Molecular ; *Ribosomal Proteins/genetics ; Sequence Analysis, DNA ; },
abstract = {The evolution of plant genomes is riddled with exchanges of genetic material within one plant (endosymbiotic gene transfer/EGT) and between unrelated plants (horizontal gene transfer/HGT). These exchanges have left their marks on plant genomes. Parasitic plants with their special evolutionary niche provide ample examples for these processes because they are under a reduced evolutionary pressure to maintain autotrophy and thus to conserve their plastid genomes. On the other hand, the close physical connections with different hosts enabled them to acquire genetic material from other plants. Based on an analysis of an extensive dataset including the parasite Cuscuta campestris and other parasitic plant species, we identified a unique evolutionary history of rpl32 genes coding for an essential plastid ribosomal subunit in Cuscuta. Our analysis suggests that the gene was most likely sequestered by HGT from a member of the Oxalidales order serving as host to an ancestor of the Cuscuta subgenus Grammica. Oxalidales had suffered an ancestral EGT of rpl32 predating the evolution of the genus Cuscuta. The HGT subsequently relieved the plastid rpl32 from its evolutionary constraint and led to its loss from the plastid genome. The HGT-based acquisition in Cuscuta is supported by a high sequence similarity of the mature L32 protein between species of the subgenus Grammica and representatives of the Oxalidales, and by a surprisingly conserved transit peptide, whose functionality in Cuscuta was experimentally verified. The findings are discussed in view of an overall pattern of EGT events for plastid ribosomal subunits in Streptophyta.},
}
@article {pmid39581254,
year = {2025},
author = {Xu, F and Xiang, Q and Xu, ML and Carter, LJ and Du, WC and Zhu, CW and Ai, FX and Yin, Y and Ji, R and Guo, HY},
title = {Elevated CO2 alters antibiotic resistome in soil amended with sulfamethazine via chemical-organic fertilization.},
journal = {Environmental research},
volume = {264},
number = {Pt 2},
pages = {120416},
doi = {10.1016/j.envres.2024.120416},
pmid = {39581254},
issn = {1096-0953},
mesh = {*Sulfamethazine ; *Soil Microbiology ; *Fertilizers/analysis ; *Carbon Dioxide ; *Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial/drug effects ; Bacteria/drug effects/genetics ; },
abstract = {Rising antimicrobial resistance (AMR) is an enormous challenge for global healthcare systems. The effects of elevated CO2 (eCO2) on AMR are poorly characterized. Using a free-air CO2 enrichment system and high-throughput qPCR arrays, we investigated the response of soil antibiotic resistome and bacterial communities to eCO2 (ambient + 200 ppm) in soils amended with sulfamethazine (SMZ) at 0.1 and 1 mg kg[-1] via chemical-organic fertilizer (COL, COH). Results showed that under ambient condition, COH significantly enhanced the diversity of high-risk antibiotic resistance genes (ARGs), relative abundance of low risk ARGs, unassessed ARGs and total ARGs compared to COL. Nevertheless, eCO2 mitigated the effects of COH, with no significant difference found between COL and COH on the above high risk, low risk, unassessed and total ARGs. Meanwhile, eCO2 decreased the relative abundance of spcN, ermA, olec, oprD, sulA-olP, tetB, tetT and vanXD in COL, and alleviated the enrichment of pikR2, ampC, lunC, oprD and pncA caused by the application of SMZ at 1 mg kg[-1]. Correlation and network analysis illustrated that changes of certain bacteria biomarkers and horizontal gene transfer of integrase gene were associated with the altered response of ARGs abundance to eCO2. This study adds knowledge of the potential risk of antibiotic resistance in agricultural exposure scenarios under increasing CO2 concentration.},
}
@article {pmid39581077,
year = {2024},
author = {Guernier-Cambert, V and Trachsel, J and Atkinson, B and Oladeinde, A and Anderson, CL and Bearson, SMD and Monson, MS and Looft, T},
title = {Tetracycline resistance gene transfer from Escherichia coli donors to Salmonella Heidelberg in chickens is impacted by the genetic context of donors.},
journal = {Veterinary microbiology},
volume = {299},
number = {},
pages = {110294},
doi = {10.1016/j.vetmic.2024.110294},
pmid = {39581077},
issn = {1873-2542},
mesh = {Animals ; *Chickens/microbiology ; *Escherichia coli/genetics/drug effects ; *Gene Transfer, Horizontal ; *Salmonella Infections, Animal/microbiology ; *Salmonella enterica/genetics/drug effects ; *Poultry Diseases/microbiology ; *Tetracycline Resistance/genetics ; Anti-Bacterial Agents/pharmacology ; Cecum/microbiology ; Tetracycline/pharmacology ; Conjugation, Genetic ; Plasmids/genetics ; },
abstract = {Chicken ceca are a rich source of bacteria, including zoonotic pathogens such as Salmonella enterica. The microbiota includes strains/species carrying antimicrobial resistance genes and horizontal transfer of resistance determinants between species may increase the risk to public health and farming systems. Possible sources of these antimicrobial resistance donors - the eggshell carrying bacteria from the hen vertically transmitted to the offspring, or the barn environment where chicks are hatched and raised - has been little explored. In this study, we used Salmonella enterica serovar Heidelberg to evaluate if layer chicks raised in different environments (using combinations of sterilized or non-sterile eggs placed in sterilized isolation chambers or non-sterile rooms) acquired transferable tetracycline resistance genes from surrounding bacteria, especially Escherichia coli. Two-day old chicks were challenged with an antibiotic-susceptible S. Heidelberg strain SH2813nal[R] and Salmonella recovered from the cecum of birds at different timepoints to test the in vivo acquisition of tetracycline resistance. Tetracycline-resistant E. coli isolates recovered from birds from the in vivo experiment were used to test the in vitro transfer of tetracycline resistance genes from E. coli to Salmonella. Even though Salmonella SH2813nal[R] colonized the 2-day old chicks after oral challenge, tetracycline-resistant Salmonella transconjugants were not recovered, as previously observed. In vitro experiments provided similar results. We discuss several hypotheses that might explain the absence of transconjugants in vitro and in vivo, despite the presence of diverse plasmids in the recovered E. coli. The factors that can inhibit/promote antimicrobial resistance transfers to Salmonella for different plasmid types need further exploration.},
}
@article {pmid39577948,
year = {2024},
author = {Sheng, H and Zhao, L and Suo, J and Yang, Q and Cao, C and Chen, J and Cui, G and Fan, Y and Ma, Y and Huo, S and Wu, X and Yang, T and Cui, X and Chen, S and Cui, S and Yang, B},
title = {Niche-specific evolution and gene exchange of Salmonella in retail pork and chicken.},
journal = {Food research international (Ottawa, Ont.)},
volume = {197},
number = {Pt 2},
pages = {115299},
doi = {10.1016/j.foodres.2024.115299},
pmid = {39577948},
issn = {1873-7145},
mesh = {Animals ; *Chickens/microbiology ; *Salmonella/genetics ; Swine ; *Food Microbiology ; China ; *Pork Meat/microbiology ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Meat/microbiology ; Drug Resistance, Bacterial/genetics ; Genetic Variation ; Red Meat/microbiology ; },
abstract = {Salmonella exhibits extensive genetic diversity, facilitated by horizontal gene transfer occurring within and between species, playing a pivotal role in this diversification. Nevertheless, most studies focus on clinical and farm animal isolates, and research on the pangenome dynamics of Salmonella isolates from retail stage of the animal food supply chain is limited. Here, we investigated the genomes of 950 Salmonella isolates recovered from retail chicken and pork meats in seven provinces and one municipality of China in 2018. We observed a strong correlation between Salmonella sublineage diversity and the accessory genome with meat type, revealing reduced diversity associated with increased resistance. Importantly, genes associated with antibiotic, biocide, and heavy metal resistance were unevenly distributed in Salmonella from retail chicken and pork. Pork Salmonella isolates showed a higher prevalence of copper and silver resistance genes, while chicken Salmonella isolates displayed a significant predominance of genetic determinants associated with cephalosporin and ciprofloxacin resistance. Moreover, co-occurrence patterns of resistance determinants and their interaction with mobile genetic elements also correlated with meat type. In summary, our findings shed light on how Salmonella achieves their ecological niche success driven by evolution and gene changes in the retail stage of the animal food supply chain.},
}
@article {pmid39577842,
year = {2024},
author = {Whangsuk, W and Dulyayangkul, P and Loprasert, S and Dubbs, JM and Vattanaviboon, P and Mongkolsuk, S},
title = {Re-sensitization of imipenem-resistant Pseudomonas aeruginosa and restoration of cephalosporins susceptibility in Enterobacteriaceae by recombinant Esterase B.},
journal = {Letters in applied microbiology},
volume = {77},
number = {12},
pages = {},
doi = {10.1093/lambio/ovae118},
pmid = {39577842},
issn = {1472-765X},
support = {//Thailand Science Research and Innovation/ ; 49892/4759806//Chulabhorn Research Institute/ ; },
mesh = {*Pseudomonas aeruginosa/genetics/drug effects/enzymology ; *Anti-Bacterial Agents/pharmacology ; *Cephalosporins/pharmacology ; *Microbial Sensitivity Tests ; *Imipenem/pharmacology ; Enterobacteriaceae/genetics/drug effects/enzymology ; Bacterial Proteins/genetics/metabolism ; Esterases/genetics/metabolism ; Bacterial Outer Membrane Proteins/genetics/metabolism ; Recombinant Proteins/genetics/metabolism ; Drug Resistance, Bacterial ; Escherichia coli/genetics/drug effects ; Plasmids/genetics ; },
abstract = {Sphingobium sp. SM42 Esterase B (EstB) is an enzyme with a dual function in degrading dibutyl phthalate and catalyzing the cleavage of the C-S bond in C3-sidechains of the dihydrothiazine ring of cephalosporins, generating more active β-lactam derivatives. Global prokaryotic genome analysis revealed the existence of a gene identical to estB in Pseudomonas aeruginosa strain PS1 suggesting a horizontal gene transfer event involving estB. To investigate the effect of ectopic expression of EstB in the periplasm of P. aeruginosa and several Enterobacteriaceae on antibiotic susceptibility levels, plasmid, pEstB, carrying a recombinant EstB fused with the signal peptide from Escherichia coli outer membrane protein A (OmpA) for periplasmic localization was constructed. The expression of EstB in the periplasm of P. aeruginosa and the Enterobacteriaceae: E. coli, Klebsiella pneumoniae, and Salmonella enterica serovar Typhi, increased susceptibility to carbapenems and cephalosporins. EstB reversed the imipenem resistance of P. aeruginosa ΔmexS and restored the changes in susceptibility to cephalosporins conferred by the downregulation of the outer membrane proteins, OmpK35 and OmpK36, in K. pneumoniae ΔramR-ompK36 to wild-type level. The introduction of EstB to the periplasmic space of Gram-negative bacteria can increase carbapenem and cephalosporin susceptibility.},
}
@article {pmid39577583,
year = {2024},
author = {Yu, K and He, B and Xiong, J and Kan, P and Sheng, H and Zhi, S and Zhu, DZ and Yao, Z},
title = {Deciphering basic and key traits of bio-pollutants in a long-term reclaimed water headwater urban stream.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177696},
doi = {10.1016/j.scitotenv.2024.177696},
pmid = {39577583},
issn = {1879-1026},
mesh = {*Environmental Monitoring ; *Rivers/microbiology/chemistry ; Water Pollutants, Chemical/analysis ; Waste Disposal, Fluid/methods ; Acinetobacter baumannii/genetics ; China ; Drug Resistance, Microbial/genetics ; },
abstract = {Reclaimed water has been recognized as a stable water resource for ecological replenishment in riverine environment. However, information about the bio-pollutants spatial and temporal distributions and the associated risk in this environment remains insufficient. Herein, the bio-pollutant profile in a long-term reclaimed water headwater urban stream, including antibiotic resistance genes (ARGs), mobile genetic elements and pathogens, were revealed by metagenomics. Notably, the temporal variation in bio-pollutant levels exceeded spatial fluctuations, possibly due to the varied rainfall intensity. Specially, multidrug resistance genes and Acinetobacter baumannii (A. baumannii) were the dominant ARGs and pathogens, respectively, exhibiting higher abundance in the dry season, especially in the downstream of the receiving point, where the bio-risk also peaked. A. baumannii and Ralstonia solanacearum were found to be the main plasmids contributors inducing the horizontal gene transfer process in this stream. Overall, A. baumannii contributed over 50 % bio-risk values in most samples, indicating that it was the "overlord" in this headwater urban stream. This study revealed characteristics of bio-pollutants in a typical long-term reclaimed water headwater urban stream, highlighting the superiority of A. baumannii in bio-pollutants, which should be a key consideration in the bio-pollutants surveillance for reclaimed waters.},
}
@article {pmid39575680,
year = {2025},
author = {Wang, H and Xu, Z and Zhang, Z and Zhong, B},
title = {Horizontal transposon transfer during plant terrestrialization.},
journal = {Journal of integrative plant biology},
volume = {67},
number = {1},
pages = {15-18},
doi = {10.1111/jipb.13809},
pmid = {39575680},
issn = {1744-7909},
support = {32122010//National Natural Science Foundation of China/ ; 32370228//National Natural Science Foundation of China/ ; },
mesh = {*Gene Transfer, Horizontal/genetics ; *DNA Transposable Elements/genetics ; *Plants/genetics ; Retroelements/genetics ; },
abstract = {During the move to land, plants acquired transposable elements by horizontal transfer from bacteria and fungi and land plants have many long non-coding RNAs derived from retrotransposons acquired by horizontal transposon transfer, including some that are highly expressed and involved in the response to drought stress and abscisic acid.},
}
@article {pmid39575186,
year = {2024},
author = {Verma, T and Hendiani, S and Carbajo, C and Andersen, SB and Hammarlund, EU and Burmølle, M and Sand, KK},
title = {Recurrence and propagation of past functions through mineral facilitated horizontal gene transfer.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1449094},
pmid = {39575186},
issn = {1664-302X},
abstract = {Horizontal gene transfer is one of the most important drivers of bacterial evolution. Transformation by uptake of extracellular DNA is traditionally not considered to be an effective mode of gene acquisition, simply because extracellular DNA is degraded in a matter of days when it is suspended in e.g. seawater. Recently the age span of stored DNA was increased to at least 2 Ma. Here, we show that Acinetobacter baylyi can incorporate 60 bp DNA fragments adsorbed to common sedimentary minerals and that the transformation frequencies scale with mineral surface properties. Our work highlights that ancient environmental DNA can fuel the evolution of contemporary bacteria. In contrast to heritable stochastic mutations, the processes by which bacteria acquire new genomic material during times of increased stress and needs, indicate a non-random mechanism that may propel evolution in a non-stochastic manner.},
}
@article {pmid39572773,
year = {2024},
author = {Hoffmann, L},
title = {Finding the sweet spot in the deep ocean.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1544},
pmid = {39572773},
issn = {2399-3642},
abstract = {‘Candidatus Endonucleobacter’ infects the nuclei of deep-sea mussels but it was unknown how they can prevent apoptosis of the host. A new study by Porras and colleagues, published in Nature Microbiology, suggests that the bacterium upregulates host-derived apoptosis inhibitors and genes for digesting sugars, lipids and amino acids acquired through horizontal gene transfer from the mussels.},
}
@article {pmid39571737,
year = {2025},
author = {Jing, T and Yang, J and Pan, J and Liu, X and Yang, X and Farhan, M and Su, H and Ma, X and Zhang, S},
title = {A near-complete genome reveals the population evolution of the cotton-melon aphid Aphis gossypii.},
journal = {Insect biochemistry and molecular biology},
volume = {176},
number = {},
pages = {104215},
doi = {10.1016/j.ibmb.2024.104215},
pmid = {39571737},
issn = {1879-0240},
mesh = {Animals ; *Aphids/genetics ; *Genome, Insect ; Male ; Female ; Telomere/genetics ; },
abstract = {The cotton-melon aphid Aphis gossypii Glover is a severe pest worldwide. Interhaplotype genomic variation can be used as a starting point to analyze the adaptability of Ap. gossypii. In this study, we utilized long-read PacBio HiFi sequencing and HiC scaffolding techniques to assemble a near telomere-to-telomere gap-free genome assembly of Hap4. The assembly had two gaps totaling 321.24 Mb. We characterized five telomeric repetitive regions (GGTTA)n, including the four found at the 3' end of the chromosomes, and obtained new structural information about the telomeres. Due to the improved sequencing technology, we also identified more than 55.03 Mb of repetitive DNA in the genome assembly of Hap4, which contributed significantly to the increase in genome size compared to that of Hap1 and Hap3. Most of the additional repetitive DNA content was located on the X chromosome, and the tandem repeat sequence occupied 16.8% of the X chromosome length. The Hap4 assembly showed that the X chromosome exhibited a greater abundance of AT-rich satDNA arrays (11 satDNA arrays longer than 100 kb) than that observed in the autosomes (A1 and A2 harboured 3 and 1 satDNA arrays). We detected presence-absence variations, insertions, and deletions events between Hap1, Hap3, and Hap4 Ap. gossypii, which had significant effects on gene expression. Additionally, we identified a male-specific glyceraldehyde-3-phosphate dehydrogenase of fungal origin in all strains of Ap. gossypii. This comprehensive genome assembly provides valuable insights into the structural characteristics of highly repetitive regions and allows comparative genomic analyses that facilitate our understanding of Ap. gossypii's adaptation and diversification.},
}
@article {pmid39571576,
year = {2024},
author = {Denoeud, F and Godfroy, O and Cruaud, C and Heesch, S and Nehr, Z and Tadrent, N and Couloux, A and Brillet-Guéguen, L and Delage, L and Mckeown, D and Motomura, T and Sussfeld, D and Fan, X and Mazéas, L and Terrapon, N and Barrera-Redondo, J and Petroll, R and Reynes, L and Choi, SW and Jo, J and Uthanumallian, K and Bogaert, K and Duc, C and Ratchinski, P and Lipinska, A and Noel, B and Murphy, EA and Lohr, M and Khatei, A and Hamon-Giraud, P and Vieira, C and Avia, K and Akerfors, SS and Akita, S and Badis, Y and Barbeyron, T and Belcour, A and Berrabah, W and Blanquart, S and Bouguerba-Collin, A and Bringloe, T and Cattolico, RA and Cormier, A and Cruz de Carvalho, H and Dallet, R and De Clerck, O and Debit, A and Denis, E and Destombe, C and Dinatale, E and Dittami, S and Drula, E and Faugeron, S and Got, J and Graf, L and Groisillier, A and Guillemin, ML and Harms, L and Hatchett, WJ and Henrissat, B and Hoarau, G and Jollivet, C and Jueterbock, A and Kayal, E and Knoll, AH and Kogame, K and Le Bars, A and Leblanc, C and Le Gall, L and Ley, R and Liu, X and LoDuca, ST and Lopez, PJ and Lopez, P and Manirakiza, E and Massau, K and Mauger, S and Mest, L and Michel, G and Monteiro, C and Nagasato, C and Nègre, D and Pelletier, E and Phillips, N and Potin, P and Rensing, SA and Rousselot, E and Rousvoal, S and Schroeder, D and Scornet, D and Siegel, A and Tirichine, L and Tonon, T and Valentin, K and Verbruggen, H and Weinberger, F and Wheeler, G and Kawai, H and Peters, AF and Yoon, HS and Hervé, C and Ye, N and Bapteste, E and Valero, M and Markov, GV and Corre, E and Coelho, SM and Wincker, P and Aury, JM and Cock, JM},
title = {Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems.},
journal = {Cell},
volume = {187},
number = {24},
pages = {6943-6965.e39},
doi = {10.1016/j.cell.2024.10.049},
pmid = {39571576},
issn = {1097-4172},
mesh = {*Phaeophyceae/genetics ; *Ecosystem ; *Phylogeny ; *Genomics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome/genetics ; },
abstract = {Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, and are under considerable threat from climate change. In this study, analysis of multiple genomes has provided insights across the entire evolutionary history of this lineage, from initial emergence, through later diversification of the brown algal orders, down to microevolutionary events at the genus level. Emergence of the brown algal lineage was associated with a marked gain of new orthologous gene families, enhanced protein domain rearrangement, increased horizontal gene transfer events, and the acquisition of novel signaling molecules and key metabolic pathways, the latter notably related to biosynthesis of the alginate-based extracellular matrix, and halogen and phlorotannin biosynthesis. We show that brown algal genome diversification is tightly linked to phenotypic divergence, including changes in life cycle strategy and zoid flagellar structure. The study also showed that integration of large viral genomes has had a significant impact on brown algal genome content throughout the emergence of the lineage.},
}
@article {pmid39568508,
year = {2024},
author = {Mukherjee, K and Moroz, LL},
title = {Evolution of g-type lysozymes in metazoa: insights into immunity and digestive adaptations.},
journal = {Frontiers in cell and developmental biology},
volume = {12},
number = {},
pages = {1487920},
pmid = {39568508},
issn = {2296-634X},
abstract = {Exploring the evolutionary dynamics of lysozymes is critical for advancing our knowledge of adaptations in immune and digestive systems. Here, we characterize the distribution of a unique class of lysozymes known as g-type, which hydrolyze key components of bacterial cell walls. Notably, ctenophores, and choanoflagellates (the sister group of Metazoa), lack g-type lysozymes. We reveal a mosaic distribution of these genes, particularly within lophotrochozoans/spiralians, suggesting the horizontal gene transfer events from predatory myxobacteria played a role in their acquisition, enabling specialized dietary and defensive adaptations. We further identify two major groups of g-type lysozymes based on their widespread distribution in gastropods. Despite their sequence diversity, these lysozymes maintain conserved structural integrity that is crucial for enzymatic activity, underscoring independent evolutionary pathways where g-type lysozymes have developed functionalities typically associated with different lysozyme types in other species. Specifically, using Aplysia californica as a reference species, we identified three distinct g-type lysozyme genes: two are expressed in organs linked to both feeding and defense, and the third exhibits broader distribution, likely associated with immune functions. These findings advance our understanding of the evolutionary dynamics shaping the recruitment and mosaic functional diversification of these enzymes across metazoans, offering new insights into ecological physiology and physiological evolution as emerging fields.},
}
@article {pmid39566460,
year = {2025},
author = {Xia, L and Wang, J and Chen, M and Li, G and Wang, W and An, T},
title = {Biofilm formation mechanisms of mixed antibiotic-resistant bacteria in water: Bacterial interactions and horizontal transfer of antibiotic-resistant plasmids.},
journal = {Journal of hazardous materials},
volume = {481},
number = {},
pages = {136554},
doi = {10.1016/j.jhazmat.2024.136554},
pmid = {39566460},
issn = {1873-3336},
mesh = {*Biofilms/drug effects/growth &amp; development ; *Plasmids/genetics ; *Gene Transfer, Horizontal ; *Escherichia coli/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Water Microbiology ; Bacteria/drug effects/genetics/metabolism ; Microbial Interactions ; },
abstract = {Over 95 % of bacteria on water supply pipeline surfaces exist in biofilms, which are hotspots for antibiotic resistance gene (ARG) transmission. This study established mixed biofilm culture systems on a metal iron substrate using Escherichia coli: antibiotic-sensitive bacteria (ASB) and antibiotic-resistant bacteria (ARB). The growth rate and extracellular polymeric substances (EPS) content of mixed biofilm surpassed single-species biofilms due to synergistic interactions among different bacteria. However, the composition of mixed biofilms formed by ASB and ARB became unstable after 72 h, linked to reduced polysaccharide proportions in EPS and inter-bacterial competition. The bacterial composition and conjugative transfer frequency of ARGs in mixed biofilms indicate that biofilm formation significantly enhances horizontal transfer of ARGs. Notably, the conjugative transfer frequency of the mixed biofilm formed by two ARB increased 100-fold within five days. In contrast, the conjugative transfer frequency in the mixed biofilm formed by ASB and ARB was unstable; inter-bacterial competition led to plasmid loss associated with horizontal transfer of ARGs, ultimately resulting in biofilm shedding. Furthermore, genes associated with ARG transfer and biofilm growth up-regulated by 1.5 - 6 and 2 - 7 times, respectively, in mixed biofilm. These findings highlight a mutually reinforcing relationship between biofilm formation and horizontal ARG transmission, with significant environmental implications.},
}
@article {pmid39565221,
year = {2025},
author = {Molano, LG and Hirsch, P and Hannig, M and Müller, R and Keller, A},
title = {The PLSDB 2025 update: enhanced annotations and improved functionality for comprehensive plasmid research.},
journal = {Nucleic acids research},
volume = {53},
number = {D1},
pages = {D189-D196},
pmid = {39565221},
issn = {1362-4962},
support = {//European Commission/ ; 466168626//DFG/ ; },
mesh = {*Plasmids/genetics ; *Molecular Sequence Annotation ; *Databases, Genetic ; Bacteria/genetics ; Software ; Artificial Intelligence ; Gene Transfer, Horizontal ; },
abstract = {Plasmids are extrachromosomal DNA molecules in bacteria and archaea, playing critical roles in horizontal gene transfer, antibiotic resistance, and pathogenicity. Since its first release in 2018, our database on plasmids, PLSDB, has significantly grown and enhanced its content and scope. From 34 513 records contained in the 2021 version, PLSDB now hosts 72 360 entries. Designed to provide life scientists with convenient access to extensive plasmid data and to support computer scientists by offering curated datasets for artificial intelligence (AI) development, this latest update brings more comprehensive and accurate information for plasmid research, with interactive visualization options. We enriched PLSDB by refining the identification and classification of plasmid host ecosystems and host diseases. Additionally, we incorporated annotations for new functional structures, including protein-coding genes and biosynthetic gene clusters. Further, we enhanced existing annotations, such as antimicrobial resistance genes and mobility typing. To accommodate these improvements and to host the increase plasmid sets, the webserver architecture and underlying data structures of PLSDB have been re-reconstructed, resulting in decreased response times and enhanced visualization of features while ensuring that users have access to a more efficient and user-friendly interface. The latest release of PLSDB is freely accessible at https://www.ccb.uni-saarland.de/plsdb2025.},
}
@article {pmid39565095,
year = {2024},
author = {Bulka, O and Mahadevan, R and Edwards, EA},
title = {Pangenomic insights into Dehalobacter evolution and acquisition of functional genes for bioremediation.},
journal = {Microbial genomics},
volume = {10},
number = {11},
pages = {},
pmid = {39565095},
issn = {2057-5858},
mesh = {*Biodegradation, Environmental ; *Phylogeny ; *Genome, Bacterial ; Evolution, Molecular ; Bacterial Proteins/genetics/metabolism ; Genomics ; Gene Transfer, Horizontal ; Metagenome ; },
abstract = {Dehalobacter is a genus of organohalide-respiring bacteria that is recognized for its fastidious growth using reductive dehalogenases (RDases). In the SC05 culture, however, a Dehalobacter population also mineralizes dichloromethane (DCM) produced by chloroform dechlorination using the mec cassette, just downstream of its active RDase. A closed genome of this DCM-mineralizing lineage has previously evaded assembly. Here, we present the genomes of two novel Dehalobacter strains, each of which was assembled from the metagenome of a distinct subculture from SC05. A pangenomic analysis of the Dehalobacter genus, including RDase synteny and phylogenomics, reveals at least five species of Dehalobacter based on average nucleotide identity, RDase and core gene synteny, as well as differential functional genes. An integration hotspot is also pinpointed in the Dehalobacter genome, in which many recombinase islands have accumulated. This nested recombinase island encodes the active RDase and mec cassette in both SC05 Dehalobacter genomes, indicating the transfer of key functional genes between species of Dehalobacter. Horizontal gene transfer between these two novel Dehalobacter strains has implications for the evolutionary history within the SC05 subcultures and of the Dehalobacter genus as a whole, especially regarding adaptation to anthropogenic chemicals.},
}
@article {pmid39564482,
year = {2024},
author = {Huang, CJ and Wu, TL and Wu, YL and Wang, RS and Lin, YC},
title = {Comparative genomic analysis uncovered phylogenetic diversity, evolution of virulence factors, and horizontal gene transfer events in tomato bacterial spot Xanthomonas euvesicatoria.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1487917},
pmid = {39564482},
issn = {1664-302X},
abstract = {INTRODUCTION: Bacterial spot, caused by diverse xanthomonads classified into four lineages within three species, poses a significant threat to global pepper and tomato production. In Taiwan, tomato bacterial spot xanthomonads phylogenetically related to an atypical Xanthomonas euvesicatoria pv. perforans (Xep) strain NI1 from Nigeria were found.<br><br>METHODS: To investigate the genetic structure of Taiwanese Xep strains and determine the phylogenetic position of the atypical strains, we completed high-quality, gap-free, circularized genomes of seven Taiwanese Xep strains and performed comparative genomic analyses with genomes of X. euvesicatoria pathovars. Average nucleotide identity, core genome analysis, and phylogenomic analysis were conducted.<br><br>RESULTS: Three sequenced strains were identified as typical Xep, while four clustered with the atypical strain NI1, forming a distinct genomovar within X. euvesicatoria, proposed as X. euvesicatoria genomovar taiwanensis (Xet). This new lineage likely originated in Taiwan and spread to Nigeria through global seed trade. At the genomovar level, chromosomes remained conserved among Taiwanese strains, while plasmids likely contributed to bacterial virulence, avirulence, and field fitness. Gap-free genomes revealed associations between the evolution of type III effectors, horizontal gene transfer events, plasmid diversity, and recombination.<br><br>DISCUSSION: This study highlights the critical roles of horizontal gene transfer and plasmids in shaping the genetic makeup, evolution, and environmental adaptation of plant pathogenic xanthomonads. The identification of a new genomovar, X. euvesicatoria genomovar taiwanensis, provides insights into the diversity and global spread of bacterial spot pathogens through seed trade.},
}
@article {pmid39562586,
year = {2024},
author = {Goh, YX and Anupoju, SMB and Nguyen, A and Zhang, H and Ponder, M and Krometis, LA and Pruden, A and Liao, J},
title = {Evidence of horizontal gene transfer and environmental selection impacting antibiotic resistance evolution in soil-dwelling Listeria.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10034},
pmid = {39562586},
issn = {2041-1723},
mesh = {*Gene Transfer, Horizontal ; *Soil Microbiology ; *Listeria/genetics/drug effects ; *Phylogeny ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Genome, Bacterial/genetics ; Evolution, Molecular ; Selection, Genetic ; },
abstract = {Soil is an important reservoir of antibiotic resistance genes (ARGs) and understanding how corresponding environmental changes influence their emergence, evolution, and spread is crucial. The soil-dwelling bacterial genus Listeria, including L. monocytogenes, the causative agent of listeriosis, serves as a key model for establishing this understanding. Here, we characterize ARGs in 594 genomes representing 19 Listeria species that we previously isolated from soils in natural environments across the United States. Among the five putatively functional ARGs identified, lin, which confers resistance to lincomycin, is the most prevalent, followed by mprF, sul, fosX, and norB. ARGs are predominantly found in Listeria sensu stricto species, with those more closely related to L. monocytogenes tending to harbor more ARGs. Notably, phylogenetic and recombination analyses provide evidence of recent horizontal gene transfer (HGT) in all five ARGs within and/or across species, likely mediated by transformation rather than conjugation and transduction. In addition, the richness and genetic divergence of ARGs are associated with environmental conditions, particularly soil properties (e.g., aluminum and magnesium) and surrounding land use patterns (e.g., forest coverage). Collectively, our data suggest that recent HGT and environmental selection play a vital role in the acquisition and diversification of bacterial ARGs in natural environments.},
}
@article {pmid39562577,
year = {2024},
author = {Chen, Y and Wang, W and Zhang, S and Zhao, Y and Feng, L and Zhu, C},
title = {Assembly and analysis of the complete mitochondrial genome of Carya illinoinensis to provide insights into the conserved sequences of tRNA genes.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {28571},
pmid = {39562577},
issn = {2045-2322},
support = {32001344//the National Natural Science Foundation of China/ ; 32001344//the National Natural Science Foundation of China/ ; 32001344//the National Natural Science Foundation of China/ ; 32001344//the National Natural Science Foundation of China/ ; 32001344//the National Natural Science Foundation of China/ ; 32001344//the National Natural Science Foundation of China/ ; BK20200290//the Natural Science Foundation of Jiangsu Province, China/ ; BK20200290//the Natural Science Foundation of Jiangsu Province, China/ ; BK20200290//the Natural Science Foundation of Jiangsu Province, China/ ; BK20200290//the Natural Science Foundation of Jiangsu Province, China/ ; BK20200290//the Natural Science Foundation of Jiangsu Province, China/ ; BK20200290//the Natural Science Foundation of Jiangsu Province, China/ ; },
mesh = {*Carya/classification/genetics ; *Genome, Mitochondrial ; *Genome, Plant ; *RNA, Transfer/chemistry/genetics ; *Conserved Sequence ; Phylogeny ; RNA Folding ; Sequence Analysis, DNA ; Codon Usage ; RNA Editing ; Gene Transfer, Horizontal ; Fagus/genetics ; },
abstract = {Carya illinoinensis is an economically important nut tree, and its chloroplast (cp.) genome has been reported; however, its mitochondrial (mt) genome remains unknown. In the present study, we assembled the first mt genome of C. illinoinensis. The circular mt genome of C. illinoinensis is 495,205 bp long, with 37 protein-coding genes(PCGs), 24 tRNA genes, and 3 rRNA genes. All the tRNAs could be folded into typical cloverleaf secondary structures, with lengths of 58-88 bp. A conserved U-U-C-x-A-x2 consensus nucleotide sequence was discovered in the Ψ-loops of tRNA sequences. In addition, 447 dispersed repeats were detected, as well as found 482 RNA editing sites and 9,960 codons in the mt genome. Furthermore, a total of 27 DNA sequences with a length of 43,277 bp were transferred from the cp. to the mt genome, and eight integrated cp-derived genes (trnL-CAA, trnV-GAC, trnD-GUC, trnW-CCA, trnN-GUU, trnH-GUG, trnM-CAU, and rps7) were identified. We also obtained 1,086 hits, including 364.023 kp of nuclear genome sequences, that were transferred to the mt genome. To determine the evolutionary position of C. illinoinensis, we conducted a phylogenetic analysis of the mitogenomes of C. illinoinensis and 14 other taxa. The results strongly suggested that C. illinoinensis and Fagus sylvatica formed a single clade with 100% bootstrap support. This study sequenced comprehensive data on the C. illinoinensis mitochondrial genome and provided insights into the conserved sequences of tRNA genes, which could facilitate evolutionary research in other Carya trees in the future.},
}
@article {pmid39555914,
year = {2024},
author = {Ulrich, NJ and Miller, SR},
title = {Integration of horizontally acquired light-harvesting genes into an ancestral regulatory network in the cyanobacterium Acaryochloris marina MBIC11017.},
journal = {mBio},
volume = {15},
number = {12},
pages = {e0242324},
pmid = {39555914},
issn = {2150-7511},
support = {NNA15BB04A//National Aeronautics and Space Administration (NASA)/ ; //Montana Space Grant Consortium (MSGC)/ ; },
mesh = {*Gene Transfer, Horizontal ; *Cyanobacteria/genetics/metabolism ; *Gene Regulatory Networks ; *Phycocyanin/genetics/metabolism ; Evolution, Molecular ; Light-Harvesting Protein Complexes/genetics/metabolism ; Chlorophyll/metabolism ; Gene Expression Regulation, Bacterial ; Bacterial Proteins/genetics/metabolism ; Transcriptome ; Light ; },
abstract = {The acquisition of new capabilities by horizontal gene transfer (HGT) shapes the distribution of traits during microbial diversification. In the Chlorophyll (Chl) d-producing cyanobacterium Acaryochloris marina, the genes involved in the production and disassembly of the light-harvesting phycobiliprotein phycocyanin (PC) were lost in the A. marina common ancestor but then subsequently regained via HGT in A. marina strain MBIC11017. However, it remains unknown how the HGT-acquired PC genes in MBIC11017 have been reintegrated into its existing regulatory network after tens of millions of years since their loss. Here, we investigated potential mechanisms of regulatory assimilation of PC genes by comparing the transcriptomes of A. marina strain MBIC11017 and a PC-lacking close relative under both low irradiance far-red light and high irradiance white light. We found that PC assembly and degradation processes have been re-assimilated into a conserved ancestral response to high light. Further, we identified putative regulatory elements that were likely co-transferred with PC genes and could be recognized by A. marina's pre-existing light response machinery. This study offers insights into how HGT-acquired genes can be reintegrated into an existing transcriptional regulatory network that has evolved in their absence.IMPORTANCEHorizontal gene transfer, the asymmetric movement of genetic information between donor and recipient organisms, is an important mechanism for acquiring new traits. In order for newly acquired gene content to be retained, it must be integrated into the genetic repertoire and regulatory networks of the recipient cell. In a strain of the Chlorophyll d-producing cyanobacterium Acaryochloris marina, the recent reacquisition of the genes required to produce the light-harvesting pigment phycocyanin offers a rare opportunity to understand the mechanisms underlying the regulatory assimilation of an acquired complex trait in bacteria. The significance in our research is in characterizing how an ancestrally lost, complex trait can be reintegrated into a conserved regulatory network, even after millions of years.},
}
@article {pmid39552541,
year = {2024},
author = {Singh, CK and Sodhi, KK},
title = {Targeting bioinformatics tools to study the dissemination and spread of antibiotic resistant genes in the environment and clinical settings.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/1040841X.2024.2429603},
pmid = {39552541},
issn = {1549-7828},
abstract = {Antibiotic resistance has expanded as a result of the careless use of antibiotics in the medical field, the food industry, agriculture, and other industries. By means of genetic recombination between commensal and pathogenic bacteria, the microbes obtain antibiotic resistance genes (ARGs). In bacteria, horizontal gene transfer (HGT) is the main mechanism for acquiring ARGs. With the development of high-throughput sequencing, ARG sequence analysis is now feasible and widely available. Preventing the spread of AMR in the environment requires the implementation of ARGs mapping. The metagenomic technique, in particular, has helped in identifying antibiotic resistance within microbial communities. Due to the exponential growth of experimental and clinical data, significant investments in computer capacity, and advancements in algorithmic techniques, the application of machine learning (ML) algorithms to the problem of AMR has attracted increasing attention over the past five years. The review article sheds a light on the application of bioinformatics for the antibiotic resistance monitoring. The most advanced tool currently being employed to catalog the resistome of various habitats are metagenomics and metatranscriptomics. The future lies in the hands of artificial intelligence (AI) and machine learning (ML) methods, to predict and optimize the interaction of antibiotic-resistant compounds with target proteins.},
}
@article {pmid39551215,
year = {2024},
author = {Bierge, P and Sánchez-Osuna, M and Duarte, B and Gómez-Sánchez, I and Espasa, M and Freitas, AR and Peixe, L and Gasch, O and Pich, OQ and Novais, C},
title = {Diverse genomic and epidemiological landscapes of redundant pbp5 genes in Enterococcus spp.: Insights into plasmid mobilization, ampicillin susceptibility, and environmental interactions.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177562},
doi = {10.1016/j.scitotenv.2024.177562},
pmid = {39551215},
issn = {1879-1026},
mesh = {*Ampicillin/pharmacology ; *Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Enterococcus/genetics/drug effects ; Phylogeny ; Bacterial Proteins/genetics ; Humans ; },
abstract = {Genetic redundancy in bacteria plays a crucial role in enhancing adaptability and accelerating evolution in response to selective pressures, particularly those associated with rapid environmental changes. Aminopenicillins like ampicillin are important therapeutic options for Enterococcus infections in both humans and animals, with resistance mostly associated with pbp5 gene mutations or overexpression. While the occurrence of redundant pbp5 genes has been occasionally reported, the advantages for the host bacteria have not been explored in detail. During a whole-genome sequencing project of Enterococcus faecium from bacteremic patients, we identified an ST592 strain (Efm57) with redundant pbp5 genes. This presented an opportunity to investigate the prevalence and implications of multiple pbp5 acquisitions in diverse Enterococcus species across various sources, geographical regions, and timeframes. The analysis of 618 complete Enterococcus genomes from public databases revealed that 3.2 % harbored redundant pbp5 genes, located on chromosomes or plasmids across different species from diverse epidemiological backgrounds. The proteins encoded by these genes showed homologies ranging from 51.1 % to 97.5 % compared to native copies. Phylogenetic analysis grouped redundant PBP5 amino acid sequences into three distinct clades, with insertion sequences (mostly IS6-like) facilitating their recent spread to diverse plasmids with varying genetic backbones. The presence of multiple antibiotic resistance genes on pbp5-plasmids, including those conferring resistance to linezolid, underscores their involvement in co-selection and recombination events with other clinically-relevant antibiotics. Conjugation experiments confirmed the transferability of a specific 24 kb pbp5-plasmid from the Efm57 strain. This plasmid was associated with higher minimum inhibitory concentrations of ampicillin and conferred bacteria growth advantages at 22 °C. In conclusion, the widespread distribution of redundant pbp5 genes among Enterococcus spp. highlights the complex interplay between genetic mobility, environmental factors, and multidrug resistance in overlapping ecosystems emphasizing the importance of understanding these dynamics to mitigate antibiotic resistance spread within the One Health framework.},
}
@article {pmid39550371,
year = {2024},
author = {Yang, JX and Peng, Y and Yu, QY and Yang, JJ and Zhang, YH and Zhang, HY and Adams, CA and Willing, CE and Wang, C and Li, QS and Han, XG and Gao, C},
title = {Gene horizontal transfers and functional diversity negatively correlated with bacterial taxonomic diversity along a nitrogen gradient.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {128},
pmid = {39550371},
issn = {2055-5008},
mesh = {*Soil Microbiology ; Soil/chemistry ; *Nitrogen/metabolism/pharmacology ; *Biodiversity ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/metabolism ; Metagenome ; *Gene Transfer, Horizontal/drug effects ; },
abstract = {Horizontal gene transfer (HGT) mediated diversification is a critical force driving evolutionary and ecological processes. However, how HGT might relate to anthropogenic activity such as nitrogen addition, and its subsequent effect on functional diversity and cooccurrence networks remain unknown. Here we approach this knowledge gap by blending bacterial 16S rRNA gene amplicon and shotgun metagenomes from a platform of cessation of nitrogen additions and continuous nitrogen additions. We found that bacterial HGT events, functional genes, and virus diversities increased whereas bacterial taxonomic diversity decreased by nitrogen additions, resulting in a counterintuitive strong negative association between bacterial taxonomic and functional diversities. Nitrogen additions, especially the ceased one, complexified the cooccurrence network by increasing the contribution of vitamin B12 auxotrophic Acidobacteria, indicating cross-feeding. These findings advance our perceptions of the causes and consequences of the diversification process in community ecology.},
}
@article {pmid39549700,
year = {2024},
author = {Siozios, S and Nadal-Jimenez, P and Azagi, T and Sprong, H and Frost, CL and Parratt, SR and Taylor, G and Brettell, L and Liew, KC and Croft, L and King, KC and Brockhurst, MA and Hypša, V and Novakova, E and Darby, AC and Hurst, GDD},
title = {Genome dynamics across the evolutionary transition to endosymbiosis.},
journal = {Current biology : CB},
volume = {34},
number = {24},
pages = {5659-5670.e7},
doi = {10.1016/j.cub.2024.10.044},
pmid = {39549700},
issn = {1879-0445},
mesh = {*Symbiosis/genetics ; *Genome, Bacterial ; Biological Evolution ; Gene Transfer, Horizontal ; Evolution, Molecular ; Enterobacteriaceae/genetics/physiology ; },
abstract = {Endosymbiosis-where a microbe lives and replicates within a host-is an important contributor to organismal function that has accelerated evolutionary innovations and catalyzed the evolution of complex life. The evolutionary processes associated with transitions to endosymbiosis, however, are poorly understood. Here, we leverage the wide diversity of host-associated lifestyles of the genus Arsenophonus to reveal the complex evolutionary processes that occur during the transition to a vertically transmitted endosymbiotic lifestyle from strains maintained solely by horizontal (infectious) transmission. We compared the genomes of 38 strains spanning diverse lifestyles from horizontally transmitted pathogens to obligate interdependent endosymbionts. Among culturable strains, we observed those with vertical transmission had larger genome sizes than closely related horizontally transmitting counterparts, consistent with evolutionary innovation and the rapid gain of new functions. Increased genome size was a consequence of prophage and plasmid acquisition, including a cargo of type III effectors, alongside the concomitant loss of CRISPR-Cas genome defense systems, enabling mobile genetic element expansion. Persistent endosymbiosis was also associated with loss of type VI secretion, which we hypothesize to be a consequence of reduced microbe-microbe competition. Thereafter, the transition to endosymbiosis with strict vertical inheritance was associated with the expected relaxation of purifying selection, gene pseudogenization, metabolic degradation, and genome reduction. We argue that reduced phage predation in endosymbiotic niches drives the loss of genome defense systems driving rapid genome expansion upon the adoption of endosymbiosis and vertical transmission. This remodeling enables rapid horizontal gene transfer-mediated evolutionary innovation and precedes the reductive evolution traditionally associated with adaptation to endosymbiosis.},
}
@article {pmid39545400,
year = {2025},
author = {Stern, DB and Raborn, RT and Lovett, SP and Boise, NR and Carrasquilla, L and Enke, S and Radune, D and Woodruff, DL and Wahl, KL and Rosovitz, MJ},
title = {Novel Toxin Biosynthetic Gene Cluster in Harmful Algal Bloom-Causing Heteroscytonema crispum: Insights into the Origins of Paralytic Shellfish Toxins.},
journal = {Genome biology and evolution},
volume = {17},
number = {1},
pages = {},
pmid = {39545400},
issn = {1759-6653},
support = {//Battelle National Biodefense Institute/ ; /DHS/DHS/United States ; //Science and Technology Directorate/ ; //National Biodefense Analysis and Countermeasures Center/ ; //Federally Funded Research and Development Center/ ; },
mesh = {*Harmful Algal Bloom ; *Multigene Family ; *Cyanobacteria/genetics/metabolism ; *Saxitoxin/genetics/biosynthesis ; *Phylogeny ; Marine Toxins/genetics/biosynthesis ; Dinoflagellida/genetics/metabolism ; Genome, Bacterial ; Gene Transfer, Horizontal ; },
abstract = {Caused by both eukaryotic dinoflagellates and prokaryotic cyanobacteria, harmful algal blooms are events of severe ecological, economic, and public health consequence, and their incidence has become more common of late. Despite coordinated research efforts to identify and characterize the genomes of harmful algal bloom-causing organisms, the genomic basis and evolutionary origins of paralytic shellfish toxins produced by harmful algal blooms remain at best incomplete. The paralytic shellfish toxin saxitoxin has an especially complex genomic architecture and enigmatic phylogenetic distribution, spanning dinoflagellates and multiple cyanobacterial genera. Using filtration and extraction techniques to target the desired cyanobacteria from nonaxenic culture, coupled with a combination of short- and long-read sequencing, we generated a reference-quality hybrid genome assembly for Heteroscytonema crispum UTEX LB 1556, a freshwater, paralytic shellfish toxin-producing cyanobacterium thought to have the largest known genome in its phylum. We report a complete, novel biosynthetic gene cluster for the paralytic shellfish toxin saxitoxin. Leveraging this biosynthetic gene cluster, we find support for the hypothesis that paralytic shellfish toxin production has appeared in divergent Cyanobacteria lineages through widespread and repeated horizontal gene transfer. This work demonstrates the utility of long-read sequencing and metagenomic assembly toward advancing our understanding of paralytic shellfish toxin biosynthetic gene cluster diversity and suggests a mechanism for the origin of paralytic shellfish toxin biosynthetic genes.},
}
@article {pmid39542384,
year = {2024},
author = {Wang, J and Wu, Y and Zhu, L and Guo, K and Gao, S and Dong, Y},
title = {Genomic evolution and patterns of horizontal gene transfer in Papilio.},
journal = {Genomics},
volume = {116},
number = {6},
pages = {110956},
doi = {10.1016/j.ygeno.2024.110956},
pmid = {39542384},
issn = {1089-8646},
mesh = {*Gene Transfer, Horizontal ; *Butterflies/genetics ; Animals ; *Evolution, Molecular ; Phylogeny ; ATP-Binding Cassette Transporters/genetics ; },
abstract = {The Papilio genus, known for its ecological and phenotypic diversity, is a valuable model for evolutionary studies. This study conducted a comparative genomic analysis of 11 Papilio species, revealing species-specific gene family expansions, including the UDP-glucosyltransferase 2 gene associated with insect detoxification, particularly expanding in Papilio polyxenes. Our analysis also revealed 199 horizontal gene transfer (HGT) acquired genes from 76 microbial species, with Pseudomonadota and Bacillota as common HGT donors across these genomes. Furthermore, we examined the evolutionary patterns of nine ABC transporter subfamilies, uncovering potential links between gene family evolution and environmental adaptation. This study provides new insights into evolutionary relationships and genomic adaptations within the Papilio genus, contributing to broader butterfly evolutionary research.},
}
@article {pmid39542270,
year = {2024},
author = {Yuan, S and Jin, G and Cui, R and Wang, X and Wang, M and Chen, Z},
title = {Transmission and control strategies of antimicrobial resistance from the environment to the clinic: A holistic review.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177461},
doi = {10.1016/j.scitotenv.2024.177461},
pmid = {39542270},
issn = {1879-1026},
mesh = {Humans ; *Gene Transfer, Horizontal ; Drug Resistance, Bacterial ; Anti-Bacterial Agents ; Drug Resistance, Microbial ; Antimicrobial Stewardship ; },
abstract = {The environment serves as a significant reservoir of antimicrobial resistance (AMR) microbes and genes and is increasingly recognized as key source of clinical AMR. Modern human activities impose an additional burden on environmental AMR, promoting its transmission to clinical setting and posing a serious threat to human health and welfare. Therefore, a comprehensive review of AMR transmission from the environment to the clinic, along with proposed effective control strategies, is crucial. This review systematically summarized current research on the transmission of environmental AMR to clinical settings. Furthermore, the transmission pathways, horizontal gene transfer (HGT) mechanisms, as well as the influential drivers including triple planetary crisis that may facilitate AMR transfer from environmental species to clinical pathogens are highlighted. In response to the growing trend of AMR transmission, we propose insightful mitigation strategies under the One Health framework, integrating advanced surveillance and tracking technologies, interdisciplinary knowledge, multisectoral interventions, alongside multiple antimicrobial use and stewardship approaches to tacking development and spread of AMR.},
}
@article {pmid39541852,
year = {2025},
author = {Wang, Q and Wang, M and Yang, Q and Feng, L and Zhang, H and Wang, R and Wang, R},
title = {The role of bacteriophages in facilitating the horizontal transfer of antibiotic resistance genes in municipal wastewater treatment plants.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122776},
doi = {10.1016/j.watres.2024.122776},
pmid = {39541852},
issn = {1879-2448},
mesh = {*Bacteriophages/genetics ; *Gene Transfer, Horizontal ; *Wastewater ; Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid ; Plasmids/genetics ; Bacteria/virology/genetics ; },
abstract = {Bacteriophages play integral roles in the ecosystem; however, their precise involvement in horizontal gene transfer and the spread of antibiotic resistance genes (ARGs) are not fully understood. In this study, a coculture system involving consortia of bacteriophages and multidrug-resistant bacteria from an aerobic tank in a municipal wastewater treatment plant (WWTP) was established to investigate the functions of bacteriophages in ARG transfer and spread. The results of the cocultivation of the MRB and bacteriophage consortia indicated that the bacterial community remained stable throughout the whole process, but the addition of bacteriophages significantly increased ARG abundance, especially in bacteriophage DNA. Nine out of the 11 identified ARGs significantly increased, indicating that more bacteriophage particles carried ARGs in the system after cocultivation. In addition, 686 plasmids were detected during cocultivation, of which only 3.36 % were identified as conjugative plasmids, which is significantly lower than the proportion found among previously published plasmids (25.2 %, totaling 14,029 plasmids). Our findings revealed that bacteriophages may play important roles in the horizontal transfer of ARGs through both bacteriophage-mediated conduction and an increase in extracellular ARGs; however, conjugative transfer may not be the main mechanism by which multidrug-resistant bacteria acquire and spread ARGs. Unlike in most previous reports, a coculture system of diverse bacteria and bacteriophages was established in this study to assess bacteriophage functions in ARG transfer and dissemination in the environment, overcoming the limitations associated with the isolation of bacteria and bacteriophages, as well as the specificity of bacteriophage hosts.},
}
@article {pmid39541851,
year = {2025},
author = {Wang, F and Huang, W and Chen, J and Luo, Y and Cao, J and Fang, F and Liu, X and Wu, Y and Luo, J},
title = {Non-antibiotic disinfectant synchronously interferes methane production and antibiotic resistance genes propagation during sludge anaerobic digestion: Activation of microbial adaptation and reconfiguration of bacteria-archaea synergies.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122773},
doi = {10.1016/j.watres.2024.122773},
pmid = {39541851},
issn = {1879-2448},
mesh = {*Sewage/microbiology ; *Methane ; Anaerobiosis ; *Disinfectants/pharmacology ; *Bacteria/drug effects/metabolism ; *Archaea/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; Bioreactors ; Waste Disposal, Fluid ; },
abstract = {Waste activated sludge (WAS) presents both resource recovery potential and pollution risks, making its efficient treatment challenging. Anaerobic digestion is broadly recognized as a green and sustainable approach to WAS treatment, whose efficiency is easily impacted by the exogeneous pollutants in WAS. However, the impact of polyhexamethylene guanidine (PHMG), as a widely-used non-antibiotic disinfectant, on WAS digestion under semi-continuous flow conditions remains unclear. In this study, CH4 production decreased from 16.1 mL/g volatile suspended solids (VSS) in the control to 13.2 mL/g VSS and 0.3 mL/g VSS under low and high PHMG exposure, respectively, while PHMG increased the number of antibiotic resistance gene (ARG) copies per bacterium by 4.6-12.7 %. Molecular docking analysis revealed that PHMG could spontaneously bind to and disintegrate WAS (binding energy:2.35 and -9.62 kcal/mol), increasing the likelihood of microbial exposure to PHMG. This led to an increase in bacterial abundance and a reduction in archaeal populations, resulting in bacterial dominance in ecological niches. The network topology index in PHMG-treated reactors was consistently lower than in the control, with a higher proportion of negatively correlated links, indicating a more antagonistic relationship between bacteria and archaea. Consequently, PHMG significantly interfered with key genes involved in CH4 biosynthesis (e.g., mch and mtd). Interestingly, methanogenic activity and archaeal chemotaxis (e.g., rfk and cheA) partially recovered under low PHMG exposure due to archaeal adaptation through quorum sensing and two-component systems. However, this adaptation process also contributed to the propagation of ARGs through horizontal gene transfer, facilitated by the enhancement of mobile genetic elements and ARGs hosts. These findings confirm the ecological risks of PHMG and highlight the need for effective WAS disposal strategies.},
}
@article {pmid39540883,
year = {2024},
author = {Garcia, LE and Sanchez-Puerta, MV},
title = {Mitochondrial Splicing Efficiency Is Lower in Holoparasites Than in Free-Living Plants.},
journal = {Plant &amp; cell physiology},
volume = {65},
number = {12},
pages = {2018-2029},
doi = {10.1093/pcp/pcae120},
pmid = {39540883},
issn = {1471-9053},
mesh = {*RNA Splicing ; *Mitochondria/genetics/metabolism ; *Introns/genetics ; Gene Transfer, Horizontal ; Magnoliopsida/genetics/parasitology ; Evolution, Molecular ; Plants/genetics/parasitology ; },
abstract = {Mitochondria play a crucial role in eukaryotic organisms, housing their own genome with genes vital for oxidative phosphorylation. Coordination between nuclear and mitochondrial genomes is pivotal for organelle gene expression. Splicing, editing and processing of mitochondrial transcripts are regulated by nuclear-encoded factors. Splicing efficiency (SEf) of the many group II introns present in plant mitochondrial genes is critical for mitochondrial function since a splicing defect or splicing deficiency can severely impact plant growth and development. This study investigates SEf in free-living and holoparasitic plants, focusing on 25 group II introns from 15 angiosperm species. Our comparative analyses reveal distinctive splicing patterns with holoparasites exhibiting significantly lower SEf, potentially linked to their unique evolutionary trajectory. Given the preponderance of horizontal gene transfer (HGT) in parasitic plants, we investigated the effect of HGT on SEf, such as the presence of foreign introns or foreign nuclear-encoded splicing factors. Contrary to expectations, the SEf reductions do not correlate with HGT events, suggesting that other factors are at play, such as the loss of photosynthesis or the transition to a holoparasitic lifestyle. The findings of this study broaden our understanding of the molecular evolution in parasitic plants and shed light on the multifaceted factors influencing organelle gene expression.},
}
@article {pmid39535289,
year = {2024},
author = {Vanhout, Z and Abdellati, S and Gestels, Z and De Baetselier, I and de Block, T and Vanbaelen, T and Manoharan-Basil, SS and Kenyon, C},
title = {Macrolide resistance is pervasive in oral streptococci in the Belgian general population: a cross-sectional survey.},
journal = {Journal of medical microbiology},
volume = {73},
number = {11},
pages = {},
doi = {10.1099/jmm.0.001932},
pmid = {39535289},
issn = {1473-5644},
mesh = {Humans ; Belgium/epidemiology ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; Child ; Cross-Sectional Studies ; *Macrolides/pharmacology ; *Drug Resistance, Bacterial ; Female ; Adult ; Male ; *Streptococcal Infections/microbiology/epidemiology ; Child, Preschool ; *Streptococcus/drug effects/genetics/isolation &amp; purification ; Mouth/microbiology ; Azithromycin/pharmacology ; Middle Aged ; Adolescent ; Young Adult ; Parents ; Prevalence ; Infant ; },
abstract = {Background. Commensal streptococci are common inhabitants of the oral microbiome and regulate its structure and function in beneficial ways for human health. They can, however, also be opportunistic pathogens and act as a reservoir of resistance genes that can be passed on to other bacteria, including pathogens. Little is known about the prevalence of these commensals in parents and their children and their antimicrobial susceptibilities in the Belgian general population.Gap Statement. The macrolide susceptibility of commensal oral Streptococci in Belgium is unknown.Methods. We assessed the prevalence and azithromycin susceptibility of commensal streptococcal species in the parents (n=38) and children (n=50) of 35 families in Belgium.Results. The most frequently detected taxonomic grouping was Streptococcus mitis/oralis, which was detected in 78/181 (43.1%) of the children's isolates and 66/128 (51.6%) of the parents' isolates. Of the 311 isolates collected in this study, 282 isolates (90.7%) had an azithromycin MIC value greater than the breakpoint of 0.25 mg l[-1] and 146 isolates (46.9%) had azithromycin MICs greater than 2 mg l[-1]. There was no difference in the azithromycin MIC distribution of all streptococcal isolates between children and parents. All individuals were colonized by streptococci with azithromycin MICs greater than 0.25 mg l[-1], and 87.5% of individuals had streptococci with MICs greater than 2 mg l[-1].Interpretation. The most prevalent species identified in both age groups was S. mitis/oralis. All individuals harboured streptococci with macrolide resistance. This highlights the need for additional antimicrobial stewardship initiatives to reduce the consumption of macrolides in the general population.},
}
@article {pmid39535230,
year = {2024},
author = {van Westerhoven, AC and Dijkstra, J and Aznar Palop, JL and Wissink, K and Bell, J and Kema, GHJ and Seidl, MF},
title = {Frequent genetic exchanges revealed by a pan-mitogenome graph of a fungal plant pathogen.},
journal = {mBio},
volume = {15},
number = {12},
pages = {e0275824},
pmid = {39535230},
issn = {2150-7511},
support = {AG-5797//Bill and Melinda Gates Foundation (GF)/ ; },
mesh = {*Genome, Mitochondrial/genetics ; *Fusarium/genetics/classification ; *Recombination, Genetic ; Evolution, Molecular ; Phylogeny ; Gene Transfer, Horizontal ; Genome, Fungal ; Plant Diseases/microbiology ; Genetic Variation ; },
abstract = {Mitochondria are present in almost all eukaryotic lineages. The mitochondrial genomes (mitogenomes) evolve separately from nuclear genomes, and they can therefore provide relevant insights into the evolution of their host species. Fusarium oxysporum is a major fungal plant pathogen that is assumed to reproduce clonally. However, horizontal chromosome transfer between strains can occur through heterokaryon formation, and recently, signs of sexual recombination have been observed. Similarly, signs of recombination in F. oxysporum mitogenomes challenged the prevailing assumption of clonal reproduction in this species. Here, we construct, to our knowledge, the first fungal pan-mitogenome graph of nearly 500 F. oxysporum mitogenome assemblies to uncover the variation and evolution. In general, the gene order of fungal mitogenomes is not well conserved, yet the mitogenome of F. oxysporum and related species are highly colinear. We observed two strikingly contrasting regions in the F. oxysporum pan-mitogenome, comprising a highly conserved core mitogenome and a long variable region (6-16 kb in size), of which we identified three distinct types. The pan-mitogenome graph reveals that only five intron insertions occurred in the core mitogenome and that the long variable regions drive the difference between mitogenomes. Moreover, we observed that their evolution is neither concurrent with the core mitogenome nor with the nuclear genome. Our large-scale analysis of long variable regions uncovers frequent recombination between mitogenomes, even between strains that belong to different taxonomic clades. This challenges the common assumption of incompatibility between genetically diverse F. oxysporum strains and provides new insights into the evolution of this fungal species.IMPORTANCEInsights into plant pathogen evolution is essential for the understanding and management of disease. Fusarium oxysporum is a major fungal pathogen that can infect many economically important crops. Pathogenicity can be transferred between strains by the horizontal transfer of pathogenicity chromosomes. The fungus has been thought to evolve clonally, yet recent evidence suggests active sexual recombination between related isolates, which could at least partially explain the horizontal transfer of pathogenicity chromosomes. By constructing a pan-genome graph of nearly 500 mitochondrial genomes, we describe the genetic variation of mitochondria in unprecedented detail and demonstrate frequent mitochondrial recombination. Importantly, recombination can occur between genetically diverse isolates from distinct taxonomic clades and thus can shed light on genetic exchange between fungal strains.},
}
@article {pmid39527185,
year = {2024},
author = {Kim, K and Islam, MM and Bang, S and Kim, J and Lee, CY and Lee, JC and Shin, M},
title = {H-NS is a Transcriptional Repressor of the CRISPR-Cas System in Acinetobacter baumannii ATCC 19606.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {62},
number = {11},
pages = {999-1012},
pmid = {39527185},
issn = {1976-3794},
support = {2022R1A2C2010683//Ministry of Science and ICT, South Korea/ ; },
mesh = {*Acinetobacter baumannii/genetics/metabolism ; *CRISPR-Cas Systems ; *Promoter Regions, Genetic ; *Bacterial Proteins/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; DNA-Binding Proteins/genetics/metabolism ; Repressor Proteins/genetics/metabolism ; CRISPR-Associated Proteins/metabolism/genetics ; },
abstract = {Acinetobacter baumannii is a multidrug-resistant opportunistic pathogen primarily associated with hospital-acquired infections. The bacterium can gain multidrug resistance through several mechanisms, including horizontal gene transfer. A CRISPR-Cas system including several Cas genes could restrict the horizontal gene transfer. However, the molecular mechanism of CRISPR- Cas transcriptional regulation remains unclear. We identified a type I-F CRISPR-Cas system in A. baumannii ATCC 19606[T] standard strain based on sequence analysis. We focused on the transcriptional regulation of Cas3, a key protein of the CRISPR-Cas system. We performed a DNA affinity chromatography-pulldown assay to identify transcriptional regulators of the Cas3 promoter. We identified several putative transcriptional factors, such as H-NS, integration host factor, and HU, that can bind to the promoter region of Cas3. We characterized AbH-NS using size exclusion chromatography and cross-linking experiments and demonstrated that the Cas3 promoter can be regulated by AbH-NS in a concentration-dependent manner via an in vitro transcription assay. CRISPR-Cas expression levels in wild-type and hns mutant strains in the early stationary phase were examined by qPCR and β-galactosidase assay. We found that H-NS can act as a repressor of Cas3. Our transformation efficiency results indicated that the hns mutation decreased the transformation efficiency, while the Cas3 mutation increased it. We report the existence and characterization of the CRISPR-Cas system in A. baumannii 19606[T] and demonstrate that AbH-NS is a transcriptional repressor of CRISPR-Cas-related genes in A. baumannii.},
}
@article {pmid39526401,
year = {2025},
author = {Jiang, Y and Wang, Y and Che, L and Yang, S and Zhang, X and Lin, Y and Shi, Y and Zou, N and Wang, S and Zhang, Y and Zhao, Z and Li, SC},
title = {GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome.},
journal = {Nucleic acids research},
volume = {53},
number = {D1},
pages = {D772-D782},
pmid = {39526401},
issn = {1362-4962},
support = {20220814183301001//Shenzhen Science and Technology Program/ ; },
mesh = {*Gene Transfer, Horizontal ; Humans ; *Gastrointestinal Microbiome/genetics ; *Databases, Genetic ; Metagenome/genetics ; Metagenomics/methods ; Bacteria/genetics/classification ; },
abstract = {Metagenomic studies have revealed the critical roles of complex microbial interactions, including horizontal gene transfer (HGT) and functional redundancy (FR), in shaping the gut microbiome's functional capacity and resilience. However, the lack of comprehensive data integration and systematic analysis approaches has limited the in-depth exploration of HGT and FR dynamics across large-scale gut microbiome datasets. To address this gap, we present GutMetaNet (https://gutmetanet.deepomics.org/), a first-of-its-kind database integrating extensive human gut microbiome data with comprehensive HGT and FR analyses. GutMetaNet contains 21 567 human gut metagenome samples with whole-genome shotgun sequencing data related to various health conditions. Through systematic analysis, we have characterized the taxonomic profiles and FR profiles, and identified 14 636 HGT events using a shared reference genome database across the collected samples. These HGT events have been curated into 8049 clusters, which are annotated with categorized mobile genetic elements, including transposons, prophages, integrative mobilizable elements, genomic islands, integrative conjugative elements and group II introns. Additionally, GutMetaNet incorporates automated analyses and visualizations for the HGT events and FR, serving as an efficient platform for in-depth exploration of the interactions among gut microbiome taxa and their implications for human health.},
}
@article {pmid39521804,
year = {2024},
author = {Jerlström-Hultqvist, J and Gallot-Lavallée, L and Salas-Leiva, DE and Curtis, BA and Záhonová, K and Čepička, I and Stairs, CW and Pipaliya, S and Dacks, JB and Archibald, JM and Roger, AJ},
title = {A unique symbiosome in an anaerobic single-celled eukaryote.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9726},
pmid = {39521804},
issn = {2041-1723},
support = {12188//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 5782//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 12188//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 12188//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; RES0043758//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en G&#xe9;nie du Canada)/ ; RES0046091//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en G&#xe9;nie du Canada)/ ; FRN-142349//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; },
mesh = {*Symbiosis ; Anaerobiosis ; In Situ Hybridization, Fluorescence ; Eukaryota/genetics/metabolism ; Phylogeny ; Gene Transfer, Horizontal ; Microscopy, Electron, Scanning ; },
abstract = {Symbiotic relationships between eukaryotes and prokaryotes played pivotal roles in the evolution of life and drove the emergence of specialized symbiotic structures in animals, plants and fungi. The host-evolved symbiotic structures of microbial eukaryotes - the vast majority of such hosts in nature - remain largely unstudied. Here we describe highly structured symbiosomes within three free-living anaerobic protists (Anaeramoeba spp.). We dissect this symbiosis using complete genome sequencing and transcriptomics of host and symbiont cells coupled with fluorescence in situ hybridization, and 3D reconstruction using focused-ion-beam scanning electron microscopy. The emergence of the symbiosome is underpinned by expansion of gene families encoding regulators of membrane trafficking and phagosomal maturation and extensive bacteria-to-eukaryote lateral transfer. The symbionts reside deep within a symbiosomal membrane network that enables metabolic syntrophy by precisely positioning sulfate-reducing bacteria alongside host hydrogenosomes. Importantly, the symbionts maintain connections to the Anaeramoeba plasma membrane, blurring traditional boundaries between ecto- and endosymbiosis.},
}
@article {pmid39518977,
year = {2024},
author = {Traglia, GM and Pasteran, F and Moheb, S and Akhtar, U and Gonzalez, S and Maldonado, C and Furtado, N and Mohamed, A and Escalante, J and Tuttobene, MR and Quillen, A and Fontan, C and Albornoz, E and Corso, A and Bonomo, RA and Rao, GG and Tolmasky, ME and Ramirez, MS},
title = {Insights into Acinetobacter baumannii AMA205's Unprecedented Antibiotic Resistance.},
journal = {International journal of molecular sciences},
volume = {25},
number = {21},
pages = {},
pmid = {39518977},
issn = {1422-0067},
support = {R01 AI100560/AI/NIAID NIH HHS/United States ; SC3GM125556 to MSR, R01AI100560, R01AI063517, R01AI072219 to RAB, and 2R15 AI047115 to MET/GF/NIH HHS/United States ; R01 AI072219/AI/NIAID NIH HHS/United States ; R01 AI063517/AI/NIAID NIH HHS/United States ; SC3 GM125556/GM/NIGMS NIH HHS/United States ; R15 AI047115/AI/NIAID NIH HHS/United States ; },
mesh = {*Acinetobacter baumannii/genetics/drug effects ; Humans ; *beta-Lactamases/genetics/metabolism ; *Acinetobacter Infections/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology ; COVID-19/virology ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Gene Transfer, Horizontal ; SARS-CoV-2/drug effects/genetics ; Genome, Bacterial ; Argentina ; Virulence Factors/genetics ; },
abstract = {The rise of antibiotic-resistant bacteria in clinical settings has become a significant global concern. Among these bacteria, Acinetobacter baumannii stands out due to its remarkable ability to acquire resistance genes and persist in hospital environments, leading to some of the most challenging infections. Horizontal gene transfer (HGT) plays a crucial role in the evolution of this pathogen. The A. baumannii AMA205 strain, belonging to sequence type ST79, was isolated from a COVID-19 patient in Argentina in 2021. This strain's antimicrobial resistance profile is notable as it harbors multiple resistance genes, some of which had not been previously described in this species. The AmpC family β-lactamase blaCMY-6, commonly found in Enterobacterales, had never been detected in A. baumannii before. Furthermore, this is the first ST79 strain known to carry the carbapenemase blaNDM-1 gene. Other acquired resistance genes include the carbapenemase blaOXA-23, further complicating treatment. Susceptibility testing revealed high resistance to most antibiotic families, including cefiderocol, with significant contributions from blaCMY-6 and blaNDM-1 genes to the cephalosporin and carbapenem resistance profiles. The A. baumannii AMA205 genome also contains genetic traits coding for 111 potential virulence factors, such as the iron-uptake system and biofilm-associated proteins. This study underscores A. baumannii's ability to acquire multiple resistance genes and highlights the need for alternative therapies and effective antimicrobial stewardship to control the spread of these highly resistant strains.},
}
@article {pmid39516559,
year = {2024},
author = {Ares-Arroyo, M and Nucci, A and Rocha, EPC},
title = {Expanding the diversity of origin of transfer-containing sequences in mobilizable plasmids.},
journal = {Nature microbiology},
volume = {9},
number = {12},
pages = {3240-3253},
pmid = {39516559},
issn = {2058-5276},
mesh = {*Plasmids/genetics ; *Escherichia coli/genetics ; *Conjugation, Genetic ; *Klebsiella pneumoniae/genetics ; *Acinetobacter baumannii/genetics/classification ; Computational Biology/methods ; Gene Transfer, Horizontal ; Replication Origin/genetics ; DNA, Bacterial/genetics/chemistry ; },
abstract = {Conjugative plasmids are important drivers of bacterial evolution. Most plasmids lack genes for conjugation and characterized origins of transfer (oriT), which has hampered our understanding of plasmid mobility. Here we used bioinformatic analyses to characterize occurrences of known oriT families across 38,057 plasmids, confirming that most conjugative and mobilizable plasmids lack identifiable oriTs. Recognizable oriT sequences tend to be intergenic, upstream of relaxase genes and specifically associated with relaxase types. We used these criteria to develop a computational method to search for and identify 21 additional families of oriT-containing sequences in plasmids from the pathogens Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii. Sequence analyses found 3,072 occurrences of these oriT-containing sequences across 2,976 plasmids, many of which encoded antimicrobial resistance genes. Six candidate oriT-containing sequences were validated experimentally and were shown to facilitate conjugation in E. coli. These findings expand our understanding of plasmid mobility.},
}
@article {pmid39515144,
year = {2024},
author = {Luo, Y and Xu, T and Li, B and Liu, F and Wu, B and Dobson, PS and Yin, H and Chen, Z and Qiu, Y and Huang, X},
title = {The effects of small plastic particles on antibiotic resistance gene transfer revealed by single cell and community level analysis.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136271},
doi = {10.1016/j.jhazmat.2024.136271},
pmid = {39515144},
issn = {1873-3336},
mesh = {*Escherichia coli/drug effects/genetics ; *Polystyrenes/toxicity/chemistry ; *Particle Size ; Microplastics/toxicity ; Gene Transfer, Horizontal ; Sewage/microbiology ; Single-Cell Analysis ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics/drug effects ; Plastics/toxicity ; Anti-Bacterial Agents/pharmacology/toxicity ; },
abstract = {Small plastic particles with sizes comparable to bacterial cells, widely exist in environment. However, their effects on antibiotic resistance gene (ARG) dissemination remain unclear. Using polystyrene (PS) particles (0.2 µm, 2 µm, 5 µm, 10 µm, 15 µm, 20 µm) as models, conjugative transfer of ARGs between the donor E. coli and different recipients (E. coli or sludge bacterial community) was investigated. Compared to the pure strain, the sludge bacterial community exposed to PS particles showed higher transfer frequencies (1.67 to 14.31 times the blank control). The transfer frequencies first decreased and then increased with particle size, and plastics similar in size to bacteria (e.g., 2 µm) appear to be a transitional zone with minimal impact on ARG transmission. Furthermore, using microfluidics, in-situ observation at single cell level found that 2 µm plastics can act as barriers between donor and recipient bacteria inhibiting growth, but conjugation events mostly occurred around them. Conversely, nanoplastics (e.g., 0.2 µm) and larger microplastics (e.g., 20 µm) significantly promote conjugation, mainly due to increased reactive oxygen species production and cell membrane permeability, or facilitating bacterial adhesion and biofilm formation, respectively. This study aids in assessing environmental risks of small plastic particles on ARG dissemination.},
}
@article {pmid39511299,
year = {2024},
author = {Hu, Y and Duan, G and Yan, H and Guo, Y and Chang, J and Zhou, M and Yan, S and Li, W and Ruan, C and Gao, S},
title = {Discovery of the first Tn630 member and the closest homolog of IS630 from viruses.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {27081},
pmid = {39511299},
issn = {2045-2322},
support = {2024-KF-03//the Open Project of Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources/ ; },
mesh = {*DNA Transposable Elements/genetics ; Phylogeny ; Viruses/genetics ; Bacteria/genetics/virology ; Animals ; Host Specificity/genetics ; },
abstract = {IS630/Tc1/mariner (ITm) represents the most widely distributed superfamily of DNA transposons in nature. Currently, bioinformatics research on ITm members primarily involves collecting data of existing and emerging members and organizing them into new groups or families. In the present study, our survey revealed that Tc1 and IS630 members have a broad host range, spanning across all six biological kingdoms (bacteria, fungi, plantae, animalia, archaea and protista) and viruses. The primary discoveries include the first Tn630 member-Tn630-NC1 and the closest homolog of IS630 from viruses-Tc1-C#1. By incorporating our discoveries into existing knowledge, we proposed a model to elucidate the formation of composite transposons. Organization of Tc1 and IS630 members into groups across biological kingdoms facilitates data collection for future research, particularly on their horizontal transfer between different kingdoms. The formation of composite transposons may result from asymmetric of terminal inverted repeats. IS630 should be merged with Tc1 into a single family IS630/Tc1. Furthermore, IS630 and its homologs constitute a valuable resource for studying horizontal gene transfer between gut bacteria and phages, opening up new avenues for research in this field.},
}
@article {pmid39510298,
year = {2024},
author = {Song, J and Huang, Z and Gao, Y and Wang, W and Guo, G and Duan, Y and Zhou, S and Tang, Z},
title = {Metagenomic insight into the enrichment of antibiotic resistance genes in activated sludge upon exposure to nanoplastics.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {363},
number = {Pt 2},
pages = {125260},
doi = {10.1016/j.envpol.2024.125260},
pmid = {39510298},
issn = {1873-6424},
mesh = {*Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; Metagenomics ; Bacteria/genetics/drug effects ; Gene Transfer, Horizontal ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Water Pollutants, Chemical/toxicity ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Activated sludge is an important reservoir for the co-occurring emerging contaminants including nanoplastics (NPs) and antibiotic resistance genes (ARGs). However, the impacts and potential mechanisms of NPs on the fate of ARGs in activated sludge are not fully understood. Herein, we used metagenomic approach to investigate the responses of ARGs, host bacteria, mobile genetic elements (MGEs), and functional genes to polystyrene (PS) NPs at environmentally relevant (0.5 mg/L) and high stress concentrations (50 mg/L) in activated sludge. The results showed that 0.5 and 50 mg/L PS NPs increased the relative abundance of ARGs in the activated sludge by 58.68% and 46.52%, respectively (p < 0.05). Host tracking analysis elucidated that the hosts of ARGs were significantly enriched by PS NPs (p < 0.05), with Proteobacteria being the predominant host bacteria. Additionally, the occurrence of new ARGs hosts and the enrichment of MGEs and functional genes (i.e., genes related to SOS response, cell membrane permeability, and secretion system, etc.) indicated that PS NPs promoted horizontal gene transfer (HGT) of ARGs. Finally, path modeling analysis revealed that the proliferation of ARGs caused by PS NPs was primarily attributed to the enhancement of HGT and the enrichment of host bacteria. Our findings contribute to a comprehensive understanding of the spread risk of ARGs in activated sludge under NPs pollution.},
}
@article {pmid39510271,
year = {2024},
author = {Xiong, J and Hu, S and Xu, Z and Li, C and Li, Z and Li, S and Ma, Y and Ren, X and Huang, B and Pan, X},
title = {Different paths, same destination: Bisphenol A and its substitute induce the conjugative transfer of antibiotic resistance genes.},
journal = {Chemosphere},
volume = {368},
number = {},
pages = {143625},
doi = {10.1016/j.chemosphere.2024.143625},
pmid = {39510271},
issn = {1879-1298},
mesh = {*Benzhydryl Compounds/toxicity ; *Phenols/toxicity ; *Escherichia coli/drug effects/genetics ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; Drug Resistance, Microbial/genetics ; Sulfones/toxicity ; Plasmids/genetics ; Reactive Oxygen Species/metabolism ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/toxicity/pharmacology ; },
abstract = {Antibiotic resistance genes are primarily spread through horizontal gene transfer in aquatic environments. Bisphenols, which are widely used in industry, are pervasive contaminants in such environments. This study investigated how environmentally relevant concentrations of bisphenol A and its substitute (bisphenol S, Bisphenol AP and Bisphenol AF) affect the spread of antibiotic resistance genes among Escherichia coli. As a result, bisphenol A and its three substitutes were found to promote the RP4 plasmid-mediated conjugative transfer of antibiotic resistance genes with different promotive efficiency. Particularly, bisphenol A and bisphenol S were found to induce more than double the incidence of conjugation at 0.1 nmol/L concentration. They therefore were selected as model compounds to investigate the involved mechanisms. Surprisingly, both slightly inhibited bacterial activity, but there was no significant increase in cell death. Bisphenols exposure changed the polymeric substances excreted by the bacteria, increased the permeability of their cell membranes, induced the secretion of antioxidant enzymes and generated reactive oxygen species. They also affected the expression of genes related to conjugative transfer by upregulating replication and DNA transfer genes and downregulating global regulatory genes. It should be noted that gene expression levels were higher in the BPS-exposed group than in the BPA-exposed group. The synthesis of bacterial metabolites and functional components was also significantly affected by bisphenols exposure. This research has helped to clarify the potential health risks of bisphenol contamination of aquatic environments.},
}
@article {pmid39508585,
year = {2024},
author = {Androsiuk, L and Maane, S and Tal, S},
title = {CRISPR spacers acquired from plasmids primarily target backbone genes, making them valuable for predicting potential hosts and host range.},
journal = {Microbiology spectrum},
volume = {12},
number = {12},
pages = {e0010424},
pmid = {39508585},
issn = {2165-0497},
abstract = {In recent years, there has been a surge in metagenomic studies focused on identifying plasmids in environmental samples. Although these studies have unearthed numerous novel plasmids, enriching our understanding of their environmental roles, a significant gap remains: the scarcity of information regarding the bacterial hosts of these newly discovered plasmids. Furthermore, even when plasmids are identified within bacterial isolates, the reported host is typically limited to the original isolate, with no insights into alternative hosts or the plasmid's potential host range. Given that plasmids depend on hosts for their existence, investigating plasmids without the knowledge of potential hosts offers only a partial perspective. This study introduces a method for identifying potential hosts and host ranges for plasmids through alignment with CRISPR spacers. To validate the method, we compared the PLSDB plasmids database with the CRISPR spacers database, yielding host predictions for 46% of the plasmids. When compared with reported hosts, our predictions achieved 84% concordance at the family level and 99% concordance at the phylum level. Moreover, the method frequently identified multiple potential hosts for a plasmid, thereby enabling predictions of alternative hosts and the host range. Notably, we found that CRISPR spacers predominantly target plasmid backbone genes while sparing functional genes, such as those linked to antibiotic resistance, aligning with our hypothesis that CRISPR spacers are acquired from plasmid-specific regions rather than insertion elements from diverse sources. Finally, we illustrate the network of connections among different bacterial taxa through plasmids, revealing potential pathways for horizontal gene transfer.IMPORTANCEPlasmids are notorious for their role in distributing antibiotic resistance genes, but they may also carry and distribute other environmentally important genes. Since plasmids are not free-living entities and rely on host bacteria for survival and propagation, predicting their hosts is essential. This study presents a method for predicting potential hosts for plasmids and offers insights into the potential paths for spreading functional genes between different bacteria. Understanding plasmid-host relationships is crucial for comprehending the ecological and clinical impact of plasmids and implications for various biological processes.},
}
@article {pmid39506544,
year = {2024},
author = {Choufa, C and Gascht, P and Leblond, H and Gauthier, A and Vos, M and Bontemps, C and Leblond, P},
title = {Conjugation Mediates Large-Scale Chromosomal Transfer in Streptomyces Driving Diversification of Antibiotic Biosynthetic Gene Clusters.},
journal = {Molecular biology and evolution},
volume = {41},
number = {11},
pages = {},
pmid = {39506544},
issn = {1537-1719},
support = {//French National Research Agency/ ; ANR-11-LABX-0002//Investissements d'Avenir program/ ; //R&#xe9;gion Grand Est/ ; },
mesh = {*Streptomyces/genetics/metabolism ; *Multigene Family ; *Gene Transfer, Horizontal ; *Chromosomes, Bacterial/genetics ; *Conjugation, Genetic ; *Anti-Bacterial Agents/biosynthesis ; },
abstract = {Streptomyces are ubiquitous soil-dwelling bacteria with large, linear genomes that are of special importance as a source of metabolites used in human and veterinary medicine, agronomy, and industry. Conjugative elements (actinomycetes integrative and conjugative elements, AICEs) are the main drivers of Streptomyces Horizontal Gene Transfer. AICE transfer has long been known to be accompanied by mobilization of chromosomal DNA. However, the magnitude of DNA transfer, or the localization of acquired DNA across their linear chromosome, has remained undetermined. We here show that conjugative crossings in sympatric strains of Streptomyces result in the large-scale, genome-wide distributed replacement of up to one-third of the recipient chromosome, a phenomenon for which we propose the name "Streptomyces Chromosomal Transfer" (SCT). Such chromosome blending results in the acquisition, loss, and hybridization of Specialized Metabolite Biosynthetic Gene Clusters, leading to a novel metabolic arsenal in exconjugant offspring. Harnessing conjugation-mediated specialized metabolite biosynthesis gene cluster diversification holds great promise in the discovery of new bioactive compounds including antibiotics.},
}
@article {pmid39504695,
year = {2025},
author = {Liu, M and Su, X and Yuan, J and Yang, X and Chen, Y and Xu, Q and Huang, X and Xu, J and He, Y},
title = {Unravelling the processes involved in biodegradation of chlorinated organic pollutant: From microbial community to isolated organohalide degraders.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122730},
doi = {10.1016/j.watres.2024.122730},
pmid = {39504695},
issn = {1879-2448},
mesh = {*Biodegradation, Environmental ; Bacteria/metabolism/genetics ; Hydrocarbons, Chlorinated/metabolism ; Microbiota ; },
abstract = {Hundreds of studies have demonstrated the bioremediation of chlorinated organic pollutants (COPs) in flooded environments. However, the role of specific functional strains in degrading COPs under complex media such as wetlands is still unclear. Here, we focused on the microbial characteristics of COP-polluted sediments, identified the bacteria responsible for degradation and conducted a genomic analysis of these bacteria. Four strains were obtained and identified as Petrimonas sulfuriphila PET, Robertmurraya sp. CYTO, Hungatella sp. CloS1 and Enterococcus avium PseS3, respectively. They were capable of degrading a typical COP, γ-hexachlorocyclohexane (γ-HCH). The residual γ-HCH concentrations were 58.8 % (PET), 45.6 % (CYTO), 60.2 % (CloS1), and 69.3 % (PseS3) of its initial value, respectively. Strain PET, CYTO and CloS1 could degrade γ-HCH to its dehalogenation product chlorobenzene. Each strain harbors genes annotated to the pathway of halogenated organic matter degradation (e.g. 2-haloacid dehalogenase) and cobalamin biosynthesis, which are involved in the degradation of COPs. Comparative genomic analysis of the four strains and other classical organohalide-respiring bacteria (e.g. Dehalococcoides mccartyi and Sulfurospirillum multivorans DSM 12446) showed that they share orthologous clusters related to the cobalamin biosynthetic process (GO:0009236). VB12 was also detected in the culture systems of the four strains, further highlighting the importance of cobalamin in COPs degradation. In the genome of the four strains, some genes were annotated to the halogenated organic matter degradation and cobalamin biosynthesis pathway within horizontal gene transfer (HGT) regions. This further indicated that microorganisms carrying these genes can adapt faster to pollution stress through HGT. Together, these findings revealed the co-evolution mechanism of functional strains and may provide novel insights into improved bioremediation strategies for COP-polluted complex media based on generalist organochlorine-degrading bacteria.},
}
@article {pmid39503503,
year = {2024},
author = {Werner Lass, S and Smith, BE and Camphire, S and Eutsey, RA and Prentice, JA and Yerneni, SS and Arun, A and Bridges, AA and Rosch, JW and Conway, JF and Campbell, P and Hiller, NL},
title = {Pneumococcal extracellular vesicles mediate horizontal gene transfer via the transformation machinery.},
journal = {mSphere},
volume = {9},
number = {12},
pages = {e0072724},
pmid = {39503503},
issn = {2379-5042},
support = {//Shurl and Kay Curci Foundation (SKCF)/ ; T32 GM133353/GM/NIGMS NIH HHS/United States ; 5T32GM133353-04//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; S10 OD025009/CD/ODCDC CDC HHS/United States ; S10 OD025009/OD/NIH HHS/United States ; //NSF | National Science Foundation Graduate Research Fellowship Program (GRFP)/ ; },
mesh = {*Gene Transfer, Horizontal ; *Extracellular Vesicles/metabolism/genetics ; *Streptococcus pneumoniae/genetics ; *Transformation, Bacterial ; *DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Humans ; },
abstract = {Bacterial cells secrete extracellular vesicles (EVs), the function of which is a matter of intense investigation. Here, we show that the EVs secreted by the human pathogen Streptococcus pneumoniae (pneumococcus) are associated with bacterial DNA on their surface and can deliver this DNA to the transformation machinery of competent cells. These findings suggest that EVs contribute to gene transfer in Gram-positive bacteria and, in doing so, may promote the spread of drug resistance genes in the population.IMPORTANCEThis work extends our understanding of horizontal gene transfer and the roles of extracellular vesicles in pneumococcus. This bacterium serves as the model for transformation, a process by which bacteria can take up naked DNA from the environment. Here, we show that extracellular vesicles secreted by the pneumococcus have DNA on their surface and that this DNA can be imported by the transformation machinery, facilitating gene transfer. Understanding EV-mediated gene transfer may provide new avenues to manage the spread of antibiotic drug resistance.},
}
@article {pmid39500921,
year = {2024},
author = {Stewart, RD and Oluwalana-Sanusi, AE and Munzeiwa, WA and Magoswana, L and Chaukura, N},
title = {Profiling the bacterial microbiome diversity and assessing the potential to detect antimicrobial resistance bacteria in wastewater in Kimberley, South Africa.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {26867},
pmid = {39500921},
issn = {2045-2322},
mesh = {*Wastewater/microbiology ; South Africa ; *Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; RNA, Ribosomal, 16S/genetics ; Anti-Bacterial Agents/pharmacology ; Phylogeny ; },
abstract = {Wastewater treatment plants (WWTPs) are hotspots for pathogens, and can facilitate horizontal gene transfer, potentially releasing harmful genetic material and antimicrobial resistance genes into the environment. Little information exists on the composition and behavior of microbes in WWTPs, especially in developing countries. This study used environmental DNA (eDNA) techniques to examine the microbiome load of wastewater from WWTPs. The DNA was isolated from wastewater samples collected from the treatment trains of three WWTPs in Kimberley, South Africa, and the microbial diversity and composition was compared through 16 S rRNA gene sequencing. The microbes detected were of the Kingdom Bacteria, and of these, 48.27% were successfully identified to genus level. The majority of reads from the combined bacterial data fall within the class Gammaproteobacteria, which is known to adversely impact ecological and human health. Arcobacteraceae constituted 19% of the bacterial reads, which is expected as this family is widespread in aquatic environments. Interestingly, the most abundant bacterial group was Bacteroides, which contain a variety of antibiotic-resistant members. Overall, various antibiotic-resistant taxa were detected in the wastewater, indicating a concerning level of antibiotic resistance within the bacterial community. Therefore, eDNA analysis can be a valuable tool in monitoring and assessing the bacterial microbiome in wastewater, thus providing important information for the optimization and improvement of wastewater treatment systems and mitigate public health risks.},
}
@article {pmid39500447,
year = {2024},
author = {Fagunwa, OE and Ashiru-Oredope, D and Gilmore, BF and Doherty, S and Oyama, LB and Huws, SA},
title = {Climate change as a challenge for pharmaceutical storage and tackling antimicrobial resistance.},
journal = {The Science of the total environment},
volume = {956},
number = {},
pages = {177367},
doi = {10.1016/j.scitotenv.2024.177367},
pmid = {39500447},
issn = {1879-1026},
mesh = {*Climate Change ; Drug Storage ; Anti-Infective Agents ; Humans ; Drug Resistance, Microbial ; },
abstract = {The rise of antimicrobial resistance (AMR) remains a pressing global health challenge. Infections that were once easily treatable with first-line antimicrobials are becoming increasingly difficult to manage. This shift directly threatens the wellness of humans, animals, plants, and the environment. While the AMR crisis can be attributed to a myriad of factors, including lack of infection prevention and control measures, over-prescription of antimicrobials, patient non-compliance, and the misuse of antimicrobials, one aspect that has garnered less attention is the role of storage conditions of these medicines. The way medications, particularly antimicrobials, are transported and stored until the point of use can influence their efficacy and, subsequently, may impact the development of resistant microbial strains. This review delves deeper into the often-overlooked domain of climate change (CC) and antimicrobial storage practices and the potential effects. Inappropriate storage conditions, such as exposure to extreme temperatures, humidity or light, can degrade the potency of antimicrobials. When these compromised medicines are administered to patients or animals alike, they may not effectively eradicate the targeted pathogens, leading to partial survival of the pathogens. These surviving pathogens, having been exposed to sub-lethal doses, are more likely to evolve and develop resistance mechanisms. The review discusses the mechanism underlying this and underscores the implications of antimicrobial storage practices in relation to two of the most pressing global health challenges: AMR and CC. The review also presents specific case studies and highlights the importance of monitoring storage practices and supply chain surveillance. Furthermore, the importance of deploying genomic tools to understand the potential impact of storage conditions on the development of AMR is discussed, and antimicrobial storage highlighted as a crucial part of comprehensive strategies in the fight against AMR.},
}
@article {pmid39500253,
year = {2024},
author = {Zhang, G and Ren, R and Yan, X and Zhang, H and Zhu, Y},
title = {Effects of microplastics on dissipation of oxytetracycline and its relevant resistance genes in soil without and with Serratia marcescens: Comparison between biodegradable and conventional microplastics.},
journal = {Ecotoxicology and environmental safety},
volume = {287},
number = {},
pages = {117235},
doi = {10.1016/j.ecoenv.2024.117235},
pmid = {39500253},
issn = {1090-2414},
mesh = {*Oxytetracycline/toxicity ; *Serratia marcescens/drug effects/genetics ; *Soil Pollutants/toxicity ; *Soil Microbiology ; *Biodegradation, Environmental ; *Microplastics/toxicity ; Soil/chemistry ; Anti-Bacterial Agents/toxicity ; Drug Resistance, Bacterial/genetics ; },
abstract = {The biodegradable (polybutylene adipate terephthalate: PBAT) and conventional (polyethylene: PE) microplastics (MPs) at 0.5 %, 1 %, and 2 % dosages (w/w) were added into soils with and without Serratia marcescens ZY01 (ZY01, a tet-host strain) to understand their different effects on the dissipation of oxytetracycline (OTC) and tet. The results showed that the dosages of PBAT MP exhibited different inhibition degrees of OTC biodegradation in soils regardless of ZY01, while the dosages of PE MP did not change the enhancement degree of OTC biodegradation in soils without ZY01. These differences were due to the higher adsorption capacity of OTC on PBAT MP and the stronger toxicity of PBAT MP to microorganisms. Besides soil organic matter, pH and total phosphorus were important factors regulating specific tet-host bacteria in soils with MPs (e.g., the nitrogen-cycling bacteria Steroidobacter and Nitrospira) and MPs + ZY01 (e.g., the phosphorus-cycling bacteria Saccharimonadales and Haliangium), respectively. Regardless of ZY01, a stronger selective harboring of tet-host bacteria in PE MP treatments than PBAT MP treatments was observed at the MP dosage of 1 % (w/w), while the opposite trend was true at the MP dosages of 0.5 % and 2 % (w/w). Some specific genera belonging to Actinobacteriota strongly associated with the class 1 integron-integrase gene (intI1), playing a critical role in the horizontal gene transfer of tet in soils especially for the co-existence of MPs and ZY01. This study will be helpful for understanding on how biodegradable and conventional MPs as hotspots affect the environmental behavior of antibiotics and ARGs in soil.},
}
@article {pmid39499398,
year = {2024},
author = {Fu, J and Zhang, P and Yin, X and Zhu, L and Zong, G and Zhong, C and Cao, G},
title = {A scientific research training programme for teaching biomedical students to identify the horizontal transfer of antibiotic resistance genes.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {39499398},
issn = {1874-9356},
support = {SDYAL2022135//the Course Construction Project of Shandong Province/ ; },
abstract = {Worldwide prevalence of multi-antibiotic resistant bacteria is rapidly increasing, and the education of undergraduates and graduates about antibiotic resistance and its associated horizontal gene transfer is critical in the general effort to confront the spread of antibiotic resistance. In this study, a deeper understanding of antibiotic resistance and horizontal gene transfer was achieved by biomedical undergraduate students through a scientific research programme. The enthusiasm of students to participate in the training programme was very high, and results revealed that each student could identify the antibiotic resistance integrative and conjugative element from the Stenotrophomonas maltophilia MER1 genome. Each student could also draw the phylogenetic relationship of the antibiotic resistance integrative and conjugative element. In addition, students proved the horizontal transfer of antibiotic resistance genes from S. maltophilia MER1 to Escherichia coli strain 25DN through conjugation and PCR assays. Each group of students was able to obtain the expected results, indicating that the outcome of the scientific research programme was highly reproducible. This programme improved the theoretical knowledge about antibiotic resistance and horizontal gene transfer and the research skills of biomedical sciences students. Through this programme, students learned that antibiotic resistance genes can be horizontally transferred among different bacteria, laying a solid foundation for students to value the importance of the appropriate use of antibiotics in their future work and life.},
}
@article {pmid39498151,
year = {2024},
author = {Dias, YJM and Dezordi, FZ and Wallau, GDL},
title = {EEfinder, a general purpose tool for identification of bacterial and viral endogenized elements in eukaryotic genomes.},
journal = {Computational and structural biotechnology journal},
volume = {23},
number = {},
pages = {3662-3668},
pmid = {39498151},
issn = {2001-0370},
abstract = {Horizontal gene transfer is a phenomenon of genetic material transmission between species with no parental relationship. It has been characterized among several major branches of life, including among prokaryotes, viruses and eukaryotes. The characterization of endogenous elements derived from viruses or bacteria provides a snapshot of past host-pathogen interactions and coevolution as well as reference information to remove false positive results from metagenomic studies. Currently there is a lack of general purpose standardized tools for endogenous elements screening which limits reproducibility and hinder comparative analysis between studies. Here we describe EEfinder, a new general purpose tool for identification and classification of endogenous elements derived from viruses or bacteria found in eukaryotic genomes. The tool was developed to include six common steps performed in this type of analysis: data cleaning, similarity search through sequence alignment, filtering candidate elements, taxonomy assignment, merging of truncated elements and flanks extraction. We evaluated the sensitivity of EEfinder to identify endogenous elements through comparative analysis using data from the literature and showed that EEfinder automatically detected 97 % of the EVEs compared to published results obtained by manual curation and detected an almost exact full integration of a Wolbachia genome described using wet-lab experiments. Therefore, EEfinder can effectively and systematically identify endogenous elements with bacterial/viral origin integrated in eukaryotic genomes. EEfinder is publicly available on https://github.com/WallauBioinfo/EEfinder.},
}
@article {pmid39498132,
year = {2024},
author = {Abe, K and Yahara, H and Nakao, R and Yamaguchi, T and Akeda, Y},
title = {A simple and cost-effective transformation system for Porphyromonas gingivalis via natural competence.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1476171},
pmid = {39498132},
issn = {1664-302X},
abstract = {Porphyromonas gingivalis is a major oral bacterial pathogen responsible for severe periodontal diseases. Numerous studies have used genetic approaches to elucidate the molecular mechanisms underlying its pathogenicity. Typically, electroporation and conjugation are utilized for mutagenesis of P. gingivalis; however, these techniques require specialized equipment such as high-voltage electroporators, conjugative plasmids and donor strains. In this study, we present a simple, cost-effective transformation method for P. gingivalis without any special equipment by exploiting its natural DNA competence. P. gingivalis ATCC 33277 was grown to the early-exponential phase and mixed with a donor DNA cassette. This mixture was then spotted onto a BHI-HM blood-agar plate and incubated for one day to promote colony biofilm formation. The resulting colony biofilm was suspended in a liquid medium and spread onto antibiotic-containing agar plates. Transformants appeared within 4 to 5 days, achieving a maximum efficiency of 7.7 × 10[6] CFU/μg. Although we optimized the transformation conditions using a representative strain ATCC 33277, but the method was also effective for other P. gingivalis strains, W83 and TDC60. Additionally, we discovered that deletion of PGN_0421 or PGN_0519, encoding putative ComEA and ComEC, abolished competency, indicating that these gene products are essential for the natural competence.},
}
@article {pmid39497365,
year = {2024},
author = {Qu, S and Zhang, Y and Weng, L and Shan, X and Cheng, P and Li, Q and Li, L},
title = {The role of bacterial extracellular vesicles in promoting antibiotic resistance.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/1040841X.2024.2423159},
pmid = {39497365},
issn = {1549-7828},
abstract = {The burgeoning proliferation of infections attributed to multidrug-resistant (MDR) bacterial pathogens is profoundly undermining conventional chemotherapeutic modalities, portending a grave menace to global public health. The propagation of drug resistance among bacteria is fundamentally facilitated by bacterial interactions, with extracellular vesicles (EVs) assuming a critical role in interbacterial communication. Here, we briefly delineate the methodologies for isolation, extraction, and characterization of EVs from both Gram-negative and Gram-positive bacterial origins. We further investigate assorted methodologies to augment EV production, embracing physical stimulation, chemical elicitation, and genetic engineering. Moreover, we expound on the pivotal involvement of EVs in the facilitation of bacterial drug resistance proliferation and anticipate future trajectories of research and application potential. This overview of EV-mediated novel mechanisms of horizontal gene transfer implicated in antibiotic resistance among bacteria aims to obstruct the transmission conduits of bacterial drug resistance and thus fortify public health integrity.},
}
@article {pmid39494898,
year = {2024},
author = {Priya, S and Rossbach, S and Eng, T and Lin, H-H and Andeer, PF and Mortimer, JC and Northen, TR and Mukhopadhyay, A},
title = {Assessing horizontal gene transfer in the rhizosphere of Brachypodium distachyon using fabricated ecosystems (EcoFABs).},
journal = {Applied and environmental microbiology},
volume = {90},
number = {11},
pages = {e0150524},
pmid = {39494898},
issn = {1098-5336},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
mesh = {*Gene Transfer, Horizontal ; *Rhizosphere ; *Brachypodium/genetics/microbiology ; *Pseudomonas putida/genetics ; *Plasmids/genetics ; *Soil Microbiology ; Ecosystem ; Plant Roots/microbiology ; Burkholderia/genetics ; Microbiota ; },
abstract = {Horizontal gene transfer (HGT) is a major process by which genes are transferred between microbes in the rhizosphere. However, examining HGT remains challenging due to the complexity of mimicking conditions within the rhizosphere. Fabricated ecosystems (EcoFABs) have been used to investigate several complex processes in plant-associated environments. Here we show that EcoFABs are efficient tools to examine and measure HGT frequency in the rhizosphere. We provide the first demonstration of gene transfer via a triparental conjugation system in the Brachypodium distachyon rhizosphere in an EcoFAB using Pseudomonas putida KT2440 as both donor and recipient bacterial strain with the donor containing a mobilizable and non-self-transmissible plasmid. We observed that the frequency of plasmid transfer in the rhizosphere is potentially dependent on the plant developmental stage and the composition and amount of root exudates. The frequency of plasmid transfer also increased with higher numbers of donor cells. We demonstrate the transfer of plasmid from P. putida to another B. distachyon root colonizer, Burkholderia sp. OAS925, showing HGT within a rhizosphere microbial community. Environmental stresses also influenced the rate and efficiency of HGT in the rhizosphere between different species and genera. This study provides a robust workflow to evaluate transfer of engineered plasmids in the rhizosphere when such plasmids are potentially introduced in a field or other plant-associated environments.IMPORTANCEWe report the use of EcoFABs to investigate the HGT process in a rhizosphere environment. It highlights the potential of EcoFABs in recapitulating the dynamic rhizosphere conditions as well as their versatility in studying plant-microbe interactions. This study also emphasizes the importance of studying the parameters impacting the HGT frequency. Several factors such as plant developmental stages, nutrient conditions, number of donor cells, and environmental stresses influence gene transfer within the rhizosphere microbial community. This study paves the way for future investigations into understanding the fate and movement of engineered plasmids in a field environment.},
}
@article {pmid39494882,
year = {2024},
author = {Oke, MT and Martz, K and Mocăniță, M and Knezevic, S and D'Costa, VM},
title = {Analysis of Acinetobacter P-type type IV secretion system-encoding plasmid diversity uncovers extensive secretion system conservation and diverse antibiotic resistance determinants.},
journal = {Antimicrobial agents and chemotherapy},
volume = {68},
number = {12},
pages = {e0103824},
pmid = {39494882},
issn = {1098-6596},
support = {PJ4-175369,PJT-178191//Canadian Government | Canadian Institutes of Health Research (CIHR)/ ; },
mesh = {*Plasmids/genetics ; *Type IV Secretion Systems/genetics ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Acinetobacter/genetics/drug effects ; Acinetobacter baumannii/genetics/drug effects ; Bacterial Proteins/genetics ; beta-Lactamases/genetics ; Acinetobacter Infections/microbiology ; Microbial Sensitivity Tests ; Phylogeny ; },
abstract = {Acinetobacter baumannii is globally recognized as a multi-drug-resistant pathogen of critical concern due to its capacity for horizontal gene transfer and resistance to antibiotics. Phylogenetically diverse Acinetobacter species mediate human infection, including many considered as important emerging pathogens. While globally recognized as a pathogen of concern, pathogenesis mechanisms are poorly understood. P-type type IV secretion systems (T4SSs) represent important drivers of pathogen evolution, responsible for horizontal gene transfer and secretion of proteins that mediate host-pathogen interactions, contributing to pathogen survival, antibiotic resistance, virulence, and biofilm formation. Genes encoding a P-type T4SS were previously identified on plasmids harboring the carbapenemase gene blaNDM-1 in several clinically problematic Acinetobacter; however, their prevalence among the genus, geographical distribution, the conservation of T4SS proteins, and full capacity for resistance genes remain unclear. Using systematic analyses, we show that these plasmids belong to a group of 53 P-type T4SS-encoding plasmids in 20 established Acinetobacter species, the majority of clinical relevance, including diverse A. baumannii sequence types and one strain of Providencia rettgeri. The strains were globally distributed in 14 countries spanning five continents, and the conjugative operon's T4SS proteins were highly conserved in most plasmids. A high proportion of plasmids harbored resistance genes, with 17 different genes spanning seven drug classes. Collectively, this demonstrates that P-type T4SS-encoding plasmids are more widespread among the Acinetobacter genus than previously anticipated, including strains of both clinical and environmental importance. This research provides insight into the spread of resistance genes among Acinetobacter and highlights a group of plasmids of importance for future surveillance.},
}
@article {pmid39493848,
year = {2024},
author = {Yang, Y and Zhang, H and Zhao, R and Qiu, X and Ye, J and Lu, W and Li, Q and Wu, G},
title = {Distribution diversity and expression regulation of class 1 integron promoters in clinical isolates of Morganella morganii.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1459162},
pmid = {39493848},
issn = {1664-302X},
abstract = {BACKGROUND: Morganella morganii is an emerging nosocomial opportunistic pathogen with increasing multidrug resistance. Antibiotic resistance, driven primarily by the horizontal transfer of resistance genes, has become a global health crisis. Integrons, mobile genetic elements, are now understood to facilitate the transfer of these genes, contributing to the rapid proliferation of resistant strains. Understanding the regulatory role of integrons in drug resistance gene expression is crucial for developing novel strategies to combat this pressing public health issue.<br><br>OBJECTIVE: To investigate the distribution of promoter types in the variable regions of class 1 integrons isolated from clinical isolates of M. morganii and their regulatory role in the expression of downstream drug resistance gene cassettes.<br><br>METHODS: Ninety seven clinical isolates of M. morganii were screened for the presence of class 1 integrons (intI1) using polymerase chain reaction (PCR). Gene cassettes within the variable regions of positive isolates were characterized, and the gene cassette promoter Pc variants and downstream auxiliary promoter P2 were identified. Enterobacterial repetitive intergenic consensus (ERIC)-PCR was employed for homology analysis. Recombinant plasmids containing different variable region promoters and gene cassettes were constructed to evaluate drug resistance genes and integrase (intI1) expression levels using reverse transcription-quantitative PCR (RT-qPCR) and antimicrobial susceptibility testing.<br><br>RESULTS: Of the clinical isolates, 28.9% (n&#x2009;=&#x2009;28/97) were positive for class 1 integrons. 24.7% (n&#x2009;=&#x2009;24/97) of these isolates carried gene cassettes encoding resistance to aminoglycosides and trimethoprim. Three Pc promoter types (PcH1, PcS, and PcW) were identified, while all P2 promoters were inactive with a 14-base pair spacing between the -35 and -10 regions. ERIC-PCR analysis classified the integron-positive strains into 6 genotypes, with high consistency in promoter types and gene cassettes within each genotype. RT-qPCR and antimicrobial susceptibility testing demonstrated that strong promoters significantly enhanced the expression of downstream drug resistance gene cassettes compared to weak promoters. Additionally, RT-qPCR revealed a negative correlation between intI1 expression and Pc promoter strength.<br><br>CONCLUSION: Class 1 integrons are prevalent in M. morganii. The promoter types within these integrons are diverse, and promoter strength is closely linked to downstream gene cassette expression. Integron-positive strains exhibit high homology, suggesting horizontal gene transfer and dissemination in clinical settings.},
}
@article {pmid39492387,
year = {2023},
author = {Duan, Z and Zhu, Y and Xia, H and Huang, K and Peng, L},
title = {A novel strategy for eliminating antibiotic resistance genes during fertilization of dewatered sludge by earthworms: Vermicomposting practice using Chinese herbal residues derived from Lianhua Qingwen as a bulking material.},
journal = {Journal of environmental management},
volume = {349},
number = {},
pages = {119444},
doi = {10.1016/j.jenvman.2023.119444},
pmid = {39492387},
issn = {1095-8630},
abstract = {Vermicomposting is a sustainable sludge recycling technology that utilizes an eco-friendly composting using earthworms and microorganisms. However, a high abundance of antibiotic resistance genes (ARGs) remains in dewatered sludge that is not satisfactorily eliminated by vermicomposting. Chinese herbs have played a major role in curing many diseases in East Asia, leading to a large amount of Chinese herbal residues (CHRs) are difficult to dispose of. The present study investigated the feasibility of CHRs on the ARGs reduction in dewatered sludge during vermicomposting. The CHRs derived from Lianhua Qingwen were added separately to sludge with weight ratios of 0%, 10%, 30%, and 50%; sludge was then vermicomposted for 30 days. The results showed that co-vermicomposting of sludge and CHRs is a feasible strategy. The CHR treatments significantly (P < 0.05) decreased antibiotic concentration and bacterial population by 23.64%-49.68% and 42.58%-93.07%, respectively, compared to counterpart. Compared to the control, the CHR addition lowered the absolute abundances of macrolide, tetracycline, and sulfonamide ARGs by 42.69%-85.15%, 22.03%-75.24%, and 23.59%-90.66%, respectively. In addition, sludge containing 30% CHRs showed significant (P < 0.05) elimination of intⅠ-1 and tnpA-4 genes with abundance reductions of 71.40% and 52.33%, respectively, relative to the control. This study suggests that the CHRs can effectively reduce ARGs content in sludge by decreasing the bacterial population and horizontal gene transfer capacity during vermicomposting.},
}
@article {pmid39491810,
year = {2025},
author = {Pereira, AB and Marano, M and Bathala, R and Zaragoza, RA and Neira, A and Samano, A and Owoyemi, A and Casola, C},
title = {Orphan genes are not a distinct biological entity.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {47},
number = {1},
pages = {e2400146},
pmid = {39491810},
issn = {1521-1878},
support = {//Texas A&amp;M AgriLife Research/ ; 1019860//USDA National Institute of Food and Agriculture/ ; //Texas&#xa0;A&amp;M&#xa0;Forest Service/ ; },
mesh = {*Evolution, Molecular ; *Phylogeny ; Animals ; Humans ; DNA Transposable Elements/genetics ; Gene Transfer, Horizontal/genetics ; Genome/genetics ; },
abstract = {The genome sequencing revolution has revealed that all species possess a large number of unique genes critical for trait variation, adaptation, and evolutionary innovation. One widely used approach to identify such genes consists of detecting protein-coding sequences with no homology in other genomes, termed orphan genes. These genes have been extensively studied, under the assumption that they represent valid proxies for species-specific genes. Here, we critically evaluate taxonomic, phylogenetic, and sequence evolution evidence showing that orphan genes belong to a range of evolutionary ages and thus cannot be assigned to a single lineage. Furthermore, we show that the processes generating orphan genes are substantially more diverse than generally thought and include horizontal gene transfer, transposable element domestication, and overprinting. Thus, orphan genes represent a heterogeneous collection of genes rather than a single biological entity, making them unsuitable as a subject for meaningful investigation of gene evolution and phenotypic innovation.},
}
@article {pmid39487157,
year = {2024},
author = {Wardi, M and Lemkhente, Z and Alla, AA and Slimani, N and Abali, M and Idaghdour, Y and Belmouden, A},
title = {Resistome analysis of wastewater treatment plants in Agadir city, Morocco, using a metagenomics approach.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {26328},
pmid = {39487157},
issn = {2045-2322},
mesh = {*Wastewater/microbiology ; Morocco ; *Metagenomics/methods ; Anti-Bacterial Agents/pharmacology ; Water Purification/methods ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; },
abstract = {Water scarcity has evolved into a pressing global issue, significantly impacting numerous regions worldwide. The use of treated wastewater stands out as a promising solution to this problem. However, the proliferation of various contaminants, primarily Antimicrobial Resistance Genes (ARGs), poses a significant challenge to its safe and sustainable use. In this study, we assessed the composition and abundance of 373 ARGs, corresponding to 31 different classes of antibiotics, in six wastewater treatment plants (WWTP) in Agadir city of Morocco. Influent and effluent samples were collected during the months of February and July in 2020, in addition to samples from the Atlantic Ocean. In total, 223 ARGs were uncovered, highlighting in particular resistance to aminoglycoside, macrolide lincosamide, beta-lactamase, chloramphenicol, sulfonamide, tetracycline, and other antibiotics. The mechanisms of action of these ARGs were mainly antibiotic inactivation, antibiotic target alteration, efflux pump and cellular protection. Mobile genetic elements (MGEs) were detected at high levels their co-occurrence with ARGs highlights their involvement in the acquisition and transmission of ARGs in microbial communities through horizontal gene transfer. While many wastewater treatment methods effectively reduce a large proportion of gene material and pathogens, a substantial fraction of ARGs and other contaminants persist in treated wastewater. This persistence poses potential risks to both human health and the environment, warranting the need of more effective treatment strategies.},
}
@article {pmid39484419,
year = {2025},
author = {Dalia, TN and Machouri, M and Lacrouts, C and Fauconnet, Y and Guerois, R and Andreani, J and Radicella, JP and Dalia, AB},
title = {DprA recruits ComM to facilitate recombination during natural transformation in Gram-negative bacteria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.21.619469},
pmid = {39484419},
issn = {2692-8205},
abstract = {UNLABELLED: Natural transformation (NT) represents one of the major modes of horizontal gene transfer in bacterial species. During NT, cells can take up free DNA from the environment and integrate it into their genome by homologous recombination. While NT has been studied for >90 years, the molecular details underlying this recombination remain poorly understood. Recent work has demonstrated that ComM is an NT-specific hexameric helicase that promotes recombinational branch migration in Gram-negative bacteria. How ComM is loaded onto the post-synaptic recombination intermediate during NT, however, remains unclear. Another NT-specific recombination mediator protein that is ubiquitously conserved in both Gram-positive and Gram-negative bacteria is DprA. Here, we uncover that DprA homologs in Gram-negative species contain a C-terminal winged helix domain that is predicted to interact with ComM by AlphaFold. Using Helicobacter pylori and Vibrio cholerae as model systems, we demonstrate that ComM directly interacts with the DprA winged-helix domain, and that this interaction is critical for DprA to recruit ComM to the recombination site to promote branch migration during NT. These results advance our molecular understanding of recombination during this conserved mode of horizontal gene transfer. Furthermore, they demonstrate how structural modeling can help uncover unexpected interactions between well-studied proteins to provide deep mechanistic insight into the molecular coordination required for their activity.<br><br>SIGNIFICANCE STATEMENT: Bacteria can acquire novel traits like antibiotic resistance and virulence through horizontal gene transfer by natural transformation. During this process, cells take up free DNA from the environment and integrate it into their genome by homologous recombination. Many of the molecular details underlying this process, however, remain incompletely understood. In this study, we identify a new protein-protein interaction between ComM and DprA, two factors that promote homologous recombination during natural transformation in Gram-negative species. Through a combination of bioinformatics, structural modeling, cell biological assays, and complementary genetic approaches, we demonstrate that this interaction is required for DprA to recruit ComM to the site of homologous recombination.},
}
@article {pmid39488185,
year = {2024},
author = {Guo, J and Jin, X and Zhou, Y and Gao, B and Li, Y and Zhou, Y},
title = {Microplastic and antibiotics in waters: Interactions and environmental risks.},
journal = {Journal of environmental management},
volume = {371},
number = {},
pages = {123125},
doi = {10.1016/j.jenvman.2024.123125},
pmid = {39488185},
issn = {1095-8630},
mesh = {*Anti-Bacterial Agents/chemistry ; *Microplastics/toxicity ; *Water Pollutants, Chemical/chemistry ; Adsorption ; Drug Resistance, Microbial/genetics ; Water/chemistry ; Environmental Monitoring ; },
abstract = {Antibiotics (ATs) are ubiquitously detected in natural waters worldwide, and their tendency to co-migrate with microplastics (MPs) post-adsorption leads to heightened environmental risk. Research on the adsorption of ATs on MPs and their subsequent effects on the environmental risks is gaining significant attention globally. This adsorption process predominantly occurs through hydrophobic forces, hydrogen bonds, and electrostatic interactions and is influenced by various environmental factors. The interaction between MPs and ATs exhibited varying degrees of efficiency across different pH levels and ionic strengths. Furthermore, this paper outlines the environmental risks associated with the co-presence of MPs and ATs in aquatic environments, emphasizing the potential effect of MPs on the distribution of antibiotic resistance genes (ARGs) and related environmental risks. The potential hazards posed by MPs and ATs in aquatic systems warrant serious consideration. Future research should concentrate on the adsorption of ATs/ARGs on MPs under real environmental conditions, horizontal gene transfer on MPs, as well as biofilm formation and agglomeration behavior on MPs that needs to be emphasized.},
}
@article {pmid39488061,
year = {2025},
author = {Zhao, Y and Zhang, J and Zheng, Y and Shi, J and Hu, Z and Xie, H and Guo, Z and Liang, S and Wu, H},
title = {Overlooked dissemination risks of antimicrobial resistance through green tide proliferation.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122714},
doi = {10.1016/j.watres.2024.122714},
pmid = {39488061},
issn = {1879-2448},
mesh = {*Seawater/microbiology ; Drug Resistance, Microbial/genetics ; Eutrophication ; Bacteria/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; Ulva ; Gene Transfer, Horizontal ; },
abstract = {Green tides, particularly those induced by Enteromorpha, pose significant environmental challenges, exacerbated by climate change, coastal eutrophication, and other anthropogenic impacts. More concerningly, these blooms may influence the spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) within ecosystems. However, the manner in which Enteromorpha blooms affect the distribution and spread of antimicrobial resistance (AMR) remains uncertain. This study investigated ARG profiles, dynamic composition, and associated health risks within the Enteromorpha phycosphere and surrounding seawater in typical bays (Jiaozhou, Aoshan, and Lingshan) in the South Yellow Sea. The Enteromorpha phycosphere exhibited significantly higher ARG abundance (p < 0.05) but lower diversity compared to the surrounding seawater. Source-tracking and metagenomic analyses revealed that the phycosphere was the main contributor to the resistome of surrounding seawater. Moreover, resistant pathogens, especially ESKAPE pathogens, with horizontal gene transfer (HGT) potential, were more abundant in the phycosphere than in the surrounding seawater. The phycosphere released high-risk ARGs to the surrounding seawater during Enteromorpha blooms, posing serious health and ecological AMR risks in marine environments. This study highlights the significant role of Enteromorpha blooms in ARG spread and associated risks, urging a reassessment of AMR burden from a public health perspective.},
}
@article {pmid39486342,
year = {2025},
author = {Dai, S and Han, Z and Liu, S and Wang, Y and Zhang, Y and Yang, M},
title = {Bacterial hosts and horizontal transfer characteristics of clinically important tet(X)-variant genes in municipal wastewater treatment plants using epicPCR-directed cultivation strategy.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122658},
doi = {10.1016/j.watres.2024.122658},
pmid = {39486342},
issn = {1879-2448},
mesh = {*Wastewater/microbiology ; Gene Transfer, Horizontal ; Polymerase Chain Reaction ; Bacteria/genetics ; Sewage/microbiology ; Genes, Bacterial ; Anti-Bacterial Agents ; Enterobacteriaceae/genetics ; Waste Disposal, Fluid ; },
abstract = {Mobile tet(X)-variant genes confer resistance to a wide range of tetracyclines, including the antibiotic of last-resort, tigecycline, raising significant concerns regarding their potential spread cross-environmental dissemination. However, the bacterial hosts and environmental spread of these genes remain poorly understood. Herein, a retrospective study unveiled the prevalence of tet(X)-variant genes (ranging from tet(X3) to tet(X6)) in activated sludge samples from five municipal wastewater treatment plants (WWTPs) from 2013 to 2021. Among these variants, tet(X4) exhibited the highest detection frequency (100 %) and abundance [(2.48 ± 3.07) × 10[7] copies/g dry weight] with an increasing trend. An epicPCR-directed cultivation strategy was proposed to facilitate the targeted isolation of tet(X4)-carrying bacterial hosts in activated sludge. This strategy involves the identification of bacterial host profiles using epicPCR and subsequent selective isolating target bacteria. Enterobacteriaceae emerged as the primary bacterial host for tet(X4), alongside previously unreported genera like Providencia, Advenella, and Moheibacter. Subsequent selective isolation of the most abundant Enterobacteriaceae based on the epicPCR-informed host spectrum yielded 39 tet(X4)-carrying Escherichia coli strains from the WWTP. Whole genome sequencing of tet(X4)-positive strains revealed that plasmid-mediated horizontal gene transfer is the primary mechanism driving tet(X4) dissemination. Plasmids including IncFIA(HI1)/IncHI1A/IncHI1B(R27) and IncX1, commonly reported in various clinical and animal settings, were identified as the predominant carriers of tet(X4). E. coli strains harbouring tet(X4) in the WWTP showed substantial genetic similarity to strains from hospital and animal sources, underscoring concerns about the potential risk of across diverse sectors. This study provided the first glimpse of the presence of mobile tet(X)-variants in WWTPs, and highlighted the promise of the epicPCR-directed cultivation strategy for exploring bacterial hosts of clinically important ARGs in different habitats from a One Health perspective.},
}
@article {pmid39481662,
year = {2024},
author = {Liu, W and Wang, Z and Huang, Y and Liu, Y and Li, R and Wang, M and Zhang, H and Meng, C and Xiao, X},
title = {Acetylshikonin reduces the spread of antibiotic resistance via plasmid conjugation.},
journal = {International journal of antimicrobial agents},
volume = {64},
number = {6},
pages = {107370},
doi = {10.1016/j.ijantimicag.2024.107370},
pmid = {39481662},
issn = {1872-7913},
mesh = {*Plasmids/genetics ; *Conjugation, Genetic ; Animals ; *Anti-Bacterial Agents/pharmacology ; Mice ; Drug Resistance, Bacterial/genetics/drug effects ; Microbial Sensitivity Tests ; Escherichia coli/drug effects/genetics ; Escherichia coli Proteins/genetics ; Anthraquinones/pharmacology ; Female ; },
abstract = {The plasmid-mediated conjugative transfer of antibiotic resistance genes (ARGs) stands out as the primary driver behind the dissemination of antimicrobial resistance (AMR). Developing effective inhibitors that target conjugative transfer represents an potential strategy for addressing the issue of AMR. Here, we studied the effect of acetylshikonin (ASK), a botanical derivative, on plasmid conjugation. The conjugative transfer of RP4-7 plasmid inter and intra species was notably reduced by ASK. The conjugation process of IncI2 and IncX4 plasmids harbouring the mobile colistin resistance gene (mcr-1), IncX4 and IncX3 plasmids containing the carbapenem resistance gene (blaNDM-5), and IncFI and IncFII plasmids possessing the tetracycline resistance gene [tet(X4)] were also reduced by ASK. Importantly, the conjugative transfer frequency of mcr-1 positive IncI2 plasmid in mouse peritoneal conjugation model and gut conjugation model was reduced by ASK. The mechanism investigation showed that ASK disrupted the functionality of the bacterial cell membrane. Furthermore, the proton motive force (PMF) was dissipated. In addition, ASK blocked the electron transmission in bacteria's electron transport chain (ETC) through disturbing the quinone interaction, resulting in an insufficient energy supply for conjugation. Collectively, ASK is a potential conjugative transfer inhibitor, providing novel strategies to prevent the spread of AMR.},
}
@article {pmid39481552,
year = {2024},
author = {Zhao, X and Qiao, Q and Qin, X and Zhao, P and Li, X and Xie, J and Zhai, F and Li, Y},
title = {Viral community and antibiotic resistance genes carried by virus in soil microbial fuel cells.},
journal = {The Science of the total environment},
volume = {955},
number = {},
pages = {177260},
doi = {10.1016/j.scitotenv.2024.177260},
pmid = {39481552},
issn = {1879-1026},
mesh = {*Soil Microbiology ; *Bioelectric Energy Sources ; *Drug Resistance, Microbial/genetics ; Soil/chemistry ; Gene Transfer, Horizontal ; Viruses/genetics ; },
abstract = {Soil microbial fuel cells (MFCs) can control the horizontal transfer of antibiotic resistance genes (ARGs) by reducing the abundance of mobile genetic elements. However, little is known about the effect of soil MFCs on the horizontal transfer pathway of ARGs transduced by viruses. In this study, the average abundance of ARGs in soil MFCs was 11 % lower than that in the open-circuit control. Lower virus abundance in soil MFCs suggested less detriment of microbial communities. The structure of the viral community was respectively shifted by the introduction of electrodes and the stimulation of biocurrent, especially for the top three viral genera Oslovirus, Tequatrovirus and Incheonvrus in soil. The ARGs aac(6)-I, cat chloramphenicol acetyltransferase, qnrA and vanY were found as the highest health risk (Rank I), and their total abundance showed the lowest in MFCs, with a decrease of 91-99 % compared to the controls. As the main carrier of ARGs, the abundance of Caudoviricetes showed a significant positive correlation with ARGs. Viral integrase was identified respectively coexisting with arnA and vanR (Rank III) in the same contig, which might aggravate their horizontal transfer. Proteobacteria was the main host of viruses carrying ARGs, which exhibited the lowest abundance in the soil MFC. The genus Pseudomonas was the host of viruses carrying ARGs, whose amount reduced by soil MFCs. This study provides an insight into the bioelectrochemical control of ARGs horizontal transfer.},
}
@article {pmid39476778,
year = {2025},
author = {Li, J and Sun, Y and Zhang, Q and Liu, S and Liu, P and Zhang, XX},
title = {Unveiling the potential role of virus-encoded polyphosphate kinases in enhancing phosphorus removal in activated sludge systems.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122678},
doi = {10.1016/j.watres.2024.122678},
pmid = {39476778},
issn = {1879-2448},
mesh = {*Viral Proteins/genetics/metabolism ; Phylogeny ; *Viruses/classification/enzymology/genetics ; Bacteria/classification/enzymology/genetics ; Water Purification ; Genetic Variation ; *Phosphotransferases (Phosphate Group Acceptor)/chemistry/genetics/metabolism ; Models, Molecular ; Protein Structure, Tertiary ; Sequence Analysis, Protein ; Sewage/virology ; },
abstract = {While microbial phosphate removal in activated sludge (AS) systems has been extensively studied, the role of viruses in this process remains largely unexplored. In this study, we identified 149 viral auxiliary metabolic genes associated with phosphorus cycling from 2,510 viral contigs (VCs) derived from AS systems. Notably, polyphosphate kinase 1 (ppk1) and polyphosphate kinase 2 (ppk2) genes, which are primarily responsible for phosphate removal, were found in five unclassified VCs. These genes exhibited conserved protein structures and active catalytic sites, indicating a pivotal role of viruses in enhancing phosphorus removal. Phylogenetic analysis demonstrated a close relationship between viral ppk genes and their bacterial counterparts, suggesting the occurrence of horizontal gene transfer. Furthermore, experimental assays validated that viral ppk genes enhanced host phosphate removal capabilities. VCs carrying ppk genes were observed across diverse ecological and geographical contexts, suggesting their potential to bolster host functions in varied environmental and nutrient settings, spanning natural and engineered systems. These findings uncover a previously underappreciated mechanism by which viruses enhance phosphate removal in wastewater treatment plants. Overall, our study highlights the potential for leveraging virus-encoded genes to improve the efficiency of biological phosphorus removal processes, offering new insights into the microbial ecology of AS systems and the role of viruses in biogeochemical cycling.},
}
@article {pmid39475308,
year = {2024},
author = {Schrago, CG and Mello, B},
title = {Challenges in Assembling the Dated Tree of Life.},
journal = {Genome biology and evolution},
volume = {16},
number = {10},
pages = {},
pmid = {39475308},
issn = {1759-6653},
mesh = {*Phylogeny ; Evolution, Molecular ; Gene Transfer, Horizontal ; },
abstract = {The assembly of a comprehensive and dated Tree of Life (ToL) remains one of the most formidable challenges in evolutionary biology. The complexity of life's history, involving both vertical and horizontal transmission of genetic information, defies its representation by a simple bifurcating phylogeny. With the advent of genome and metagenome sequencing, vast amounts of data have become available. However, employing this information for phylogeny and divergence time inference has introduced significant theoretical and computational hurdles. This perspective addresses some key methodological challenges in assembling the dated ToL, namely, the identification and classification of homologous genes, accounting for gene tree-species tree mismatch due to population-level processes along with duplication, loss, and horizontal gene transfer, and the accurate dating of evolutionary events. Ultimately, the success of this endeavor requires new approaches that integrate knowledge databases with optimized phylogenetic algorithms capable of managing complex evolutionary models.},
}
@article {pmid39474943,
year = {2024},
author = {Sharma, P and Kishore, A and Singh, M},
title = {Single-use polyethylene terephthalate bottle-derived nanoplastics propagate antibiotic resistance in bacteria via transformation and outer membrane vesicle secretion.},
journal = {Nanoscale},
volume = {16},
number = {46},
pages = {21360-21378},
doi = {10.1039/d4nr02613f},
pmid = {39474943},
issn = {2040-3372},
mesh = {*Polyethylene Terephthalates/chemistry ; *Escherichia coli/drug effects/metabolism ; Microplastics/chemistry ; Gene Transfer, Horizontal ; Drug Resistance, Microbial/drug effects ; Plasmids/metabolism ; Nanoparticles/chemistry ; Drug Resistance, Bacterial/drug effects ; Bacterial Outer Membrane/metabolism/drug effects ; Transformation, Bacterial ; },
abstract = {Plastic pollution arising from single-use plastic bottles (SUPBs) and containers leads to the formation of micro/nanoplastics (NPs). These NPs raise concerns due to their potential toxicity and interactions with microorganisms. In various environments, including our digestive system, both microorganisms and plastics coexist. The interactions between these NPs and microorganisms can have far-reaching consequences, potentially affecting the ecosystems and human health. Therefore, understanding these interactions is crucial for addressing the challenges posed by plastic pollution. This study investigated the role of NPs in propagating antibiotic resistance (AR), specifically through outer membrane vesicles (OMVs), which is a mechanism that has not been fully explored to date in terms of NPs' effects. To explore this, NPs were synthesized using polyethylene terephthalate (PET) SUPBs, mimicking the natural chemical composition of environmental nanoplastics, unlike previous studies, which used pure PET, polystyrene (PS) or other pure plastic materials. The resulting PET bottle-derived nanoplastics (PBNPs), which exhibited diverse shapes and sizes (50-850 nm), were found to facilitate horizontal gene transfer (HGT) through transformation and outer membrane vesicles (OMVs), enabling the transport of plasmids among bacteria. In transformation, PBNPs physically carried plasmids across the bacterial membrane. In another scenario, PBNPs induced oxidative stress and bacterial surface damage, which led to the upregulation of stress response-associated genes and the escalation of OMV secretion in E. coli. This novel pathway highlights how PBNPs contribute to AR gene dissemination, potentially exacerbating the global antibiotic resistance crisis. Furthermore, PBNPs mediate cross-species gene transfer from E. coli to Lactobacillus acidophilus, underscoring their impact on diverse microorganisms, including those in the human gut. Our findings suggest that nanoplastics may be an unrecognized contributor to the rising tide of antibiotic resistance, with significant consequences for human health and the environment. Molecular analyses revealed the upregulated expression of genes associated with stress response and OMV secretion, offering deeper insights into the biological mechanisms affected by PBNPs. This study offers crucial insights into the interactions of NPs and microorganisms for developing strategies to address the ecological and health implications of nanoplastic contamination.},
}
@article {pmid39472795,
year = {2024},
author = {Andriyanov, P and Zhurilov, P and Menshikova, A and Tutrina, A and Yashin, I and Kashina, D},
title = {Large-scale genomic analysis of Elizabethkingia anophelis.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1015},
pmid = {39472795},
issn = {1471-2164},
mesh = {*Flavobacteriaceae/genetics ; *Genome, Bacterial ; *Phylogeny ; *Genomics/methods ; Gene Transfer, Horizontal ; Humans ; Flavobacteriaceae Infections/microbiology ; Animals ; Drug Resistance, Bacterial/genetics ; },
abstract = {The recent emergence of Elizabethkingia anophelis as a human pathogen is a major concern for global public health. This organism has the potential to cause severe infections and has inherent antimicrobial resistance. The potential for widespread outbreaks and rapid global spread highlights the critical importance of understanding the biology and transmission dynamics of this infectious agent. We performed a large-scale analysis of available 540 E. anophelis, including one novel strain isolated from raw milk and sequenced in this study. Pan-genome analysis revealed an open and diverse pan-genome in this species, characterized by the presence of many accessory genes. This suggests that the species has a high level of adaptability and can thrive in a variety of environments. Phylogenetic analysis has also revealed a complex population structure, with limited source-lineage correlation. We identified diverse antimicrobial resistance factors, including core-genome and accessory ones often associated with mobile genetic elements within specific lineages. Mobilome analysis revealed a dynamic landscape primarily composed of genetic islands, integrative and conjugative elements, prophage elements, and small portion of plasmids emphasizing a complex mechanism of horizontal gene transfer. Our study underscores the adaptability of E. anophelis, characterized by a diverse range of antimicrobial resistance genes, putative virulence factors, and genes enhancing fitness. This adaptability is also supported by the organism's ability to acquire genetic material through horizontal gene transfer, primarily facilitated by mobile genetic elements such as integrative and conjugative elements (ICEs). The potential for rapid evolution of this emerging pathogen poses a significant challenge to public health efforts.},
}
@article {pmid39471530,
year = {2025},
author = {Qi, H and Lv, J and Liao, J and Jin, J and Ren, Y and Tao, Y and Wang, D and Alvarez, PJJ and Yu, P},
title = {Metagenomic insights into microalgae-bacterium-virus interactions and viral functions in phycosphere facing environmental fluctuations.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122676},
doi = {10.1016/j.watres.2024.122676},
pmid = {39471530},
issn = {1879-2448},
mesh = {*Microalgae/virology ; Bacteria/genetics ; Metagenomics ; Phylogeny ; Symbiosis ; Gene Transfer, Horizontal ; Viruses/genetics ; },
abstract = {Despite the ecological and biotechnological significance of microalgae-bacterium symbionts, the response of host-virus interactions to external environmental fluctuations and the role of viruses in phycosphere remain largely unexplored. Herein, we employed algal-bacterial granular sludge (ABGS) with varying light intensity and organic carbon loading to investigate the mechanisms of microalgae-bacterium-virus symbionts in response to environmental fluctuations. Metagenomics revealed that enhanced light intensity decreased the diversity of microalgae, so did the diversity of symbiotic bacteria and viruses. As carbon sources decreased, bacteria prompted horizontal gene transfer in phycosphere by 12.76 %-157.40 %, increased the proportion of oligotrophs as keystone species (0.00 % vs 14.29 %) as well as viruses using oligotrophs as hosts (18.52 % vs 25.00 %). Furthermore, virus-carried auxiliary metabolic genes (AMGs) and biosynthetic gene clusters (BGCs) encoding vitamin B12 synthesis (e.g., cobS), antioxidation (e.g., queC), and microbial aggregation (e.g., cysE). Additionally, phylogenetic and similarity analysis further revealed the evolutionary origin and potential horizontal transfer of the AMGs and BGCs, which could potentially enhance the adaptability of bacteria and eukaryotic microalgae. Overall, our research demonstrates that environmental fluctuations have cascading effects on the microalgae-bacteria-virus interactions, and emphasizes the important role of viruses in maintaining the stability of the phycosphere symbiotic community.},
}
@article {pmid39470278,
year = {2024},
author = {Scherff, N and Rothgänger, J and Weniger, T and Mellmann, A and Harmsen, D},
title = {Real-time plasmid transmission detection pipeline.},
journal = {Microbiology spectrum},
volume = {12},
number = {12},
pages = {e0210024},
pmid = {39470278},
issn = {2165-0497},
abstract = {UNLABELLED: The spread of antimicrobial resistance among bacteria by horizontal plasmid transmissions poses a major challenge for clinical microbiology. Here, we evaluate a new real-time plasmid transmission detection pipeline implemented in the SeqSphere[+] (Ridom GmbH, Münster, Germany) software. Within the pipeline, a local Mash plasmid database is created, and Mash searches with a distance threshold of 0.001 are used to trigger plasmid transmission early warning alerts (EWAs). Clonal transmissions are detected using core-genome multi-locus sequence typing allelic differences. The tools MOB-suite, NCBI AMRFinderPlus, CGE MobileElementFinder, pyGenomeViz, and MUMmer, integrated in SeqSphere+, are used to characterize plasmids and for visual pairwise plasmid comparisons, respectively. We evaluated the pipeline using published hybrid assemblies (Oxford Nanopore Technology/Illumina) of a surveillance and outbreak data set with plasmid transmissions. To emulate prospective usage, samples were imported in chronological order of sampling date. Different combinations of the user-adjustable parameters sketch size (1,000 vs 10,000) and plasmid size correction were tested, and discrepancies between resulting clusters were analyzed with Quast. When using a sketch size of 1,000 with size correction turned on, the SeqSphere[+] pipeline agreed with the published data and produced the same clonal and carbapenemase-carrying plasmid clusters. EWAs were in the correct chronological order. In summary, the developed pipeline presented here is suitable for integration into clinical microbiology settings with limited bioinformatics knowledge due to its automated analyses and alert system, which are combined with the GUI-based SeqSphere[+] platform. Thus, with its integrated sample database, (near) real-time plasmid transmission detection is within reach in bacterial routine-diagnostic settings when long-read sequencing is employed.<br><br>IMPORTANCE: Plasmid-mediated spread of antimicrobial resistance is a major challenge for clinical microbiology, and monitoring of potential plasmid transmissions is essential to combat further dissemination. Whole-genome sequencing is often used to surveil nosocomial transmissions but usually limited to the detection of clonal transmissions (based on chromosomal markers). Recent advances in long-read sequencing technologies enable full reconstruction of plasmids and the detection of very similar plasmids, but so far, easy-to-use bioinformatic tools for this purpose have been missing. Here, we present an evaluation of an innovative real-time plasmid transmission detection pipeline. It is integrated into the GUI-based SeqSphere[+] software, which already offers core-genome multi-locus sequence typing-based pathogen outbreak detection. It requires very limited bioinformatics knowledge, and its database, automated analyses, and alert system make it well suited for prospective clinical application.},
}
@article {pmid39467614,
year = {2024},
author = {Gobbo, A and Fraiture, MA and Van Poelvoorde, L and De Keersmaecker, SCJ and Garcia-Graells, C and Van Hoorde, K and Verhaegen, B and Huwaert, A and Maloux, H and Hutse, V and Ceyssens, PJ and Roosens, N},
title = {Strategy to develop and validate digital droplet PCR methods for global antimicrobial resistance wastewater surveillance.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {96},
number = {11},
pages = {e11145},
doi = {10.1002/wer.11145},
pmid = {39467614},
issn = {1554-7531},
support = {//Sciensano (contract NAP-AMR)/ ; },
mesh = {*Wastewater/microbiology ; Real-Time Polymerase Chain Reaction/methods ; Environmental Monitoring/methods ; Polymerase Chain Reaction/methods ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; },
abstract = {According to World Health Organization (WHO), antimicrobial resistance (AMR) is currently one of the world's top 10 health threats, causing infections to become difficult or impossible to treat, increasing the risk of disease spread, severe illness, disability, and death. Accurate surveillance is a key component in the fight against AMR. Wastewater is progressively becoming a new player in AMR surveillance, with the promise of a cost-effective real-time tracking of global AMR profiles in specific regions. One of the most useful analytical methods for wastewater surveillance is currently based on real-time PCR (qPCR) and digital droplet PCR (ddPCR) technologies. As stated in the EU Wastewater Treatment Directive proposal, methodological standardization, including a workflow for method development and validation, will play a crucial role in global monitoring of AMR in wastewater. However, according to our knowledge, there are currently no qPCR and ddPCR methods for AMR surveillance available that have been validated according to international standard performance criteria. Therefore, this study proposes a workflow for the development and validation of PCR-based methods for a harmonized and global AMR surveillance, including the construction of specific sequence databases and microbial collections for an efficient method development and method specificity evaluation. Following this strategy, we have developed and validated four duplex ddPCR methods responding to international standard performance criteria, focusing on seven AMR genes (ARG's), including extended spectrum beta-lactam (blaCTX-M), carbapenem (blaKPC-2/3), tetracycline (tet(M)), erythromycin (erm(B)), vancomycin (vanA), sulfonamide (sul2), and aminoglycoside (aac(3)-IV), as well as one indicator of antibiotic (multi-) resistance and horizontal gene transfer, named the class I integron (intl1). The performance of these ddPCR methods was successfully assessed for their specificity, as no false-positive and false-negative results were observed. These ddPCR methods were also considered to be highly sensitive as showing a limit of detection below 25 copies of the targets. In addition, their applicability was confirmed using 14 wastewater samples collected from two Belgian water resource recovery facilities. The proposed study represents therefore a step forward to reinforce method harmonization in the context of the global AMR surveillance in wastewater. PRACTITIONER POINTS: In the context of wastewater surveillance, no PCR-based methods for global AMR monitoring are currently validated according to international standards. Consequently, we propose a workflow to develop and validate PCR-based methods for a harmonized and global AMR surveillance. This workflow resulted here in four duplex ddPCR methods targeting seven ARGs and one general indicator for mobilizable resistance genes. The applicability of these validated ddPCR methods was confirmed on 14 wastewater samples from two Belgian water resource recovery facilities.},
}
@article {pmid39460620,
year = {2025},
author = {Zhu, Q and Chen, Q and Gao, S and Li, Z and Zhou, H and Cui, Z and Fan, G and Liu, X and Wu, X and Ma, J and Kan, B and Hu, S and Wu, L and Lu, X},
title = {PIPdb: a comprehensive plasmid sequence resource for tracking the horizontal transfer of pathogenic factors and antimicrobial resistance genes.},
journal = {Nucleic acids research},
volume = {53},
number = {D1},
pages = {D169-D178},
pmid = {39460620},
issn = {1362-4962},
support = {2021YFF0703805//National Key Research and Development Program of China/ ; XDB0830000//Chinese Academy of Sciences/ ; 2022YFC2602301//National Key Research and Development Program of China/ ; 22193064//National Natural Science Foundation of China/ ; SRPG22007//Self-supporting Program of Guangzhou National Laboratory/ ; },
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Virulence Factors/genetics ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Humans ; Databases, Genetic ; Genome, Bacterial ; },
abstract = {Plasmids, as independent genetic elements, carrying resistance or virulence genes and transfer them among different pathogens, posing a significant threat to human health. Under the 'One Health' approach, it is crucial to control the spread of plasmids carrying such genes. To achieve this, a comprehensive characterization of plasmids in pathogens is essential. Here we present the Plasmids in Pathogens Database (PIPdb), a pioneering resource that includes 792 964 plasmid segment clusters (PSCs) derived from 1 009 571 assembled genomes across 450 pathogenic species from 110 genera. To our knowledge, PIPdb is the first database specifically dedicated to plasmids in pathogenic bacteria, offering detailed multi-dimensional metadata such as collection date, geographical origin, ecosystem, host taxonomy, and habitat. PIPdb also provides extensive functional annotations, including plasmid type, insertion sequences, integron, oriT, relaxase, T4CP, virulence factors genes, heavy metal resistance genes and antibiotic resistance genes. The database features a user-friendly interface that facilitates studies on plasmids across diverse host taxa, habitats, and ecosystems, with a focus on those carrying antimicrobial resistance genes (ARGs). We have integrated online tools for plasmid identification and annotation from assembled genomes. Additionally, PIPdb includes a risk-scoring system for identifying potentially high-risk plasmids. The PIPdb web interface is accessible at https://nmdc.cn/pipdb.},
}
@article {pmid39459963,
year = {2024},
author = {Pu, F and Zhang, N and Pang, J and Zeng, N and Baloch, FB and Li, Z and Li, B},
title = {Deciphering the Genetic Architecture of Staphylococcus warneri Prophage vB_G30_01: A Comprehensive Molecular Analysis.},
journal = {Viruses},
volume = {16},
number = {10},
pages = {},
pmid = {39459963},
issn = {1999-4915},
support = {31271818//National Natural Science Foundation of China/ ; 2023-01//International Cooperation Project of Universities in Liaoning Province/ ; 2022030673-JH5/104//Liaoning Province Rural Science and Technology Special Action Project/ ; 22-319-2-13//Shenyang Science and Technology Project/ ; 202108857002//China Scholarship Council/ ; },
mesh = {*Genome, Viral ; *Staphylococcus/virology/genetics ; *Prophages/genetics/physiology ; *Phylogeny ; *Host Specificity ; *Open Reading Frames ; *Staphylococcus Phages/genetics/classification/physiology/ultrastructure ; *Lysogeny ; DNA, Viral/genetics ; Genomics/methods ; },
abstract = {The current knowledge of Staphylococcus warneri phages is limited, with few genomes sequenced and characterized. In this study, a prophage, vB_G30_01, isolated from Staphylococcus warneri G30 was characterized and evaluated for its lysogenic host range. The phage was studied using transmission electron microscopy and a host range. The phage genome was sequenced and characterized in depth, including phylogenetic and taxonomic analyses. The linear dsDNA genome of vB_G30_01 contains 67 predicted open reading frames (ORFs), classifying it within Bronfenbrennervirinae. With a total of 10 ORFs involved in DNA replication-related and transcriptional regulator functions, vB_G30_01 may play a role in the genetics and transcription of a host. Additionally, vB_G30_01 possesses a complete set of genes related to host lysogeny and lysis, implying that vB_G30_01 may influence the survival and adaptation of its host. Furthermore, a comparative genomic analysis reveals that vB_G30_01 shares high genomic similarity with other Staphylococcus phages and is relatively closely related to those of Exiguobacterium and Bacillus, which, in combination with the cross-infection assay, suggests possible cross-species infection capabilities. This study enhances the understanding of Staphylococcus warneri prophages, providing insights into phage-host interactions and potential horizontal gene transfer.},
}
@article {pmid39458330,
year = {2024},
author = {Dixson, JD and Vumma, L and Azad, RK},
title = {An Analysis of Combined Molecular Weight and Hydrophobicity Similarity between the Amino Acid Sequences of Spike Protein Receptor Binding Domains of Betacoronaviruses and Functionally Similar Sequences from Other Virus Families.},
journal = {Microorganisms},
volume = {12},
number = {10},
pages = {},
pmid = {39458330},
issn = {2076-2607},
abstract = {Recently, we proposed a new method, based on protein profiles derived from physicochemical dynamic time warping (PCDTW), to functionally/structurally classify coronavirus spike protein receptor binding domains (RBD). Our method, as used herein, uses waveforms derived from two physicochemical properties of amino acids (molecular weight and hydrophobicity (MWHP)) and is designed to reach into the twilight zone of homology, and therefore, has the potential to reveal structural/functional relationships and potentially homologous relationships over greater evolutionary time spans than standard primary sequence alignment-based techniques. One potential application of our method is inferring deep evolutionary relationships such as those between the RBD of the spike protein of betacoronaviruses and functionally similar proteins found in other families of viruses, a task that is extremely difficult, if not impossible, using standard multiple alignment-based techniques. Here, we applied PCDTW to compare members of four divergent families of viruses to betacoronaviruses in terms of MWHP physicochemical similarity of their RBDs. We hypothesized that some members of the families Arteriviridae, Astroviridae, Reoviridae (both from the genera rotavirus and orthoreovirus considered separately), and Toroviridae would show greater physicochemical similarity to betacoronaviruses in protein regions similar to the RBD of the betacoronavirus spike protein than they do to other members of their respective taxonomic groups. This was confirmed to varying degrees in each of our analyses. Three arteriviruses (the glycoprotein-2 sequences) clustered more closely with ACE2-binding betacoronaviruses than to other arteriviruses, and a clade of 33 toroviruses was found embedded within a clade of non-ACE2-binding betacoronaviruses, indicating potentially shared structure/function of RBDs between betacoronaviruses and members of other virus clades.},
}
@article {pmid39455017,
year = {2024},
author = {Zhou, Y and Yang, Y and Wu, C and Zhou, P and Gao, H and Wang, B and Zhao, H and Xu, Y and Yu, F},
title = {LuxS/AI-2 system facilitates the dissemination of antibiotic-resistant plasmids in Klebsiella pneumoniae.},
journal = {International journal of antimicrobial agents},
volume = {64},
number = {6},
pages = {107361},
doi = {10.1016/j.ijantimicag.2024.107361},
pmid = {39455017},
issn = {1872-7913},
mesh = {*Klebsiella pneumoniae/genetics/drug effects ; *Plasmids/genetics ; *Bacterial Proteins/genetics/metabolism ; *Carbon-Sulfur Lyases/genetics ; *Conjugation, Genetic ; *Quorum Sensing/genetics ; Homoserine/analogs &amp; derivatives/metabolism ; Lactones/metabolism/pharmacology ; Gene Expression Regulation, Bacterial ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Plasmid conjugation is a central mechanism driving the dissemination of antibiotic resistance in Klebsiella pneumoniae. However, the conjugative operon requires specific stimuli for activation. Identifying signals and elucidating the underlying mechanisms is crucial in combating plasmid spread. This study uncovers a key mechanism promoting the dissemination of high-risk plasmids, including IncFII, IncX3, and IncX4 types, in K. pneumoniae. In this study, increased donor density significantly enhanced conjugation, and transcript levels of both conjugation and AI-2 quorum sensing genes were markedly upregulated. Mutating the luxS and lsrR genes in K. pneumoniae 1678 decreased plasmid conjugation efficiency in the 1678ΔluxS mutant, and significantly increased plasmid conjugation efficiency in the 1678ΔlsrR mutant. RT-qPCR and β-galactosidase assays showed that LsrR represses transcription of relaxosome and T4CP genes, whereas AI-2 (synthesised by LuxS) activates their expression. AlphaFold 3 docking models indicate that LsrR may bind directly to IncX plasmid relaxase promoters, inhibiting their expression. Adding external AI-2 signals revealed no effect on plasmid conjugation when LsrR was absent, confirming the dependence of AI-2 signals on LsrR repression. In conclusion, AI-2-mediated signalling enhances donor density effects on plasmid conjugation by de-repressing LsrR-mediated suppression.},
}
@article {pmid39454331,
year = {2024},
author = {Wang, Y and Ren, Z and Wu, Y and Li, Y and Han, S},
title = {Antibiotic resistance genes transfer risk: Contributions from soil erosion and sedimentation activities, agricultural cycles, and soil chemical contamination.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136227},
doi = {10.1016/j.jhazmat.2024.136227},
pmid = {39454331},
issn = {1873-3336},
mesh = {*Agriculture ; *Soil Pollutants/toxicity/analysis ; *Drug Resistance, Microbial/genetics ; *Soil/chemistry ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/toxicity ; Soil Microbiology ; Geologic Sediments/chemistry ; },
abstract = {The transfer of antibiotic resistance genes (ARGs) pose environmental risks that are influenced by soil activity and pollution. Soil erosion and sedimentation accelerate degradation and migration, thereby affecting soil distribution and contamination. This study quantified the vertical and horizontal transfer capabilities of ARGs and simulated soil environments under various scenarios, such as erosion, agricultural cycles, and chemical pollution. The results showed that slope, runoff, and sediment volume significantly affected soil erosion and ARG transfer risks. The response of environmental factors to the transfer risk of ARGs is as follows: the promotion effect of soil deposition (average: 21.41 %) is significantly greater than the inhibitory effect of soil erosion (average: -11.31 %); the planting period (average: -64.654) is greater than the harvest period (average: -56.225); the response to soil chemical pollution is: the impact of phosphate fertilizer residues, antibiotics, and pesticide pollution is more significant. This study constructed a vertical and horizontal transfer system of ARGs in soil erosion and sedimentation environments and proposed a response analysis method for the impact of factors, such as soil erosion and sedimentation activities, agricultural cycles, and soil chemical pollution, on ARGs transfer capabilities.},
}
@article {pmid39453690,
year = {2024},
author = {Toppings, N and Marshall, M and Smirnova, AV and Sheremet, A and Pasala, AS and Nwosu, FC and Hepburn, M and Lewis, I and Coleman, NV and Dunfield, PF},
title = {Ethylene and epoxyethane metabolism in methanotrophic bacteria: comparative genomics and physiological studies using Methylohalobius crimeensis.},
journal = {Microbial genomics},
volume = {10},
number = {10},
pages = {},
pmid = {39453690},
issn = {2057-5858},
mesh = {*Ethylenes/metabolism ; *Multigene Family ; *Genomics/methods ; Oxidation-Reduction ; Methane/metabolism ; Phylogeny ; Epoxy Compounds/metabolism ; Oxygenases/genetics/metabolism ; Genome, Bacterial ; Bacterial Proteins/genetics/metabolism ; Methylococcaceae/genetics/metabolism ; },
abstract = {The genome of the methanotrophic bacterium Methylohalobius crimeensis strain 10Ki contains a gene cluster that encodes a putative coenzyme-M (CoM)-dependent pathway for oxidation of epoxyethane, based on homology to genes in bacteria that grow on ethylene and propylene as sole substrates. An alkene monooxygenase was not detected in the M. crimeensis genome, so epoxyethane is likely produced from co-oxidation of ethylene by the methane monooxygenase enzyme. Similar gene clusters were detected in about 10% of available genomes from aerobic methanotrophic bacteria, primarily strains grown from rice paddies and other wetlands. The sparse occurrence of the gene cluster across distant phylogenetic groups suggests that multiple lateral gene transfer events have occurred in methanotrophs. In support of this, the gene cluster in M. crimeensis was detected within a large genomic island predicted using multiple methods. Growth studies, reverse transcription-quantitative PCR (RT-qPCR) and proteomics were performed to examine the expression of these genes in M. crimeensis. Growth and methane oxidation activity were completely inhibited by the addition of >0.5% (v/v) ethylene to the headspace of cultures, but at 0.125% and below, the inhibition was only partial, and ethylene was gradually oxidized. The etnE gene encoding epoxyalkane:CoM transferase was strongly upregulated in ethylene-exposed cells based on RT-qPCR. Proteomics analysis confirmed that EtnE and nine other proteins encoded in the same gene cluster became much more predominant after cells were exposed to ethylene. The results suggest that ethylene is strongly inhibitory to M. crimeensis, but the bacterium responds to ethylene exposure by expressing an epoxide oxidation system similar to that used by bacteria that grow on alkenes. In the obligate methanotroph M. crimeensis, this system does not facilitate growth on ethylene but likely alleviates toxicity of epoxyethane formed through ethylene co-oxidation by particulate methane monooxygenase. The presence of predicted epoxide detoxification systems in several other wetland methanotrophs suggests that co-oxidation of ambient ethylene presents a stress for methanotrophic bacteria in these environments and that epoxyethane removal has adaptive value.},
}
@article {pmid39452755,
year = {2024},
author = {Sabin, SJ and Beesley, CA and Marston, CK and Paisie, TK and Gulvik, CA and Sprenger, GA and Gee, JE and Traxler, RM and Bell, ME and McQuiston, JR and Weiner, ZP},
title = {Investigating Anthrax-Associated Virulence Genes among Archival and Contemporary Bacillus cereus Group Genomes.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {10},
pages = {},
pmid = {39452755},
issn = {2076-0817},
mesh = {*Bacillus cereus/genetics/pathogenicity ; *Virulence Factors/genetics ; *Genome, Bacterial/genetics ; *Anthrax/microbiology ; Virulence/genetics ; *Phylogeny ; Humans ; Whole Genome Sequencing ; Bacillus anthracis/genetics/pathogenicity ; },
abstract = {Bacillus anthracis causes anthrax through virulence factors encoded on two plasmids. However, non-B. anthracis organisms within the closely related, environmentally ubiquitous Bacillus cereus group (BCG) may cause an anthrax-like disease in humans through the partial adoption of anthrax-associated virulence genes, challenging the definition of anthrax disease. To elucidate these phenomena and their evolutionary past, we performed whole-genome sequencing on non-anthracis BCG isolates, including 93 archival (1967-2003) and 5 contemporary isolates (2019-2023). We produced annotated genomic assemblies and performed a pan-genome analysis to identify evidence of virulence gene homology and virulence gene acquisition by linear inheritance or horizontal gene transfer. At least one anthrax-associated virulence gene was annotated in ten isolates. Most homologous sequences in archival isolates showed evidence of pseudogenization and subsequent gene loss. The presence or absence of accessory genes, including anthrax-associated virulence genes, aligned with the phylogenetic structure of the BCG core genome. These findings support the hypothesis that anthrax-associated virulence genes were inherited from a common ancestor in the BCG and were retained or lost across different lineages, and contribute to a growing body of work informing public health strategies related to anthrax surveillance and identification.},
}
@article {pmid39452226,
year = {2024},
author = {Durocher, AF and Paquet, VE and St-Laurent, RE and Duchaine, C and Charette, SJ},
title = {Impact of Predation by Ciliate Tetrahymena borealis on Conjugation in Aeromonas salmonicida subsp. salmonicida.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {10},
pages = {},
pmid = {39452226},
issn = {2079-6382},
support = {539024-2019//Natural Sciences and Engineering Research Council/ ; },
abstract = {BACKGROUND/OBJECTIVES: Antibiotic resistance gene (ARG) spread is driven by horizontal gene transfer (HGT). Ciliated protozoa may contribute to this process, as their predation has been shown to facilitate HGT in certain bacteria. Here, this phenomenon was further investigated using A. salmonicida subsp. salmonicida. This fish pathogen bears an extensive and dynamic plasmidome, suggesting a high potential for HGT.<br><br>METHODS: A. salmonicida strains carrying one of three conjugative plasmids bearing ARGs (pSN254b, pRAS1b or pAsa4b) were cocultured with a recipient, either A. salmonicida, E. coli or A. hydrophila. Conjugation rates were assessed in the presence and absence of the ciliate Tetrahymena borealis. PCR genotyping confirmed the acquisition of the conjugative plasmids and was used to verify the mobilization of other plasmids.<br><br>RESULTS: The basal rate of conjugation observed was high. Under the conditions studied, ciliate predation did not appear to influence the conjugation rate, except at higher proportions of ciliates, which typically hampered conjugation. Microscopy revealed that most bacteria were digested in these conditions. PCR screening demonstrated that small mobilizable plasmids from A. salmonicida (pAsa1, pAsa2, pAsa3, and pAsal1) were acquired by the recipients along with the conjugative plasmids, with a slight effect of the ciliates in some donor/recipient cell combination.<br><br>CONCLUSIONS: These results highlight how A. salmonicida can conjugate efficiently with different species and how complex its relationship with ciliates is.},
}
@article {pmid39452131,
year = {2024},
author = {Xiong, Z and Zhang, W and Yin, H and Wan, J and Wu, Z and Gao, Y},
title = {Diversity and Evolution of NLR Genes in Citrus Species.},
journal = {Biology},
volume = {13},
number = {10},
pages = {},
pmid = {39452131},
issn = {2079-7737},
support = {32060615//National Natural Science Foundation of China/ ; jxsq2020102134//Double Thousand Plan of Jiangxi Province/ ; },
abstract = {NLR genes are crucial components of the effector-triggered immunity (ETI) system, responsible for recognizing pathogens and initiating immune responses. Although NLR genes in many plant species have been extensively studied, the diversity of NLR genes in citrus remains largely unknown. Our analysis revealed significant variations in the copy numbers of NLR genes among these species. Gene duplication and recombination were identified as the major driving forces behind this diversity. Additionally, horizontal gene transfer (HGT) emerged as the principal mechanism responsible for the increase in NLR gene copy number in A. buxifolia. The citrus NLR genes were classified into four categories: TIR-NBS-LRR (TNL), CC-NBS-LRR (CNL), RPW8-NBS-LRR (RNL), and NL. Our findings indicate that TNL, RNL, and CNL genes originated from NL genes through the acquisition of TIR and RPW8 domains, along with CC motifs, followed by the random loss of corresponding domains. Phylogenetic analysis suggested that citrus NLR genes originated alongside the species and underwent adaptive evolution, potentially playing crucial roles in the global colonization of citrus. This study provides important insights into the diversity of citrus NLR genes and serves as a foundational dataset for future research aimed at breeding disease-resistant citrus varieties.},
}
@article {pmid39450285,
year = {2024},
author = {Agudo, R and Reche, MP},
title = {Revealing antibiotic resistance's ancient roots: insights from pristine ecosystems.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1445155},
pmid = {39450285},
issn = {1664-302X},
abstract = {The prevailing belief that antibiotic resistance mechanisms emerged with human antibiotic use has been challenged. Evidence indicates that some antibiotic resistance genes (ARGs) have a long evolutionary history, predating the advent of antibiotics in human medicine, thereby demonstrating that resistance is an ancient phenomenon. Despite extensive surveys of resistance elements in environments impacted by human activity, limited data are available from remote and pristine habitats. This minireview aims to compile the most relevant research on the origins and evolution of ARGs in these habitats, which function as reservoirs for ancient resistance mechanisms. These studies indicate that ancient ARGs functionally similar to modern resistance genes, highlighting the general role of natural antimicrobial substances in fostering the evolution and exchange of diverse resistance mechanisms through horizontal gene transfer over time. This minireview underscores that antibiotic resistance was present in ancestral microbial communities and emphasizes the ecological role of antibiotics and resistance determinants. Understanding ancient ARGs is crucial for predicting and managing the evolution of antibiotic resistance. Thus, these insights provide a foundational basis for developing new antibiotics and strategies for microbial resistance management.},
}
@article {pmid39448149,
year = {2025},
author = {Fang, M and Yuan, Y and Fox, EM and Wu, K and Tian, X and Zhang, L and Feng, H and Li, R and Bai, L and Wang, X and Yang, Z and Zhang, R and Wang, J},
title = {Prevalence and genomic characteristics of becAB-carrying Clostridium perfringens strains.},
journal = {Food microbiology},
volume = {125},
number = {},
pages = {104640},
doi = {10.1016/j.fm.2024.104640},
pmid = {39448149},
issn = {1095-9998},
mesh = {*Clostridium perfringens/genetics/classification/isolation &amp; purification ; *Clostridium Infections/microbiology/epidemiology/veterinary ; China/epidemiology ; Prevalence ; Humans ; *Bacterial Toxins/genetics ; Animals ; Genome, Bacterial ; Plasmids/genetics ; Genomics ; Phylogeny ; },
abstract = {Clostridium perfringens, as a foodborne pathogen, can cause various intestinal diseases in both humans and animals according to its repertoire of toxins. In recent years, a multitude of studies have highlighted its threat to infants and young children. C. perfringens carries numerous toxins, with the newly identified BEC toxin confirmed as the second toxin to cause diarrheal illness, after CPE. However, the global dissemination of C. perfringens strains carrying becAB genes, which encode BEC toxins, has not been extensively studied. Following epidemiological surveillance of the prevalence of C. perfringens from different sources in various provinces of China, we identified two becAB-carrying strains and one strain carrying a sequence similar to becAB from distinct provinces and sources. When combined with genomic analysis of other becAB-carrying C. perfringens strains from public databases, we found that becAB was present in strains from different lineages. Our analysis of the plasmid and genetic environment corroborates previous findings on becAB-carrying strains, confirming that it currently achieves horizontal transmission through one type of evolutionarily conserved Pcp plasmid. This study provides a comprehensive analysis of the prevalence and transmission patterns of the newly emerged toxin gene locus, becAB, in C. perfringens. Despite the relatively low identification rate of becAB-carrying strains, their potential impact requires ongoing surveillance and investigation of their features, particularly their antimicrobial resistance.},
}
@article {pmid39446960,
year = {2024},
author = {Li, L and Ge, Z and Liu, S and Zheng, K and Li, Y and Chen, K and Fu, Y and Lei, X and Cui, Z and Wang, Y and Huang, J and Liu, Y and Duan, M and Sun, Z and Chen, J and Li, L and Shen, P and Wang, G and Chen, J and Li, R and Li, C and Yang, Z and Ning, Y and Luo, A and Chen, B and Seim, I and Liu, X and Wang, F and Yao, Y and Guo, F and Yang, M and Liu, CH and Fan, G and Wang, L and Yang, D and Zhang, L},
title = {Multi-omics landscape and molecular basis of radiation tolerance in a tardigrade.},
journal = {Science (New York, N.Y.)},
volume = {386},
number = {6720},
pages = {eadl0799},
doi = {10.1126/science.adl0799},
pmid = {39446960},
issn = {1095-9203},
mesh = {Animals ; DNA Damage ; *DNA Repair ; Gene Transfer, Horizontal ; Genome ; Mitochondrial Proteins/metabolism/genetics ; Multiomics ; NAD/metabolism ; Poly (ADP-Ribose) Polymerase-1/metabolism/genetics ; Proteome ; *Radiation Tolerance/genetics ; *Tardigrada/genetics/metabolism/radiation effects ; *Transcriptome ; },
abstract = {Tardigrades are captivating organisms known for their resilience in extreme environments, including ultra-high-dose radiation, but the underlying mechanisms of this resilience remain largely unknown. Using genome, transcriptome, and proteome analysis of Hypsibius henanensis sp. nov., we explored the molecular basis contributing to radiotolerance in this organism. A putatively horizontally transferred gene, DOPA dioxygenase 1 (DODA1), responds to radiation and confers radiotolerance by synthesizing betalains-a type of plant pigment with free radical-scavenging properties. A tardigrade-specific radiation-induced disordered protein, TRID1, facilitates DNA damage repair through a mechanism involving phase separation. Two mitochondrial respiratory chain complex assembly proteins, BCS1 and NDUFB8, accumulate to accelerate nicotinamide adenine dinucleotide (NAD[+]) regeneration for poly(adenosine diphosphate-ribosyl)ation (PARylation) and subsequent poly(adenosine diphosphate-ribose) polymerase 1 (PARP1)-mediated DNA damage repair. These three observations expand our understanding of mechanisms of tardigrade radiotolerance.},
}
@article {pmid39446952,
year = {2024},
author = {Sheahan, ML and Flores, K and Coyne, MJ and García-Bayona, L and Chatzidaki-Livanis, M and Holst, AQ and Smith, RC and Sundararajan, A and Barquera, B and Comstock, LE},
title = {A ubiquitous mobile genetic element changes the antagonistic weaponry of a human gut symbiont.},
journal = {Science (New York, N.Y.)},
volume = {386},
number = {6720},
pages = {414-420},
doi = {10.1126/science.adj9504},
pmid = {39446952},
issn = {1095-9203},
support = {R01 AI093771/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Bacteroides fragilis/genetics ; Conjugation, Genetic ; *Gastrointestinal Microbiome/genetics ; *Gene Transfer, Horizontal ; Genetic Fitness ; Genome, Bacterial ; *Interspersed Repetitive Sequences ; *Symbiosis ; *Type VI Secretion Systems/genetics ; *DNA, Bacterial/genetics ; },
abstract = {DNA transfer is ubiquitous in the human gut microbiota, especially among species of the order Bacteroidales. In silico analyses have revealed hundreds of mobile genetic elements shared between these species, yet little is known about the phenotypes they encode, their effects on fitness, or pleiotropic consequences for the recipient's genome. In this work, we show that acquisition of a ubiquitous integrative conjugative element (ICE) encoding a type VI secretion system (T6SS) shuts down the native T6SS of Bacteroides fragilis. Despite inactivating this T6SS, ICE acquisition increases the fitness of the B. fragilis transconjugant over its progenitor by arming it with the new T6SS. DNA transfer causes the strain to change allegiances so that it no longer targets ecosystem members with the same element yet is armed for communal defense.},
}
@article {pmid39443865,
year = {2024},
author = {Xiong, Y and Lei, X and Xiong, Y and Liu, Y and Dong, Z and Zhao, J and Yu, Q and Ma, X},
title = {Factors contributing to organelle genomes size variation and the intracellular DNA transfer in Polygonaceae.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {994},
pmid = {39443865},
issn = {1471-2164},
support = {32271753//National Natural Science Foundation of China/ ; 2022YFQ0076//Sichuan Province regional innovation cooperation project/ ; 2023YFSY0012//Cooperation project of provincial college, and provincial school/ ; },
mesh = {*Genome, Mitochondrial ; *Genome, Chloroplast ; *Polygonaceae/genetics ; *Genome Size ; *Phylogeny ; Evolution, Molecular ; Genome, Plant ; Gene Transfer, Horizontal ; },
abstract = {The use of complete organelle genomes, including chloroplast and mitochondrial genomes, is a powerful molecular method for studying biological evolution and gene transfer. However, in the case of Polygonaceae, an important family with numerous edible, medicinal, and ornamental species, the mitochondrial genomes of only three species have been sequenced and analyzed. In this study, we present the mitochondrial and chloroplast genomes of two important Tibetan medicinal plants, Bistorta viviparum and B. macrophyllum. All the organelle genomes are assembled into a single circular structure and contain a common set of 32 protein-coding genes (PCGs). Some genes such as rps2 and ndhF were found to have high nucleotide polymorphism (Pi) in the chloroplast genomes, while cox1, mttB and rps12 showed pronounced Pi values in the mitochondrial genomes. Furthermore, our analysis revealed that most chloroplast genes and mitochondrial PCGs in Polygonaceae plants are under purifying selection. However, a few genes, including the chloroplast gene psaJ and the mitochondrial genes ccmFc, atp8 and nad4, showed positive selection in certain Polygonaceae plants, as indicated by a Ka/Ks ratio greater than one. Structural variation analysis revealed a wealth of differences between the mitochondrial genomes of five Polygonaceae species, with a particularly notable large-scale inversion observed between Reynoutria japonica and Fallopia aubertii. Furthermore, an analysis of the homologous sequences in the chloroplast and mitochondrial genomes revealed that the rps7 has been transferred from the chloroplast to the mitochondrial genome in all five Polygonaceae species. Finally, ecological niche models were constructed for B. viviparum and B. macrophyllum, indicating that mean annual temperature and altitude are the main climatic factors influencing the distribution of both species. Although the current distribution of B. viviparum is significantly wider than that of B. macrophyllum, projections suggest that the optimal growth ranges of both species will expand in the future, with B. macrophyllum potentially exceeding B. viviparum. This study not only contributes to the plastid genome database for Polygonaceae plants, but also provides theoretical insights into the adaptive evolution of these plants.},
}
@article {pmid39441990,
year = {2024},
author = {Uppal, S and Waterworth, SC and Nick, A and Vogel, H and Flórez, LV and Kaltenpoth, M and Kwan, JC},
title = {Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39441990},
issn = {1751-7370},
support = {ERC CoG 819585//European Research Council through an ERC Consolidator/ ; 1845890//National Science Foundation/ ; },
mesh = {Animals ; *Symbiosis ; *Coleoptera/microbiology ; *Burkholderia/genetics/metabolism/classification/physiology ; Phylogeny ; Metagenomics ; Genome, Bacterial ; Gene Transfer, Horizontal ; },
abstract = {Microbial symbionts associate with multicellular organisms on a continuum from facultative associations to mutual codependency. In the oldest intracellular symbioses there is exclusive vertical symbiont transmission, and co-diversification of symbiotic partners over millions of years. Such symbionts often undergo genome reduction due to low effective population sizes, frequent population bottlenecks, and reduced purifying selection. Here, we describe multiple independent acquisition events of closely related defensive symbionts followed by genome erosion in a group of Lagriinae beetles. Previous work in Lagria villosa revealed the dominant genome-eroded symbiont of the genus Burkholderia produces the antifungal compound lagriamide, protecting the beetle's eggs and larvae from antagonistic fungi. Here, we use metagenomics to assemble 11 additional genomes of lagriamide-producing symbionts from 7 different host species within Lagriinae from 5 countries, to unravel the evolutionary history of this symbiotic relationship. In each host, we detected one dominant genome-eroded Burkholderia symbiont encoding the lagriamide biosynthetic gene cluster. However, we did not find evidence for host-symbiont co-diversification or for monophyly of the lagriamide-producing symbionts. Instead, our analyses support a single ancestral acquisition of the gene cluster followed by at least four independent symbiont acquisitions and subsequent genome erosion in each lineage. By contrast, a clade of plant-associated relatives retained large genomes but secondarily lost the lagriamide gene cluster. Our results, therefore, reveal a dynamic evolutionary history with multiple independent symbiont acquisitions characterized by a high degree of specificity and highlight the importance of the specialized metabolite lagriamide for the establishment and maintenance of this defensive symbiosis.},
}
@article {pmid39441515,
year = {2024},
author = {Cardoso, EM and Dea Lindner, J and Ferreira, FA},
title = {Genomic analysis of Salmonella Heidelberg isolated from the Brazilian poultry farms.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {55},
number = {4},
pages = {4129-4137},
pmid = {39441515},
issn = {1678-4405},
mesh = {Animals ; Brazil ; *Salmonella Infections, Animal/microbiology ; Chickens/microbiology ; *Poultry Diseases/microbiology ; *Genome, Bacterial ; Virulence Factors/genetics ; Anti-Bacterial Agents/pharmacology ; Farms ; Polymorphism, Single Nucleotide ; *Salmonella enterica/genetics/isolation &amp; purification/drug effects/classification ; Phylogeny ; Genomics ; *Salmonella/genetics/isolation &amp; purification/classification ; Genomic Islands ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {The rapid expansion of broiler chicken production in Brazil has presented significant sanitation challenges within the poultry industry. Among these challenges, Salmonella enterica subsp. enterica serotype Heidelberg stands as a contributor to global salmonellosis outbreaks. This study analyzed 13 draft genomes of Salmonella Heidelberg isolated from the pre-slaughter broiler chickens farms in Brazil. By conducting in silico analysis of these genomes, the study investigated genome similarity based on single nucleotide polymorphisms (SNPs) and identified genes encoding resistance to antimicrobials, sanitizers, and virulence factors. Furthermore, mobile genetic elements (MGE) were identified to assess their potential role in propagating genes through horizontal gene transfer. A risk classification was also applied based on the resistomes. The genomes revealed a high prevalence of genes conferring resistance to aminoglycosides, fosfomycin, sulfonamides, tetracycline, and genes linked to quaternary ammonium resistance. The study also uncovered six Salmonella pathogenicity islands (SPI) and over 100 genes encoding virulence factors. The association of MGE with antibiotic-resistant genes sul2 and blaCMY-2 raised concerns about the potential transfer to other bacteria, posing a substantial risk for spreading resistance mechanisms according to established risk protocols. Additionally, SNP analysis indicated close phylogenetic relationships among some isolates, suggesting a common origin. This study enhances our understanding of Salmonella Heidelberg strains by identifying key risk factors for transmission and revealing the association between resistance genes and MGEs. This insight provides a foundation for developing and implementing effective control, monitoring, and treatment strategies in the poultry industry.},
}
@article {pmid39441253,
year = {2024},
author = {Varshith, MR and Ghosh Dastidar, R and Shrilaxmi, MS and Bhattacharya, R and Jha, S and Choudhary, S and Varny, E and Carvalho, RA and John, L and Sundaramoorthy, V and Smith, CM and Damerla, RR and Herai, RH and Biswas, SR and Lal, PB and Mukhopadhyay, C and Ghosh Dastidar, S},
title = {Virulome and phylogenomic profiling of a novel Burkholderia pseudomallei strain from an Indian clinical isolate.},
journal = {Molecular genetics and genomics : MGG},
volume = {299},
number = {1},
pages = {98},
pmid = {39441253},
issn = {1617-4623},
support = {102. IFD/SAN/2549/2019-20 Dated 29-10-2019//Department of Biotechnology, Ramalingaswami re-entry Fellowship/ ; },
mesh = {*Burkholderia pseudomallei/genetics/isolation &amp; purification/pathogenicity ; Humans ; *Melioidosis/microbiology ; *Virulence Factors/genetics ; India ; *Phylogeny ; Genome, Bacterial/genetics ; Genomic Islands/genetics ; Whole Genome Sequencing/methods ; Virulence/genetics ; },
abstract = {Highly pathogenic Burkholderia pseudomallei is the causative agent of melioidosis, a neglected tropical disease endemic in Southeast Asian tropical region. This bacterium encompasses diverse virulence factors which further undergo dynamic gene-expression flux as it transits through distinct environmental niches within the host which may lead to manifestation of differential clinical symptoms. B. pseudomallei, is classified as a Tier 1 select agent in the United States and regarded as a risk group 3 organism in India with the potential to be used as bioweapon. Considering these facts, it is vital to uncover both physiological and genetic heterogeneity of B. pseudomallei, particularly to identify any novel virulence factors that may contribute to pathogenicity. B. pseudomallei strain CM000113 was isolated from a clinical case in India, characterized it for its physiological, biochemical, and prominently genetic traits through WGS. It has a type 2 morphotype with faster doubling time and high biofilm producing capacity as compared to Pseudomonas aeruginosa. The genome size is 7.3 Mbp and it is phylogenetically close to B. pseudomallei strain Mahidol 1106a and Burkholderia mallei Turkey 2. We observed genetic heterogeneity, as key virulence factors that were identified shows sequence dissimilarity with reference strains. Additionally, presence of genomic islands, harbouring two virulence factors, GmhA and GmhB2, associated with pathogenesis indicates possibility of horizontal gene transfer. These results emphasize the need for an extensive study focusing the genome of B. pseudomallei and its associated heterogeneity, to identify molecular biomarkers aiding to develop point-of-care diagnostic kits for early diagnosis of melioidosis.},
}
@article {pmid39441081,
year = {2025},
author = {Li, Y and Feng, X and Chen, X and Yang, S and Zhao, Z and Chen, Y and Li, SC},
title = {PlasmidScope: a comprehensive plasmid database with rich annotations and online analytical tools.},
journal = {Nucleic acids research},
volume = {53},
number = {D1},
pages = {D179-D188},
pmid = {39441081},
issn = {1362-4962},
support = {32061160472//NSFC-RGC Joint Research Scheme/ ; 32300527//National Natural Science Foundation of China/ ; 2022A1515110784//Guangdong Basic and Applied Basic Research Foundation/ ; 20220814183301001//Shenzhen Science and Technology Program/ ; },
mesh = {*Plasmids/genetics ; *Molecular Sequence Annotation ; *Databases, Genetic ; Software ; Internet ; Bacteria/genetics ; CRISPR-Cas Systems ; },
abstract = {Plasmids are extrachromosomal genetic molecules that replicate independent of chromosomes in bacteria, archaea, and eukaryotic organisms. They contain diverse functional elements and are capable of horizontal gene transfer among hosts. While existing plasmid databases have archived plasmid sequences isolated from individual microorganisms or natural environments, there is a need for a comprehensive, standardized, and annotated plasmid database to address the vast accumulation of plasmid sequences. Here, we propose PlasmidScope (https://plasmid.deepomics.org/), a plasmid database offering comprehensive annotations, automated online analysis, and interactive visualization. PlasmidScope harbors a substantial collection of 852 600 plasmids curated from 10 repositories. Along with consolidated background information, PlasmidScope utilizes 12 state-of-the-art tools and provides comprehensive annotations for the curated plasmids, covering genome completeness, topological structure, mobility, host source, tRNA, tmRNA, signal peptides, transmembrane proteins and CRISPR/Cas systems. PlasmidScope offers diverse functional annotations for its 25 231 059 predicted genes from 9 databases as well as corresponding protein structures predicted by ESMFold. In addition, PlasmidScope integrates online analytical modules and interactive visualization, empowering researchers to delve into the complexities of plasmids.},
}
@article {pmid39437930,
year = {2024},
author = {Da, YM and Yang, XR and Li, MJ and Li, SS and Gao, ZP and Zhang, Y and Su, JQ and Zhou, GW},
title = {Promotion of antibiotic-resistant genes dissemination by the micro/nanoplastics in the gut of snail Achatina fulica.},
journal = {The Science of the total environment},
volume = {955},
number = {},
pages = {176829},
doi = {10.1016/j.scitotenv.2024.176829},
pmid = {39437930},
issn = {1879-1026},
mesh = {Animals ; *Snails ; *Gastrointestinal Microbiome/drug effects ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Nanoparticles ; Microplastics ; Water Pollutants, Chemical ; RNA, Ribosomal, 16S ; },
abstract = {Terrestrial animal intestines are hotspots for the enrichment of micro/nano plastics (M/NPs) and antibiotic-resistant genes (ARGs). However, little is known about the further impact of M/NPs on the spread of ARGs in animal guts. This study investigates the role of M/NPs (polystyrene) with varying particle sizes (0.082, 42, and 182 μm), concentrations (10 and 100 mg/L), and exposure durations (4 and 16 days) in the ARGs dissemination via conjugation in the edible snail (Achatina fulica) gut. Combination of qPCR with 16S rRNA-based sequencing, we found that PS exposure caused intestinal cell impairment and shifts in the gut microbial community of snails. Conjugation rate increased with PS particle sizes in the snail gut. After 4 days of exposure, significantly higher conjugation rates were observed in the gut exposed to 100 mg/L PS compared to 10 mg/L, however, this trend reversed after 16 days. Consistently, the abundances of conjugation relevant genes trfA and trbB shared similar trends to the conjugation ratios in the snail gut after PS exposure. Transconjugant diversity was much lower in 10 mg/L PS groups than in 100 mg/L PS treatments. Therefore, this study suggests that the presence of M/NPs would complicate management of ARG spread. The selection pressure exerted by M/NPs may sustain or even amplify the spread of ARGs in the gut of terrestrial animals even in the absence of antibiotics. It highlights the necessity of avoiding M/NPs intake as a part of comprehensive strategy for cubing ARG dissemination in the gut of animals.},
}
@article {pmid39437688,
year = {2024},
author = {Zhang, B and Hu, X and Zhao, D and Wang, Y and Qu, J and Tao, Y and Kang, Z and Yu, H and Zhang, J and Zhang, Y},
title = {Harnessing microbial biofilms in soil ecosystems: Enhancing nutrient cycling, stress resilience, and sustainable agriculture.},
journal = {Journal of environmental management},
volume = {370},
number = {},
pages = {122973},
doi = {10.1016/j.jenvman.2024.122973},
pmid = {39437688},
issn = {1095-8630},
mesh = {*Biofilms ; *Agriculture/methods ; *Soil/chemistry ; *Soil Microbiology ; *Ecosystem ; Nutrients/metabolism ; },
abstract = {Soil ecosystems are complex networks of microorganisms that play pivotal roles in nutrient cycling, stress resilience, and the provision of ecosystem services. Among these microbial communities, soil biofilms, and complex aggregations of microorganisms embedded within extracellular polymeric substances (EPS) exert significant influence on soil health and function. This review delves into the dynamics of soil biofilms, highlighting their structural intricacies and the mechanisms by which they facilitate nutrient cycling, and discusses how biofilms enhance the degradation of pollutants through the action of extracellular enzymes and horizontal gene transfer, contributing to soil detoxification and fertility. Furthermore, the role of soil biofilms in stress resilience is underscored, as they form symbiotic relationships with plants, bolstering their growth and resistance to environmental stressors. The review also explores the ecological functions of biofilms in enhancing soil structure stability by promoting aggregate formation, which is crucial for water retention and aeration. By integrating these insights, we aim to provide a comprehensive understanding of the multifaceted benefits of biofilms in soil ecosystems. This knowledge is essential for developing strategies to manipulate soil biofilms to improve agricultural productivity and ecological sustainability. This review also identifies research gaps and emphasizes the need for practical applications of biofilms in sustainable agriculture.},
}
@article {pmid39436807,
year = {2024},
author = {Koleva, DT and Bengochea, AW and Mellor, SB and Ochoa-Fernandez, R and Nelson, DR and Møller, BL and Gillam, EMJ and Sørensen, M},
title = {Sequence diversity in the monooxygenases involved in oxime production in plant defense and signaling: a conservative revision in the nomenclature of the highly complex CYP79 family.},
journal = {The Plant journal : for cell and molecular biology},
volume = {120},
number = {3},
pages = {1236-1256},
doi = {10.1111/tpj.17044},
pmid = {39436807},
issn = {1365-313X},
support = {//Villum Fonden/ ; CF19-0301//Carlsbergfondet/ ; CF20-0352//Carlsbergfondet/ ; NNF21OC0071074//Novo Nordisk Fonden/ ; },
mesh = {*Cytochrome P-450 Enzyme System/genetics/metabolism ; *Phylogeny ; *Oximes/metabolism ; Plant Proteins/genetics/metabolism ; Signal Transduction ; Plants/enzymology/genetics ; Evolution, Molecular ; Substrate Specificity ; Amino Acid Sequence ; },
abstract = {Cytochrome P450 monooxygenases of the CYP79 family catalyze conversion of specific amino acids into oximes feeding into a variety of metabolic plant pathways. Here we present an extensive phylogenetic tree of the CYP79 family built on carefully curated sequences collected across the entire plant kingdom. Based on a monophyletic origin of the P450s, a set of evolutionarily distinct branches was identified. Founded on the functionally characterized CYP79 sequences, sequence features of the individual substrate recognition sites (SRSs) were analyzed. Co-evolving amino acid residues were identified using co-evolutionary sequence analysis. SRS4 possesses a specific sequence pattern when tyrosine is a substrate. Except for the CYP79Cs and CYP79Fs, substrate preferences toward specific amino acids could not be assigned to specific subfamilies. The highly diversified CYP79 tree, reflecting recurrent independent evolution of CYP79s, may relate to the different roles of oximes in different plant species. The sequence differences across individual CYP79 subfamilies may facilitate the in vivo orchestration of channeled metabolic pathways based on altered surface charge domains of the CYP79 protein. Alternatively, they may serve to optimize dynamic interactions with oxime metabolizing enzymes to enable optimal ecological interactions. The outlined detailed curation of the CYP79 sequences used for building the phylogenetic tree made it appropriate to make a conservative phylogenetic tree-based revision of the naming of the sequences within this highly complex cytochrome P450 family. The same approach may be used in other complex P450 subfamilies. The detailed phylogeny of the CYP79 family will enable further exploration of the evolution of function in these enzymes.},
}
@article {pmid39433770,
year = {2024},
author = {Yoon, EJ and Choi, YJ and Won, D and Choi, JR and Jeong, SH},
title = {Klebsiella pneumoniae, a human-dog shuttle organism for the genes of CTX-M ESBL.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {24725},
pmid = {39433770},
issn = {2045-2322},
support = {2019ER540402//Korea Disease Control and Prevention Agency/ ; },
mesh = {*Klebsiella pneumoniae/genetics/drug effects/isolation &amp; purification ; *beta-Lactamases/genetics ; Humans ; Animals ; Dogs ; *Plasmids/genetics ; *Escherichia coli/genetics/drug effects ; *Klebsiella Infections/microbiology ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Genome, Bacterial ; Escherichia coli Infections/microbiology/veterinary ; },
abstract = {Antimicrobials reserved for human medicines are permitted for companion animals and it is important to understand multidrug-resistant pathogens recovered from companion animals in terms of epidemiological correlation with human pathogens and possibility of transmission to human-beings. Seventeen of each CTX-M-type extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) and Klebsiella pneumoniae (ESBL-KP) canine isolates were assessed. Entire genomes of the 34 isolates were sequenced. Plasmid transfer and relative growth rates were assessed at differed temperature conditions indicating the body temperature of dogs, that of human-beings, and environment. ESBL-ECs were clonally diverse, while ESBL-KPs were not. The ESBL-ECs carried the blaCTX-M-15 gene in plasmids and the blaCTX-M-14-like gene either in chromosomes or in plasmids. The ESBL-KPs possessed the blaCTX-M-15 gene in plasmids (n = 15). One of the isolates carried another blaCTX-M-15 gene in a chromosome simultaneously and the other isolate had an additional blaCTX-M-9 gene-harbouring plasmid, together. Two ESBL-KP isolates carried the blaCTX-M-14 gene in plasmids. Plasmid transfer ESBL-EC to K. pneumoniae was efficient and the differed biological costs by temperature was much more in ESBL-EC than in ESBL-KP. Intersectoral dissemination of ESBL-ECs occurred mainly by horizontal gene transfer, while that of ESBL-KPs occurred by clonal dissemination.},
}
@article {pmid39431893,
year = {2024},
author = {Kim, DH and Seo, H and Jung, S and Kim, B-J},
title = {Global prevalence of Mycobacterium massiliense strains with recombinant rpoB genes (Rec-Mas) horizontally transferred from Mycobacterium abscessus: two major types, dominant circulating clone 7 and MLST ST46 sequence type.},
journal = {Microbiology spectrum},
volume = {12},
number = {12},
pages = {e0193524},
pmid = {39431893},
issn = {2165-0497},
abstract = {UNLABELLED: Mycobacterium abscessus is a group of emerging antimicrobial-resistant nontuberculous mycobacteria that causes severe lung disease in infected patients globally. Recently, molecular epidemiology studies have indicated that horizontal gene transfer (HGT) events in the rpoB gene are prevalent between M. abscessus subspecies. To determine the global prevalence of M. abscessus strains subjected to rpoB HGT, we performed phylogenetic inference using a 711-bp rpoB sequence extracted from 1,786 M. abscessus isolates for which the whole-genome sequence was publicly available. Our data showed that a total of 74 isolates (4.1%) from 1,786 strains are subject to rpoB HGT, which is more prevalent than strains with hsp65 HGT (19 isolates from 1,786, 1.1%). Most of these (69 isolates) belong to two major groups of Mycobacterium massiliense, of which the rpoB gene is horizontally transferred from M. abscessus (Rec-mas), dominant circulating clone 7 (DCC7) (44 isolates) and ST46 type by multilocus sequence typing (25 isolates). The Rec-mas strains of the two groups have distinct geographical patient distributions, of which the former is mainly distributed in the United States, while the latter is prevalent in Asia. Our further genome-based analysis indicated that the ST46 type is a novel DCC candidate of M. massiliense that is responsible for dissemination between noncystic fibrosis patients in Asia. In conclusion, our global phylogenetic analysis revealed two major Rec-mas clones with distinct geographical distributions, namely, DCC7 and ST46. This study provides insights into the genetic clustering and person-to-person transmission of globally dominant and area-specific strains harboring the HGT rpoB gene.<br><br>IMPORTANCE: Horizontal gene transfer (HGT) events play a pivotal role in the evolution of Mycobacterium abscessus into dominant circulating clones (DCCs), which is capable of causing patient-to-patient transmission. In particular, HGT of the rpoB gene between strains of different subspecies of M. abscessus could also compromise differentiation between strains of M. abscessus. Here, for the first time, using 1,786 M. abscessus genome sequences, we evaluated the global prevalence of M. abscessus strains subjected to rpoB HGT. We found a greater prevalence of M. abscessus subjected to rpoB HGT than to those subjected to hsp65 HGT, which is mainly due to two Rec-mas clones, dominant circulating clone 7 and ST46, which are responsible for dissemination between non-CF patients in Asia. Our data highlight the importance of rpoB HGT in the evolution of M. abscessus, particularly Mycobacterium massiliense, into virulent DCC clones.},
}
@article {pmid39431819,
year = {2024},
author = {Qian, Y and Lai, L and Cheng, M and Fang, H and Fan, D and Zylstra, GJ and Huang, X},
title = {Identification, characterization, and distribution of novel amidase gene aphA in sphingomonads conferring resistance to amphenicol antibiotics.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {11},
pages = {e0151224},
pmid = {39431819},
issn = {1098-5336},
support = {42277016//MOST | National Natural Science Foundation of China (NSFC)/ ; 41977119//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology ; *Thiamphenicol/analogs &amp; derivatives/pharmacology ; *Amidohydrolases/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism ; Sphingomonadaceae/genetics/enzymology/drug effects ; Chloramphenicol/pharmacology ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; },
abstract = {Amphenicol antibiotics, such as chloramphenicol (CHL), thiamphenicol (TAP), and florfenicol (Ff), are high-risk emerging pollutants. Their extensive usage in aquaculture, livestock, and poultry farming has led to an increase in bacterial antibiotic resistance and facilitated the spread of resistance genes. Yet, limited research has been conducted on the co-resistance of CHL, TAP, and Ff. Herein, a novel amidase AphA was identified from a pure cultured strain that can concurrently mediate the hydrolytic inactivation of CHL, TAP, and Ff, yielding products p-nitrophenylserinol, thiamphenicol amine (TAP-amine), and florfenicol amine (Ff-amine), respectively. The antibacterial activity of these antibiotic hydrolysates exhibited a significant reduction or complete loss in comparison to the parent compounds. Notably, AphA shared less than 26% amino acid sequence identity with previously reported enzymes and exhibited high conservation within the sphingomonad species. Through enzymatic kinetic analysis, the AphA exhibited markedly superior affinity and catalytic activity toward Ff in comparison to CHL and TAP. Site-directed mutagenesis analysis revealed the indispensability of catalytic triad residues, particularly serine 153 and histidine 277, in forming crucial hydrogen bonds essential for AphA's hydrolytic activity. Comparative genomic analysis showed that aphA genes in some species are closely adjacent to various transposable elements, indicating that there is a high potential risk of horizontal gene transfer (HGT). This study established a hydrolysis resistance mechanism of amphenicol antibiotics in sphingomonads, which offers theoretical guidance and a novel marker gene for assessing the prevalent risk of amphenicol antibiotics in the environment.IMPORTANCEAmphenicol antibiotics are pervasive emerging contaminants that present a substantial threat to ecological systems. Few studies have elucidated resistance genes or mechanisms that can act on CHL, TAP, and Ff simultaneously. The results of this study fill this knowledge gap and identify a novel amidase AphA from the bacterium Sphingobium yanoikuyae B1, which mediates three typical amphenicol antibiotic inactivation, and the molecular mechanism is elucidated. The diverse types of transposable elements were identified in the flanking regions of the aphA gene, indicating the risk of horizontal transfer of this antibiotic resistance genes (ARG). These findings offer new insights into the bacterial resistance to amphenicol antibiotics. The gene reported herein can be utilized as a novel genetic diagnostic marker for monitoring the environmental fate of amphenicol antibiotics, thereby enriching risk assessment efforts within the context of antibiotic resistance.},
}
@article {pmid39430728,
year = {2025},
author = {Zhang, Y and Xue, B and Mao, Y and Chen, X and Yan, W and Wang, Y and Wang, Y and Liu, L and Yu, J and Zhang, X and Chao, S and Topp, E and Zheng, W and Zhang, T},
title = {High-throughput single-cell sequencing of activated sludge microbiome.},
journal = {Environmental science and ecotechnology},
volume = {23},
number = {},
pages = {100493},
pmid = {39430728},
issn = {2666-4984},
abstract = {Wastewater treatment plants (WWTPs) represent one of biotechnology's largest and most critical applications, playing a pivotal role in environmental protection and public health. In WWTPs, activated sludge (AS) plays a major role in removing contaminants and pathogens from wastewater. While metagenomics has advanced our understanding of microbial communities, it still faces challenges in revealing the genomic heterogeneity of cells, uncovering the microbial dark matter, and establishing precise links between genetic elements and their host cells as a bulk method. These issues could be largely resolved by single-cell sequencing, which can offer unprecedented resolution to show the unique genetic information. Here we show the high-throughput single-cell sequencing to the AS microbiome. The single-amplified genomes (SAGs) of 15,110 individual cells were clustered into 2,454 SAG bins. We find that 27.5% of the genomes in the AS microbial community represent potential novel species, highlighting the presence of microbial dark matter. Furthermore, we identified 1,137 antibiotic resistance genes (ARGs), 10,450 plasmid fragments, and 1,343 phage contigs, with shared plasmid and phage groups broadly distributed among hosts, indicating a high frequency of horizontal gene transfer (HGT) within the AS microbiome. Complementary analysis using 1,529 metagenome-assembled genomes from the AS samples allowed for the taxonomic classification of 98 SAG bins, which were previously unclassified. Our study establishes the feasibility of single-cell sequencing in characterizing the AS microbiome, providing novel insights into its ecological dynamics, and deepening our understanding of HGT processes, particularly those involving ARGs. Additionally, this valuable tool could monitor the distribution, spread, and pathogenic hosts of ARGs both within AS environments and between AS and other environments, which will ultimately contribute to developing a health risk evaluation system for diverse environments within a One Health framework.},
}
@article {pmid39427888,
year = {2024},
author = {Wang, S and Li, W and Xi, B and Cao, L and Huang, C},
title = {Mechanisms and influencing factors of horizontal gene transfer in composting system: A review.},
journal = {The Science of the total environment},
volume = {955},
number = {},
pages = {177017},
doi = {10.1016/j.scitotenv.2024.177017},
pmid = {39427888},
issn = {1879-1026},
mesh = {*Gene Transfer, Horizontal ; *Composting/methods ; Drug Resistance, Microbial/genetics ; Quorum Sensing ; Bacteria/genetics ; Soil Microbiology ; },
abstract = {Organic solid wastes such as livestock manure and sewage sludge are important sources and repositories of antibiotic resistance genes (ARGs). Composting, a solid waste treatment technology, has demonstrated efficacy in degrading various antibiotics and reducing ARGs. However, some recalcitrant ARGs (e.g., sul1, sul2) will enrich during the composting maturation period. These ARGs persist in compost products and spread through horizontal gene transfer (HGT). We analyzed the reasons behind the increase of ARGs during the maturation phase. It was found that the proliferation of ARG-host bacteria and HGT process play an important role. This article revealed that microbial physiological responses, environmental factors, pollutants, and quorum sensing (QS) can all influence the HGT process in composting systems. We examined the influence of these factors on HGT in the compost system and summarized potential mechanisms by analyzing the alterations in microbial communities. We comprehensively summarized the HGT hazards that these factors may present in composting systems. Finally, we summarized methods to inhibit HGT in compost, such as using additives, quorum sensing inhibitors (QSIs), microbial inoculation, and predicting HGT events. Overall, the HGT mechanism and driving force in complex composting systems are still insufficiently studied. In view of the current situation, using predictions to assess the risk of HGT in composting may be advisable.},
}
@article {pmid39426452,
year = {2024},
author = {Jaffer, YD and Abdolahpur Monikh, F and Uli, K and Grossart, HP},
title = {Tire wear particles enhance horizontal gene transfer of antibiotic resistance genes in aquatic ecosystems.},
journal = {Environmental research},
volume = {263},
number = {Pt 3},
pages = {120187},
doi = {10.1016/j.envres.2024.120187},
pmid = {39426452},
issn = {1096-0953},
mesh = {*Gene Transfer, Horizontal ; *Escherichia coli/drug effects/genetics ; *Pseudomonas/genetics/drug effects ; Microplastics/toxicity ; Lakes/microbiology ; Drug Resistance, Microbial/genetics ; Ecosystem ; Water Pollutants, Chemical/toxicity/analysis ; },
abstract = {Microplastics (MPs) have introduced new surfaces for biofilm development and gene exchange among bacteria. We investigated Tire Wear Particles (TWPs) for their involvement in horizontal gene transfer (HGT), particularly in relation to associated metals in the matrices of TWPs. We employed red-fluorescently tagged E. coli strain as a donor with green-fluorescently tagged, broad-host-range plasmid pKJK5, resistant to trimethoprim. As a recipient, we utilized Pseudomonas sp. and a natural lake microbial community. HGT activity on TWPs was determined and compared with that on polystyrene (PS) (with and without metals), and chitosan, which was used as a natural surface. Exposure to TWPs significantly enhanced HGT frequency of antibiotic resistance gene (ARG) from donor to recipient compared to PS and chitosan, and metals of TWPs further promoted HGT. HGT frequency on TWPs with Pseudomonas sp. was found to be 10[-3] at 30 °C. in the lake community, it was similarly high already at 25 °C suggesting a higher permissiveness of the natural microbial community towards ARG at lower temperatures. This study sheds light on the potential impact of TWPs in promoting HGT, forming the basis for health risk assessments of TWPs and more generally of MP pollution in various aquatic ecosystems.},
}
@article {pmid39423639,
year = {2024},
author = {Xu, Y and Li, H and Ding, Y and Zhang, D and Liu, W},
title = {How nanoscale plastics facilitate the evolution of antibiotic resistance?.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136157},
doi = {10.1016/j.jhazmat.2024.136157},
pmid = {39423639},
issn = {1873-3336},
mesh = {*Serratia marcescens/drug effects/genetics/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Plastics/chemistry ; Gene Transfer, Horizontal ; Nanoparticles/chemistry ; Drug Resistance, Microbial/genetics ; },
abstract = {The plastic can enhance the proliferation of antibiotic resistance genes (ARGs), however, the effect of nanoplastics (NPLs) on bacterial antibiotic resistance has not been clearly explained. Herein, we explored the effects and mechanisms of NPLs of different sizes (200 and 600 nm) on the evolution of antibiotic resistance in Serratia marcescens. The results indicated that the evolution of bacterial antibiotic resistance could be promoted under NPLs exposure, which the median of relative abundance of ARGs was 1.11-1.46 times compared to the treatment without NPLs. Transcriptomic analysis showed that the larger size of NPLs mainly increased the permeability of bacterial cell membranes to efflux antibiotics, thus potentiating antibiotic resistance. While, the smaller NPLs is more than that, its enhanced the expression of antibiotic resistance by modulating bacterial metabolic processes. The genome SNP analysis found that the NPLs could cause the genetic mutation occurrence to alter the membrane transport and metabolism processes, and it increased at a size of 200 nm more than at 600 nm NPLs. Importantly, we demonstrated that the horizontal transfer of ARGs was augmented due to the NPLs could dock to bacterial surface proteins and pull their movement to contact with other bacteria (binding energy of membrane proteins: -8.54 kcal/mol), especially the smaller size. It suggests that NPLs will also contribute to the proliferation of ARGs in the environment. This study provides data for understanding the risk of bacterial resistance.},
}
@article {pmid39423563,
year = {2024},
author = {Gomberg, AF and Grossman, AD},
title = {It's complicated: relationships between integrative and conjugative elements and their bacterial hosts.},
journal = {Current opinion in microbiology},
volume = {82},
number = {},
pages = {102556},
pmid = {39423563},
issn = {1879-0364},
support = {R35 GM148343/GM/NIGMS NIH HHS/United States ; },
mesh = {*Conjugation, Genetic ; *Bacteria/genetics/metabolism ; *DNA Transposable Elements/genetics ; Chromosomes, Bacterial/genetics ; Gene Transfer, Horizontal ; },
abstract = {Integrative and conjugative elements (ICEs) are typically found integrated in a bacterial host chromosome. They can excise, replicate, and transfer from cell to cell. Many contain genes that confer phenotypes to host cells, including antibiotic resistances, specialized metabolisms, phage defense, and symbiosis or pathogenesis determinants. Recent studies revealed that at least three ICEs (ICEclc, Tn916, and TnSmu1) cause growth arrest or death of host cells upon element activation. This review highlights the complex interactions between ICEs and their hosts, including the recent examples of the significant costs to host cells. We contrast two examples of killing, ICEclc and Tn916, in which killing, respectively, benefits or impairs conjugation and emphasize the importance of understanding the impacts of ICE-host relationships on conjugation. ICEs are typically only active in a small fraction of cells in a population, and we discuss how phenotypes normally occurring in a small subset of host cells can be uncovered.},
}
@article {pmid39417646,
year = {2024},
author = {Wang, Q and Geng, L and Gao, Z and Sun, Y and Li, X and Sun, S and Luo, Y},
title = {Microalgae Enhances the Adaptability of Epiphytic Bacteria to Sulfamethoxazole Stress and Proliferation of Antibiotic Resistance Genes Mediated by Integron.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {43},
pages = {19397-19407},
doi = {10.1021/acs.est.4c04925},
pmid = {39417646},
issn = {1520-5851},
mesh = {*Microalgae/drug effects ; *Sulfamethoxazole/pharmacology ; *Drug Resistance, Microbial/genetics ; *Bacteria/drug effects/genetics/metabolism ; Integrons ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The transmission of ARGs in the microalgae-associated epiphytic bacteria remains unclear under antibiotic exposure, apart from altering the microbial community structure. In this study, Chlorella vulgaris cocultured with bacteria screened from surface water was examined to explore the spread of ARGs in the presence of sulfamethoxazole (SMX). The extracellular polymers released by Chlorella vulgaris could reduce antibiotic-induced collateral damage to bacteria, thus increasing the diversity of the microalgae-associated epiphytic bacteria. The abundances of sul1 and intI1 in the phycosphere at 1 mg/L SMX dose increased by 290 and 28 times, respectively. Metagenomic sequencing further confirmed that SMX bioaccumulation stimulated the horizontal transfer of sul1 mediated by intI1 in the microalgae-associated epiphytic bacteria, while reactive oxygen species (ROS)-mediated oxidative stress induced the SOS response and thus enhanced the transformation of sul1 in the J group. This is the first study to verify that microalgae protect bacteria from antibiotic damage and hinder the spread of ARGs mediated by SOS response, while the transfer of ARGs mediated by integron is promoted due to the bioaccumulation of SMX in the phycosphere. The results contribute to present comprehensive understanding of the risk of ARG proliferation by the presence of emerging contaminants residues in river.},
}
@article {pmid39417302,
year = {2024},
author = {Li, J and Fang, W and Li, C and Cui, M and Qian, L and Jiang, Z and Jiang, Y and Shi, L and Xie, X and Guo, H and Li, P and Dong, Y and Xiu, W and Wang, Y and Wang, Y},
title = {Dissimilatory Iodate-Reducing Microorganisms Contribute to the Enrichment of Iodine in Groundwater.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {43},
pages = {19255-19265},
doi = {10.1021/acs.est.4c04455},
pmid = {39417302},
issn = {1520-5851},
mesh = {*Groundwater/microbiology ; *Iodates/metabolism ; *Iodine/metabolism ; China ; },
abstract = {Iodate reduction by dissimilatory iodate-reducing microorganisms (DIRMs) plays a crucial role in the biogeochemical cycling of iodine on Earth. However, the occurrence and distribution of DIRMs in iodine-rich groundwater remain unclear. In this study, we isolated the dissimilatory iodate-reducing bacteriumAzonexus hydrophilusstrain NCP973 from a geogenic high-iodine groundwater of China for the first time. The analysis of genome, transcriptome, and heterologous expression revealed that strain NCP973 uses the dissimilatory iodate-reducing enzyme IdrABP1P2 to reduce dissolved or in situ sediment-bound iodate to iodide. The location of IdrABP1P2 in the conjugative plasmid of strain NCP973 implies that IdrABP1P2 could be spread by horizontal gene transfer and allow the recipient microorganisms to participate in the enrichment of iodide in aquifers. Based on the global iodine-rich groundwater metagenomes and genomes, the identification of idrA showed that phylogenetically diverse DIRMs are widely distributed not only in geogenic high-iodine groundwater of China but also in radionuclide-contaminated groundwater of USA as well as in subsurface cavern waters in Germany and Italy. Moreover, the abundance of idrA was found to be higher in groundwater with a relatively high iodine content. Collectively, these results suggest that terrestrial iodine-affected groundwater systems are another important habitat for DIRMs in addition to marine environments, and their activity in aquifers triggers the mobilization and enrichment of iodine in groundwater worldwide.},
}
@article {pmid39416196,
year = {2024},
author = {Heredia, AG and Grossman, AD},
title = {Regulation of the SOS response and homologous recombination by an integrative and conjugative element.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39416196},
issn = {2692-8205},
support = {R35 GM122538/GM/NIGMS NIH HHS/United States ; R35 GM148343/GM/NIGMS NIH HHS/United States ; },
abstract = {Integrative and conjugative elements (ICEs) are mobile genetic elements that transfer between bacteria and influence host physiology and promote evolution. ICEBs1 of Bacillus subtilis modulates the host DNA damage response by reducing RecA filament formation. We found that the two ICEBs1-encoded proteins, RamT and RamA that modulate the SOS response in donors also function in recipient cells to inhibit both the SOS response and homologous recombination following transfer of the element. Expression of RamT and RamA caused a decrease in binding of the host single strand binding protein SsbA to ssDNA. We found that RamA interacted with PcrA, the host DNA translocase that functions to remove RecA from DNA, likely functioning to modulate the SOS response and recombination by stimulating PcrA activity. These findings reveal how ICEBs1 can modulate key host processes, including the SOS response and homologous recombination, highlighting the complex interplay between mobile genetic elements and their bacterial hosts in adaptation and evolution.},
}
@article {pmid39416164,
year = {2024},
author = {McKeithen-Mead, S and Anderson, ME and García-Heredia, A and Grossman, AD},
title = {Activation and modulation of the host response to DNA damage by an integrative and conjugative element.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39416164},
issn = {2692-8205},
support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; R35 GM122538/GM/NIGMS NIH HHS/United States ; R35 GM148343/GM/NIGMS NIH HHS/United States ; T32 GM007287/GM/NIGMS NIH HHS/United States ; },
abstract = {Mobile genetic elements help drive horizontal gene transfer and bacterial evolution. Conjugative elements and temperate bacteriophages can be stably maintained in host cells. They can alter host physiology and regulatory responses and typically carry genes that are beneficial to their hosts. We found that ICEBs1, an integrative and conjugative element of Bacillus subtilis, inhibits the host response to DNA damage (the SOS response). Activation of ICEBs1 before DNA damage reduced host cell lysis that was caused by SOS-mediated activation of two resident prophages. Further, activation of ICEBs1 itself activated the SOS response in a subpopulation of cells, and this activation was attenuated by the functions of the ICEBs1 genes ydcT and yddA (now ramT and ramA, for RecA modulator). Double mutant analyses indicated that RamA functions to inhibit and RamT functions to both inhibit and activate the SOS response. Both RamT and RamA caused a reduction in RecA filaments, one of the early steps in activation of the SOS response. We suspect that there are several different mechanisms by which mobile genetic elements that generate ssDNA during their lifecycle inhibit the host SOS response and RecA function, as RamT and RamA differ from the known SOS inhibitors encoded by conjugative elements.},
}
@article {pmid39415115,
year = {2024},
author = {Bao, D and Chen, L and Shen, W and Xu, X and Zhu, L and Wang, Y and Wu, Y and He, X and Zhu, F and Li, H},
title = {Genomic epidemiology of ceftriaxone-resistant non-typhoidal Salmonella enterica strain in China.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {974},
pmid = {39415115},
issn = {1471-2164},
support = {LQ24H200003//Zhejiang Provincial Natural Science Foundation of China/ ; 2023KY414//Zhejiang Provincial Medical and Health Science and Technology Plan/ ; 2024KY1441//Zhejiang Provincial Medical and Health Science and Technology Plan/ ; },
mesh = {*Ceftriaxone/pharmacology ; China/epidemiology ; *Salmonella enterica/genetics/drug effects ; Humans ; *Salmonella Infections/microbiology/epidemiology/drug therapy ; *Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; *Phylogeny ; Drug Resistance, Multiple, Bacterial/genetics ; Multilocus Sequence Typing ; Microbial Sensitivity Tests ; Molecular Epidemiology ; },
abstract = {Non-typhoidal Salmonella (NTS) is one of the top causes of diarrhea worldwide. Ceftriaxone is commonly recommended as the initial treatment option for Salmonella infections due to its antibacterial effectiveness. The objective of this study was to investigate the molecular epidemiological characteristics of NTS and to compare the phenotypic and genotypic profiles of antimicrobial resistance in multidrug-resistant Salmonella strains by sequencing 329 NTS strains collected from a county-level hospital between 2018 and 2021. Multi-locus sequence typing (MLST), antimicrobial resistance genes and plasmid types were identified by BacWGSTdb 2.0 webserver. Phylogenetic analysis of all NTS strains was carried out using Snippy and Gubbins software. The transferability of ceftriaxone resistant plasmids was confirmed through plasmid conjugation assays, and verified by S1-PFGE-Southern blot assays. The predominant serotypes among all NTS strains were Typhimurium (161/329), Enteritidis (49/329) and London (45/329). The most common sequence type observed was ST34 (86/329), followed by ST19 (72/329) and ST11 (47/329). The antimicrobial resistance of Salmonella to a wide range of antimicrobials showed an overall increase. Out of these 37 (11.24%) ceftriaxone-resistant strains, with the majority of them (33/37) being blaCTX-M. The predominant plasmid types identified were IncHI2 (14/21) and IncI1 (6/21), ranging in size from 70 kb to 360 kb. The conjugation efficiency was calculated with the high conjugation efficiency of 1.1 × 10[- 5] to 9.3 × 10[- 2]. The strains varied widely, ranging from 3 to 45,024 single nucleotide polymorphisms (SNPs). There are close linkages observed among the predominant lineage, with an average of 78 SNPs between each pair of ST34 strains. The findings contribute to our understanding of the transmission and resistance mechanisms of multidrug-resistant Salmonella, thereby facilitating the development of effective control strategies.},
}
@article {pmid39414627,
year = {2024},
author = {Aggarwal, T and Kondabagil, K},
title = {Proteome-scale structural prediction of the giant Marseillevirus reveals conserved folds and putative homologs of the hypothetical proteins.},
journal = {Archives of virology},
volume = {169},
number = {11},
pages = {222},
pmid = {39414627},
issn = {1432-8798},
support = {CRG/2023/00131//Science and Engineering Research Board/ ; 58/14/11/2020-BRNS/37188//Board of Research in Nuclear Sciences/ ; BT/PR35928/BRB/10/1979/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {*Proteome ; *Viral Proteins/genetics/chemistry ; *Genome, Viral/genetics ; Protein Folding ; Amino Acid Sequence ; Computational Biology/methods ; Giant Viruses/genetics/classification/chemistry ; Protein Conformation ; },
abstract = {A significant proportion of the highly divergent and novel proteins of giant viruses are termed "hypothetical" due to the absence of detectable homologous sequences in the existing databases. The quality of genome and proteome annotations often relies on the identification of signature sequences and motifs in order to assign putative functions to the gene products. These annotations serve as the first set of information for researchers to develop workable hypotheses for further experimental research. The structure-function relationship of proteins suggests that proteins with similar functions may also exhibit similar folding patterns. Here, we report the first proteome-wide structure prediction of the giant Marseillevirus. We use AlphaFold-predicted structures and their comparative analysis with the experimental structures in the PDB database to preliminarily annotate the viral proteins. Our work highlights the conservation of structural folds in proteins with highly divergent sequences and reveals potentially paralogous relationships among them. We also provide evidence for gene duplication and fusion as contributing factors to giant viral genome expansion and evolution. With the easily accessible AlphaFold and other advanced bioinformatics tools for high-confidence de novo structure prediction, we propose a combined sequence and predicted-structure-based proteome annotation approach for the initial characterization of novel and complex organisms or viruses.},
}
@article {pmid39414103,
year = {2024},
author = {Zhao, W and Ye, C and Li, J and Yu, X},
title = {Increased risk of antibiotic resistance in surface water due to global warming.},
journal = {Environmental research},
volume = {263},
number = {Pt 2},
pages = {120149},
doi = {10.1016/j.envres.2024.120149},
pmid = {39414103},
issn = {1096-0953},
mesh = {*Global Warming ; Water Microbiology ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Drug Resistance, Microbial/genetics ; },
abstract = {As the pace of global warming accelerates, so do the threats to human health, urgent priority among them being antibiotic-resistant infections. In the context of global warming, this review summarises the direct and indirect effects of rising surface water temperatures on the development of bacterial antibiotic resistance. First, the resistance of typical pathogens such as E. coli increased with average temperature. This is not only related to increased bacterial growth rate and horizontal gene transfer frequency at high temperatures but also heat shock responses and cumulative effects. Secondly, the acceleration of bacterial growth indirectly promotes antibiotic residues in surface water, which is conducive to the growth and spread of resistant bacteria. Furthermore, the cascading effects of global warming, including the release of nutrients into the water and the resulting increase of bacteria and algae, indirectly promote the improvement of resistance. Water treatment processes exposed to high temperatures also increase the risk of resistance in surface water. The fitness costs of antibiotic resistance under these dynamic conditions are also discussed, concluding the relationship between various factors and resistance persistence. It was expected to provide a comprehensive basis for mitigating antibiotic resistance in the face of global warming.},
}
@article {pmid39412865,
year = {2024},
author = {Bartlett, KV and Luo, TL and Ong, AC and Maybank, RA and Stribling, W and Thompson, B and Powell, A and Kwak, YI and Bennett, JW and Lebreton, F and Mc Gann, PT},
title = {Tn4661-mediated transfer of bla CTX-M-15 from Klebsiella michiganensis to an outbreak clone of Pseudomonas aeruginosa.},
journal = {Microbial genomics},
volume = {10},
number = {10},
pages = {},
pmid = {39412865},
issn = {2057-5858},
mesh = {*beta-Lactamases/genetics ; *Pseudomonas aeruginosa/genetics/drug effects/isolation &amp; purification ; Humans ; *Disease Outbreaks ; *Plasmids/genetics ; *Pseudomonas Infections/microbiology/epidemiology ; Klebsiella/genetics/isolation &amp; purification/drug effects ; DNA Transposable Elements ; Gene Transfer, Horizontal ; },
abstract = {Carriage of CTX-M-type extended-spectrum β-lactamase (ESBL) is rare in Pseudomonas aeruginosa. During routine surveillance of an endemic ST-621 P. aeruginosa at a large hospital, isolate MRSN 100690 carrying bla CTX-M-15 was cultured from a patient (P2). This was the first detection of this ESBL in the endemic ST-621 lineage. All 1 488 bacterial isolates collected from the same facility in the 12 months prior to the incidence of 100 690 were screened for the presence of bla CTX-M-15. A set of 183 isolates was identified, in which corresponding patient metadata was evaluated for spatiotemporal overlaps with P2. The resulting three isolates, along with 100 690, were long-read sequenced using the Oxford Nanopore MinION platform to determine a potential donor of bla CTX-M-15. The screen revealed a single Klebsiella michiganensis isolate, MRSN 895358, which carried an IncA/C2 plasmid harbouring bla CTX-M-15. Notably, the patient harbouring 895358, P1, occupied the same hospital room as P2 9 months prior. Genomic alignment revealed that both isolates shared an identical 80.8 kb region containing the IncA/C2 plasmid replicon and bla CTX-M-15. This region was plasmid bound in 895 358, but chromosomally bound in 100 690 due to Tn4661-mediated transposition. ESBL bla CTX-M-15 was acquired and subsequently integrated into the chromosome of a ST-621 P. aeruginosa, likely initiated by plasmid transfer from a K. michiganensis strain.},
}
@article {pmid39411937,
year = {2024},
author = {Sekar, G and Bahot, A and Bansode, M and Phadnis, A and Sarode, SC and Sharma, NK},
title = {Potentiation of Tumor Hallmarks by the Loss of GULO, a Vitamin C Biosynthesis Gene in Humans.},
journal = {Current molecular medicine},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115665240328074241003110326},
pmid = {39411937},
issn = {1875-5666},
abstract = {Vitamin C plays a significant role in various physiological functions. Humans depend on external sources of vitamin C due to the loss of the L-gulono-γ-lactone oxidase (GULO) gene that contributes to the synthesis of vitamin C. During the evolutionary loss of the GULO gene, physical, chemical, and biological factors were different from the present environmental settings. Besides the evolutionary genetic loss of the GULO gene, there is a gap in the insightful discussion on the potential implications of the non-functional GULO gene towards the predisposition of humans to cancer that faces hostile and carcinogenic environments. Various methods by which vitamin C modulates cellular processes related to cancer, including DNA repair, epigenetic changes, and redox balance, are discussed. Furthermore, we present experimental and clinical evidence indicating that vitamin C deficiency promotes tumor growth, metastasis, and therapy resistance, emphasizing its potential as a cancer phenotypic modulator. Therapeutic implications of restoring vitamin C levels in cancer treatment range from improving the efficacy of conventional medicines to exploiting metabolic vulnerabilities in tumors. The relevance of assessing vitamin C status in cancer patients and the basis for additional research into vitamin C supplementation as an adjuvant therapy is emphasized. This paper presents a comprehensive overview of the implications associated with the functional deficiency of the GULO gene in human subjects exhibiting diverse tumor hallmarks, encompassing ECM remodeling, hypoxia, epigenetic reprogramming, oxidative stress, and drug responsiveness.},
}
@article {pmid39411151,
year = {2024},
author = {Meza-Padilla, I and McConkey, BJ and Nissimov, JI},
title = {Structural models predict a significantly higher binding affinity between the NblA protein of cyanophage Ma-LMM01 and the phycocyanin of Microcystis aeruginosa NIES-298 compared to the host homolog.},
journal = {Virus evolution},
volume = {10},
number = {1},
pages = {veae082},
pmid = {39411151},
issn = {2057-1577},
abstract = {Horizontal gene transfer events between viruses and hosts are widespread across the virosphere. In cyanophage-host systems, such events often involve the transfer of genes involved in photosynthetic processes. The genome of the lytic cyanophage Ma-LMM01 infecting the toxic, bloom-forming, freshwater Microcystis aeruginosa NIES-298 contains a homolog of the non-bleaching A (nblA) gene, which was probably transferred from a cyanobacterial host. The function of the NblA protein is to disassemble phycobilisomes, cyanobacterial light-harvesting complexes that can comprise up to half of the cellular soluble protein content. NblA thus plays an essential dual role in cyanobacteria: it protects the cell from high-light intensities and increases the intracellular nitrogen pool under nutrient limitation. NblA has previously been shown to interact with phycocyanin, one of the main components of phycobilisomes. Using structural modeling and protein-protein docking, we show that the NblA dimer of Ma-LMM01 is predicted to have a significantly higher binding affinity for M. aeruginosa NIES-298 phycocyanin (αβ)6 hexamers, compared to the host homolog. Protein-protein docking suggests that the viral NblA structural model is able to bind deeper into the phycocyanin groove. The main structural difference between the virus and host NblA appears to be an additional α-helix near the N-terminus of the viral NblA, which interacts with the inside of the phycocyanin groove and could thus be considered partly responsible for this deeper binding. Interestingly, phylogenetic analyses indicate that this longer nblA was probably acquired from a different Microcystis host. Based on infection experiments and previous findings, we propose that a higher binding affinity of the viral NblA to the host phycocyanin may represent a selective advantage for the virus, whose infection cycle requires an increased phycobilisome degradation rate that is not fulfilled by the NblA of the host.},
}
@article {pmid39405618,
year = {2025},
author = {Tan, Y and Yu, P and Yu, Z and Xuan, F and Zhu, L},
title = {Deciphering defense system modulating bacteria-mobile genetic elements symbiosis in microbial aggregates under elevated hydraulic stress.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122590},
doi = {10.1016/j.watres.2024.122590},
pmid = {39405618},
issn = {1879-2448},
mesh = {*Bacteria/genetics ; *Symbiosis ; Bioreactors ; Interspersed Repetitive Sequences ; Sewage/microbiology ; Biofilms ; Gene Transfer, Horizontal ; Plasmids/genetics ; },
abstract = {Bacterial defense systems are under strong evolutionary pressures to defend against mobile genetic elements (MGEs), yet their distribution in microbial aggregates in engineered systems remains largely unexplored. Herein, we investigated the bacterial defensome and MGEs within activated sludge flocs (AS) and membrane-attached biofilm (MF) in a full-scale membrane bioreactor. Similar distribution pattern of bacterial defense systems (63 types) was observed in prokaryotic genome in AS and MF, including RM system (∼40 %), Cas system (∼18 %) and TA-Abi system (∼28 %), exhibiting a dependency on the genome size and bacterial taxonomy in microbial aggregates under elevated hydraulic stress (MF). In contrast to plasmid and provirus, which carried defense systems (22 types) similar to their associated hosts, virome (61 %) carried novel defense systems (40 types) absent in their associated hosts. With 54 % of which involved in MGEs geneflow network, 69 % of high quality bacterial genome bins were associated with horizontal gene transfer (HGT), facilitating the exchange of mobile core functional genes. This potentially conferred competitive advantages to hosts through habitat-specific payload genes related to biotic defense, antibiotic resistance, and nitrogen metabolism. The longer growth cycle and varied defense gene density suggested the potential defense redundancy and trade-off of metabolic expense and immunity in bacterial host-MGE symbionts. Furthermore, enhanced cooperative network modules of cross-feeding and defense were observed in the MF, potentially helped the symbiotic microbial communities in coping with hostile conditions under elevated hydraulic stress. These findings shed light on the dynamics of bacterial defense systems in host-MGE coevolution and provide new perspectives of microbial aggregates manipulation for ecological and engineering application.},
}
@article {pmid39404847,
year = {2024},
author = {Bethke, JH and Kimbrel, J and Jiao, Y and Ricci, D},
title = {Toxin-Antitoxin Systems Reflect Community Interactions Through Horizontal Gene Transfer.},
journal = {Molecular biology and evolution},
volume = {41},
number = {10},
pages = {},
pmid = {39404847},
issn = {1537-1719},
mesh = {*Gene Transfer, Horizontal ; *Toxin-Antitoxin Systems/genetics ; *Plasmids/genetics ; Bacteria/genetics ; },
abstract = {Bacterial evolution through horizontal gene transfer (HGT) reflects their community interactions. In this way, HGT networks do well at mapping community interactions, but offer little toward controlling them-an important step in the translation of synthetic strains into natural contexts. Toxin-antitoxin (TA) systems serve as ubiquitous and diverse agents of selection; however, their utility is limited by their erratic distribution in hosts. Here we examine the heterogeneous distribution of TAs as a consequence of their mobility. By systematically mapping TA systems across a 10,000 plasmid network, we find HGT communities have unique and predictable TA signatures. We propose these TA signatures arise from plasmid competition and have further potential to signal the degree to which plasmids, hosts, and phage interact. To emphasize these relationships, we construct an HGT network based solely on TA similarity, framing specific selection markers in the broader context of bacterial communities. This work both clarifies the evolution of TA systems and unlocks a common framework for manipulating community interactions through TA compatibility.},
}
@article {pmid39404832,
year = {2024},
author = {Díaz-Martínez, C and Bolívar, A and Mercanoglu Taban, B and Kanca, N and Pérez-Rodríguez, F},
title = {Exploring the antibiotic resistance of Listeria monocytogenes in food environments - a review.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-24},
doi = {10.1080/1040841X.2024.2412007},
pmid = {39404832},
issn = {1549-7828},
abstract = {Listeria monocytogenes, a resilient bacterium in diverse food conditions, such as refrigeration, reduced water activity and low pH, poses a significant threat to the food industry and public health. In recent years, it has been documented an increase in the antibiotic resistance of zoonotic pathogens, including L. monocytogenes. This review provides new insight into the molecular mechanisms involved in both intrinsic and acquired antibiotic resistance of L. monocytogenes with an emphasis on the effect of different environmental and food-related factors. It also explores the relationship of these resistance mechanisms with virulence factors. An analysis of literature data (2009-2021) was conducted to investigate statistically and graphically potential associations between specific antibiotic resistance patterns in the pathogen and food categories using an unbiased variance analysis. The results evidenced that food type had an influence on the antibiotic resistance profiles of L. monocytogenes, with meat and vegetables being the food categories exhibiting the most prevalent profiles. The frequent detection of resistance to ampicillin, penicillin, and tetracycline (non-intrinsic resistances) indicates that specific processing conditions along the food chain may induce them. Many questions remain about the impact of food chain factors (e.g. thermal treatments, cold chain, preservatives, etc.) and food type (low pH, reduced water activity, etc.) on the antibiotic resistance patterns of the pathogen, particularly concerning food-related sources, the resistance mechanisms involved (e.g. cross-protection, horizontal gene transfer, etc.), and the evolutionary processes of antibiotic-resistant microbial populations. Metagenomics, in addition to other -omics technologies (metabolomics and transcriptomics), allows a better understanding of the processes involved in the acquisition of resistance.},
}
@article {pmid39402773,
year = {2025},
author = {Dunmyre, A and Vinayamohan, P and Locke, SR and Cheng, TY and Schaffner, V and Habing, G},
title = {Characterisation of Antimicrobial Resistance in Special-Fed Veal Production Environments.},
journal = {Zoonoses and public health},
volume = {72},
number = {1},
pages = {75-83},
pmid = {39402773},
issn = {1863-2378},
support = {//U.S. Department of Agriculture/ ; 018- 68003-27466//National Institute of Food and Agriculture/ ; //USDA National Institute of Food and Agriculture/ ; //Agricultural and Food Research Initiative Competitive Program/ ; 2018-68003-27466//Agriculture Economics and Rural Communities/ ; },
mesh = {Animals ; *Escherichia coli/drug effects ; Cattle ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial ; Animal Husbandry ; Abattoirs ; Escherichia coli Infections/veterinary/microbiology/epidemiology ; Drug Resistance, Multiple, Bacterial ; },
abstract = {INTRODUCTION: Antimicrobial resistance (AMR) is one of the leading public health threats globally. AMR genes can be transferred between bacteria through lateral gene transfer, and AMR organisms can spread through environments by contaminated water, agriculture and animals. Thus, widespread environmental dissemination of bacteria and lateral gene transfer facilitate AMR transmission pathways. Farm environments in dairy and calf production are known to harbour AMR bacteria that pose a risk for food contamination and to workers in direct or indirect contact with animals. Escherichia coli is present in farm environments and is known to participate in lateral gene transfer, providing a good marker of resistance genes in each environment.<br><br>METHODS: In this study, E. coli from nine cohorts of calves was isolated at different time points from nine barns, nine trailers and one slaughterhouse environment in a single special-fed veal calf production facility. The antimicrobial susceptibility to 15 antimicrobials, classified as highly or critically important by the World Health Organization, was characterised for E. coli isolates using Kirby-Bauer disk diffusion.<br><br>RESULTS: The highest proportion of isolates showing multidrug resistance was present in barn environments (51.7%), where calves were housed from their arrival at <&#x2009;2&#x2009;weeks of age until they were transported to slaughter. Additionally, 15 E. coli isolates were resistant to 11 of the 15 antimicrobials tested. Trailer and slaughterhouse environments had greater prevalence of resistance after accommodating calves, including resistance to third-generation cephalosporins.<br><br>CONCLUSION: These data highlight the importance of calf environments in the dissemination of resistant bacteria and gives insight into where interventions could be most effective in combatting antimicrobial-resistant bacteria that could infect humans and livestock.},
}
@article {pmid39401218,
year = {2024},
author = {Mazzamurro, F and Chirakadavil, JB and Durieux, I and Poiré, L and Plantade, J and Ginevra, C and Jarraud, S and Wilharm, G and Charpentier, X and P C Rocha, E},
title = {Intragenomic conflicts with plasmids and chromosomal mobile genetic elements drive the evolution of natural transformation within species.},
journal = {PLoS biology},
volume = {22},
number = {10},
pages = {e3002814},
pmid = {39401218},
issn = {1545-7885},
mesh = {*Plasmids/genetics ; *Interspersed Repetitive Sequences/genetics ; *Legionella pneumophila/genetics ; Humans ; Acinetobacter baumannii/genetics ; Phylogeny ; Evolution, Molecular ; Chromosomes, Bacterial/genetics ; Transformation, Bacterial ; Gene Transfer, Horizontal ; },
abstract = {Natural transformation is the only mechanism of genetic exchange controlled by the recipient bacteria. We quantified its rates in 786 clinical strains of the human pathogens Legionella pneumophila (Lp) and 496 clinical and environmental strains of Acinetobacter baumannii (Ab). The analysis of transformation rates in the light of phylogeny revealed they evolve by a mixture of frequent small changes and a few large quick jumps across 6 orders of magnitude. In standard conditions close to half of the strains of Lp and a more than a third in Ab are below the detection limit and thus presumably non-transformable. Ab environmental strains tend to have higher transformation rates than the clinical ones. Transitions to non-transformability were frequent and usually recent, suggesting that they are deleterious and subsequently purged by natural selection. Accordingly, we find that transformation decreases genetic linkage in both species, which might accelerate adaptation. Intragenomic conflicts with chromosomal mobile genetic elements (MGEs) and plasmids could explain these transitions and a GWAS confirmed systematic negative associations between transformation and MGEs: plasmids and other conjugative elements in Lp, prophages in Ab, and transposable elements in both. In accordance with the hypothesis of modulation of transformation rates by genetic conflicts, transformable strains have fewer MGEs in both species and some MGEs inactivate genes implicated in the transformation with heterologous DNA (in Ab). Innate defense systems against MGEs are associated with lower transformation rates, especially restriction-modification systems. In contrast, CRISPR-Cas systems are associated with higher transformation rates suggesting that adaptive defense systems may facilitate cell protection from MGEs while preserving genetic exchanges by natural transformation. Ab and Lp have different lifestyles, gene repertoires, and population structure. Nevertheless, they exhibit similar trends in terms of variation of transformation rates and its determinants, suggesting that genetic conflicts could drive the evolution of natural transformation in many bacteria.},
}
@article {pmid39395971,
year = {2024},
author = {Li, Z and Ran, Z and Xiao, X and Yan, C and Xu, J and Tang, M and An, M},
title = {Comparative analysis of the whole mitochondrial genomes of four species in sect. Chrysantha (Camellia L.), endemic taxa in China.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {955},
pmid = {39395971},
issn = {1471-2229},
support = {2022&#xff08;072&#xff09;//Guizhou Provincial Basic Research Program (Natural Science)/ ; 32360101//National Natural Science Foundation of China/ ; 31960043//National Natural Science Foundation of China/ ; },
mesh = {*Genome, Mitochondrial ; China ; *Camellia/genetics ; Phylogeny ; RNA Editing ; Genome, Plant ; Base Composition ; },
abstract = {BACKGROUND: The sect. Chrysantha Chang of plants with yellow flowers of Camellia species as the "Queen of the Tea Family", most of these species are narrowly distributed endemics of China and are currently listed Grde-II in National Key Protected Wild Plant of China. They are commercially important plants with horticultural medicinal and scientific research value. However, the study of the sect. Chrysantha species genetics are still in its infancy, to date, the mitochondrial genome in sect. Chrysantha has been still unexplored.<br><br>RESULTS: In this study, we provide a comprehensive assembly and annotation of the mitochondrial genomes for four species within the sect. Chrysantha. The results showed that the mitochondrial genomes were composed of closed-loop DNA molecules with sizes ranging from 850,836&#xa0;bp (C. nitidissima) to 1,098,121&#xa0;bp (C. tianeensis) with GC content of 45.71-45.78% and contained 48-58 genes, including 28-37 protein-coding genes, 17-20 tRNA genes and 2 rRNA genes. We also examined codon usage, sequence repeats, RNA editing and selective pressure in the four species. Then, we performed a comprehensive comparison of their basic structures, GC contents, codon preferences, repetitive sequences, RNA editing sites, Ka/Ks ratios, haplotypes, and RNA editing sites. The results showed that these plants differ little in gene type and number. C. nitidissima has the greatest variety of genes, while C. tianeensis has the greatest loss of genes. The Ka/Ks values of the atp6 gene in all four plants were greater than 1, indicating positive selection. And the codons ending in A and T were highly used. In addition, the RNA editing sites differed greatly in number, type, location, and efficiency. Twelve, six, five, and twelve horizontal gene transfer (HGT) fragments were found in C. tianeensis, Camellia huana, Camellia liberofilamenta, and C. nitidissima, respectively. The phylogenetic tree clusters the four species of sect. Chrysantha plants into one group, and C. huana and C. liberofilamenta have closer affinities.<br><br>CONCLUSIONS: In this study, the mitochondrial genomes of four sect. Chrysantha plants were assembled and annotated, and these results contribute to the development of new genetic markers, DNA barcode databases, genetic improvement and breeding, and provide important references for scientific research, population genetics, and kinship identification of sect. Chrysantha plants.},
}
@article {pmid39395498,
year = {2024},
author = {Hou, H and Zou, D and Shi, W and Wang, Y and Ma, D and Wang, Y and Li, Q and Gao, Y and Gao, B},
title = {Localized heating coupling with radical oxidation eliminating antibiotic resistance genes (ARGs) in interfacial photothermal Fenton-like disinfection process.},
journal = {The Science of the total environment},
volume = {955},
number = {},
pages = {176779},
doi = {10.1016/j.scitotenv.2024.176779},
pmid = {39395498},
issn = {1879-1026},
mesh = {*Disinfection/methods ; *Hydrogen Peroxide/chemistry ; *Oxidation-Reduction ; *Drug Resistance, Microbial/genetics ; Escherichia coli/drug effects ; Iron/chemistry ; Anti-Bacterial Agents/pharmacology/chemistry ; Reactive Oxygen Species/metabolism ; },
abstract = {Conventional oxidative disinfection processes are inefficient in eliminating intracellular antibiotic resistance genes (iARGs) due to the barrier of the cell membrane and the competitive reaction of cellular constituents within antibiotic-resistant bacteria (ARB), resulting in the widespread prevalence of ARGs in recycled water. This study presented the first application of localized heating coupling with advanced oxidation to destroy the resistant Escherichia coli cells and improved subsequent iARGs (blaTEM-1) degradation in a novel photothermal Fenton-like disinfection process. The Fe-Mn@CNT microfiltration membrane, comprising carbon nanotubes wrapped with Fe and Mn nanoparticles (Fe-Mn@CNT), was employed as a nanomaterial for photothermal conversion and H2O2 activation. The highly efficient absorption of full-spectrum photons by CNTs enabled the Fe-Mn@CNT membrane to concentrate light to generate localized intense heat, resulting in the destruction of ARB nearby, and the subsequent release of iARGs. Interfacial heat favored Fe-Mn-induced H2O2 activation, leading to the production of more ·OH, which in turn promoted the oxidation for ARG degradation and ARB cell damage. The results of the acetylcysteine quenching experiments indicated that interfacial heating and radical oxidation-induced accumulation of intracellular reactive oxygen species contributed to the elimination of about 1-log iARGs through direct attack. The integrity of the cell membrane, the morphology of ARB and the variation of i/e ARG copy numbers were observed to reveal that the introduction of interfacial heating aggravated the cell lysis and accelerated the iARGs release, resulting in the inactivation of 7.27-log ARB and the elimination of 4.64-log iARGs and 2.23-log eARGs. Localized heating coupling with ·OH oxidation achieved a 143 % increase in iARGs removal compared to the conventional Fenton-like oxidation. The interfacial photothermal Fenton-like disinfection process exhibited remarkable material stability, robust disinfection performance, and effective suppression of horizontal gene transfer, underscoring its immense potential to mitigate the risk of ARG dissemination in reclaimed water systems.},
}
@article {pmid39387591,
year = {2024},
author = {Zhang, M and Yin, Z and Chen, B and Yu, Z and Liang, J and Tian, X and Li, D and Deng, X and Peng, L},
title = {Investigation of Citrobacter freundii clinical isolates in a Chinese hospital during 2020-2022 revealed genomic characterization of an extremely drug-resistant C. freundii ST257 clinical strain GMU8049 co-carrying blaNDM-1 and a novel blaCMY variant.},
journal = {Microbiology spectrum},
volume = {12},
number = {11},
pages = {e0425423},
pmid = {39387591},
issn = {2165-0497},
support = {2023A1515220222//the Guangdong Basic and Applied Basic Research Foundation: Provincal-Enterprise Joint Fund/ ; 2024SRP134//Research Ability Enhancement Program of Guangzhou Medical University/ ; 2022A1515012504//the National Science Foundation of Guangdong Province/ ; },
mesh = {*Citrobacter freundii/genetics/drug effects/isolation &amp; purification/enzymology ; *beta-Lactamases/genetics ; Humans ; *Drug Resistance, Multiple, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; China ; *Plasmids/genetics ; *Whole Genome Sequencing ; *Enterobacteriaceae Infections/microbiology ; Genome, Bacterial/genetics ; Genomics ; Hospitals ; Azabicyclo Compounds/pharmacology ; Bacterial Proteins/genetics/metabolism ; Ceftazidime/pharmacology ; },
abstract = {The emergence of multidrug-resistant Citrobacter freundii poses a significant threat to public health. C. freundii isolates were collected from clinical patients in a Chinese hospital during 2020-2022. An unusual strain, GMU8049, was not susceptible to any of the antibiotics tested, including the novel β-lactam/β-lactamase inhibitor combination ceftazidime-avibactam. Whole-genome sequencing (WGS) revealed that GMU8049 harbors a circular chromosome belonging to the rare ST257 and an IncX3 resistance plasmid. Genomic analysis revealed the coexistence of two β-lactamase genes, including plasmid-mediated blaNDM-1 and chromosomal blaCMY encoding a novel CMY variant, combined with an outer membrane porin deficiency, which may account for the extreme resistance to β-lactams. Conjugation experiment confirmed that the blaNDM-1 resistance gene located on pGMU8049 could be successfully transferred to Escherichia coli EC600. The novel CMY variant had an amino acid substitution at position 106 (N106S) compared to the closely related CMY-51. Additionally, a GMU8049-specific truncation in an OmpK37 variant that produces a premature stop codon. Moreover, a variety of chromosome-located efflux pump coding genes and virulence-related genes were also identified. Analysis of strain GMU8049 in the context of other C. freundii strains reveals an open pan-genome and the presence of mobile genetic elements that can mediate horizontal gene transfer of antimicrobial resistance and virulence genes. Our work provides comprehensive insights into the genetic mechanisms of highly resistant C. freundii, highlighting the importance of genomic surveillance of this opportunistic pathogen as a high-risk population for emerging resistance and pathogenicity.IMPORTANCEEmerging pathogens exhibiting multi-, extremely, and pan-drug resistance are a major concern for hospitalized patients and the healthcare community due to limited antimicrobial treatment options and the potential for spread. Genomic technologies have enabled clinical surveillance of emerging pathogens and modeling of the evolution and transmission of antimicrobial resistance and virulence. Here, we report the genomic characterization of an extremely drug-resistant ST257 Citrobacter freundii clinical isolate. Genomic analysis of GMU8049 with a rare ST type and unusual phenotypes can provide information on how this extremely resistant clinical isolate has evolved, including the acquisition of blaNDM-1 via the IncX3 plasmid and accumulation through chromosomal mutations leading to a novel CMY variant and deficiency of the outer membrane porin OmpK37. Our work highlights that the emergence of extremely resistant C. freundii poses a significant challenge to the treatment of clinical infections. Therefore, great efforts must be made to specifically monitor this opportunistic pathogen.},
}
@article {pmid39394251,
year = {2024},
author = {Hossain, M and Aslan, B and Hatoum-Aslan, A},
title = {Tandem mobilization of anti-phage defenses alongside SCCmec elements in staphylococci.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8820},
pmid = {39394251},
issn = {2041-1723},
support = {R01 AI173022/AI/NIAID NIH HHS/United States ; R01AI 173022-01//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 1020298//Burroughs Wellcome Fund (BWF)/ ; },
mesh = {*Genomic Islands/genetics ; Staphylococcus/genetics ; Recombinases/metabolism/genetics ; Methicillin Resistance/genetics ; Staphylococcus Phages/genetics ; Gene Transfer, Horizontal ; Methicillin-Resistant Staphylococcus aureus/genetics ; Bacteriophages/genetics/physiology ; Chromosomes, Bacterial/genetics ; },
abstract = {Recent research has identified multiple immune systems that bacteria use to protect themselves from viral infections. However, little is known about the mechanisms by which these systems horizontally spread, especially among bacterial pathogens. Here, we investigate antiviral defenses in staphylococci, opportunistic pathogens that constitute leading causes of antibiotic-resistant infections. We show that these organisms harbor a variety of anti-phage defenses encoded within or near SCC (staphylococcal cassette chromosome) mec cassettes, mobile genomic islands that confer methicillin resistance. Importantly, we demonstrate that SCCmec-encoded recombinases mobilize not only SCCmec, but also tandem SCC-like cassettes enriched in genes coding for diverse defense systems. Further, we show that phage infection stimulates cassette mobilization (i.e. excision and circularization). Thus, our findings indicate that SCC/SCCmec cassettes not only spread antibiotic resistance but can also play a role in mobilizing anti-phage defenses.},
}
@article {pmid39394195,
year = {2024},
author = {Chu, J and Choi, J and Ji, SK and Park, C and Jung, SH and Park, SH and Lee, DG},
title = {An outbreak of blaKPC-4- and blaVIM-1-producing Klebsiella pneumoniae and Klebsiella variicola at a single hospital in South Korea.},
journal = {Antimicrobial resistance and infection control},
volume = {13},
number = {1},
pages = {123},
pmid = {39394195},
issn = {2047-2994},
support = {HI22C0226//Korea Health Industry Development Institute/Republic of Korea ; 2021R1A2C1009867//National Research Foundation of Korea/ ; },
mesh = {Humans ; *beta-Lactamases/genetics/metabolism ; *Disease Outbreaks ; *Klebsiella pneumoniae/genetics/isolation &amp; purification ; Republic of Korea/epidemiology ; *Klebsiella Infections/epidemiology/microbiology/transmission ; *Klebsiella/genetics ; *Plasmids/genetics ; Cross Infection/microbiology/epidemiology ; Bacterial Proteins/genetics/metabolism ; Hospitals ; Whole Genome Sequencing ; Gene Transfer, Horizontal ; Female ; Anti-Bacterial Agents/pharmacology ; Male ; },
abstract = {BACKGROUND: The dissemination of Klebsiella spp. producing multiple carbapenemases has been increasingly recognized. Between July 2019 and August 2021, ten patients were found to carry Klebsiella spp. co-harboring blaKPC-4 and blaVIM-1 across multiple wards at a Korean hospital, and one isolate was recovered from a hand-washing sink, more than a year after the outbreak. This study aimed to investigate the outbreak and conduct a genomic study of these isolates.<br><br>METHODS: Whole-genome sequencing, including long-read sequencing, was performed to analyze plasmid structures and mobile genetic elements (MGEs). Bioinformatics analyses were performed to trace clonal transmission chains and horizontal gene transfer.<br><br>RESULTS: The findings suggested that the inter-ward spread of Klebsiella spp. seemed to be facilitated by healthcare worker contact or patient movement. Of the nine isolates collected (eight clinical and one environmental), seven (including the environmental isolate) were identified as K. pneumoniae (ST3680) and two were K. variicola (single-locus variant of ST5252). These isolates showed high genetic relatedness within their species and harbored the IncHI5B plasmid carrying both blaKPC-4 and blaVIM-1 (pKPCVIM.1). On this plasmid, blaVIM-1 was located in the Class 1 integron associated with IS1326::IS1353 (In2), and Tn4401b carrying blaKPC-4 was inserted into IS1326::IS1353, creating a novel MGE construct (In2_blaVIM-1-Tn4401b_blaKPC-4).<br><br>CONCLUSION: The hospital-wide spread of blaKPC-4 and blaVIM-1 was facilitated by clonal spread and horizontal plasmid transfer. The persistence of this strain in the hospital sink suggests a potential reservoir of the strain. Understanding the transmission mechanisms of persistent pathogens is important for improving infection control strategies in hospitals.},
}
@article {pmid39393940,
year = {2024},
author = {Hall, JPJ},
title = {Loading and unloading plasmid cargoes.},
journal = {Trends in microbiology},
volume = {32},
number = {12},
pages = {1150-1152},
doi = {10.1016/j.tim.2024.09.012},
pmid = {39393940},
issn = {1878-4380},
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Bacteria/genetics/metabolism ; Chromosomes, Bacterial/genetics ; },
abstract = {Plasmids are vehicles for horizontal gene transfer between cells, but they also exchange genes with associated chromosomes in a process termed 'intracellular mobility'. I discuss a recent article by Kadibalban et al. mapping such plasmid-chromosomal sequence similarities across diverse bacteria.},
}
@article {pmid39389705,
year = {2024},
author = {Zhen, Q and Wang, X and Cheng, X and Fang, W},
title = {Remediation of toxic metal and metalloid pollution with plant symbiotic fungi.},
journal = {Advances in applied microbiology},
volume = {129},
number = {},
pages = {171-187},
doi = {10.1016/bs.aambs.2024.04.001},
pmid = {39389705},
issn = {0065-2164},
mesh = {*Plants/microbiology ; *Symbiosis ; *Biodegradation, Environmental ; *Metalloids/metabolism/toxicity ; *Soil Pollutants/metabolism/toxicity ; *Fungi/metabolism/genetics ; *Mycorrhizae/metabolism/physiology ; Endophytes/metabolism/physiology/isolation &amp; purification/genetics ; Metals/metabolism/toxicity ; Soil Microbiology ; },
abstract = {Anthropogenic activities have dramatically accelerated the release of toxic metal(loid)s into soil and water, which can be subsequently accumulated in plants and animals, threatening biodiversity, human health, and food security. Compared to physical and chemical remediation, bioremediation of metal(loid)-polluted soil using plants and/or plant symbiotic fungi is usually low-cost and environmentally friendly. Mycorrhizal fungi and endophytic fungi are two major plant fungal symbionts. Mycorrhizal fungi can immobilize metal(loid)s via constitutive mechanisms, including intracellular sequestration with vacuoles and vesicles and extracellular immobilization by cell wall components and extracellular polymeric substances such as glomalin. Mycorrhizal fungi can improve the efficacy of phytoremediation by promoting plant symplast and apoplast pathways. Endophytic fungi also use constitutive cellular components to immobilize metal(loid)s and to reduce the accumulation of metal(loid)s in plants by modifying plant physiological status. However, a specific mechanism for the removal of methylmercury pollution was recently discovered in the endophytic fungi Metarhizium, which could be acquired from bacteria via horizontal gene transfer. In contrast to mycorrhizal fungi that are obligate biotrophs, some endophytic fungi, such as Metarhizium and Trichoderma, can be massively and cost-effectively produced, so they seem to be well-placed for remediation of metal(loid)-polluted soil on a large scale.},
}
@article {pmid39389327,
year = {2025},
author = {Narain Singh, D and Pandey, P and Shankar Singh, V and Kumar Tripathi, A},
title = {Evidence for high-risk pollutants and emerging microbial contaminants at two major bathing ghats of the river Ganga using high-resolution mass spectrometry and metagenomics.},
journal = {Gene},
volume = {933},
number = {},
pages = {148991},
doi = {10.1016/j.gene.2024.148991},
pmid = {39389327},
issn = {1879-0038},
mesh = {*Rivers/microbiology/chemistry ; *Metagenomics/methods ; *Wastewater/microbiology ; Bacteria/genetics/isolation &amp; purification/classification ; Water Pollutants, Chemical/analysis ; India ; Mass Spectrometry/methods ; Environmental Monitoring/methods ; Water Microbiology ; },
abstract = {An efficient wastewater treatment plant is imperative to limit the entry of emerging pollutants (EPs) and emerging microbial contaminants (EMCs) in the river ecosystem. The detection of emerging EPs in aquatic environments is challenging due to complex sample preparation methods, and the need for sophisticated accurate analytical tools. In Varanasi (India), the river Ganga holds immense significance as a holy river but is consistently polluted with municipal (MWW) and hospital wastewater (HWW). We developed an efficient method for untargeted detection of EPs in the water samples using High-resolution mass spectrometry (HRMS), and identified 577 and 670 chemicals (or chemical components) in the water samples from two major bathing ghats, Assi Ghat (AG) and Dashashwamedh Ghat (DG), respectively. The presence of EPs of different categories viz chemicals from research labs, diagnostic labs, lifestyle and industrial chemicals, toxins, flavor and food additives indicated the unsafe disposal of MWW and HWW or inefficient wastewater treatment plants (WWTPs). Besides, shotgun metagenomic analysis depicted the presence of bacteria associated with MWW viz Cloacibacterium normanse, Sphaerotilus natans (sewage fungi), E. coli, and Prevotella. Also, the presence of human pathogens Arcobacter, Polynucleobacter, Pseudomonas, Klebsiella, Aeromonas, Acinetobacter, Vibrio, and Campylobacter suggests the discharge of HWW. EPs are linked to the development, and transmission of antimicrobial resistance (AMR). Occurrence of antibiotic resistance genes (ARGs), plasmid-borne β-lactamases, aminoglycoside transferases, and ARGs associated with integrons, transposons and plasmids viz mcr-3 gene that confer resistance to colistin, the last resort of antibiotics confirmed the presence of emerging microbial contaminants. Subsequent genome reconstruction studies showed the presence of uncultivable ARB and transmission of ARGs through horizontal gene transfer. This study can be used to monitor the health of aquatic bodies as well as the efficiency of WWTPs and raise an urgent need for efficient WWTPs to safeguard the river, Ganga.},
}
@article {pmid39386473,
year = {2024},
author = {Dalia, TN and Dalia, AB},
title = {SbcB facilitates natural transformation in Vibrio cholerae in an exonuclease-independent manner.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.25.615017},
pmid = {39386473},
issn = {2692-8205},
abstract = {UNLABELLED: Natural transformation (NT) is a conserved mechanism of horizontal gene transfer in bacterial species. During this process, DNA is taken up into the cytoplasm where it can be integrated into the host genome by homologous recombination. We have previously shown that some cytoplasmic exonucleases inhibit NT by degrading ingested DNA prior to its successful recombination. However, one exonuclease, SbcB, counterintuitively promotes NT in Vibrio cholerae . Here, through a systematic analysis of the distinct steps of NT, we show that SbcB acts downstream of DNA uptake into the cytoplasm, but upstream of recombinational branch migration. Through mutational analysis, we show that SbcB promotes NT in a manner that does not rely on its exonuclease activity. Finally, we provide genetic evidence that SbcB directly interacts with the primary bacterial recombinase, RecA. Together, these data advance our molecular understanding of horizontal gene transfer in V. cholerae , and reveal that SbcB promotes homologous recombination during NT in a manner that does not rely on its canonical exonuclease activity.<br><br>IMPORTANCE: Horizontal gene transfer by natural transformation contributes to the spread of antibiotic resistance and virulence factors in bacterial species. Here, we study how one protein, SbcB, helps facilitate this process in the facultative bacterial pathogen Vibrio cholerae . SbcB is a well-known for its exonuclease activity (i . e ., the ability to degrade the ends of linear DNA). Through this study we uncover that while SbcB is important for natural transformation, it does not facilitate this process using its exonuclease activity. Thus, this work helps further our understanding of the molecular events required for this conserved evolutionary process, and uncovers a function for SbcB beyond its canonical exonuclease activity.},
}
@article {pmid39385022,
year = {2024},
author = {Samuel, B and Mittelman, K and Croitoru, SY and Ben Haim, M and Burstein, D},
title = {Diverse anti-defence systems are encoded in the leading region of plasmids.},
journal = {Nature},
volume = {635},
number = {8037},
pages = {186-192},
pmid = {39385022},
issn = {1476-4687},
mesh = {*Conjugation, Genetic ; CRISPR-Cas Systems/genetics ; DNA, Single-Stranded/genetics ; *Escherichia coli/genetics/immunology ; Gene Transfer, Horizontal ; *Plasmids/genetics ; Promoter Regions, Genetic/genetics ; SOS Response, Genetics/genetics ; },
abstract = {Plasmids are major drivers of gene mobilization by means of horizontal gene transfer and play a key role in spreading antimicrobial resistance among pathogens[1,2]. Despite various bacterial defence mechanisms such as CRISPR-Cas, restriction-modification systems and SOS-response genes that prevent the invasion of mobile genetic elements[3], plasmids robustly transfer within bacterial populations through conjugation[4,5]. Here we show that the leading region of plasmids, the first to enter recipient cells, is a hotspot for an extensive repertoire of anti-defence systems, encoding anti-CRISPR, anti-restriction, anti-SOS and other counter-defence proteins. We further identified in the leading region a prevalence of promoters known to allow expression from single-stranded DNA[6], potentially facilitating rapid protection against bacterial immunity during the early stages of plasmid establishment. We demonstrated experimentally the importance of anti-defence gene localization in the leading region for efficient conjugation. These results indicate that focusing on the leading region of plasmids could lead to the discovery of diverse anti-defence genes. Combined, our findings show a new facet of plasmid dissemination and provide theoretical foundations for developing efficient conjugative delivery systems for natural microbial communities.},
}
@article {pmid39384008,
year = {2024},
author = {Gentile, A and Di Stasio, L and Oliva, G and Vigliotta, G and Cicatelli, A and Guarino, F and Nissim, WG and Labra, M and Castiglione, S},
title = {Antibiotic resistance in urban soils: Dynamics and mitigation strategies.},
journal = {Environmental research},
volume = {263},
number = {Pt 2},
pages = {120120},
doi = {10.1016/j.envres.2024.120120},
pmid = {39384008},
issn = {1096-0953},
mesh = {*Drug Resistance, Microbial/genetics ; *Soil Microbiology ; *Soil/chemistry ; *Anti-Bacterial Agents/pharmacology ; Cities ; Soil Pollutants/toxicity ; Humans ; },
abstract = {Antibiotic resistance (AR) is a critical global health issue with significant clinical and economic implications. AR occurs when microorganisms develop mechanisms to withstand the effects of antibiotics, reducing treatment efficacy and increasing the risk of mortality and healthcare costs. While the connection between antibiotic use in clinical and agricultural settings and the emergence of AR is well-established, the role of urban soils as reservoirs and spreaders of AR is underexplored. This review examines the complex dynamics of AR in urban soils, highlighting the various sources of antibiotics, including domestic wastewater, industrial effluents, urban agricultural practices, but also microplastics and domestic animal excrements. The selective pressure exerted by these anthropogenic sources promotes the proliferation of antibiotic-resistant bacteria, particularly through horizontal gene transfer, which facilitates the transmission of resistance genes among soil microorganisms in urban environments. About that, the presence of antibiotics in urban soils poses a significant threat to public health by potentially transferring resistance genes to human pathogens through multiple pathways, including direct contact, food consumption, and water ingestion. Furthermore, AR in urban soils disrupts microbial community dynamics, impacting soil fertility, plant growth, and overall environmental quality. Therefore, this review aims to address gaps in understanding AR in urban soils, offering insights into its implications for human health and ecosystem integrity. By identifying these gaps and suggesting evidence-based strategies, this review proposes valid and sustainable solutions to mitigate and counteract the spread of AR in urban environments.},
}
@article {pmid39383948,
year = {2024},
author = {Rao, M and Teixeira, JS and Flint, A and Tamber, S},
title = {Hazard Characterization of Antibiotic-resistant Aeromonas spp. Isolated from Mussel and Oyster Shellstock Available for Retail Purchase in Canada.},
journal = {Journal of food protection},
volume = {87},
number = {11},
pages = {100374},
doi = {10.1016/j.jfp.2024.100374},
pmid = {39383948},
issn = {1944-9097},
mesh = {*Aeromonas/isolation &amp; purification/drug effects ; Animals ; Canada ; *Anti-Bacterial Agents/pharmacology ; *Bivalvia/microbiology ; Humans ; *Ostreidae/microbiology ; Shellfish/microbiology ; Microbial Sensitivity Tests ; Drug Resistance, Bacterial ; Food Microbiology ; Food Contamination/analysis ; },
abstract = {Surveillance and monitoring of foods for the presence of antimicrobial-resistant (AMR) bacteria are required to assess the risks these bacteria pose to human health. Frequently consumed raw or lightly cooked, live bivalve shellfish such as mussels and oysters can be a source of exposure to AMR bacteria. This study sought to determine the prevalence of third-generation cephalosporin (3GC) and carbapenem-resistant bacteria in live mussel and oyster shellstock available for retail purchase through the course of one calendar year. Just over half of the 180 samples (52%) tested positive for the presence of 3GC-resistant bacteria belonging to thirty distinct bacterial species. Speciation of the isolates was carried out using the Bruker MALDI Biotyper. Serratia spp., Aeromonas spp., and Rahnella spp. were the most frequently isolated groups of bacteria. Antibiotic resistance testing confirmed reduced susceptibility for 3GCs and/or carbapenems in 15 of the 29 Aeromonas isolates. Based on AMR patterns, and species identity, a subset of ten Aeromonas strains was chosen for further characterization by whole genome sequence analysis. Genomic analysis revealed the presence of multiple antibiotic resistance and virulence genes. A number of mobile genetic elements were also identified indicating the potential for horizontal gene transfer. Differences in gene detection by the bioinformatic tools and databases used (ResFinder. CARD RGI, PlasmidFinder, and MobSuite) are discussed. This study highlights the strengths and limitations of using genomics tools to perform hazard characterization of diverse foodborne bacterial species.},
}
@article {pmid39383803,
year = {2025},
author = {Xiang, Y and Song, X and Yang, Y and Deng, S and Fu, L and Yang, C and Chen, M and Pu, J and Zhang, H and Chai, H},
title = {Comammox rather than AOB dominated the efficient autotrophic nitrification-denitrification process in an extremely oxygen-limited environment.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122572},
doi = {10.1016/j.watres.2024.122572},
pmid = {39383803},
issn = {1879-2448},
mesh = {*Nitrification ; *Denitrification ; *Oxygen/metabolism ; *Autotrophic Processes ; *Ammonia/metabolism ; *Bacteria/metabolism/genetics ; *RNA, Ribosomal, 16S/genetics ; Nitrogen/metabolism ; Oxidation-Reduction ; Bioreactors/microbiology ; },
abstract = {The discovery of complete ammonia oxidizer (comammox) has challenged the traditional understanding of the two-step nitrification process. However, their functions in the oxygen-limited autotrophic nitrification-denitrification (OLAND) process remain unclear. In this study, OLAND was achieved using comammox-dominated nitrifying bacteria in an extremely oxygen-limited environment with a dissolved oxygen concentrations of 0.05 mg/L. The ammonia removal efficiency exceeded 97 %, and the total nitrogen removal efficiency reached 71 % when sodium bicarbonate was used as the carbon source. The pseudo-first- and second-order models were found to best fit the ammonia removal processes under low and high loads, respectively, suggesting distinct ammonia removal pathways. Full-length 16S rRNA gene sequencing and metagenomic results revealed that comammox-dominated under different oxygen levels, in conjunction with anammox and heterotrophic denitrifiers. The abundance of enzymes involved in energy metabolism indicates the coexistence of anammox and autotrophic nitrification-heterotrophic denitrification pathways. The binning results showed that comammox bacteria engaged in horizontal gene transfer with nitrifiers, anammox bacteria, and denitrifiers to adapt to an obligate environments. Therefore, this study demonstrated that comammox, anammox, and heterotrophic denitrifiers play important roles in the OLAND process and provide a reference for further reducing aeration energy in the autotrophic nitrogen removal process.},
}
@article {pmid39376581,
year = {2024},
author = {Du, Y and Qian, C and Li, X and Zheng, X and Huang, S and Yin, Z and Chen, T and Pan, L},
title = {Unveiling intraspecific diversity and evolutionary dynamics of the foodborne pathogen Bacillus paranthracis through high-quality pan-genome analysis.},
journal = {Current research in food science},
volume = {9},
number = {},
pages = {100867},
pmid = {39376581},
issn = {2665-9271},
abstract = {Understanding the evolutionary dynamics of foodborne pathogens throughout host-associated habitats is of utmost importance. Bacterial pan-genomes, as dynamic entities, are strongly influenced by ecological lifestyles. As a phenotypically diverse species in the Bacillus cereus group, Bacillus paranthracis is recognized as an emerging foodborne pathogen and a probiotic simultaneously. This poorly understood species is a suitable study model for adaptive pan-genome evolution. In this study, we determined the biogeographic distribution, abundance, genetic diversity, and genotypic profiles of key genetic elements of B. paranthracis. Metagenomic read recruitment analyses demonstrated that B. paranthracis members are globally distributed and abundant in host-associated habitats. A high-quality pan-genome of B. paranthracis was subsequently constructed to analyze the evolutionary dynamics involved in ecological adaptation comprehensively. The open pan-genome indicated a flexible gene repertoire with extensive genetic diversity. Significant divergences in the phylogenetic relationships, functional enrichment, and degree of selective pressure between the different components demonstrated different evolutionary dynamics between the core and accessory genomes driven by ecological forces. Purifying selection and gene loss are the main signatures of evolutionary dynamics in B. paranthracis pan-genome. The plasticity of the accessory genome is characterized by horizontal gene transfer (HGT), massive gene losses, and weak purifying or positive selection, which might contribute to niche-specific adaptation. In contrast, although the core genome dominantly undergoes purifying selection, its association with HGT and positively selected mutations indicates its potential role in ecological diversification. Furthermore, host fitness-related dynamics are characterized by the loss of secondary metabolite biosynthesis gene clusters (BGCs) and CAZyme-encoding genes and the acquisition of antimicrobial resistance (AMR) and virulence genes via HGT. This study offers a case study of pan-genome evolution to investigate the ecological adaptations reflected by biogeographical characteristics, thereby advancing the understanding of intraspecific diversity and evolutionary dynamics of foodborne pathogens.},
}
@article {pmid39375624,
year = {2024},
author = {Männer, L and Schell, T and Spies, J and Galià-Camps, C and Baranski, D and Ben Hamadou, A and Gerheim, C and Neveling, K and Helfrich, EJN and Greve, C},
title = {Chromosome-level genome assembly of the sacoglossan sea slug Elysia timida (Risso, 1818).},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {941},
pmid = {39375624},
issn = {1471-2164},
mesh = {Animals ; *Gastropoda/genetics ; *Molecular Sequence Annotation ; *Genome ; *Chromosomes/genetics ; Genomics/methods ; },
abstract = {BACKGROUND: Sequencing and annotating genomes of non-model organisms helps to understand genome architecture, the genetic processes underlying species traits, and how these genes have evolved in closely-related taxa, among many other biological processes. However, many metazoan groups, such as the extremely diverse molluscs, are still underrepresented in the number of sequenced and annotated genomes. Although sequencing techniques have recently improved in quality and quantity, molluscs are still neglected due to difficulties in applying standardized protocols for obtaining genomic data.<br><br>RESULTS: In this study, we present the chromosome-level genome assembly and annotation of the sacoglossan sea slug&#xa0;species Elysia timida, known for its ability to store the chloroplasts of its food algae. In particular, by optimizing the long-read and chromosome conformation capture library preparations, the genome assembly was performed using PacBio HiFi and Arima HiC data. The scaffold and contig N50s, at 41.8&#xa0;Mb and 1.92&#xa0;Mb, respectively, are approximately 30-fold and fourfold higher compared to other published sacoglossan genome assemblies. Structural annotation resulted in 19,904 protein-coding genes, which are more contiguous and complete compared to publicly available annotations of Sacoglossa with respect to metazoan BUSCOs. We found no evidence for horizontal gene transfer (HGT), i.e. no photosynthetic genes encoded in the sacoglossan nucleus genome. However, we detected genes encoding polyketide synthases in E. timida, indicating that polypropionates are produced. HPLC-MS/MS analysis confirmed the presence of a large number of polypropionates, including known and yet uncharacterised compounds.<br><br>CONCLUSIONS: We can show that our methodological approach helps to obtain a high-quality genome assembly even for a "difficult-to-sequence" organism, which may facilitate genome sequencing in molluscs. This will enable a better understanding of complex biological processes in molluscs, such as functional kleptoplasty in Sacoglossa, by significantly improving the quality of genome assemblies and annotations.},
}
@article {pmid39373502,
year = {2025},
author = {Liu, G and Li, X and Guan, J and Tai, C and Weng, Y and Chen, X and Ou, HY},
title = {oriTDB: a database of the origin-of-transfer regions of bacterial mobile genetic elements.},
journal = {Nucleic acids research},
volume = {53},
number = {D1},
pages = {D163-D168},
pmid = {39373502},
issn = {1362-4962},
support = {2023YFC2307103//National Key Research and Development Program of China/ ; 32070572//National Natural Science Foundation of China/ ; SHDC2022CRD039//Shanghai Hospital Development Center Foundation/ ; GWV1-11.2-XD01//Talent Program on Public Health System Construction of Shanghai/ ; 20240818//Shanghai Jiao Tong University School of Medicine/ ; },
mesh = {*Interspersed Repetitive Sequences ; Gene Transfer, Horizontal ; Plasmids/genetics ; Conjugation, Genetic ; Bacteria/genetics/classification ; Databases, Genetic ; Genome, Bacterial ; Bacterial Proteins/genetics/metabolism ; Databases, Nucleic Acid ; DNA, Bacterial/genetics ; },
abstract = {Conjugation and mobilization are two important pathways of horizontal transfer of bacterial mobile genetic elements (MGEs). The origin-of-transfer (oriT) region is crucial for this process, serving as a recognition site for relaxase and containing the DNA nicking site (nic site), which initiates the conjugation or mobilization. Here, we present a database of the origin-of-transfer regions of bacterial MGEs, oriTDB (https://bioinfo-mml.sjtu.edu.cn/oriTDB2/). Incorporating data from text mining and genome analysis, oriTDB comprises 122 experimentally validated and 22 927 predicted oriTs within bacterial plasmids, Integrative and Conjugative Elements, and Integrative and Mobilizable Elements. Additionally, oriTDB includes details about associated relaxases, auxiliary proteins, type IV coupling proteins, and a gene cluster encoding the type IV secretion system. The database also provides predicted secondary structures of oriT sequences, dissects oriT regions into pairs of inverted repeats, nic sites, and their flanking conserved sequences, and offers an interactive visual representation. Furthermore, oriTDB includes an enhanced oriT prediction pipeline, oriTfinder2, which integrates a functional annotation module for cargo genes in bacterial MGEs. This resource is intended to support research on bacterial conjugative or mobilizable elements and promote an understanding of their cargo gene functions.},
}
@article {pmid39368562,
year = {2024},
author = {Hu, JC and Han, M and Yan, RY and Hua, MM and Li, J and Shen, H and Cao, XL},
title = {Mobile genetic elements contributing to horizontal gene transfer of blaNDM among Escherichia coli in the community setting.},
journal = {Microbial pathogenesis},
volume = {196},
number = {},
pages = {106996},
doi = {10.1016/j.micpath.2024.106996},
pmid = {39368562},
issn = {1096-1208},
mesh = {*Gene Transfer, Horizontal ; Humans ; *Escherichia coli/genetics/drug effects/isolation &amp; purification ; *beta-Lactamases/genetics ; *Interspersed Repetitive Sequences/genetics ; *Anti-Bacterial Agents/pharmacology ; *Whole Genome Sequencing ; China/epidemiology ; *Feces/microbiology ; *Plasmids/genetics ; Microbial Sensitivity Tests ; Phylogeny ; Carbapenem-Resistant Enterobacteriaceae/genetics/isolation &amp; purification ; Escherichia coli Proteins/genetics ; Escherichia coli Infections/microbiology/epidemiology ; Citrobacter freundii/genetics/drug effects/isolation &amp; purification ; Genotype ; Carbapenems/pharmacology ; Klebsiella/genetics/drug effects/enzymology ; },
abstract = {OBJECTIVE: To investigate the distribution of carbapenem-resistant Enterobacterales (CRE) in the community and to describe the genomic characteristics.<br><br>METHODS: CRE screened from fecal samples in healthy people at the health examination center of a tertiary hospital in China underwent Whole genome sequencing (WGS) to analyze genotypic characteristics of CRE. The flanking DNA sequence of blaNDM-5 and mcr1.1 genes were analyzed by Gcluster software.<br><br>RESULTS: A total of 7187 fecal samples were screened, and CRE carriage was detected in 0.4&#xa0;% of the sampled population. In total, 30 Escherichia coli, one Citrobacter freundii and one Klebsiella aerogene were screened. The 30 carbapenem-resistant Escherichia coli (CREC) isolates displayed slight resistance to amikacin (13.3&#xa0;%) and aztreonam (20.0&#xa0;%). All the CRE isolates contained blaNDM, and blaNDM-5 (84.4&#xa0;%) was the most common one. B1 (n&#xa0;=&#xa0;11) and A (n&#xa0;=&#xa0;7) were predominant phylogroups. Furthermore, 34 distinct plasmid replicons, 67 different VFs, 22 distinct STs, 17 different FimH types, 26 O:H serotypes as well as 74 MGEs including 61 insertion sequences and 13 transposons were identified. The flanking DNA sequence analysis of blaNDM-5 and mcr1.1 genes indicates the key role of horizontal transfer of blaNDM-5 in the CRE development evidenced by diverse STs and phylogenetic tree.<br><br>CONCLUSION: E. coli was the most predominant CRE isolates in community setting, and blaNDM (blaNDM-5) was the main CH&#x3b2;L encoding genes. The high prevalence of ARGs was associated with high resistance to commonly used antimicrobials. Besides, the genetic diversity of these isolates suggested the key role of blaNDM horizontal transfer in the CRE development. Thus, active screening of blaNDM in communities is particularly important for the prevention and control of CRE.},
}
@article {pmid39368190,
year = {2024},
author = {Jiao, P and Zhou, Y and Zhang, X and Jian, H and Zhang, XX and Ma, L},
title = {Mechanisms of horizontal gene transfer and viral contribution to the fate of intracellular and extracellular antibiotic resistance genes in anaerobic digestion supplemented with conductive materials under ammonia stress.},
journal = {Water research},
volume = {267},
number = {},
pages = {122549},
doi = {10.1016/j.watres.2024.122549},
pmid = {39368190},
issn = {1879-2448},
mesh = {*Gene Transfer, Horizontal ; *Ammonia ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; Sewage ; },
abstract = {The addition of conductive materials (CMs) is an effective strategy for mitigating ammonia inhibition during anaerobic digestion (AD). However, the introduction of CMs can result in increased antibiotic resistance genes (ARGs) pollution, potentially facilitated by enhanced horizontal gene transfer (HGT). The complex dynamics of intracellular and extracellular ARGs (iARGs/eARGs) and the mechanisms underlying their transfer, mediated by CMs, in ammonia-stressed AD systems remain unclear. In this study, we investigated the effects of three commonly used CMs-nano magnetite (Mag), nano zero-valent iron (nZVI), and granular activated carbon (GAC)-on the fate of iARGs and eARGs during the AD of waste activated sludge under ammonia stress. The results revealed an unexpected enrichment of iARGs by 1.5 %-10.9 % and a reduction of eARGs by 14.1 %-25.2 % in CM-supplemented AD. This discrepancy in the dynamics of iARGs and eARGs may be attributed to changes in microbial hosts and the horizontal transfer of ARGs. Notably, CMs activated prophages within antibiotic-resistant bacteria (ARB) and their symbiotic partners involved in vitamin B12 provision, leading to the lysis of ARB and the subsequent release of eARGs for transformation. Additionally, the abundance of potentially mobile ARGs, which co-occurred with mobile genetic elements, increased by 56.6 %-134.5 % with CM addition, highlighting an enhanced potential for the HGT of ARGs. Specifically, Mag appeared to promote both transformation and conjugation processes, while nZVI only promoted conjugation. Moreover, none of the three CMs had any discernible impact on transduction. GAC proved superior to both nano Mag and nZVI in controlling the enrichment of iARGs, reducing eARGs, and limiting HGTs simultaneously. Overall, these findings provide novel insights into the role of viruses and the mechanisms of ARG spread in CM-assisted AD, offering valuable information for developing strategies to mitigate ARG pollution in practical applications.},
}
@article {pmid39368156,
year = {2024},
author = {Zhou, Y and Zhang, G and Zhang, D and Zhu, N and Bo, J and Meng, X and Chen, Y and Qin, Y and Liu, H and Li, W},
title = {Microplastic biofilms promote the horizontal transfer of antibiotic resistance genes in estuarine environments.},
journal = {Marine environmental research},
volume = {202},
number = {},
pages = {106777},
doi = {10.1016/j.marenvres.2024.106777},
pmid = {39368156},
issn = {1879-0291},
mesh = {*Biofilms/drug effects ; *Gene Transfer, Horizontal ; *Microplastics/toxicity ; *Estuaries ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Bacteria/genetics/drug effects ; Water Pollutants, Chemical/toxicity ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology/toxicity ; },
abstract = {As emerging pollutants, microplastics can aggregate microorganisms on their surfaces and form biofilms, enriching antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Consequently, microplastic biofilms have become a focal point of research. Horizontal gene transfer is one of the primary mechanisms by which bacteria acquire antibiotic resistance, with much of the research focusing on suspended bacteria. However, microplastic biofilms, as hotspots for horizontal gene transfer, also merit significant investigation. This study primarily explored and compared the frequency of ARG conjugative transfer between suspended bacteria and microplastic biofilms. The results demonstrated that, compared to suspended bacteria, microplastic biofilms enhanced the frequency of ARG conjugative transfer by 7.2-19.6 times. Among them, biofilms on polyethylene microplastics showed the strongest promotion of conjugation. After the formation of microplastic biofilms, there was a significant increase in bacterial density within the biofilms, which raised the collision frequency of donor and recipient bacteria. Then microplastic biofilms facilitated the gene expression levels of outer membrane proteins, enhanced bacterial gene transfer capabilities, promoted the synthesis of conjugative pili, accelerated the formation of conjugative pairing systems, and elevated the expression levels of genes related to DNA replication and transfer systems, thereby enhancing the conjugative transfer of ARGs within microplastic biofilms. Among different types of microplastic biofilms, polyethylene biofilms exhibited the highest bacterial density, thus showing the highest frequency of ARG conjugation. This study highlights the risks associated with ARG conjugative transfer following the formation of microplastic biofilms and provides insights into the risks of microplastic and antibiotic resistance propagation in estuarine environments.},
}
@article {pmid39366749,
year = {2024},
author = {Leclerc, L and Mattick, J and Burns, BP and Sassera, D and Hotopp, JD and Lo, N},
title = {Metatranscriptomics provide insights into the role of the symbiont Midichloria mitochondrii in Ixodes ticks.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {12},
pages = {},
pmid = {39366749},
issn = {1574-6941},
support = {//The Linnean Society of New South Wales/ ; //University of New South Wales/ ; },
mesh = {*Ixodes/microbiology/genetics ; Animals ; *Symbiosis ; *Transcriptome ; Gene Transfer, Horizontal ; Nymph/microbiology/growth &amp; development/genetics ; Gene Expression Profiling ; },
abstract = {Ticks are important vectors of bacterial, viral, and protozoan pathogens of humans and animals worldwide. Candidatus Midichloria mitochondrii is a highly abundant bacterial endosymbiont found in many tick species, including two medically important ticks respectively found in Europe and Australia, Ixodes ricinus and Ixodes holocyclus. The present study aimed to determine the symbiont's biological role by identifying lateral gene transfer (LGT) events, characterizing the transcriptome, and performing differential expression analyses. Metatranscriptomic data revealed that M. mitochondrii species in I. ricinus and I. holocyclus were equipped with the metabolic potential and were actively transcribing the genes for several important roles including heme, biotin and folate synthesis, oxidative stress response, osmotic regulation, and ATP production in microaerobic conditions. Differential expression analyses additionally showed an upregulation in stringent response and DNA repair genes in M. mitochondrii of I. holocyclus nymphs compared to adults. Low rates of differential expression suggest the symbiont may lack global gene regulation, as observed in other endosymbionts. Moreover, the identification of an LGT event and the proposed specialization of the M. mitochondrii strains, mIxholo1 and mIxholo2, for different I. holocyclus life stages highlight the complex interactions between M. mitochondrii and their tick hosts.},
}
@article {pmid39366703,
year = {2024},
author = {Gomez-Simmonds, A and Annavajhala, MK and Seeram, D and Hokunson, TW and Park, H and Uhlemann, AC},
title = {Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of bla KPC.},
journal = {Genome research},
volume = {34},
number = {11},
pages = {1895-1907},
pmid = {39366703},
issn = {1549-5469},
support = {K99 AI163348/AI/NIAID NIH HHS/United States ; P30 DK132710/DK/NIDDK NIH HHS/United States ; R01 AI116939/AI/NIAID NIH HHS/United States ; K24 AI183182/AI/NIAID NIH HHS/United States ; K23 AI137316/AI/NIAID NIH HHS/United States ; R01 AI175414/AI/NIAID NIH HHS/United States ; U54 DK104309/DK/NIDDK NIH HHS/United States ; },
mesh = {*Plasmids/genetics ; *beta-Lactamases/genetics ; Humans ; *Gene Transfer, Horizontal ; *Bacterial Proteins/genetics ; *Carbapenems/pharmacology ; New York City/epidemiology ; Carbapenem-Resistant Enterobacteriaceae/genetics ; Enterobacteriaceae Infections/microbiology/epidemiology/transmission ; Klebsiella pneumoniae/genetics/drug effects ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Molecular Epidemiology ; Multilocus Sequence Typing ; },
abstract = {Transmission of carbapenem-resistant Enterobacterales (CRE) in hospitals has been shown to occur through complex, multifarious networks driven by both clonal spread and horizontal transfer mediated by plasmids and other mobile genetic elements. We performed nanopore long-read sequencing on CRE isolates from a large urban hospital system to determine the overall contribution of plasmids to CRE transmission and identify specific plasmids implicated in the spread of bla KPC (the Klebsiella pneumoniae carbapenemase [KPC] gene). Six hundred and five CRE isolates collected between 2009 and 2018 first underwent Illumina sequencing for genome-wide genotyping; 435 bla KPC-positive isolates were then successfully nanopore sequenced to generate hybrid assemblies including circularized bla KPC-harboring plasmids. Phylogenetic analysis and Mash clustering were used to define putative clonal and plasmid transmission clusters, respectively. Overall, CRE isolates belonged to 96 multilocus sequence types (STs) encoding bla KPC on 447 plasmids which formed 54 plasmid clusters. We found evidence for clonal transmission in 66% of CRE isolates, over half of which belonged to four clades comprising K. pneumoniae ST258. Plasmid-mediated acquisition of bla KPC occurred in 23%-27% of isolates. While most plasmid clusters were small, several plasmids were identified in multiple different species and STs, including a highly promiscuous IncN plasmid and an IncF plasmid putatively spreading bla KPC from ST258 to other clones. Overall, this points to both the continued dominance of K. pneumoniae ST258 and the dissemination of bla KPC across clones and species by diverse plasmid backbones. These findings support integrating long-read sequencing into genomic surveillance approaches to detect the hitherto silent spread of carbapenem resistance driven by mobile plasmids.},
}
@article {pmid39367299,
year = {2024},
author = {Wang, J and Liu, X and Zhang, M and Liu, R},
title = {The mitochondrial genome of Lavandula angustifolia Mill. (Lamiaceae) sheds light on its genome structure and gene transfer between organelles.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {929},
pmid = {39367299},
issn = {1471-2164},
support = {No. 2022BCA022//Hubei Province key research and development project/ ; },
mesh = {*Genome, Mitochondrial ; *Lavandula/genetics ; *Phylogeny ; RNA, Transfer/genetics ; Organelles/genetics ; Gene Transfer, Horizontal ; RNA Editing ; Molecular Sequence Annotation ; Genome, Plant ; Evolution, Molecular ; },
abstract = {BACKGROUND: Lavandula angustifolia holds importance as an aromatic plant with extensive applications spanning the fragrance, perfume, cosmetics, aromatherapy, and spa sectors. Beyond its aesthetic and sensory applications, this plant offers medicinal benefits as a natural herbal remedy and finds use in household cleaning products. While extensive genomic data, inclusive of plastid and nuclear genomes, are available for this species, researchers have yet to characterize its mitochondrial genome. This gap in knowledge hampers deeper understanding of the genome organization and its evolutionary significance.<br><br>RESULTS: Through the course of this study, we successfully assembled and annotated the mitochondrial genome of L. angustifolia, marking a first in this domain. This assembled genome encompasses 61 genes, which comprise 34 protein-coding genes, 24 transfer RNA genes, and three ribosomal RNA genes. We identified a chloroplast sequence insertion into the mitogenome, which spans a length of 10,645&#xa0;bp, accounting for 2.94% of the mitogenome size. Within these inserted sequences, there are seven intact tRNA genes (trnH-GUG, trnW-CCA, trnD-GUC, trnS-GGA, trnN-GUU, trnT-GGU, trnP-UGG) and four complete protein-coding genes (psbA, rps15, petL, petG) of chloroplast derivation. Additional discoveries include 88 microsatellites, 15 tandem repeats, 74 palindromic repeats, and 87 forward long repeats. An RNA editing analysis highlighted an elevated count of editing sites in the cytochrome c oxidase genes, notably ccmB with 34 editing sites, ccmFN with 32, and ccmC with 29. All protein-coding genes showed evidence of cytidine-to-uracil conversion. A phylogenetic analysis, utilizing common protein-coding genes from 23 Lamiales species, yielded a tree with consistent topology, supported by high confidence values.<br><br>CONCLUSIONS: Analysis of the current mitogenome resource revealed its typical circular genome structure. Notably, sequences originally from the chloroplast genome were found within the mitogenome, pointing to the occurrence of horizontal gene transfer between organelles. This assembled mitogenome stands as a valuable resource for subsequent studies on mitogenome structures, their evolution, and molecular biology.},
}
@article {pmid39366964,
year = {2024},
author = {Kawaichi, S and Kotoky, R and Fiutowski, J and Rotaru, AE},
title = {Adaptation of a methanogen to Fe[0] corrosion via direct contact.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {100},
pmid = {39366964},
issn = {2055-5008},
support = {ERC CoG 101045149//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; UFM 5229-00010B//Uddannelses- og Forskningsministeriet (Ministry of Higher Education and Science)/ ; },
mesh = {*Methanococcus/genetics/metabolism ; Corrosion ; *Adaptation, Physiological ; *Hydrogenase/genetics/metabolism ; Gene Transfer, Horizontal ; Methane/metabolism ; Iron/metabolism ; },
abstract = {Due to unique genomic adaptations, Methanococcus maripaludis Mic1c10 is highly corrosive when in direct contact with Fe[0]. A critical adaptation involves increased glycosylation of an extracellular [NiFe]-hydrogenase, facilitating its anchoring to cell surface proteins. Corrosive strains adapt to the constructed environment via horizontal gene transfer while retaining ancestral genes important for intraspecies competition and surface attachment. This calls for a reevaluation of how the built environment impacts methane cycling.},
}
@article {pmid39365569,
year = {2024},
author = {Gniewosz, M and Andrzejczak-Grządko, S},
title = {[Characterization of KPC-type drug resistance in bacteria].},
journal = {Postepy biochemii},
volume = {70},
number = {3},
pages = {315-324},
doi = {10.18388/pb.2021_555},
pmid = {39365569},
issn = {0032-5422},
mesh = {*beta-Lactamases/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Humans ; Carbapenems/pharmacology ; Bacteria/genetics/drug effects ; Gene Transfer, Horizontal ; },
abstract = {One of the main problems of modern medicine is the phenomenon of drug resistance. Inappropriate use of antibiotics is considered to be the most important reason for the emergence of new resistance mechanisms in microorganisms. Carbapenems, which belong to the β-lactams, are considered the most effective group of antimicrobial agents. Unfortunately, as a result of prolonged exposure to the aforementioned drugs, bacteria have developed several mechanisms for survival. The most important of these is the production of hydrolytic enzymes (carbapenemases), which cleave the β-lactam ring and inactivate the antibiotics. The mentioned enzymes are encoded by blaKPC genes, which are located in so-called mobile genetic elements (i.e. plasmids and transposons). Such localization is associated with their ease of transfer between different bacterial species in the process of horizontal gene transfer.},
}
@article {pmid39364782,
year = {2024},
author = {Bellinazzo, F and Nadal Bigas, J and Hogers, RAH and Kodde, J and van der Wal, F and Kokkinopoulou, P and Duijts, KTM and Angenent, GC and van Dijk, ADJ and van Velzen, R and Immink, RGH},
title = {Evolutionary origin and functional investigation of the widely conserved plant PEBP gene STEPMOTHER OF FT AND TFL1 (SMFT).},
journal = {The Plant journal : for cell and molecular biology},
volume = {120},
number = {4},
pages = {1410-1420},
doi = {10.1111/tpj.17057},
pmid = {39364782},
issn = {1365-313X},
support = {//KAVB Productgroep Tulp/ ; //Stimuflori/ ; VICI16129//NWO/ ; ALWGR.2017.008//NWO/ ; VICI192033//NWO/ ; },
mesh = {*Evolution, Molecular ; *Phosphatidylethanolamine Binding Protein/genetics/metabolism ; *Phylogeny ; Plant Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Arabidopsis/genetics/metabolism ; Arabidopsis Proteins/genetics/metabolism ; },
abstract = {Genes of the family PHOSPHATIDYLETHANOLAMINE-BINDING PROTEINS (PEBP) have been intensely studied in plants for their role in cell (re)programming and meristem differentiation. Recently, sporadic reports of the presence of a new type of PEBP in plants became available, highly similar to the YY-PEBPs of prokaryotes. A comprehensive investigation of their spread, origin, and function revealed conservation across the plant kingdom. The YY-PEBP clade in plants seems to have resulted from a single Horizontal Gene Transfer (HGT) episode from a prokaryotic organism to an ancestral streptophyte. YY-PEBPs are also present in other eukaryotes, such as certain fungi, diatoms, and rotifers, and these cases derive from independent HGT events. Reciprocally, the occurrence of the eukaryotic CETS/RKIP type PEBPs (CR-PEBPs) was noticed in bacteria of the genus Nocardia, showing that HGT has occurred as well from eukaryotes to prokaryotes. Based on these observations, we propose that the current model of the PEBP family in plants needs to be updated with the clade STEPMOTHER OF FT AND TFL1 (SMFT). SMFT genes not only share high sequence conservation but also show specific expression in homologous plant structures that serve as propagules. Functional analysis of Arabidopsis smft mutant lines pointed to a function for this gene in regulating seed germination, both concerning primary dormancy release and in response to adverse high-temperature conditions. Overall, our study reveals an increasing complexity in the evolutionary history of the PEBP gene family, unlocking new potential in understanding the evolution and functional spectrum of these important key regulatory genes.},
}
@article {pmid39360841,
year = {2024},
author = {Smith, AC and Shrivastava, A and Cartee, JC and Bélanger, M and Sharpe, S and Lewis, J and Budionno, S and Gomez, R and Khubbar, MK and , and Pham, CD and Gernert, KM and Schmerer, MW and Raphael, BH and Learner, ER and Kersh, EN and Joseph, SJ},
title = {Whole-genome sequencing resolves biochemical misidentification of Neisseria species from urogenital specimens.},
journal = {Journal of clinical microbiology},
volume = {62},
number = {11},
pages = {e0070424},
pmid = {39360841},
issn = {1098-660X},
mesh = {Humans ; *Whole Genome Sequencing ; *Neisseria gonorrhoeae/genetics/classification/isolation &amp; purification ; *Genome, Bacterial/genetics ; *Gonorrhea/microbiology/diagnosis ; Neisseria meningitidis/genetics/isolation &amp; purification/classification ; Urogenital System/microbiology ; Gene Transfer, Horizontal ; Male ; Female ; Diagnostic Errors ; },
abstract = {Neisseria meningitidis (Nm) and Neisseria gonorrhoeae (Ng) are human pathogens that sometimes occupy the same anatomical niche. Ng, the causative agent of gonorrhea, infects 87 million individuals annually worldwide and is an urgent threat due to increasing drug resistance. Ng is a pathogen of the urogenital tract and may infect the oropharyngeal or rectal site, often asymptomatically. Conversely, Nm is an opportunistic pathogen. While often a commensal in the oropharyngeal tract, it is also the leading cause of bacterial meningitis with 1.2 million cases globally, causing significant morbidity and mortality. Horizontal gene transfer (HGT) is likely to occur between Ng and Nm due to their shared anatomical niches and genetic similarity, which poses challenges for accurate detection and treatment. Routine surveillance through the Gonococcal Isolate Surveillance Project and Strengthening the U.S. Response to Resistant Gonorrhea detected six concerning urogenital Neisseria isolates with contradicting species identification in Milwaukee (MIL). While all six isolates were positive for Ng using nucleic acid amplification testing (NAAT) and matrix-assisted laser desorption/ionization time of flight identified the isolates as Ng, two biochemical tests, Gonochek-II and API NH, classified them as Nm. To address this discrepancy, we performed whole-genome sequencing (WGS) using Illumina MiSeq on all isolates and employed various bioinformatics tools. Species detection analysis using BMScan, which uses WGS data, identified all isolates as Ng. Furthermore, Kraken revealed over 98% of WGS reads mapped to the Ng genome and <1% to Nm. Recombination analysis identified putative HGT in all MIL isolates within the γ-glutamyl transpeptidase (ggt) gene, a key component in the biochemical tests used to differentiate between Nm and Ng. Further analysis identified Nm as the source of HGT event. Specifically, the active Nm ggt gene replaced the Ng pseudogenes, ggt1 and ggt2. Together, this study demonstrates that closely related Neisseria species sharing a niche underwent HGT, which led to the misidentification of species following biochemical testing. Importantly, NAAT accurately detected Ng. The misidentification highlights the importance of using WGS to continually evaluate diagnostic or bacterial identification tests.},
}
@article {pmid39360838,
year = {2024},
author = {Ott, L and Smith, C and Mellata, M},
title = {Dietary zinc supplementation inhibits bacterial plasmid conjugation in vitro by regulating plasmid replication (rep) and transfer (tra) genes.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {10},
pages = {e0148024},
pmid = {39360838},
issn = {1098-5336},
support = {IOW05679//USDA | National Institute of Food and Agriculture (NIFA)/ ; IOW05700//U.S. Department of Agriculture (USDA)/ ; IOW04202//U.S. Department of Agriculture (USDA)/ ; },
mesh = {*Plasmids/genetics ; *Zinc/pharmacology ; *Dietary Supplements ; *Escherichia coli/genetics/drug effects ; *Conjugation, Genetic ; Animals ; Humans ; Gene Transfer, Horizontal ; Escherichia coli Proteins/genetics ; },
abstract = {Humans use dietary supplements for several intended effects, such as supplementing malnutrition. While these compounds have been developed for host end benefits, their ancillary impact on the gut microbiota remains unclear. The human gut has been proposed as a reservoir for the prevalent lateral transfer of antimicrobial resistance and virulence genes in bacteria through plasmid conjugation. Here, we studied the effect of dietary zinc supplements on the incidence of plasmid conjugation in vitro. Supplement effects were analyzed through standardized broth conjugation assays. The avian pathogenic Escherichia coli (APEC) strain APEC-O2-211 was a donor of the multidrug resistance plasmid pAPEC-O2-211A-ColV, and the human commensal isolate E. coli HS-4 was the plasmid-free recipient. Bacterial strains were standardized and mixed 1:1 and supplemented 1:10 with water, or zinc derived from either commercial zinc supplements or zinc gluconate reagent at varying concentrations. We observed a significant reduction in donors, recipients, and transconjugant populations in conjugations supplemented with zinc, with a dose-dependent relationship. Additionally, we observed a significant reduction (P < 0.05) in log conjugation efficiency in zinc-treated reactions. Upregulation of the mRNA for the plasmid replication initiation gene repA and the subset of transfer genes M, J, E, K, B, P, C, W, U, N, F, Q, D, I, and X was observed. Furthermore, we observed a downregulation of the conjugal propilin gene traA and the entry exclusion gene traS. This study demonstrates the effect of dietary zinc supplements on the conjugal transfer of a multidrug resistance plasmid between pathogenic and commensal bacteria during in vitro conditions.IMPORTANCEThis study identifies dietary zinc supplementation as a potential novel intervention for mitigating the emergence of multidrug resistance in bacteria, thus preventing antibiotic treatment failure and death in patients and animals. Further studies are required to determine the applicability of this approach in an in vivo model.},
}
@article {pmid39359630,
year = {2024},
author = {Wang, Y and Chen, P and Lin, Q and Zuo, L and Li, L},
title = {Endophytic bacteria with allelopathic potential regulate gene expression and metabolite production in host Casuarina equisetifolia.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1435440},
pmid = {39359630},
issn = {1664-462X},
abstract = {INTRODUCTION: Casuarina equisetifolia is a common protective forest in coastal areas. However, artificial C. equisetifolia forests cannot self-renew, mainly due to the accumulation of allelochemicals. Endophytic bacteria may alleviate the root growth inhibition caused by allelochemicals in C. equisetifolia seedlings. B. amyloliquefaciens and B. aryabhattai were endophytic bacteria with strong allelopathy in C. equisetifolia root. The allelopathy mechanism of these two endophytes and their interaction with C. equisetifolia remains to be studied.<br><br>METHODS: Whole-genome sequencing of B. amyloliquefaciens and B. aryabhattai isolated from the roots of allelochemical-accumulating C. equisetifolia was performed using Illumina Hiseq and PacBio single-molecule sequencing platforms. Sterile seedlings of C. equisetifolia were treated with either individual or mixed bacterial cultures through root drenching. Transcriptional and metabolomics analyses were conducted after 3 days of infection.<br><br>RESULTS AND DISCUSSION: Whole-genome sequencing of Bacillus aryabhattai and Bacillus amyloliquefaciens showed that the two strains contained various horizontal gene transfer elements such as insertion sequence, prophage and transposon. In addition, these two strains also contain numerous genes related to the synthesis and catabolism of allelochemicals. After these two strains of bacteria were individually or mixed infected with C. equisetifolia, metabolomics and transcriptomic analysis of C. equisetifolia showed the 11 important secondary metabolite biosynthesis among them alkaloids biosynthesis, phenylpropanoid and terpenes biosynthesis and related genes were putatively regulated. Correlation analysis revealed that 48 differentially expressed genes had strong positive correlations with 42 differential metabolites, and 48 differentially expressed genes had strong negative correlations with 36 differential metabolites. For example, CMBL gene showed positive correlations with the allelochemical (-)-Catechin gallate, while Bp10 gene showed negative correlations with (-)-Catechin gallate.<br><br>CONCLUSION: The intergenerational accumulation of allelochemicals may induce horizontal gene transfer in endogenic bacteria of Casuarina equisetifolia root. Endophytic Bacillus plays an allelopathic role by assisting the host in regulating gene expression and the production and/or variety of allelochemicals. This comprehensive study sheds light on the intricate genetic and metabolic interactions between Bacillus endophytes and C. equisetifolia. These findings provide insights into endophyte-mediated allelopathy and its potential uses in plant biology and forest sustainability.},
}
@article {pmid39357349,
year = {2024},
author = {Zhang, K and Gao, J and Lu, T and Wang, Y and Zhang, J and An, J and Xu, H},
title = {Evolution of microbial community and resistance genes in denitrification system under single and combined exposure to benzethonium chloride and methylparaben.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136010},
doi = {10.1016/j.jhazmat.2024.136010},
pmid = {39357349},
issn = {1873-3336},
mesh = {*Parabens/toxicity ; *Denitrification/drug effects ; *Water Pollutants, Chemical/toxicity ; *Benzethonium/toxicity ; Microbiota/drug effects ; Sewage/microbiology ; Wastewater ; Genes, Bacterial/drug effects ; Gene Transfer, Horizontal ; },
abstract = {Benzethonium chloride (BZC) and methylparaben (MeP) are commonly added into cosmetics as preservatives, which are frequently detected in wastewater treatment plants. Different response patterns of denitrification system were proposed under single and combined exposure to BZC and MeP (0, 0.5, 5 mg/L) by evaluating system performance, functional genes, extracellular polymeric substance (EPS), cytotoxicity, microbial community structure and resistance genes (RGs). The inhibition effect of BZC on denitrification system was stronger than MeP, and the co-exposure of BZC and MeP showed synergistic effect, enhancing the inhibition effect of BZC single exposure. BZC and/or MeP could promote the diffusion of RGs in sludge, including intracellular RGs (si-RGs) and extracellular RGs (se-RGs). Moreover, the single exposure of BZC and co-exposure of BZC and MeP increased the dissemination risks of RGs in water (w-RGs). IntI1 and tnpA-04, mobile genetic elements (MGEs), correlated positively with diverse RGs from different fractions. Notably, the spread of RGs through horizontal gene transfer mediated by MGEs and the flow of si-RGs into extracellular and water were observed in this study.},
}
@article {pmid39352766,
year = {2024},
author = {Ling, X and Gu, X and Shen, Y and Fu, C and Zhou, Y and Yin, Y and Gao, Y and Zhu, Y and Lou, Y and Zheng, M},
title = {Comparative genomic analysis of Acanthamoeba from different sources and horizontal transfer events of antimicrobial resistance genes.},
journal = {mSphere},
volume = {9},
number = {10},
pages = {e0054824},
pmid = {39352766},
issn = {2379-5042},
mesh = {*Acanthamoeba/genetics/classification/microbiology ; *Gene Transfer, Horizontal ; *Phylogeny ; Humans ; *Acanthamoeba Keratitis/parasitology/microbiology ; Genomics ; Genome, Protozoan ; Genetic Variation ; Whole Genome Sequencing ; Drug Resistance/genetics ; },
abstract = {UNLABELLED: Acanthamoeba species are among the most common free-living amoeba and ubiquitous protozoa, mainly distributed in water and soil, and cause Acanthamoeba keratitis (AK) and severe visual impairment in patients. Although several studies have reported genomic characteristics of Acanthamoeba, limited sample sizes and sources have resulted in an incomplete understanding of the genetic diversity of Acanthamoeba from different sources. While endosymbionts exert a significant influence on the phenotypes of Acanthamoeba, including pathogenicity, virulence, and drug resistance, the species diversity and functional characterization remain largely unexplored. Herein, our study sequenced and analyzed the whole genomes of 19 Acanthamoeba pathogenic strains that cause AK, and by integrating publicly available genomes, we sampled 29 Acanthamoeba strains from ocular, environmental, and other sources. Combined pan-genomic and comparative functional analyses revealed genetic differences and evolutionary relationships among the different sources of Acanthamoeba, as well as classification into multiple functional groups, with ocular isolates in particular showing significant differences that may account for differences in pathogenicity. Phylogenetic and rhizome gene mosaic analyses of ocular Acanthamoeba strains suggested that genomic exchanges between Acanthamoeba and endosymbionts, particularly potential antimicrobial resistance genes trafficking including the adeF, amrA, and amrB genes exchange events, potentially contribute to Acanthamoeba drug resistance. In conclusion, this study elucidated the adaptation of Acanthamoeba to different ecological niches and the influence of gene exchange on the evolution of ocular Acanthamoeba genome, guiding the clinical diagnosis and treatment of AK and laying a theoretical groundwork for developing novel therapeutic approaches.<br><br>IMPORTANCE: Acanthamoeba causes a serious blinding keratopathy, Acanthamoeba keratitis, which is currently under-recognized by clinicians. In this study, we analyzed 48 strains of Acanthamoeba using a whole-genome approach, revealing differences in pathogenicity and function between strains of different origins. Horizontal transfer events of antimicrobial resistance genes can help provide guidance as potential biomarkers for the treatment of specific Acanthamoeba keratitis cases.},
}
@article {pmid39350642,
year = {2024},
author = {Saha, S and Kanaujia, SP},
title = {Decoding Substrate Selectivity of an Archaeal RlmCD-like Methyltransferase Through Its Salient Traits.},
journal = {Biochemistry},
volume = {63},
number = {19},
pages = {2477-2492},
doi = {10.1021/acs.biochem.4c00401},
pmid = {39350642},
issn = {1520-4995},
mesh = {Substrate Specificity ; *Archaeal Proteins/metabolism/genetics/chemistry ; *Methyltransferases/metabolism/chemistry/genetics ; Pyrococcus horikoshii/enzymology/genetics ; Models, Molecular ; Crystallography, X-Ray ; S-Adenosylmethionine/metabolism ; Amino Acid Sequence ; },
abstract = {5-Methyluridine (m[5]U) rRNA modifications frequently occur at U747 and U1939 (Escherichia coli numbering) in domains II and IV of the 23S rRNA in Gram-negative bacteria, with the help of S-adenosyl-l-methionine (SAM)-dependent rRNA methyltransferases (MTases), RlmC and RlmD, respectively. In contrast, Gram-positive bacteria utilize a single SAM-dependent rRNA MTase, RlmCD, to modify both corresponding sites. Notably, certain archaea, specifically within the Thermococcales group, have been found to possess two genes encoding SAM-dependent archaeal (tRNA and rRNA) m[5]U (Arm[5]U) MTases. Among these, a tRNA-specific Arm[5]U MTase (PabTrmU54) has already been characterized. This study focused on the structural and functional characterization of the rRNA-specific Arm[5]U MTase from the hyperthermophilic archaeon Pyrococcus horikoshii (PhRlmCD). An in-depth structural examination revealed a dynamic hinge movement induced by the replacement of the iron-sulfur cluster with disulfide bonds, obstructing the substrate-binding site. It revealed distinctive characteristics of PhRlmCD, including elongated positively charged loops in the central domain and rotational variations in the TRAM domain, which influence substrate selectivity. Additionally, the results suggested that two potential mini-rRNA fragments interact in a similar manner with PhRlmCD at a positively charged cleft at the interface of domains and facilitate dual MTase activities akin to the protein RlmCD. Altogether, these observations showed that Arm[5]U MTases originated from horizontal gene transfer events, most likely from Gram-positive bacteria.},
}
@article {pmid39348487,
year = {2024},
author = {Ishida, JK and Costa, EC},
title = {What we know so far and what we can expect next: A molecular investigation of plant parasitism.},
journal = {Genetics and molecular biology},
volume = {47Suppl 1},
number = {Suppl 1},
pages = {e20240051},
pmid = {39348487},
issn = {1415-4757},
abstract = {The review explores parasitic plants' evolutionary success and adaptability, highlighting their widespread occurrence and emphasizing the role of an invasive organ called haustorium in nutrient acquisition from hosts. It discusses the genetic and physiological adaptations that facilitate parasitism, including horizontal gene transfer, and the impact of environmental factors like climate change on these relationships. It addresses the need for further research into parasitic plants' genomes and interactions with their hosts to better predict environmental changes' impacts.},
}
@article {pmid39348416,
year = {2024},
author = {Mayfield, JA and Raman, S and Ramnarine, AK and Mishra, VK and Huang, AD and Dudoit, S and Buter, J and Cheng, TY and Young, DC and Nair, YM and Ouellet, IG and Griebel, BT and Ma, S and Sherman, DR and Mallet, L and Rhee, KY and Minnaard, AJ and Branch Moody, D},
title = {Mycobacteria that cause tuberculosis have retained ancestrally acquired genes for the biosynthesis of chemically diverse terpene nucleosides.},
journal = {PLoS biology},
volume = {22},
number = {9},
pages = {e3002813},
pmid = {39348416},
issn = {1545-7885},
support = {U19 AI162598/AI/NIAID NIH HHS/United States ; U19 AI162584/AI/NIAID NIH HHS/United States ; DP2 AI164249/AI/NIAID NIH HHS/United States ; R01 AI165573/AI/NIAID NIH HHS/United States ; R01 AI146194/AI/NIAID NIH HHS/United States ; },
mesh = {*Mycobacterium tuberculosis/metabolism/genetics ; *Tuberculosis/microbiology ; *Terpenes/metabolism ; Humans ; *Nucleosides/metabolism ; Adenosine/metabolism/analogs &amp; derivatives ; Lipidomics/methods ; Mass Spectrometry ; Bacterial Proteins/metabolism/genetics ; Genes, Bacterial ; Lipids ; },
abstract = {Mycobacterium tuberculosis (Mtb) releases the unusual terpene nucleoside 1-tuberculosinyladenosine (1-TbAd) to block lysosomal function and promote survival in human macrophages. Using conventional approaches, we found that genes Rv3377c and Rv3378c, but not Rv3376, were necessary for 1-TbAd biosynthesis. Here, we introduce linear models for mass spectrometry (limms) software as a next-generation lipidomics tool to study the essential functions of lipid biosynthetic enzymes on a whole-cell basis. Using limms, whole-cell lipid profiles deepened the phenotypic landscape of comparative mass spectrometry experiments and identified a large family of approximately 100 terpene nucleoside metabolites downstream of Rv3378c. We validated the identity of previously unknown adenine-, adenosine-, and lipid-modified tuberculosinol-containing molecules using synthetic chemistry and collisional mass spectrometry, including comprehensive profiling of bacterial lipids that fragment to adenine. We tracked terpene nucleoside genotypes and lipid phenotypes among Mycobacterium tuberculosis complex (MTC) species that did or did not evolve to productively infect either human or nonhuman mammals. Although 1-TbAd biosynthesis genes were thought to be restricted to the MTC, we identified the locus in unexpected species outside the MTC. Sequence analysis of the locus showed nucleotide usage characteristic of plasmids from plant-associated bacteria, clarifying the origin and timing of horizontal gene transfer to a pre-MTC progenitor. The data demonstrated correlation between high level terpene nucleoside biosynthesis and mycobacterial competence for human infection, and 2 mechanisms of 1-TbAd biosynthesis loss. Overall, the selective gain and evolutionary retention of tuberculosinyl metabolites in modern species that cause human TB suggest a role in human TB disease, and the newly discovered molecules represent candidate disease-specific biomarkers.},
}
@article {pmid39343406,
year = {2024},
author = {Lin, L and Sun, M and Pan, X and Zhang, W and Yang, Y and Yang, Y},
title = {Absence of synergistic effects between microplastics and copper ions on the spread of antibiotic resistance genes within aquatic bacteria at the community level.},
journal = {The Science of the total environment},
volume = {954},
number = {},
pages = {176591},
doi = {10.1016/j.scitotenv.2024.176591},
pmid = {39343406},
issn = {1879-1026},
mesh = {*Copper/toxicity ; *Microplastics/toxicity ; *Water Pollutants, Chemical/toxicity ; *Bacteria/drug effects/genetics ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; },
abstract = {Microplastics and copper ions (Cu[2+]) are favorable in accelerating the propagation of antibiotic resistance genes (ARGs) in the plastisphere, however, their combined effects on the ARG spread within the bacterial community of the natural environment were less understood. The influence of microplastic types and Cu[2+] concentrations on the horizontal gene transfer (HGT) of ARGs mediated by RP4 plasmid within natural bacterial communities in aquatic environments was investigated. Both biodegradable polybutylene succinate (PBS) and non-biodegradable polyvinyl chloride (PVC) microplastics significantly enhanced the transfer of ARGs, with PBS showing a significant higher effect compared to PVC. Cu[2+] also increased transconjugation rates at environmentally relevant concentrations (5 μg L[-1]), but higher levels (50 μg L[-1]) lead to decreased rates due to severe bacterial cell membrane damage. The transconjugation rates in the presence of both microplastics and Cu[2+] were lower than the sum of their individual effects, indicating no synergistic effects between them on transconjugation. Proteobacteria dominated the composition of transconjugates for all the treatment. Transmission electron microscope images and reactive oxygen species production in bacterial cells indicated that the increased contact frequency due to extracellular polymeric substances, combined with enhanced membrane permeability induced by microplastics and Cu[2+], accounted for the increasing transconjugation rates. The study provides valuable insight into the potential effects of microplastics and heavy metals on the spread of ARGs from donors to bacterial communities in natural environments.},
}
@article {pmid39343112,
year = {2024},
author = {Tao, Y and Zeng, Z and Deng, Y and Zhang, M and Wang, F and Wang, Y},
title = {Phylogeny and evolution of dissimilatory sulfite reduction in prokaryotes.},
journal = {Molecular phylogenetics and evolution},
volume = {201},
number = {},
pages = {108208},
doi = {10.1016/j.ympev.2024.108208},
pmid = {39343112},
issn = {1095-9513},
mesh = {*Phylogeny ; *Sulfites/metabolism ; *Oxidation-Reduction ; *Evolution, Molecular ; Bacteria/genetics/classification/metabolism ; Gene Transfer, Horizontal ; Archaea/genetics/classification/metabolism ; Prokaryotic Cells/classification/metabolism ; Sequence Analysis, DNA ; },
abstract = {Sulfate is the second most common nonmetallic ion in modern oceans, as its concentration dramatically increased alongside tectonic activity and atmospheric oxidation in the Proterozoic. Microbial sulfate/sulfite metabolism, involving organic carbon or hydrogen oxidation, is linked to sulfur and carbon biogeochemical cycles. However, the coevolution of microbial sulfate/sulfite metabolism and Earth's history remains unclear. Here, we conducted a comprehensive phylogenetic analysis to explore the evolutionary history of the dissimilatory sulfite reduction (Dsr) pathway. The phylogenies of the Dsr-related genes presented similar branching patterns but also some incongruencies, indicating the complex origin and evolution of Dsr. Among these genes, dsrAB is the hallmark of sulfur-metabolizing prokaryotes. Our detailed analyses suggested that the evolution of dsrAB was shaped by vertical inheritance and multiple horizontal gene transfer events and that selection pressure varied across distinct lineages. Dated phylogenetic trees indicated that key evolutionary events of dissimilatory sulfur-metabolizing prokaryotes were related to the Great Oxygenation Event (2.4-2.0 Ga) and several geological events in the "Boring Billion" (1.8-0.8 Ga), including the fragmentation of the Columbia supercontinent (approximately 1.6 Ga), the rapid increase in marine sulfate (1.3-1.2 Ga), and the Neoproterozoic glaciation event (approximately 1.0 Ga). We also proposed that the voluminous iron formations (approximately 1.88 Ga) might have induced the metabolic innovation of iron reduction. In summary, our study provides new insights into Dsr evolution and a systematic view of the coevolution of dissimilatory sulfur-metabolizing prokaryotes and the Earth's environment.},
}
@article {pmid39343029,
year = {2024},
author = {Fernie, AR and de Vries, S and de Vries, J},
title = {Evolution of plant metabolism: the state-of-the-art.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1914},
pages = {20230347},
pmid = {39343029},
issn = {1471-2970},
mesh = {*Plants/metabolism/genetics ; Biological Evolution ; Metabolic Networks and Pathways/genetics ; Evolution, Molecular ; },
abstract = {Immense chemical diversity is one of the hallmark features of plants. This chemo-diversity is mainly underpinned by a highly complex and biodiverse biochemical machinery. Plant metabolic enzymes originated and were inherited from their eukaryotic and prokaryotic ancestors and further diversified by the unprecedentedly high rates of gene duplication and functionalization experienced in land plants. Unlike prokaryotic microbes, which display frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO2 and have experienced relatively few gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner using existing networks as a starting point and under various evolutionary constraints. That said, until recently, the evolution of only a handful of metabolic traits had been extensively investigated and as such, the evolution of metabolism has received a fraction of the attention of, the evolution of development, for example. Advances in metabolomics and next-generation sequencing have, however, recently led to a deeper understanding of how a wide range of plant primary and specialized (secondary) metabolic pathways have evolved both as a consequence of natural selection and of domestication and crop improvement processes. This article is part of the theme issue 'The evolution of plant metabolism'.},
}
@article {pmid39339889,
year = {2024},
author = {Arhab, Y and Pestova, TV and Hellen, CUT},
title = {Translation of Overlapping Open Reading Frames Promoted by Type 2 IRESs in Avian Calicivirus Genomes.},
journal = {Viruses},
volume = {16},
number = {9},
pages = {},
pmid = {39339889},
issn = {1999-4915},
support = {5 R01 GM097014//NIH (NIGMS)/ ; 5 R35 GM122602//NIH (NIGMS)/ ; },
mesh = {*Open Reading Frames ; *Genome, Viral ; Animals ; *Internal Ribosome Entry Sites/genetics ; *Caliciviridae/genetics ; *Protein Biosynthesis ; RNA, Viral/genetics ; 5' Untranslated Regions/genetics ; Ribosomes/metabolism/genetics ; },
abstract = {Caliciviruses have positive-sense RNA genomes, typically with short 5'-untranslated regions (5'UTRs) that precede the long open reading frame 1 (ORF1). Exceptionally, some avian caliciviruses have long 5'UTRs containing a picornavirus-like internal ribosomal entry site (IRES), which was likely acquired by horizontal gene transfer. Here, we identified numerous additional avian calicivirus genomes with IRESs, predominantly type 2, and determined that many of these genomes contain a ~200-300 codon-long ORF (designated ORF1*) that overlaps the 5'-terminal region of ORF1. The activity of representative type 2 IRESs from grey teal calicivirus (GTCV) and Caliciviridae sp. isolate yc-13 (RaCV1) was confirmed by in vitro translation. Toeprinting showed that in cell-free extracts and in vitro reconstituted reactions, ribosomal initiation complexes assembled on the ORF1* initiation codon and at one or two AUG codons in ORF1 at the 3'-border and/or downstream of the IRES. Initiation at all three sites required eIF4A and eIF4G, which bound to a conserved region of the IRES; initiation on the ORF1* and principal ORF1 initiation codons involved eIF1/eIF1A-dependent scanning from the IRES's 3'-border. Initiation on these IRESs was enhanced by the IRES trans-acting factors (ITAFs) Ebp1/ITAF45, which bound to the apical subdomain Id of the IRES, and PTB (GTCV) or PCBP2 (RaCV1).},
}
@article {pmid39338985,
year = {2024},
author = {Sung, K and Nawaz, M and Park, M and Chon, J and Khan, SA and Alotaibi, K and Khan, AA},
title = {Comprehensive Genomic Analysis of Uropathogenic E. coli: Virulence Factors, Antimicrobial Resistance, and Mobile Genetic Elements.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {9},
pages = {},
pmid = {39338985},
issn = {2076-0817},
support = {E0770601//United States Food and Drug Administration/ ; },
mesh = {*Uropathogenic Escherichia coli/genetics/drug effects/pathogenicity ; Humans ; *Virulence Factors/genetics ; *Escherichia coli Infections/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology ; *Interspersed Repetitive Sequences/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; Genome, Bacterial ; Genomics/methods ; Urinary Tract Infections/microbiology/drug therapy ; Genomic Islands/genetics ; Whole Genome Sequencing ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Female ; Male ; },
abstract = {Our whole-genome sequencing analysis of sixteen uropathogenic E. coli isolates revealed a concerning picture of multidrug resistance and potentially virulent bacteria. All isolates belonged to four distinct clonal groups, with the highly prevalent ST131 lineage being associated with extensive antibiotic resistance and virulence factors. Notably, all isolates exhibited multidrug resistance, with some resistant to as many as 12 antibiotics. Fluoroquinolone resistance stemmed primarily from efflux pumps and mutations in gyrase and topoisomerase genes. Additionally, we identified genes encoding resistance to extended-spectrum cephalosporins, trimethoprim/sulfamethoxazole, and various heavy metals. The presence of diverse plasmids and phages suggests the potential for horizontal gene transfer and the dissemination of virulence factors. All isolates harbored genomic islands containing virulence factors associated with adhesion, biofilm formation, and invasion. Genes essential for iron acquisition, flagella biosynthesis, secretion systems, and toxin production were also prevalent. Adding further complexity to understanding the isolates' genetic makeup, we identified CRISPR-Cas systems. This study underscores the need for continued genomic surveillance in understanding the pathogenic mechanisms and resistance profiles of uropathogenic E. coli to aid in developing targeted therapeutic strategies.},
}
@article {pmid39338594,
year = {2024},
author = {Oliveira, M and Antunes, W and Mota, S and Madureira-Carvalho, &#xc1; and Dinis-Oliveira, RJ and Dias da Silva, D},
title = {An Overview of the Recent Advances in Antimicrobial Resistance.},
journal = {Microorganisms},
volume = {12},
number = {9},
pages = {},
pmid = {39338594},
issn = {2076-2607},
support = {UIDP/04378/2020, UIDB/04378/2020, LA/P/0140/2020, UIDB/50006//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; },
abstract = {Antimicrobial resistance (AMR), frequently considered a major global public health threat, requires a comprehensive understanding of its emergence, mechanisms, advances, and implications. AMR's epidemiological landscape is characterized by its widespread prevalence and constantly evolving patterns, with multidrug-resistant organisms (MDROs) creating new challenges every day. The most common mechanisms underlying AMR (i.e., genetic mutations, horizontal gene transfer, and selective pressure) contribute to the emergence and dissemination of new resistant strains. Therefore, mitigation strategies (e.g., antibiotic stewardship programs-ASPs-and infection prevention and control strategies-IPCs) emphasize the importance of responsible antimicrobial use and surveillance. A One Health approach (i.e., the interconnectedness of human, animal, and environmental health) highlights the necessity for interdisciplinary collaboration and holistic strategies in combating AMR. Advancements in novel therapeutics (e.g., alternative antimicrobial agents and vaccines) offer promising avenues in addressing AMR challenges. Policy interventions at the international and national levels also promote ASPs aiming to regulate antimicrobial use. Despite all of the observed progress, AMR remains a pressing concern, demanding sustained efforts to address emerging threats and promote antimicrobial sustainability. Future research must prioritize innovative approaches and address the complex socioecological dynamics underlying AMR. This manuscript is a comprehensive resource for researchers, policymakers, and healthcare professionals seeking to navigate the complex AMR landscape and develop effective strategies for its mitigation.},
}
@article {pmid39338472,
year = {2024},
author = {Gonzalez, V and Abarca-Hurtado, J and Arancibia, A and Claverías, F and Guevara, MR and Orellana, R},
title = {Novel Insights on Extracellular Electron Transfer Networks in the Desulfovibrionaceae Family: Unveiling the Potential Significance of Horizontal Gene Transfer.},
journal = {Microorganisms},
volume = {12},
number = {9},
pages = {},
pmid = {39338472},
issn = {2076-2607},
support = {11190863//ANID/Fondecyt/ ; 1211977//ANID/Fondecyt/ ; PAI79170091//ANID/ ; FOVI 230154//ANID/ ; Milenio-NCN2023_054//ANID/ ; Scholarship 21231799/2023//ANID/ ; },
abstract = {Some sulfate-reducing bacteria (SRB), mainly belonging to the Desulfovibrionaceae family, have evolved the capability to conserve energy through microbial extracellular electron transfer (EET), suggesting that this process may be more widespread than previously believed. While previous evidence has shown that mobile genetic elements drive the plasticity and evolution of SRB and iron-reducing bacteria (FeRB), few have investigated the shared molecular mechanisms related to EET. To address this, we analyzed the prevalence and abundance of EET elements and how they contributed to their differentiation among 42 members of the Desulfovibrionaceae family and 23 and 59 members of Geobacteraceae and Shewanellaceae, respectively. Proteins involved in EET, such as the cytochromes PpcA and CymA, the outer membrane protein OmpJ, and the iron-sulfur cluster-binding CbcT, exhibited widespread distribution within Desulfovibrionaceae. Some of these showed modular diversification. Additional evidence revealed that horizontal gene transfer was involved in the acquiring and losing of critical genes, increasing the diversification and plasticity between the three families. The results suggest that specific EET genes were widely disseminated through horizontal transfer, where some changes reflected environmental adaptations. These findings enhance our comprehension of the evolution and distribution of proteins involved in EET processes, shedding light on their role in iron and sulfur biogeochemical cycling.},
}
@article {pmid39337307,
year = {2024},
author = {Zhang, J and Zhu, S and Sun, J and Liu, Y},
title = {Bisphenol S Promotes the Transfer of Antibiotic Resistance Genes via Transformation.},
journal = {International journal of molecular sciences},
volume = {25},
number = {18},
pages = {},
pmid = {39337307},
issn = {1422-0067},
support = {BE2023332//Key R&amp;D Program of Jiangsu Province (Modern Agriculture)/ ; ZDYF2024SHFZ050//Science and Technology special fund of Hainan Province/ ; },
mesh = {*Phenols ; *Escherichia coli/genetics/drug effects ; *Sulfones/pharmacology ; *Plasmids/genetics ; Reactive Oxygen Species/metabolism ; Transformation, Bacterial ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Benzhydryl Compounds ; Citric Acid Cycle/drug effects/genetics ; },
abstract = {The antibiotic resistance crisis has seriously jeopardized public health and human safety. As one of the ways of horizontal transfer, transformation enables bacteria to acquire exogenous genes naturally. Bisphenol compounds are now widely used in plastics, food, and beverage packaging, and have become a new environmental pollutant. However, their potential relationship with the spread of antibiotic resistance genes (ARGs) in the environment remains largely unexplored. In this study, we aimed to assess whether the ubiquitous bisphenol S (BPS) could promote the transformation of plasmid-borne ARGs. Using plasmid pUC19 carrying the ampicillin resistance gene as an extracellular ARG and model microorganism E. coli DH5α as the recipient, we established a transformation system. Transformation assays revealed that environmentally relevant concentrations of BPS (0.1-10 μg/mL) markedly enhanced the transformation frequency of plasmid-borne ARGs into E. coli DH5α up to 2.02-fold. Fluorescent probes and transcript-level analyses suggest that BPS stimulated increased reactive oxygen species (ROS) production, activated the SOS response, induced membrane damage, and increased membrane fluidity, which weakened the barrier for plasmid transfer, allowing foreign DNA to be more easily absorbed. Moreover, BPS stimulates ATP supply by activating the tricarboxylic acid (TCA) cycle, which promotes flagellar motility and expands the search for foreign DNA. Overall, these findings provide important insight into the role of bisphenol compounds in facilitating the horizontal spread of ARGs and emphasize the need to monitor the residues of these environmental contaminants.},
}
@article {pmid39336804,
year = {2024},
author = {Opazo-Capurro, A and Xanthopoulou, K and Arazo Del Pino, R and González-Muñoz, P and Matus-Köhler, M and Amsteins-Romero, L and Jerez-Olate, C and Hormazábal, JC and Vera, R and Aguilera, F and Fuller, S and Higgins, PG and González-Rocha, G},
title = {Co-Occurrence of Two Plasmids Encoding Transferable blaNDM-1 and tet(Y) Genes in Carbapenem-Resistant Acinetobacter bereziniae.},
journal = {Genes},
volume = {15},
number = {9},
pages = {},
pmid = {39336804},
issn = {2073-4425},
support = {FONDECYT 1220708//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; FONDECYT Iniciacion 11190602//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; FONDEQUIP EQM200056//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; },
mesh = {*Plasmids/genetics ; *Acinetobacter/genetics/drug effects ; *beta-Lactamases/genetics ; Humans ; *Carbapenems/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Acinetobacter Infections/microbiology/drug therapy/epidemiology ; Bacterial Proteins/genetics ; Whole Genome Sequencing ; COVID-19 ; },
abstract = {Acinetobacter bereziniae has emerged as a significant human pathogen, acquiring multiple antibiotic resistance genes, including carbapenemases. This study focuses on characterizing the plasmids harboring the blaNDM-1 and tet(Y) genes in two carbapenem-resistant A. bereziniae isolates (UCO-553 and UCO-554) obtained in Chile during the COVID-19 pandemic. Methods: Antibiotic susceptibility testing was conducted on UCO-553 and UCO-554. Both isolates underwent whole-genome sequencing to ascertain their sequence type (ST), core genome multilocus sequence-typing (cgMLST) profile, antibiotic resistance genes, plasmids, and mobile genetic elements. Conjugation experiments were performed for both isolates. Results: Both isolates exhibited broad resistance, including resistance to carbapenems, third-generation cephalosporins, fluoroquinolones, tetracycline, cotrimoxazole, and aminoglycosides. Both isolates belong to sequence type ST[PAS]1761, with a difference of 17 out of 2984 alleles. Each isolate carried a 47,274 bp plasmid with blaNDM-1 and aph(3')-VI genes and two highly similar plasmids: a 35,184 bp plasmid with tet(Y), sul2, aph(6)-Id, and aph(3″)-Ib genes, and a 6078 bp plasmid containing the ant(2″)-Ia gene. Quinolone-resistance mutations were identified in the gyrA and parC genes of both isolates. Importantly, blaNDM-1 was located within a Tn125 transposon, and tet(Y) was embedded in a Tn5393 transposon. Conjugation experiments successfully transferred blaNDM-1 and tet(Y) into the A. baumannii ATCC 19606 strain, indicating the potential for horizontal gene transfer. Conclusions: This study highlights the critical role of plasmids in disseminating resistance genes in A. bereziniae and underscores the need for the continued genomic surveillance of this emerging pathogen. The findings emphasize the importance of monitoring A. bereziniae for its potential to cause difficult-to-treat infections and its capacity to spread resistance determinants against clinically significant antibiotics.},
}
@article {pmid39335078,
year = {2024},
author = {Tarrah, A and Zhang, D and Darvishzadeh, P and LaPointe, G},
title = {The Contribution of Dairy Bedding and Silage to the Dissemination of Genes Coding for Antimicrobial Resistance: A Narrative Review.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {9},
pages = {},
pmid = {39335078},
issn = {2079-6382},
abstract = {Antimicrobial resistance (AMR) is a concern in the dairy industry. Recent studies have indicated that bedding serves as a reservoir for antimicrobial-resistant bacteria and antimicrobial-resistance genes (ARGs), while silage has been proposed as another possible source. The impact of AMR in dairy farming can be significant, resulting in decreased productivity and economic losses for farmers. Several studies have highlighted the safety implications of AMR bacteria and genes in bedding and silage, emphasizing the need for further research on how housing, bedding, and silage management affect AMR in farm environments. Exposure to sub-lethal concentrations of antibiotics, such as those from contaminated bedding and silage, can prompt bacteria to develop resistance mechanisms. Thus, even if antimicrobial usage is diminished, ARGs may be maintained in the dairy farm environment. By implementing proactive measures to tackle AMR in dairy farming, we can take steps to preserve the health and productivity of dairy cattle while also protecting public health. This involves addressing the prudent use of antibiotics during production and promoting animal welfare, hygiene, and management practices in bedding and farm environments to minimize the risk of AMR development and spread. This narrative review compiles the growing research, positioning the contribution of bedding and silage to the prevalence and dissemination of AMR, which can elicit insights for researchers and policymakers.},
}
@article {pmid39334999,
year = {2024},
author = {Mitchell, TM and Ho, T and Salinas, L and VanderYacht, T and Walas, N and Trueba, G and Graham, JP},
title = {Analysis of Antibiotic Resistance Genes (ARGs) across Diverse Bacterial Species in Shrimp Aquaculture.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {9},
pages = {},
pmid = {39334999},
issn = {2079-6382},
abstract = {There is little information available on antibiotic resistance (ABR) within shrimp aquaculture environments. The aim of this study was to investigate the presence of antibiotic resistance genes (ARGs) in shrimp farming operations in Atacames, Ecuador. Water samples (n = 162) and shrimp samples (n = 54) were collected from three shrimp farming operations. Samples were cultured and a subset of isolates that grew in the presence of ceftriaxone, a third-generation cephalosporin, were analyzed using whole-genome sequencing (WGS). Among the sequenced isolates (n = 44), 73% of the isolates contained at least one ARG and the average number of ARGs per isolate was two, with a median of 3.5 ARGs. Antibiotic resistance genes that confer resistance to the β-lactam class of antibiotics were observed in 65% of the sequenced isolates from water (20/31) and 54% of the isolates from shrimp (7/13). We identified 61 different ARGs across the 44 sequenced isolates, which conferred resistance to nine antibiotic classes. Over half of all sequenced isolates (59%, n = 26) carried ARGs that confer resistance to more than one class of antibiotics. ARGs for certain antibiotic classes were more common, including beta-lactams (26 ARGs); aminoglycosides (11 ARGs); chloramphenicol (three ARGs); and trimethoprim (four ARGs). Sequenced isolates consisted of a diverse array of bacterial orders and species, including Escherichia coli (48%), Klebsiella pneumoniae (7%), Aeromonadales (7%), Pseudomonadales (16%), Enterobacter cloacae (2%), and Citrobacter freundii (2%). Many ARGs were shared across diverse species, underscoring the risk of horizontal gene transfer in these environments. This study indicated the widespread presence of extended-spectrum β-lactamase (ESBL) genes in shrimp aquaculture, including blaCTX-M, blaSHV, and blaTEM genes. Increased antibiotic resistance surveillance of shrimp farms and identification of aquaculture operation-level risk factors, such as antibiotic use, will likely be important for mitigating the spread of ARGs of clinical significance.},
}
@article {pmid39334992,
year = {2024},
author = {Liu, L and Zou, X and Cheng, Y and Li, H and Zhang, X and Yuan, Q},
title = {Contrasting Dynamics of Intracellular and Extracellular Antibiotic Resistance Genes in Response to Nutrient Variations in Aquatic Environments.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {9},
pages = {},
pmid = {39334992},
issn = {2079-6382},
support = {No. 42377436 and 42177348//National Natural Science Foundation of China/ ; 2022YFC3205400//China National Key R&amp;D Program/ ; },
abstract = {The propagation of antibiotic resistance in environments, particularly aquatic environments that serve as primary pathways for antibiotic resistance genes (ARGs), poses significant health risks. The impact of nutrients, as key determinants of bacterial growth and metabolism, on the propagation of ARGs, particularly extracellular ARGs (eARGs), remains poorly understood. In this study, we collected microorganisms from the Yangtze River and established a series of microcosms to investigate how variations in nutrient levels and delivery frequency affect the relative abundance of intracellular ARGs (iARGs) and eARGs in bacterial communities. Our results show that the relative abundance of 7 out of 11 representative eARGs in water exceeds that of iARGs, while 8 iARGs dominate in biofilms. Notably, iARGs and eARGs consistently exhibited opposite responses to nutrient variation. When nutrient levels increased, iARGs in the water also increased, with the polluted group (COD = 333.3 mg/L, COD:N:P = 100:3:0.6, m/m) and the eutrophic group (COD = 100 mg/L, COD:N:P = 100:25:5, m/m) showing 1.2 and 3.2 times higher levels than the normal group (COD = 100 mg/L, COD:N:P = 100:10:2, m/m), respectively. In contrast, eARGs decreased by 6.7% and 8.4% in these groups. On the other hand, in biofilms, higher nutrient levels led to an increase in eARGs by 1.5 and 1.7 times, while iARGs decreased by 17.5% and 50.1% in the polluted and eutrophic groups compared to the normal group. Moreover, while increasing the frequency of nutrient delivery (from 1 time/10 d to 20 times/10 d) generally did not favor iARGs in either water or biofilm, it selectively enhanced eARGs in both. To further understand these dynamics, we developed an ARGs-nutrient model by integrating the Lotka-Volterra and Monod equations. The results highlight the complex interplay of bacterial growth, nutrient availability, and mechanisms such as horizontal gene transfer and secretion influencing ARGs' propagation, driving the opposite trend between these two forms of ARGs. This contrasting response between iARGs and eARGs contributes to a dynamic balance that stabilizes bacterial resistance levels amid nutrient fluctuations. This study offers helpful implications regarding the persistence of bacterial resistance in the environment.},
}
@article {pmid39329926,
year = {2024},
author = {Syed, K},
title = {Ferredoxins: Functions, Evolution, Potential Applications, and Challenges of Subtype Classification.},
journal = {Current issues in molecular biology},
volume = {46},
number = {9},
pages = {9659-9673},
pmid = {39329926},
issn = {1467-3045},
abstract = {Ferredoxins are proteins found in all biological kingdoms and are involved in essential biological processes including photosynthesis, lipid metabolism, and biogeochemical cycles. Ferredoxins are classified into different groups based on the iron-sulfur (Fe-S) clusters that they contain. A new subtype classification and nomenclature system, based on the spacing between amino acids in the Fe-S binding motif, has been proposed in order to better understand ferredoxins' biological diversity and evolutionary linkage across different organisms. This new classification system has revealed an unparalleled diversity between ferredoxins and has helped identify evolutionarily linked ferredoxins between species. The current review provides the latest insights into ferredoxin functions and evolution, and the new subtype classification, outlining their potential biotechnological applications and the future challenges in streamlining the process.},
}
@article {pmid39328914,
year = {2024},
author = {Yan, J and Doublet, B and Wiedemann, A},
title = {Trends in horizontal gene transfer research in Salmonella antimicrobial resistance: a bibliometric analysis.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1439664},
pmid = {39328914},
issn = {1664-302X},
abstract = {Horizontal gene transfer (HGT) favors the acquisition and spread of antimicrobial resistance (AMR) genes in Salmonella, making it a major public health concern. We performed a bibliometric analysis to provide the current landscape of HGT in research on Salmonella AMR and identify emerging trends and potential research directions for the future. Data were collected from the Web of Science Core Collection and limited to articles and reviews published between 1999 and 2024 in English. VOSviewer 1.6.19 and CiteSpace 6.2.R1 software were used to conduct bibliometric analysis and visualize co-occurring keywords. A total of 1,467 publications were retrieved for analysis. American researchers contributed the most articles (n = 310). In the meantime, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement have the highest citation/publication rate of 85.6. Recent studies have focused on the application of whole genome sequencing (WGS), Salmonella quinolone and colistin resistance, and the biocontrol of Salmonella AMR. These findings provide new insights into the role of HGT and help identify new targets for controlling the spread of AMR in Salmonella populations.},
}
@article {pmid39327210,
year = {2025},
author = {García-Lozano, M and Salem, H},
title = {Microbial bases of herbivory in beetles.},
journal = {Trends in microbiology},
volume = {33},
number = {2},
pages = {151-163},
doi = {10.1016/j.tim.2024.08.004},
pmid = {39327210},
issn = {1878-4380},
mesh = {Animals ; *Coleoptera/microbiology/physiology ; *Herbivory/physiology ; Gene Transfer, Horizontal ; Symbiosis ; Bacteria/genetics/metabolism ; *Microbiota ; },
abstract = {The ecological radiation of herbivorous beetles is among the most successful in the animal kingdom. It coincided with the rise and diversification of flowering plants, requiring beetles to adapt to a nutritionally imbalanced diet enriched in complex polysaccharides and toxic secondary metabolites. In this review, we explore how beetles overcame these challenges by coopting microbial genes, enzymes, and metabolites, through both horizontal gene transfer (HGT) and symbiosis. Recent efforts revealed the functional convergence governing both processes and the unique ways in which microbes continue to shape beetle digestion, development, and defense. The development of genetic and experimental tools across a diverse set of study systems has provided valuable mechanistic insights into how microbes spurred metabolic innovation and facilitated an herbivorous transition in beetles.},
}
@article {pmid39326418,
year = {2024},
author = {Liu, Y and Miao, B and Li, W and Hu, X and Bai, F and Abuduresule, Y and Liu, Y and Zheng, Z and Wang, W and Chen, Z and Zhu, S and Feng, X and Cao, P and Ping, W and Yang, R and Dai, Q and Liu, F and Tian, C and Yang, Y and Fu, Q},
title = {Bronze Age cheese reveals human-Lactobacillus interactions over evolutionary history.},
journal = {Cell},
volume = {187},
number = {21},
pages = {5891-5900.e8},
doi = {10.1016/j.cell.2024.08.008},
pmid = {39326418},
issn = {1097-4172},
mesh = {Humans ; *Cheese/microbiology ; *Lactobacillus/genetics ; Kefir/microbiology ; History, Ancient ; Phylogeny ; China ; Biological Evolution ; Fermentation ; Asia, Eastern ; },
abstract = {Despite the long history of consumption of fermented dairy, little is known about how the fermented microbes were utilized and evolved over human history. Here, by retrieving ancient DNA of Bronze Age kefir cheese (∼3,500 years ago) from the Xiaohe cemetery, we explored past human-microbial interactions. Although it was previously suggested that kefir was spread from the Northern Caucasus to Europe and other regions, we found an additional spreading route of kefir from Xinjiang to inland East Asia. Over evolutionary history, the East Asian strains gained multiple gene clusters with defensive roles against environmental stressors, which can be a result of the adaptation of Lactobacillus strains to various environmental niches and human selection. Overall, our results highlight the role of past human activities in shaping the evolution of human-related microbes, and such insights can, in turn, provide a better understanding of past human behaviors.},
}
@article {pmid39324609,
year = {2024},
author = {Liu, QH and Yuan, L and Li, ZH and Leung, KMY and Sheng, GP},
title = {Natural Organic Matter Enhances Natural Transformation of Extracellular Antibiotic Resistance Genes in Sunlit Water.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {40},
pages = {17990-17998},
doi = {10.1021/acs.est.4c08211},
pmid = {39324609},
issn = {1520-5851},
mesh = {*Drug Resistance, Microbial/genetics ; *Sunlight ; Anti-Bacterial Agents/pharmacology ; Reactive Oxygen Species/metabolism ; },
abstract = {Antibiotic resistance genes (ARGs) as emerging environmental contaminants exacerbate the risk of spreading antibiotic resistance. Natural organic matter (NOM) is ubiquitous in aquatic environments and plays a crucial role in biogeochemical cycles. However, its impact on the dissemination of extracellular antibiotic resistance genes (eARGs) under sunlight exposure remains elusive. This study reveals that environmentally relevant levels of NOM (0.1-20 mg/L) can significantly enhance the natural transformation frequency of the model bacterium Acinetobacter baylyi ADP1 by up to 7.6-fold under simulated sunlight. Similarly, this enhancement was consistently observed in natural water and wastewater systems. Further mechanism analysis revealed that reactive oxygen species (ROS) generated by NOM under sunlight irradiation, primarily singlet oxygen and hydroxyl radicals, play a crucial role in this process. These ROS induce intracellular oxidative stress and elevated cellular membrane permeability, thereby indirectly boosting ATP production and enhancing cell competence of extracellular DNA uptake and integration. Our findings highlight a previously underestimated role of natural factors in the dissemination of eARGs within aquatic ecosystems and deepen our understanding of the complex interplay between NOM, sunlight, and microbes in environmental water bodies. This underscores the importance of developing comprehensive strategies to mitigate the spread of antibiotic resistance in aquatic environments.},
}
@article {pmid39322056,
year = {2024},
author = {Chen, J and Lin, Y and Zhu, Y and Zhang, Y and Qian, Q and Chen, C and Xie, S},
title = {Spatiotemporal profiles and underlying mechanisms of the antibiotic resistome in two water-diversion lakes.},
journal = {Environmental research},
volume = {263},
number = {Pt 1},
pages = {120051},
doi = {10.1016/j.envres.2024.120051},
pmid = {39322056},
issn = {1096-0953},
mesh = {*Lakes/microbiology ; China ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Seasons ; Drug Resistance, Microbial/genetics ; Spatio-Temporal Analysis ; Environmental Monitoring ; Bacteria/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; },
abstract = {Human-induced interventions have altered the local characteristics of the lake ecosystems through changes in hydraulic exchange, which in turn impacts the ecological processes of antibiotic resistance genes (ARGs) in the lakes. However, the current understanding of the spatiotemporal patterns and driving factors of ARGs in water-diversion lakes is still seriously insufficient. In the present study, we investigated antibiotic resistome in the main regulation and storage hubs, namely Nansi Lake and Dongping Lake, of the eastern part of the South-to-North Water Diversion project in Shandong Province (China) using a metagenomic-based approach. A total of 653 ARG subtypes belonging to 25 ARG types were detected with a total abundance of 0.125-0.390 copies/cell, with the dominance of bacitracin, multidrug, and macrolide-lincosamide streptogramin resistance genes. The ARG compositions were sensitive to seasonal variation and also interfered by artificial regulation structures along the way. Human pathogenic bacteria such as Acinetobacter calcoaceticus, Acinetobacter lwoffii, Klebsiella pneumoniae, along with the multidrug resistance genes they carried, were the focus of risk control in the two studied lakes, especially in summer. Plasmids were the key mobile genetic elements (MGEs) driving the horizontal gene transfer of ARGs, especially multidrug and sulfonamide resistance genes. The null model revealed that stochastic process was the main driver of ecological drift for ARGs in the lakes. The partial least squares structural equation model further determined that seasonal changes of pH and temperature drove a shift in the bacterial community, which in turn shaped the profile of ARGs by altering the composition of MGEs, antibacterial biocide- and metal-resistance genes (BMGs), and virulence factor genes (VFGs). Our results highlighted the importance of seasonal factors in determining the water transfer period. These findings can aid in a deeper understanding of the spatiotemporal variations of ARGs in lakes and their driving factors, offering a scientific basis for antibiotic resistance management.},
}
@article {pmid39321940,
year = {2024},
author = {Wang, P and Li, L and Zhang, Y and Ren, D and Feng, Y and Li, X and Wu, D and Xie, B and Ma, J},
title = {Triclosan facilitates the dissemination of antibiotic resistance genes during anaerobic digestion: Focusing on horizontal transfer and microbial response.},
journal = {Bioresource technology},
volume = {413},
number = {},
pages = {131522},
doi = {10.1016/j.biortech.2024.131522},
pmid = {39321940},
issn = {1873-2976},
mesh = {*Triclosan/pharmacology ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Bioreactors ; },
abstract = {The present study aims to investigate the mechanism by which triclosan influences the dissemination of antibiotic resistance genes (ARGs) during the whole anaerobic digestion process. qPCR and metagenomic analyses revealed that triclosan facilitated ARGs dissemination in a dose- and time-dependent manner. Furthermore, integrons exhibited a significant correlation with the majority of quantified ARGs, and various ARGs were frequently linked on integron gene cassettes. Microbial community and redundancy analyses indicated that triclosan altered the components of dominant ARGs hosts Firmicutes, Synergistetes and Bacteroidetes. Path modeling analysis confirmed integrons were the main driving force for facilitating ARGs dissemination. The promoted ARGs dissemination may be associated with the increased reactive oxygen species generation, cell membrane permeability, close-connected the ARGs transfer related regulatory proteins induced by triclosan. This study broadens the understanding of triclosan facilitates ARGs dissemination through anaerobic treatment, the strategies for preventing potential risks should be proposed in practice.},
}
@article {pmid39321479,
year = {2024},
author = {Rong, L and Wu, L and Zong, L and Wang, W and Xiao, Y and Yang, C and Pan, H and Zou, X},
title = {Evolution of the Black solider fly larvae gut antibiotic resistome during kitchen waste disposal.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135878},
doi = {10.1016/j.jhazmat.2024.135878},
pmid = {39321479},
issn = {1873-3336},
mesh = {Animals ; *Larva/drug effects ; *Gastrointestinal Microbiome/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; Refuse Disposal ; Gene Transfer, Horizontal ; Diptera/genetics/microbiology/drug effects ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; },
abstract = {Kitchen waste (KW) is an important reservoir of antibiotic resistance genes (ARGs). Black solider fly larvae (BSFL) are extensively employed in KW disposal, closely linking to their robust gut microbes. However, antibiotic resistome in BSFL gut during the KW disposal processes and the mechanism remain unclear. In the present study, the antibiotic resistome in BSFL gut within the 12 days KW disposal processes were investigated. Results showed that, ARGs abundance initially increased and subsequently decreased, the five most prevalent core ARG classes were tetracycline, aminoglycoside, cephalosporin, lincosamide and multidrug. A total of 7 MGE types were observed and the horizontal gene transfer (HGT) of ARGs was predominantly mediated by plasmids. Host microbes were mainly categorized into Proteobacteria (98.12 %) and their assemblies were mainly classified into the deterministic processes. To elucidate the driving mechanisms, the mantel test and the structural equation model (SEM) were developed. Results indicated that microbial functions (0.912, p < 0.0001) and microbial community (1.014, p = 0.036), consistently showed very significant relationships with the patterns of ARGs, which presented higher direct effects than indirect effects. Overall, this study makes an initial contribution to a more deepgoing comprehension of the gut antibiotic resistome of BSFL during KW disposal.},
}
@article {pmid39319368,
year = {2024},
author = {Pierpont, CL and Baroch, JJ and Church, MJ and Miller, SR},
title = {Idiosyncratic genome evolution of the thermophilic cyanobacterium Synechococcus at the limits of phototrophy.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39319368},
issn = {1751-7370},
support = {IOS-1755407//National Science Foundation/ ; },
mesh = {*Synechococcus/genetics ; *Genome, Bacterial ; *Evolution, Molecular ; *Phylogeny ; Phototrophic Processes ; Gene Transfer, Horizontal ; Thermotolerance/genetics ; Hot Temperature ; },
abstract = {Thermophilic microorganisms are expected to have smaller cells and genomes compared with mesophiles, a higher proportion of horizontally acquired genes, and distinct nucleotide and amino acid composition signatures. Here, we took an integrative approach to investigate these apparent correlates of thermophily for Synechococcus A/B cyanobacteria, which include the most heat-tolerant phototrophs on the planet. Phylogenomics confirmed a unique origin of different thermotolerance ecotypes, with low levels of continued gene flow between ecologically divergent but overlapping populations, which has shaped the distribution of phenotypic traits along these geothermal gradients. More thermotolerant strains do have smaller genomes, but genome reduction is associated with a decrease in community richness and metabolic diversity, rather than with cell size. Horizontal gene transfer played only a limited role during Synechococcus evolution, but, the most thermotolerant strains have acquired a Thermus tRNA modification enzyme that may stabilize translation at high temperatures. Although nucleotide base composition was not associated with thermotolerance, we found a general replacement of aspartate with glutamate, as well as a dramatic remodeling of amino acid composition at the highest temperatures that substantially differed from previous predictions. We conclude that Synechococcus A/B genome diversification largely does not conform to the standard view of temperature adaptation. In addition, carbon fixation was more thermolabile than photosynthetic oxygen evolution for the most thermotolerant strains compared with less tolerant lineages. This suggests that increased flow of reducing power generated during the light reactions to an electron sink(s) beyond carbon dioxide has emerged during temperature adaptation of these bacteria.},
}
@article {pmid39316921,
year = {2024},
author = {Liu, Z and Feng, L and Li, B and Lü, C and Sun, J and Giannakis, S},
title = {Crouching bacteria, hidden tetA genes in natural waters: Intracellular damage via double persulfate activation (UVA/Fe[2+]/PDS) effectively alleviates the spread of antibiotic resistance.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135854},
doi = {10.1016/j.jhazmat.2024.135854},
pmid = {39316921},
issn = {1873-3336},
mesh = {*Ultraviolet Rays ; *Sulfates/chemistry ; Drug Resistance, Bacterial/genetics/drug effects ; Anti-Bacterial Agents/pharmacology/chemistry/toxicity ; Escherichia coli/drug effects/genetics ; Iron/chemistry ; Gene Transfer, Horizontal ; Bacteria/drug effects/genetics ; Water Microbiology ; Rivers/chemistry/microbiology ; Peroxides ; },
abstract = {In this study, we elucidated the chemical and biological inactivation mechanisms of peroxydisulfate (PDS) activated by UVA and Fe[2+] (UVA/Fe[2+]/PDS) in wild-type antibiotic-resistant bacteria (ARB) isolated from a river in Inner Mongolia. Among the screened wild-type ARB, the relative abundance of unidentified Enterobacteriaceae, Stenotrophomonas, and Ralstonia was high. A ratio of 1:1 for Fe[2+] and PDS under 18 W·m[-2] UVA radiation (sunny days) completely inactivated the environmental ARB isolates. In the macro view of the inactivation process, Fe[2+] first activates PDS rapidly, and later the UVA energy accumulated starts to activate PDS; HO• then becomes the main active species at a rate-limiting step. From a micro perspective, damage to the cell wall, intracellular proteins, inactivation of antioxidant enzymes, and genetic material degradation are the inactivation series of events by UVA/Fe[2+]/PDS, contributing to the 97.8 % inactivation of ARB at the initial stage. No regrowth of sublethal ARBs was observed. The transfer of tetracycline resistance genes from ARB to lab E. coli was evaluated by horizontal gene transfer (HGT), in which no HGT occurred when ARB was eliminated by UVA/Fe[2+]/PDS. Moreover, the sulfate and iron residuals in the effluents of treated water were lower than the drinking water standards. In summary, PDS, UVA, and Fe[2+] activation effectively inactivated wild ARB with a low concentration of reagents, while inhibiting their regrowth and spread of resistance due to the contribution of intracellular inactivation pathways.},
}
@article {pmid39316269,
year = {2024},
author = {Wang, L and Yu, L and Cai, B},
title = {Characteristics of tetracycline antibiotic resistance gene enrichment and migration in soil-plant system.},
journal = {Environmental geochemistry and health},
volume = {46},
number = {11},
pages = {427},
pmid = {39316269},
issn = {1573-2983},
support = {LH2023C088//the Natural Science Foundation of Heilongjiang Province of China/ ; LH2023C088//the Natural Science Foundation of Heilongjiang Province of China/ ; LH2023C088//the Natural Science Foundation of Heilongjiang Province of China/ ; HST2022TR002//the Scientific Research Project on Ecological Environmental Protection in Heilongjiang Province/ ; HST2022TR002//the Scientific Research Project on Ecological Environmental Protection in Heilongjiang Province/ ; HST2022TR002//the Scientific Research Project on Ecological Environmental Protection in Heilongjiang Province/ ; 2023SYSJJ15//2023 Open Fund Subjects of the Key Laboratory of Agro-ecological Safety in Hebei Province Project/ ; 2023SYSJJ15//2023 Open Fund Subjects of the Key Laboratory of Agro-ecological Safety in Hebei Province Project/ ; 2023SYSJJ15//2023 Open Fund Subjects of the Key Laboratory of Agro-ecological Safety in Hebei Province Project/ ; },
mesh = {*Soil Microbiology ; *Soil Pollutants ; *Tetracycline Resistance/genetics ; *Gene Transfer, Horizontal ; Plants/microbiology ; Humans ; Bacteria/genetics/drug effects ; Soil/chemistry ; Tetracycline/pharmacology ; },
abstract = {Tetracycline Resistance Genes (TRGs) have received widespread attention in recent years, as they are a novel environmental pollutant that can rapidly accumulate and migrate in soil plant systems through horizontal gene transfer (HGT), posing a potential threat to food safety and public health. This article systematically reviews the pollution sources, enrichment, and migration characteristics of TRGs in soil. The main sources of TRGs include livestock manure and contaminated wastewater, especially in intensive farming environments where TRGs pollution is more severe. In soil, TRGs diffuse horizontally between bacteria and migrate to plant tissues through mechanisms such as plasmid conjugation, integron mediation, and phage transduction. The migration of TRGs is not limited to the soil interior, and increasing evidence suggests that they can also enter the plant system through plant root absorption and the HGT pathway of endophytic bacteria, ultimately accumulating in plant roots, stems, leaves, fruits, and other parts. This process has a direct impact on human health, especially when TRGs are found in crops such as vegetables, which may be transmitted to the human body through the food chain. In addition, this article also deeply analyzed various factors that affect the migration of TRGs, including the residual level of tetracycline in soil, the type and concentration of microorganisms, heavy metal pollution, and the presence of new pollutants such as microplastics. These factors significantly affect the enrichment rate and migration mode of TRGs in soil. In addition, two technologies that can effectively eliminate TRGs in livestock breeding environments were introduced, providing reference for healthy agricultural production. The article concludes by summarizing the shortcomings of current research on TRGs, particularly the limited understanding of TRG migration pathways and their impact mechanisms. Future research should focus on revealing the migration mechanisms of TRGs in soil plant systems and developing effective control and governance measures to reduce the environmental transmission risks of TRGs and ensure the safety of ecosystems and human health.},
}
@article {pmid39312572,
year = {2024},
author = {Gonçalves, C and Harrison, MC and Steenwyk, JL and Opulente, DA and LaBella, AL and Wolters, JF and Zhou, X and Shen, XX and Groenewald, M and Hittinger, CT and Rokas, A},
title = {Diverse signatures of convergent evolution in cactus-associated yeasts.},
journal = {PLoS biology},
volume = {22},
number = {9},
pages = {e3002832},
pmid = {39312572},
issn = {1545-7885},
support = {R01 AI153356/AI/NIAID NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; },
mesh = {*Cactaceae/microbiology/genetics ; Phylogeny ; Yeasts/genetics ; Genome, Fungal/genetics ; Biological Evolution ; Evolution, Molecular ; Phenotype ; Gene Transfer, Horizontal ; Thermotolerance/genetics ; Ascomycota/genetics/pathogenicity ; Machine Learning ; },
abstract = {Many distantly related organisms have convergently evolved traits and lifestyles that enable them to live in similar ecological environments. However, the extent of phenotypic convergence evolving through the same or distinct genetic trajectories remains an open question. Here, we leverage a comprehensive dataset of genomic and phenotypic data from 1,049 yeast species in the subphylum Saccharomycotina (Kingdom Fungi, Phylum Ascomycota) to explore signatures of convergent evolution in cactophilic yeasts, ecological specialists associated with cacti. We inferred that the ecological association of yeasts with cacti arose independently approximately 17 times. Using a machine learning-based approach, we further found that cactophily can be predicted with 76% accuracy from both functional genomic and phenotypic data. The most informative feature for predicting cactophily was thermotolerance, which we found to be likely associated with altered evolutionary rates of genes impacting the cell envelope in several cactophilic lineages. We also identified horizontal gene transfer and duplication events of plant cell wall-degrading enzymes in distantly related cactophilic clades, suggesting that putatively adaptive traits evolved independently through disparate molecular mechanisms. Notably, we found that multiple cactophilic species and their close relatives have been reported as emerging human opportunistic pathogens, suggesting that the cactophilic lifestyle-and perhaps more generally lifestyles favoring thermotolerance-might preadapt yeasts to cause human disease. This work underscores the potential of a multifaceted approach involving high-throughput genomic and phenotypic data to shed light onto ecological adaptation and highlights how convergent evolution to wild environments could facilitate the transition to human pathogenicity.},
}
@article {pmid39309771,
year = {2024},
author = {Westerström, P and Gabrielsen Ås, C and Bak Dragsted, U},
title = {Characterising virulence in a nontoxigenic non-O1/non-O139 Vibrio cholerae isolate imported from Vietnam.},
journal = {Heliyon},
volume = {10},
number = {18},
pages = {e37205},
pmid = {39309771},
issn = {2405-8440},
abstract = {Vibrio cholerae is a major human pathogen that can cause life-threatening acute diarrhea. V. cholerae are classified according to O-antigen polysaccharide outer membrane properties, where the serotypes O1 and O139 are strains that cause pandemics and epidemics while non-O1/non-O139 usually cause mild disease. The dynamic evolution of V. cholerae involves acquisition of new virulence factors through horizontal gene transfer and formerly nontoxigenic serogroups are increasingly being reported to cause severe forms of human disease. In this study we have serotyped one isolate (ST588-CPH) of imported V. cholerae from Vietnam to Denmark and performed whole genome sequencing to identify known virulence genes and furthermore studied the pattern of virulence in closely related pathogenic strains of V. cholerae. ST558-CPH was found to be a non-O1/non-O139 strain. Initial analysis from the whole genome sequencing gave a 96,6 % match to the O139-specific wbfZ gene, but in a second analysis with a higher identification threshold, the wbfZ gene was absent. We suggest a "de novo" display of a database misannotation, which explains the conflicting results. The MLST analysis revealed that the isolate belongs to the nontoxigenic non-O1/non-O139 sequence type ST558. ST558 has recently been reported as a sequence type forming a cluster of ST's that should be monitored, as it has shown to have virulence causing moderate to severe illness. Our analysis of virulence genes identified MakA, a recently discovered toxin, which seems to be generally present in both toxigenic and nontoxigenic strains.},
}
@article {pmid39308980,
year = {2024},
author = {Mendoza, H and Lamb, EA and Thomas, J and Tavares, DG and Schroeder, LA and Müller, C and Agrawal, N and Schirawski, J and Perlin, MH},
title = {Comparative mitogenomic analysis of Sporisorium reilianum f. sp. zeae suggests recombination events during its evolutionary history.},
journal = {Frontiers in physiology},
volume = {15},
number = {},
pages = {1264359},
pmid = {39308980},
issn = {1664-042X},
abstract = {INTRODUCTION: Modern understanding of the concept of genetic diversity must include the study of both nuclear and organellar DNA, which differ greatly in terms of their structure, organization, gene content and distribution. This study comprises an analysis of the genetic diversity of the smut fungus Sporisorium reilianum f. sp. zeae from a mitochondrial perspective.<br><br>METHODS: Whole-genome sequencing data was generated from biological samples of S. reilianum collected from different geographical regions. Multiple sequence alignment and gene synteny analysis were performed to further characterize genetic diversity in the context of mitogenomic polymorphisms.<br><br>RESULTS: Mitochondria of strains collected in China contained unique sequences. The largest unique sequence stretch encompassed a portion of cox1, a mitochondrial gene encoding one of the subunits that make up complex IV of the mitochondrial electron transport chain. This unique sequence had high percent identity to the mitogenome of the related species Sporisorium scitamineum and Ustilago bromivora.<br><br>DISCUSSION: The results of this study hint at potential horizontal gene transfer or mitochondrial genome recombination events during the evolutionary history of basidiomycetes. Additionally, the distinct polymorphic region detected in the Chinese mitogenome provides the ideal foundation to develop a diagnostic method to discern between mitotypes and enhance knowledge on the genetic diversity of this organism.},
}
@article {pmid39306135,
year = {2024},
author = {Wang, B and Farhan, MHR and Yuan, L and Sui, Y and Chu, J and Yang, X and Li, Y and Huang, L and Cheng, G},
title = {Transfer dynamics of antimicrobial resistance among gram-negative bacteria.},
journal = {The Science of the total environment},
volume = {954},
number = {},
pages = {176347},
doi = {10.1016/j.scitotenv.2024.176347},
pmid = {39306135},
issn = {1879-1026},
mesh = {*Gram-Negative Bacteria/drug effects ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Bacteriophages/physiology ; Plasmids/genetics ; },
abstract = {Antimicrobial resistance (AMR) in gram-negative bacteria (GNBs) is a significant global health concern, exacerbated by mobile genetic elements (MGEs). This review examines the transfer of antibiotic resistance genes (ARGs) within and between different species of GNB facilitated by MGEs, focusing on the roles of plasmids and phages. The impact of non-antibiotic chemicals, environmental factors affecting ARG transfer frequency, and underlying molecular mechanisms of bacterial resistance evolution are also discussed. Additionally, the study critically assesses the impact of fitness costs and compensatory evolution driven by MGEs in host organisms, shedding light on the transfer frequency of ARGs and host evolution within ecosystems. Overall, this comprehensive review highlights the factors and mechanisms influencing ARG movement among diverse GNB species and underscores the importance of implementing holistic One-Health strategies to effectively address the escalating public health challenges associated with AMR.},
}
@article {pmid39305601,
year = {2024},
author = {Wang, F and Hu, Z and Wang, W and Wang, J and Xiao, Y and Shi, J and Wang, C and Mai, W and Li, G and An, T},
title = {Selective enrichment of high-risk antibiotic resistance genes and priority pathogens in freshwater plastisphere: Unique role of biodegradable microplastics.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135901},
doi = {10.1016/j.jhazmat.2024.135901},
pmid = {39305601},
issn = {1873-3336},
mesh = {*Microplastics/toxicity ; *Drug Resistance, Microbial/genetics ; *Fresh Water/microbiology ; Water Pollutants, Chemical/toxicity ; Biofilms/drug effects ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Virulence Factors/genetics ; Polyhydroxyalkanoates ; Polyesters/metabolism ; Microbiota/drug effects/genetics ; Biodegradation, Environmental ; Biodegradable Plastics ; },
abstract = {Microplastics (MPs) has been concerned as emerging vectors for spreading antibiotic resistance and pathogenicity in aquatic environments, but the role of biodegradable MPs remains largely unknown. Herein, field in-situ incubation method combined with metagenomic sequencing were employed to reveal the dispersal characteristics of microbial community, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factors (VFs) enriched by MPs biofilms. Results showed that planktonic microbes were more prone to enrich on biodegradable MPs (i.e., polyhydroxyalkanoate and polylactic acid) than non-biodegradable MPs (i.e., polystyrene, polypropylene and polyethylene). Distinctive microbial communities were assembled on biodegradable MPs, and the abundances of ARGs, MGEs, and VFs on biofilms of biodegradable MPs were much higher than that of non-biodegradable MPs. Notably, network analysis showed that the biodegradable MPs selectively enriched pathogens carrying ARGs, VFs and MGEs concurrently, suggesting a strong potential risks of co-spreading antibiotic resistance and pathogenicity through horizontal gene transfer. According to WHO priority list of Antibiotic Resistant Pathogens (ARPs) and ARGs health risk assessment framework, the highest abundances of Priority 1 ARPs and Rank I risk ARGs were found on polylactic acid and polyhydroxyalkanoate, respectively. These findings elucidate the unique and critical role of biodegradable MPs for selective enrichment of high-risk ARGs and priority pathogens in freshwater environments.},
}
@article {pmid39305593,
year = {2024},
author = {Shen, Y and Zhang, B and Yao, Y and Wang, H and Chen, Z and Hao, A and Guo, P},
title = {Insights into the interactions of plant-associated bacteria and their role in the transfer of antibiotic resistance genes from soil to plant.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135881},
doi = {10.1016/j.jhazmat.2024.135881},
pmid = {39305593},
issn = {1873-3336},
mesh = {*Soil Microbiology ; *Rhizosphere ; *Bacteria/genetics/metabolism/classification ; *Plant Roots/microbiology ; Plants/microbiology ; Microbiota ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Plant Shoots/microbiology/growth &amp; development ; Gene Transfer, Horizontal ; },
abstract = {This study discussed the role of plant-associated microbiome in regulating ARG transfer in soil-plant systems. Results showed that target ARGs in plants were mainly derived from rhizosphere soil. Cooperative interactions among bacteria in rhizosphere soil, plant-roots, plant-shoots, and soil-roots-shoots systems occurred during ARG transfer. The number of modules and keystone taxa identified as positively correlated with ARG transfer in rhizosphere soil, roots, and shoots was 3 and 49, 3 and 41, 2 and 5, respectively. Among these modules, module 3 in roots was significantly positively correlated with module 3 in rhizosphere soils and module 2 in shoots, indicating that module 3 in roots played central hub roles in ARG transfer from rhizosphere soil to roost and shoots. This may be because module 3 in roots increased cell motility and xenobiotics biodegradation and metabolism. These keystone taxa mainly belonged to Proteobacteria that can carry ARGs to transfer in soil-plant systems, especially Clostridium-sensu_stricito and Pseudomonas in rhizosphere soil carried ARGs into the shoot. Additionally, they promoted ARG transfer by increasing plant biomass, net photosynthetic rate and water use efficiency. The findings helped reveal the mechanism of plant-associated bacterial interactions and provided understanding for potential risks of ARG transfer from soil to plants.},
}
@article {pmid39304531,
year = {2024},
author = {Umar, M and Merlin, TS and Puthiyedathu Sajeevan, T},
title = {Genomic insights into symbiosis and host adaptation of sponge-associated novel bacterium, Rossellomorea orangium sp. nov.},
journal = {FEMS microbiology letters},
volume = {371},
number = {},
pages = {},
doi = {10.1093/femsle/fnae074},
pmid = {39304531},
issn = {1574-6968},
support = {BT/PR41474/NDB/39/760/2020//Higher Education Department, Government of Kerala/ ; 1422/2021/HEDN//Performance Linked Encouragement for Academic Studies and Endeavour (PLEASE)/ ; CUSAT/PL(UGC).A1/2314/2023//Rashtriya Uchchatar Shiksha Abhiyan/ ; //Kerala State Council for Science, Technology and Environment/ ; //University Grants Commission India/ ; },
mesh = {*Symbiosis ; *Porifera/microbiology ; Animals ; *Genome, Bacterial ; *Phylogeny ; Genomics ; Multigene Family ; Adaptation, Physiological ; Flavobacteriaceae/genetics/classification ; Secondary Metabolism ; Gene Transfer, Horizontal ; },
abstract = {Sponge-associated microorganisms play vital roles in marine sponge ecology. This study presents a genomic investigation of Rossellomorea sp. MCCB 382, isolated from Stelletta sp., reveals insights into its adaptations and symbiotic roles. Phylogenomic study and Overall Genomic Relatedness Index (OGRI) classify MCCB 382 as a novel species, Rossellomorea orangium sp. nov. The genome encodes numerous carbohydrate metabolism enzymes (CAZymes), likely aiding nutrient cycling in the sponge host. Unique eukaryotic-like protein domains hint at potential mechanisms of symbiosis. Defence mechanisms include CRISPR, restriction-modification systems, DNA phosphorothioation, toxin-antitoxin systems, and heavy metal and multidrug resistance genes, indicating adaptation to challenging marine environments. Unlike obligate mutualists, MCCB 382 shows no genome reduction. Furthermore, the presence of mobile genetic elements, horizontal gene transfer, and prophages suggest genetic versatility, implying flexible metabolic potential and capacity for rapid adaptation and symbiosis shifts. MCCB 382 possesses six biosynthetic gene clusters for secondary metabolites, including both type II and III polyketide synthases (PKS), terpenes, (NRPS), NRPS-independent-siderophore, and lassopeptide. Further genome mining using BiGScape revealed four distinct gene cluster families, T2PKS, NRPS-independent-siderophore, lasso peptide, and terpene, presenting opportunities for novel compound elucidation. Our study reveals a symbiotic lifestyle of MCCB 382 with the host sponge, highlighting symbiont factors that aid in establishing and sustaining this relationship. This is the pioneering genomic characterization of a novel Rossellomorea sp. within the sponge Stelletta sp. holobiont.},
}
@article {pmid39304387,
year = {2024},
author = {Vos, M and Buckling, A and Kuijper, B and Eyre-Walker, A and Bontemps, C and Leblond, P and Dimitriu, T},
title = {Why do mobile genetic elements transfer DNA of their hosts?.},
journal = {Trends in genetics : TIG},
volume = {40},
number = {11},
pages = {927-938},
doi = {10.1016/j.tig.2024.07.008},
pmid = {39304387},
issn = {0168-9525},
mesh = {*Gene Transfer, Horizontal/genetics ; *Interspersed Repetitive Sequences/genetics ; Selection, Genetic/genetics ; DNA Transposable Elements/genetics ; Bacteria/genetics ; },
abstract = {The prokaryote world is replete with mobile genetic elements (MGEs) - self-replicating entities that can move within and between their hosts. Many MGEs not only transfer their own DNA to new hosts but also transfer host DNA located elsewhere on the chromosome in the process. This could potentially lead to indirect benefits to the host when the resulting increase in chromosomal variation results in more efficient natural selection. We review the diverse ways in which MGEs promote the transfer of host DNA and explore the benefits and costs to MGEs and hosts. In many cases, MGE-mediated transfer of host DNA might not be selected for because of a sex function, but evidence of MGE domestication suggests that there may be host benefits of MGE-mediated sex.},
}
@article {pmid39304140,
year = {2024},
author = {Qi, Q and Ghaly, TM and Rajabal, V and Russell, DH and Gillings, MR and Tetu, SG},
title = {Vegetable phylloplane microbiomes harbour class 1 integrons in novel bacterial hosts and drive the spread of chlorite resistance.},
journal = {The Science of the total environment},
volume = {954},
number = {},
pages = {176348},
doi = {10.1016/j.scitotenv.2024.176348},
pmid = {39304140},
issn = {1879-1026},
mesh = {*Integrons/genetics ; *Microbiota/drug effects/genetics ; *Vegetables/microbiology ; Chlorides ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects ; Gene Transfer, Horizontal ; },
abstract = {Bacterial hosts in vegetable phylloplanes carry mobile genetic elements, such as plasmids and transposons that are associated with integrons. These mobile genetic elements and their cargo genes can enter human microbiomes via consumption of fresh agricultural produce, including uncooked vegetables. This presents a risk of acquiring antimicrobial resistance genes from uncooked vegetables. To better understand horizontal gene transfer of class 1 integrons in these compartments, we applied epicPCR, a single-cell fusion-PCR surveillance technique, to link the class 1 integron integrase (intI1) gene with phylogenetic markers of their bacterial hosts. Ready-to-eat salads carried class 1 integrons from the phyla Bacteroidota and Pseudomonadota, including four novel genera that were previously not known to be associated with intI1. We whole-genome sequenced Pseudomonas and Erwinia hosts of pre-clinical class 1 integrons that are embedded in Tn402-like transposons. The proximal gene cassette in these integrons was identified as a chlorite dismutase gene cassette, which we showed experimentally to confer chlorite resistance. Chlorine-derived compounds such as acidified sodium chlorite and chloride dioxide are used to disinfectant raw vegetables in food processing facilities, suggesting selection for chlorite resistance in phylloplane integrons. The spread of integrons conferring chlorite resistance has the potential to exacerbate integron-mediated antimicrobial resistance (AMR) via co-selection of chlorite resistance and AMR, thus highlighting the importance of monitoring chlorite residues in agricultural produce. These results demonstrate the strength of combining epicPCR and culture-based isolation approaches for identifying hosts and dissecting the molecular ecology of class 1 integrons.},
}
@article {pmid39303860,
year = {2024},
author = {Yong, Y and Hu, S and Zhong, M and Wen, Y and Zhou, Y and Ma, R and Jiang, X and Zhang, Q},
title = {Horizontal gene transfer from chloroplast to mitochondria of seagrasses in the yellow-Bohai seas.},
journal = {Genomics},
volume = {116},
number = {5},
pages = {110940},
doi = {10.1016/j.ygeno.2024.110940},
pmid = {39303860},
issn = {1089-8646},
mesh = {*Gene Transfer, Horizontal ; Genome, Mitochondrial ; Chloroplasts/genetics ; Genome, Chloroplast ; Alismatales/genetics/metabolism ; Phylogeny ; Mitochondria/genetics/metabolism ; },
abstract = {Seagrasses are ideal for studying plant adaptation to marine environments. In this study, the mitochondrial (mt) and chloroplast (cp) genomes of Ruppia sinensis were sequenced. The results showed an extensive gene loss in seagrasses, including a complete loss of cp-rpl19 genes in Zosteraceae, most cp-ndh genes in Hydrocharitaceae, and mt-rpl and mt-rps genes in all seagrasses, except for the mt-rpl16 gene in Phyllospadix iwatensis. Notably, most ribosomal protein genes were lost in the mt and cp genomes. The deleted cp genes were not transferred to the mt genomes through horizontal gene transfer. Additionally, a significant DNA transfer between seagrass organelles was found, with the mt genomes of Zostera containing numerous sequences from the cp genome. Rearrangement analyses revealed an unreported inversion of the cp genome in R. sinensis. Moreover, four positively selected genes (atp8, nad5, atp4, and ccmFn) and five variable regions (matR, atp4, atp8, rps7, and ccmFn) were identified.},
}
@article {pmid39303615,
year = {2024},
author = {Li, X and Cai, S and Xu, M},
title = {Nanoscale zero-valent iron alleviated horizontal transfer of antibiotic resistance genes in soil: The important role of extracellular polymeric substances.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135902},
doi = {10.1016/j.jhazmat.2024.135902},
pmid = {39303615},
issn = {1873-3336},
mesh = {*Iron/chemistry/metabolism ; *Soil Microbiology ; *Gene Transfer, Horizontal ; *Extracellular Polymeric Substance Matrix/metabolism ; *Soil Pollutants ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; Tetracycline/pharmacology ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; },
abstract = {Extracellular polymeric substances (EPS) are tightly related to the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs), but often neglected in soil. In this study, nanoscale zero-valent iron (nZVI) was utilized for attenuation of ARGs in contaminated soil, with an emphasis on its effects on EPS secretion and HGT. Results showed during soil microbe cultivation exposed to tetracycline, more EPS was secreted and significant increase of tet was observed due to facilitated HGT. Notably, copies of EPS-tet accounted for 71.39 % of the total tet, implying vital effects of EPS on ARGs proliferation. When co-exposed to nZVI, EPS secretion was decreased by 38.36-71.46 %, for that nZVI could alleviate the microbial oxidative stress exerted by tetracycline resulting in downregulation of genes expression related to the c-di-GMP signaling system. Meanwhile, the abundance of EPS-tet was obviously reduced from 7.04 to 5.12-6.47 log unit, directly causing decrease of total tet from 7.19 to 5.68-6.69 log unit. For the reduced tet, it was mainly due to decreased EPS secretion induced by nZVI resulting in inhibition of HGT especially transformation of the EPS-tet. This work gives an inspiration for attenuation of ARGs dissemination in soil through an EPS regulation strategy.},
}
@article {pmid39301187,
year = {2024},
author = {Xu, M and Ke, H and Zang, Y and Gou, H and Yang, D and Shi, K and Zhang, K and Li, Y and Jiang, Z and Chu, P and Zhai, S and Li, C},
title = {Outer membrane vesicles secreted from Actinobacillus pleuropneumoniae isolate disseminating the floR resistance gene to Enterobacteriaceae.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1467847},
pmid = {39301187},
issn = {1664-302X},
abstract = {Actinobacillus pleuropneumoniae, a significant respiratory pig pathogen, is causing substantial losses in the global swine industry. The resistance spectrum of A. pleuropneumoniae is expanding, and multidrug resistance is a severe issue. Horizontal gene transfer (HGT) plays a crucial role in the development of the bacterial genome by facilitating the dissemination of resistance determinants. However, the horizontal transfer of resistance genes via A. pleuropneumoniae-derived outer membrane vesicles (OMVs) has not been previously reported. In this study, we used Illumina NovaSeq and PacBio SequeI sequencing platforms to determine the whole genome sequence of A. pleuropneumoniae GD2107, a multidrug-resistant (MDR) isolate from China. We detected a plasmid in the isolate named pGD2107-1; the plasmid was 5,027 bp in size with 7 putative open reading frames (ORF) and included the floR resistance genes. The carriage of resistance genes in A. pleuropneumoniae OMVs was identified using a polymerase chain reaction (PCR) assay, and then we thoroughly evaluated the influence of OMVs on the horizontal transfer of drug-resistant plasmids. The transfer of the plasmid to recipient bacteria via OMVs was confirmed by PCR. In growth competition experiments, all recipients carrying the pGD2107-1 plasmid exhibited a fitness cost compared to the corresponding original recipients. This study revealed that OMVs could mediate interspecific horizontal transfer of the resistance plasmid pGD2107-1 into Escherichia coli recipient strains and significantly enhance the resistance of the transformants. In summary, A. pleuropneumoniae-OMVs play the pivotal role of vectors for dissemination of the floR gene spread and may contribute to more antimicrobial resistance gene transfer in other Enterobacteriaceae.},
}
@article {pmid39299886,
year = {2024},
author = {Urquhart, A and Vogan, AA and Gluck-Thaler, E},
title = {Starships: a new frontier for fungal biology.},
journal = {Trends in genetics : TIG},
volume = {40},
number = {12},
pages = {1060-1073},
doi = {10.1016/j.tig.2024.08.006},
pmid = {39299886},
issn = {0168-9525},
mesh = {*DNA Transposable Elements/genetics ; *Genome, Fungal/genetics ; *Evolution, Molecular ; *Fungi/genetics ; Gene Transfer, Horizontal/genetics ; Symbiosis/genetics ; },
abstract = {Transposable elements (TEs) are semiautonomous genetic entities that proliferate in genomes. We recently discovered the Starships, a previously hidden superfamily of giant TEs found in a diverse subphylum of filamentous fungi, the Pezizomycotina. Starships are unlike other eukaryotic TEs because they have evolved mechanisms for both mobilizing entire genes, including those encoding conditionally beneficial phenotypes, and for horizontally transferring between individuals. We argue that Starships have unrivaled capacity to engage their fungal hosts as genetic parasites and mutualists, revealing unexplored terrain for investigating the ecoevolutionary dynamics of TE-eukaryote interactions. We build on existing models of fungal genome evolution by conceptualizing Starships as a distinct genomic compartment whose dynamics profoundly shape fungal biology.},
}
@article {pmid39296779,
year = {2024},
author = {Thomy, J and Sanchez, F and Prioux, C and Yau, S and Xu, Y and Mak, J and Sun, R and Piganeau, G and Yung, CCM},
title = {Unveiling Prasinovirus diversity and host specificity through targeted enrichment in the South China Sea.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae109},
pmid = {39296779},
issn = {2730-6151},
abstract = {Unicellular green picophytoplankton from the Mamiellales order are pervasive in marine ecosystems and susceptible to infections by prasinoviruses, large double-stranded DNA viruses within the Nucleocytoviricota phylum. We developed a double-stranded DNA virus enrichment and shotgun sequencing method, and successfully assembled 80 prasinovirus genomes from 43 samples in the South China Sea. Our research delivered the first direct estimation of 94% accuracy in correlating genome similarity to host range. Stirkingly, our analyses uncovered unexpected host-switching across diverse algal lineages, challenging the existing paradigms of host-virus co-speciation and revealing the dynamic nature of viral evolution. We also detected six instances of horizontal gene transfer between prasinoviruses and their hosts, including a novel alternative oxidase. Additionally, diversifying selection on a major capsid protein suggests an ongoing co-evolutionary arms race. These insights not only expand our understanding of prasinovirus genomic diversity but also highlight the intricate evolutionary mechanisms driving their ecological success and shaping broader virus-host interactions in marine environments.},
}
@article {pmid39294579,
year = {2024},
author = {Shabbir, MAB and Shamim, M and Tahir, AH and Sattar, A and Qin, W and Ahmad, W and Ahmad, W and Khan, FA and Ashraf, MA},
title = {Potential of ZnO nanoparticles for multi-drug resistant Escherichia coli having CRISPR-Cas from poultry market in Lahore.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {355},
pmid = {39294579},
issn = {1471-2180},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *CRISPR-Cas Systems ; *Drug Resistance, Multiple, Bacterial/genetics ; *Escherichia coli/genetics/drug effects ; *Escherichia coli Infections/microbiology/veterinary ; Microbial Sensitivity Tests ; Nanoparticles ; Poultry/microbiology ; *Poultry Diseases/microbiology ; *Zinc Oxide/pharmacology ; },
abstract = {BACKGROUND AND OBJECTIVES: Apart from known factors such as irrational use of antibiotics and horizontal gene transfer, it is now reported that clustered regularly interspaced short palindromic repeats (CRISPR) are also associated with increased antimicrobial resistance. Hence, it is critical to explore alternatives to antibiotics to control economic losses. Therefore, the present study aimed to determine not only the association of CRISPR-Cas system with antibiotic resistance but also the potential of Zinc Oxide nanoparticles (ZnO-NPs) for avian pathogenic Escherichia coli (APEC) isolated from poultry market Lahore.<br><br>MATERIALS AND METHODS: Samples (n&#x2009;=&#x2009;100) were collected from live bird markets of Lahore, and isolates were confirmed as Escherichia coli (E. coli) using the Remel One fast kit, and APEC was identified using PCR. The antibiotic resistance pattern in APEC was determined using the minimum inhibitory concentration (MIC), followed by genotypic confirmation of antibiotic-resistant genes using the PCR. The CRISPR-Cas system was also identified in multidrug-resistant (MDR) isolates, and its association with antibiotics was determined using qRT-PCR. The potential of ZnO-NPs was evaluated for multidrug-resistant (MDR) isolates by MIC.<br><br>RESULTS: All isolates of APEC were resistant to nalidixic acid, whereas 95% were resistant to chloramphenicol and 89% were resistant to streptomycin. Nineteen MDR APEC were found in the present study and the CRISPR-Cas system was detected in all of these MDR isolates. In addition, an increased expression of CRISPR-related genes was observed in the standard strain and MDR isolates of APEC.&#xa0;ZnO-NPs inhibited the growth of resistant isolates.<br><br>CONCLUSIONS: The findings showed the presence of the CRISPR-Cas system in MDR strains of APEC, along with the potential of ZnO-NPs for a possible solution to proceed. This highlights the importance of regulating antimicrobial resistance in poultry to reduce potential health consequences.},
}
@article {pmid39293438,
year = {2024},
author = {Zhang, ZJ and Cole, CG and Coyne, MJ and Lin, H and Dylla, N and Smith, RC and Pappas, TE and Townson, SA and Laliwala, N and Waligurski, E and Ramaswamy, R and Woodson, C and Burgo, V and Little, JC and Moran, D and Rose, A and McMillin, M and McSpadden, E and Sundararajan, A and Sidebottom, AM and Pamer, EG and Comstock, LE},
title = {Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species- and strain-level diversity and evolution.},
journal = {Cell host &amp; microbe},
volume = {32},
number = {10},
pages = {1853-1867.e5},
pmid = {39293438},
issn = {1934-6069},
support = {P01 CA023766/CA/NCI NIH HHS/United States ; T32 GM144292/GM/NIGMS NIH HHS/United States ; U01 AI124275/AI/NIAID NIH HHS/United States ; R01 AI093771/AI/NIAID NIH HHS/United States ; R01 AI042135/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Phylogeny ; *Genome, Bacterial ; Bacteroidetes/genetics/classification/isolation &amp; purification ; Gene Transfer, Horizontal ; Genetic Variation ; Metabolomics ; Evolution, Molecular ; DNA, Bacterial/genetics ; Genomics ; Sequence Analysis, DNA ; },
abstract = {Species of the Bacteroidales order are among the most abundant and stable bacterial members of the human gut microbiome, with diverse impacts on human health. We cultured and sequenced the genomes of 408 Bacteroidales isolates from healthy human donors representing nine genera and 35 species and performed comparative genomic, gene-specific, metabolomic, and horizontal gene transfer analyses. Families, genera, and species could be grouped based on many distinctive features. We also observed extensive DNA transfer between diverse families, allowing for shared traits and strain evolution. Inter- and intra-species diversity is also apparent in the metabolomic profiling studies. This highly characterized and diverse Bacteroidales culture collection with strain-resolved genomic and metabolomic analyses represents a valuable resource to facilitate informed selection of strains for microbiome reconstitution.},
}
@article {pmid39288183,
year = {2024},
author = {Tuffet, R and Carvalho, G and Godeux, AS and Mazzamurro, F and Rocha, EPC and Laaberki, MH and Venner, S and Charpentier, X},
title = {Manipulation of natural transformation by AbaR-type islands promotes fixation of antibiotic resistance in Acinetobacter baumannii.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {39},
pages = {e2409843121},
pmid = {39288183},
issn = {1091-6490},
support = {ANR-20-CE12-0004//Agence Nationale de la Recherche (ANR)/ ; ANR-11-LABX-0048//Agence Nationale de la Recherche (ANR)/ ; PhD grant//VetAgro Sup (VetAgro-Sup)/ ; 80|PRIME//Centre National de la Recherche Scientifique (CNRS)/ ; },
mesh = {*Acinetobacter baumannii/genetics/drug effects ; *Genomic Islands ; Drug Resistance, Multiple, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Transformation, Bacterial ; Polymorphism, Single Nucleotide ; Bacterial Proteins/genetics/metabolism ; },
abstract = {The opportunistic pathogen Acinetobacter baumannii, carries variants of A. baumannii resistance islands (AbaR)-type genomic islands conferring multidrug resistance. Their pervasiveness in the species has remained enigmatic. The dissemination of AbaRs is intricately linked to their horizontal transfer via natural transformation, a process through which bacteria can import and recombine exogenous DNA, effecting allelic recombination, genetic acquisition, and deletion. In experimental populations of the closely related pathogenic Acinetobacter nosocomialis, we quantified the rates at which these natural transformation events occur between individuals. When integrated into a model of population dynamics, they lead to the swift removal of AbaRs from the population, contrasting with the high prevalence of AbaRs in genomes. Yet, genomic analyses show that nearly all AbaRs specifically disrupt comM, a gene encoding a helicase critical for natural transformation. We found that such disruption impedes gene acquisition, and deletion, while moderately impacting acquisition of single nucleotide polymorphism. A mathematical evolutionary model demonstrates that AbaRs inserted into comM gain a selective advantage over AbaRs inserted in sites that do not inhibit or completely inhibit transformation, in line with the genomic observations. The persistence of AbaRs can be ascribed to their integration into a specific gene, diminishing the likelihood of their removal from the bacterial genome. This integration preserves the acquisition and elimination of alleles, enabling the host bacterium-and thus its AbaR-to adapt to unpredictable environments and persist over the long term. This work underscores how manipulation of natural transformation by mobile genetic elements can drive the prevalence of multidrug resistance.},
}
@article {pmid39287446,
year = {2024},
author = {Contarin, R and Drapeau, A and François, P and Madec, J-Y and Haenni, M and Dordet-Frisoni, E},
title = {The interplay between mobilome and resistome in Staphylococcus aureus.},
journal = {mBio},
volume = {15},
number = {10},
pages = {e0242824},
pmid = {39287446},
issn = {2150-7511},
support = {//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE)/ ; //Agence Nationale de S&#xe9;curit&#xe9; Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES)/ ; },
mesh = {*Staphylococcus aureus/genetics/drug effects ; Humans ; *Staphylococcal Infections/microbiology ; Animals ; *Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; *Plasmids/genetics ; *Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial/genetics ; Genes, Bacterial/genetics ; },
abstract = {Antibiotic resistance genes (ARGs) in Staphylococcus aureus can disseminate vertically through successful clones, but also horizontally through the transfer of genes conveyed by mobile genetic elements (MGEs). Even though underexplored, MGE/ARG associations in S. aureus favor the emergence of multidrug-resistant clones, which are challenging therapeutic success in both human and animal health. This study investigated the interplay between the mobilome and the resistome of more than 10,000 S. aureus genomes from human and animal origin. The analysis revealed a remarkable diversity of MGEs and ARGs, with plasmids and transposons being the main carriers of ARGs. Numerous MGE/ARG associations were identified, suggesting that MGEs play a critical role in the dissemination of resistance. A high degree of similarity was observed in MGE/ARG associations between human and animal isolates, highlighting the potential for unrestricted spread of ARGs between hosts. Our results showed that in parallel to clonal expansion, MGEs and their associated ARGs can spread across different strain types sequence types (STs), favoring the evolution of these clones and their adaptation in selective environments. The high variability of MGE/ARG associations within individual STs and their spread across several STs highlight the crucial role of MGEs in shaping the S. aureus resistome. Overall, this study provides valuable insights into the complex interplay between MGEs and ARGs in S. aureus, emphasizing the need to elucidate the mechanisms governing the epidemic success of MGEs, particularly those implicated in ARG transfer.IMPORTANCEThe research presented in this article highlights the importance of understanding the interactions between mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs) carried by Staphylococcus aureus, a versatile bacterium that can be both a harmless commensal and a dangerous pathogen for humans and animals. S. aureus has a great capacity to acquire and disseminate ARGs, enabling efficient adaption to various environmental or clinical conditions. By analyzing a large data set of S. aureus genomes, we highlighted the substantial role of MGEs, particularly plasmids and transposons, in disseminating ARGs within and between S. aureus populations, bypassing host barriers. Given that multidrug-resistant S. aureus strains are classified as a high-priority pathogen by global health organizations, this knowledge is crucial for understanding the complex dynamics of transmission of antibiotic resistance in this species.},
}
@article {pmid39287432,
year = {2024},
author = {Nwokocha, GC and Ghosh, A and Grove, A},
title = {Regulation of bacterial virulence genes by PecS family transcription factors.},
journal = {Journal of bacteriology},
volume = {206},
number = {10},
pages = {e0030224},
pmid = {39287432},
issn = {1098-5530},
support = {MCB-2153410//National Science Foundation (NSF)/ ; },
mesh = {*Gene Expression Regulation, Bacterial ; *Transcription Factors/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism ; Virulence/genetics ; Virulence Factors/genetics/metabolism ; },
abstract = {Bacterial plant pathogens adjust their gene expression programs in response to environmental signals and host-derived compounds. This ensures that virulence genes or genes encoding proteins, which promote bacterial fitness in a host environment, are expressed only when needed. Such regulation is in the purview of transcription factors, many of which belong to the ubiquitous multiple antibiotic resistance regulator (MarR) protein family. PecS proteins constitute a subset of this large protein family. PecS has likely been distributed by horizontal gene transfer, along with the divergently encoded efflux pump PecM, suggesting its integration into existing gene regulatory networks. Here, we discuss the roles of PecS in the regulation of genes associated with virulence and fitness of bacterial plant pathogens. A comparison of phenotypes and differential gene expression associated with the disruption of pecS shows that functional consequences of PecS integration into existing transcriptional networks are highly variable, resulting in distinct PecS regulons. Although PecS universally binds to the pecS-pecM intergenic region to repress the expression of both genes, binding modes differ. A particularly relaxed sequence preference appears to apply for Dickeya dadantii PecS, perhaps to optimize its integration as a global regulator and regulate genes ancestral to the acquisition of pecS-pecM. Even inducing ligands for PecS are not universally conserved. It appears that PecS function has been optimized to match the unique regulatory needs of individual bacterial species and that its roles must be appreciated in the context of the regulatory networks into which it was recruited.},
}
@article {pmid39287139,
year = {2024},
author = {Pu, L and Shamir, R},
title = {4CAC: 4-class classifier of metagenome contigs using machine learning and assembly graphs.},
journal = {Nucleic acids research},
volume = {52},
number = {19},
pages = {e94},
pmid = {39287139},
issn = {1362-4962},
support = {1339/18//Israel Science Foundation/ ; //Edmond J. Safra Center for Bioinformatics at Tel-Aviv University/ ; //Planning &amp; Budgeting Committee/ ; //Council for Higher Education/ ; },
mesh = {*Machine Learning ; *Metagenome/genetics ; Bacteria/genetics/classification ; Plasmids/genetics ; Archaea/genetics/classification ; Software ; Metagenomics/methods ; Viruses/genetics/classification ; Contig Mapping/methods ; Algorithms ; },
abstract = {Microbial communities usually harbor a mix of bacteria, archaea, plasmids, viruses and microeukaryotes. Within these communities, viruses, plasmids, and microeukaryotes coexist in relatively low abundance, yet they engage in intricate interactions with bacteria. Moreover, viruses and plasmids, as mobile genetic elements, play important roles in horizontal gene transfer and the development of antibiotic resistance within microbial populations. However, due to the difficulty of identifying viruses, plasmids, and microeukaryotes in microbial communities, our understanding of these minor classes lags behind that of bacteria and archaea. Recently, several classifiers have been developed to separate one or more minor classes from bacteria and archaea in metagenome assemblies. However, these classifiers often overlook the issue of class imbalance, leading to low precision in identifying the minor classes. Here, we developed a classifier called 4CAC that is able to identify viruses, plasmids, microeukaryotes, and prokaryotes simultaneously from metagenome assemblies. 4CAC generates an initial four-way classification using several sequence length-adjusted XGBoost models and further improves the classification using the assembly graph. Evaluation on simulated and real metagenome datasets demonstrates that 4CAC substantially outperforms existing classifiers and combinations thereof on short reads. On long reads, it also shows an advantage unless the abundance of the minor classes is very low. 4CAC runs 1-2 orders of magnitude faster than the other classifiers. The 4CAC software is available at https://github.com/Shamir-Lab/4CAC.},
}
@article {pmid39282498,
year = {2024},
author = {Jiang, C and Yang, J and Xiao, G and Xiao, N and Hu, J and Yang, Y and Sun, Z and Li, Y},
title = {The ISVsa3-ORF2-abh-tet(X4) circular intermediate-mediated transmission of tigecycline resistance in Escherichia coli isolates from duck farms.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1444031},
pmid = {39282498},
issn = {2235-2988},
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; China ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; *Ducks/microbiology ; *Escherichia coli/genetics/drug effects/isolation &amp; purification ; *Escherichia coli Infections/veterinary/microbiology ; Escherichia coli Proteins/genetics ; *Farms ; Feces/microbiology ; Gene Transfer, Horizontal ; Genotype ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Plasmids/genetics ; Poultry Diseases/microbiology ; *Tigecycline/pharmacology ; *Whole Genome Sequencing ; },
abstract = {Tigecycline is a last-resort drug used to treat serious infections caused by multidrug-resistant bacteria. tet(X4) is a recently discovered plasmid-mediated tigecycline resistance gene that confers high-level resistance to tigecycline and other tetracyclines. Since the first discovery of tet(X4) in 2019, it has spread rapidly worldwide, and as a consequence, tigecycline has become increasingly ineffective in the clinical treatment of multidrug-resistant infections. In this study, we identified and analyzed tet(X4)-positive Escherichia coli isolates from duck farms in Hunan Province, China. In total, 976 samples were collected from nine duck farms. Antimicrobial susceptibility testing and whole-genome sequencing (WGS) were performed to establish the phenotypes and genotypes of tet(X4)-positive isolates. In addition, the genomic characteristics and transferability of tet(X4) were determined based on bioinformatics analysis and conjugation. We accordingly detected an E. coli strain harboring tet(X4) and seven other resistance genes in duck feces. Multi-locus sequence typing analysis revealed that this isolate belonged to a new clone, and subsequent genetic analysis indicated that tet(X4) was carried in a 4608-bp circular intermediate, flanked by ISVsa3-ORF2-abh elements. Moreover, it exhibited transferability to E. coli C600 with a frequency of 10[-5]. The detection of tet(X4)-harboring E, coli strains on duck farms enhances our understanding of tigecycline resistance dynamics. The transferable nature of the circular intermediate of tet(X4) contributing to the spread of tigecycline resistance genes poses a substantial threat to healthcare. Consequently, vigilant monitoring and proactive measures are necessary to prevent their spread.},
}
@article {pmid39278585,
year = {2024},
author = {Yang, B and Sun, J and Zhu, S and Wang, Z and Liu, Y},
title = {Exposure to bisphenol compounds accelerates the conjugative transfer of antibiotic resistance plasmid.},
journal = {Environmental research},
volume = {263},
number = {Pt 1},
pages = {120002},
doi = {10.1016/j.envres.2024.120002},
pmid = {39278585},
issn = {1096-0953},
mesh = {*Phenols/toxicity ; *Plasmids/genetics ; Animals ; *Gene Transfer, Horizontal ; Mice ; Benzhydryl Compounds/toxicity ; Conjugation, Genetic/drug effects ; Drug Resistance, Microbial/genetics ; Endocrine Disruptors/toxicity ; },
abstract = {Antimicrobial resistance poses the most formidable challenge to public health, with plasmid-mediated horizontal gene transfer playing a pivotal role in its global spread. Bisphenol compounds (BPs), a group of environmental contaminants with endocrine-disrupting properties, are extensively used in various plastic products and can be transmitted to food. However, the impact of BPs on the plasmid-mediated horizontal transfer of antibiotic resistance genes (ARGs) has not yet been elucidated. Herein, we demonstrate that BPs could promote the conjugative transfer frequency of RP4-7 and clinically multidrug-resistant plasmids. Furthermore, the promoting effect of BPs on the plasmid transfer was also confirmed in a murine model. Microbial diversity analysis of transconjugants indicated an increase in α diversity in the BPAF-treated group, along with the declined richness of some beneficial bacteria and elevated richness of Faecalibaculum rodentium, which might serve as an intermediate repository for resistance plasmids. The underlying mechanisms driving the enhanced conjugative transfer upon BPAF treatment include exacerbated oxidative stress, disrupted membrane homeostasis, augmented energy metabolism, and the increased expression of conjugation-related genes. Collectively, our findings highlight the potential risk associated with the exacerbated dissemination of AMR both in vitro and in vivo caused by BPs exposure.},
}
@article {pmid39277355,
year = {2024},
author = {Gao, Y and Guo, Y and Wang, L and Guo, L and Shi, B and Zhu, L and Wang, J and Kim, YM and Wang, J},
title = {Tebuconazole exacerbates co-occurrence and horizontal transfer of antibiotic resistance genes.},
journal = {Pesticide biochemistry and physiology},
volume = {204},
number = {},
pages = {106026},
doi = {10.1016/j.pestbp.2024.106026},
pmid = {39277355},
issn = {1095-9939},
mesh = {*Triazoles/toxicity/pharmacology ; *Gene Transfer, Horizontal ; *Fungicides, Industrial/toxicity/pharmacology ; *Biofilms/drug effects ; Drug Resistance, Microbial/genetics ; Plasmids/genetics ; Genes, Bacterial ; },
abstract = {As one of the most widely used pesticides in the global fungicide market, tebuconazole has become heavily embedded in soil along with antibiotic resistance genes (ARGs). However, it remains unclear whether the selective pressure produced by tebuconazole affects ARGs and their horizontal transfer. In this experiment, we simulated a tebuconazole-contaminated soil ecosystem and observed changes in the abundance of ARGs and mobile genetic element (MGEs) due to tebuconazole exposure. We also established a plasmid RP4-mediated conjugative transfer system to investigate in depth the impact of tebuconazole on the horizontal transfer of ARGs and its mechanism of action. The results showed that under tebuconazole treatment at concentrations ranging from 0 to 10 mg/L, there was a gradual increase in the frequency of plasmid conjugative transfer, peaking at 10 mg/L which was 7.93 times higher than that of the control group, significantly promoting horizontal transfer of ARGs. Further analysis revealed that the conjugative transfer system under tebuconazole stress exhibited strong ability to form biofilm, and the conjugative transfer frequency ratio of biofilm to planktonic bacteria varied with the growth cycle of biofilm. Additionally, scanning electron microscopy and flow cytometry demonstrated increased cell membrane permeability in both donor and recipient bacteria under tebuconazole stress, accompanied by upregulation of ompA gene expression controlling cell membrane permeability. Furthermore, enzyme activity assays indicated significant increases in CAT, SOD activity, and GSH content in recipient bacteria under tebuconazole stress. Moreover, expression levels of transmembrane transporter gene trfAp as well as genes involved in oxidative stress and SOS response were found to be correlated with the frequency of plasmid conjugative transfer.},
}
@article {pmid39276831,
year = {2024},
author = {Li, C and Zhang, Y and Shi, W and Peng, Y and Han, Y and Jiang, S and Dong, X and Zhang, R},
title = {Viral diversity within marine biofilms and interactions with corrosive microbes.},
journal = {Environmental research},
volume = {263},
number = {Pt 1},
pages = {119991},
doi = {10.1016/j.envres.2024.119991},
pmid = {39276831},
issn = {1096-0953},
mesh = {*Biofilms/growth &amp; development ; Corrosion ; Bacteria/genetics ; Viruses/genetics/classification ; Phylogeny ; Metagenome ; Archaea/virology/genetics ; },
abstract = {In marine environments, a wide variety of microbes like bacteria, and archaea influence on the corrosion of materials. Viruses are widely distributed in biofilms among these microbes and may affect the corrosion process through interactions with key corrosive prokaryotes. However, understanding of the viral communities within biofilms and their interactions with corrosive microbes remains is limited. To improve this knowledge gap, 53 metagenomes were utilized to investigate the diversity of viruses within biofilms on 8 different materials and their interactions with corrosive microbes. Notably, the viruses within biofilms predominantly belonged to Caudoviricetes, and phylogenetic analysis of Caudoviricetes and protein-sharing networks with other environments revealed the presence of numerous novel viral clades in biofilms. The virus‒host linkages revealed a close association between viruses and corrosive microbes in biofilms. This means that viruses may modulate host corrosion-related metabolism through auxiliary metabolic genes. It was observed that the virus could enhance host resistance to metals and antibiotics via horizontal gene transfer. Interestingly, viruses could protect themselves from host antiviral systems through anti-defense systems. This study illustrates the diversity of viruses within biofilms formed on materials and the intricate interactions between viruses and corrosive microbes, showing the potential roles of viruses in corrosive biofilms.},
}
@article {pmid39270765,
year = {2024},
author = {Bjornson, S and Verbruggen, H and Upham, NS and Steenwyk, JL},
title = {Reticulate evolution: Detection and utility in the phylogenomics era.},
journal = {Molecular phylogenetics and evolution},
volume = {201},
number = {},
pages = {108197},
doi = {10.1016/j.ympev.2024.108197},
pmid = {39270765},
issn = {1095-9513},
mesh = {*Phylogeny ; Genomics ; Gene Transfer, Horizontal ; Hybridization, Genetic ; Genetic Speciation ; Models, Genetic ; Biological Evolution ; Evolution, Molecular ; Animals ; },
abstract = {Phylogenomics has enriched our understanding that the Tree of Life can have network-like or reticulate structures among some taxa and genes. Two non-vertical modes of evolution - hybridization/introgression and horizontal gene transfer - deviate from a strictly bifurcating tree model, causing non-treelike patterns. However, these reticulate processes can produce similar patterns to incomplete lineage sorting or recombination, potentially leading to ambiguity. Here, we present a brief overview of a phylogenomic workflow for inferring organismal histories and compare methods for distinguishing modes of reticulate evolution. We discuss how the timing of coalescent events can help disentangle introgression from incomplete lineage sorting and how horizontal gene transfer events can help determine the relative timing of speciation events. In doing so, we identify pitfalls of certain methods and discuss how to extend their utility across the Tree of Life. Workflows, methods, and future directions discussed herein underscore the need to embrace reticulate evolutionary patterns for understanding the timing and rates of evolutionary events, providing a clearer view of life's history.},
}
@article {pmid39270668,
year = {2024},
author = {Aserse, AA and Nimusiima, J and Tumuhairwe, JB and Yli-Halla, M and Lindström, K},
title = {Phylogenetic diversity of Rhizobium species recovered from nodules of common beans (Phaseolus vulgaris L.) in fields in Uganda: R. phaseoli, R. etli, and R. hidalgonense.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {11},
pages = {},
pmid = {39270668},
issn = {1574-6941},
support = {319&#x2009;874//Academy of Finland/ ; 0116947-3//Finnish Cultural Foundation/ ; },
mesh = {*Phylogeny ; *Rhizobium/genetics/classification/isolation &amp; purification ; Uganda ; *Phaseolus/microbiology ; *Root Nodules, Plant/microbiology ; Symbiosis ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Genetic Variation ; Bacterial Proteins/genetics ; Rec A Recombinases/genetics ; },
abstract = {A total of 75 bacterial isolates were obtained from nodules of beans cultivated across 10 sites in six agro-ecological zones in Uganda. Using recA gene sequence analysis, 66 isolates were identified as members of the genus Rhizobium, while 9 were related to Agrobacterium species. In the recA gene tree, most Rhizobium strains were classified into five recognized species. Phylogenetic analysis based on six concatenated sequences (recA-rpoB-dnaK-glnII-gyrB-atpD) placed 32 representative strains into five distinct Rhizobium species, consistent with the species groups observed in the recA gene tree: R. phaseoli, R. etli, R. hidalgonense, R. ecuadorense, and R. sophoriradicis, with the first three being the predominant. The rhizobial strains grouped into three nodC subclades within the symbiovar phaseoli clade, encompassing strains from distinct phylogenetic groups. This pattern reflects the conservation of symbiotic genes, likely acquired through horizontal gene transfer among diverse rhizobial species. The 32 representative strains formed symbiotic relationships with host beans, while the Agrobacterium strains did not form nodules and lacked symbiotic genes. Multivariate analysis revealed that species distribution was influenced by the environmental factors of the sampling sites, emphasizing the need to consider these factors in future effectiveness studies to identify effective nitrogen-fixing strains for specific locations.},
}
@article {pmid39269515,
year = {2024},
author = {Amara, Y and Mahjoubi, M and Souissi, Y and Cherif, H and Naili, I and ElHidri, D and Kadidi, I and Mosbah, A and Masmoudi, AS and Cherif, A},
title = {Tapping into haloalkaliphilic bacteria for sustainable agriculture in treated wastewater: insights into genomic fitness and environmental adaptation.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {1},
pages = {1},
pmid = {39269515},
issn = {1572-9699},
support = {No 688320//European Union's Horizon 2020, MADFORWATER/ ; No 688320//European Union's Horizon 2020, MADFORWATER/ ; No 688320//European Union's Horizon 2020, MADFORWATER/ ; No 688320//European Union's Horizon 2020, MADFORWATER/ ; },
mesh = {*Wastewater/microbiology ; *Phylogeny ; *Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; Salinity ; Rhizosphere ; Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Agriculture/methods ; Tunisia ; Adaptation, Physiological ; Olea/microbiology ; Genome, Bacterial ; },
abstract = {The increasing salinity and alkalinity of soils pose a global challenge, particularly in arid regions such as Tunisia, where about 50% of lands are sensitive to soil salinization. Anthropogenic activities, including the use of treated wastewater (TWW) for irrigation, exacerbate these issues. Haloalkaliphilic bacteria, adapted to TWW conditions and exhibiting plant-growth promotion (PGP) and biocontrol traits, could offer solutions. In this study, 24 haloalkaliphilic bacterial strains were isolated from rhizosphere sample of olive tree irrigated with TWW for more than 20 years. The bacterial identification using 16S rRNA gene sequencing showed that the haloalkaliphilic isolates, capable of thriving in high salinity and alkaline pH, were primarily affiliated to Bacillota (Oceanobacillus and Staphylococcus). Notably, these strains exhibited biofertilization and enzyme production under both normal and saline conditions. Traits such as phosphate solubilization, and the production of exopolysaccharide, siderophore, ammonia, and hydrogen cyanide were observed. The strains also demonstrated enzymatic activities, including protease, amylase, and esterase. Four selected haloalkaliphilic PGPR strains displayed antifungal activity against Alternaria terricola, with three showing tolerances to heavy metals and pesticides. The strain Oceanobacillus picturea M4W.A2 was selected for genome sequencing. Phylogenomic analyses indicated that the extreme environmental conditions probably influenced the development of specific adaptations in M4W.A2 strain, differentiating it from other Oceanobacillus picturae strains. The presence of the key genes associated with plant growth promotion, osmotic and oxidative stress tolerance, antibiotic and heavy metals resistance hinted the functional capabilities might help the strain M4W.A2 to thrive in TWW-irrigated soils. By demonstrating this connection, we aim to improve our understanding of genomic fitness to stressed environments. Moreover, the identification of gene duplication and horizontal gene transfer events through mobile genetic elements allow the comprehension of these adaptation dynamics. This study reveals that haloalkaliphilc bacteria from TWW-irrigated rhizosphere exhibit plant-growth promotion and biocontrol traits, with genomic adaptations enabling their survival in high salinity and alkaline conditions, offering potential solutions for soil salinization issues.},
}
@article {pmid39268957,
year = {2024},
author = {Yang, P and Li, J and Lv, M and He, P and Song, G and Shan, B and Yang, X},
title = {Molecular Epidemiology and Horizontal Transfer Mechanism of optrA-Carrying Linezolid-Resistant Enterococcus faecalis.},
journal = {Polish journal of microbiology},
volume = {73},
number = {3},
pages = {349-362},
pmid = {39268957},
issn = {2544-4646},
mesh = {*Enterococcus faecalis/genetics/drug effects ; *Linezolid/pharmacology ; *Gene Transfer, Horizontal ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Gram-Positive Bacterial Infections/microbiology/epidemiology ; China/epidemiology ; Bacterial Proteins/genetics/metabolism ; Molecular Epidemiology ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Drug Resistance, Multiple, Bacterial/genetics ; Whole Genome Sequencing ; Conjugation, Genetic ; },
abstract = {The aim of this work was to provide a theoretical and scientific basis for the treatment, prevention, and control of clinical drug-resistant bacterial infections by studying the molecular epidemiology and horizontal transfer mechanism of optrA-carrying linezolid-resistant Enterococcus faecalis strains (LREfs) that were clinically isolated in a tertiary hospital in Kunming, China. Non-repetitive LREfs retained in a tertiary A hospital in Kunming, China. The strains were identified by Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The transferability and horizontal transfer mechanism of optrA gene were analyzed using polymerase chain reaction (PCR), whole-genome sequencing (WGS), and conjugation experiments. A total of 39 LREfs strains were collected, and all of them were multi-drug resistant. There were 30 LREfs strains (76.9%) carrying the optrA gene, The cfr, poxtA genes and mutations in the 23S rRNA gene were not detected. The conjugation experiments showed that only three of 10 randomly selected optrA-carrying LREfs were successfully conjugated with JH2-2. Further analysis of one successfully conjugated strain revealed that the optrA gene, located in the donor bacterium, formed the IS1216E-erm(A)-optrA-fexA-IS1216E transferable fragment under the mediation of the mobile genetic element (MGE) IS1216E, which was then transferred to the recipient bacterium via horizontal plasmid transfer. Carrying the optrA gene is the primary resistance mechanism of LREfs strains. The optrA gene could carry the erm(A) and fexA genes to co-transfer among E. faecalis. MGEs such as insertion sequence IS1216E play an important role in the horizontal transfer of the optrA gene.},
}
@article {pmid39268528,
year = {2024},
author = {Riva, F and Dechesne, A and Eckert, EM and Riva, V and Borin, S and Mapelli, F and Smets, BF and Crotti, E},
title = {Conjugal plasmid transfer in the plant rhizosphere in the One Health context.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1457854},
pmid = {39268528},
issn = {1664-302X},
abstract = {INTRODUCTION: Horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) is one of the primary routes of antimicrobial resistance (AMR) dissemination. In the One Health context, tracking the spread of mobile genetic elements (MGEs) carrying ARGs in agri-food ecosystems is pivotal in understanding AMR diffusion and estimating potential risks for human health. So far, little attention has been devoted to plant niches; hence, this study aimed to evaluate the conjugal transfer of ARGs to the bacterial community associated with the plant rhizosphere, a hotspot for microbial abundance and activity in the soil. We simulated a source of AMR determinants that could enter the food chain via plants through irrigation.<br><br>METHODS: Among the bacterial strains isolated from treated wastewater, the strain Klebsiella variicola EEF15 was selected as an ARG donor because of the relevance of Enterobacteriaceae in the AMR context and the One Health framework. The strain ability to recolonize lettuce, chosen as a model for vegetables that were consumed raw, was assessed by a rifampicin resistant mutant. K. variicola EEF15 was genetically manipulated to track the conjugal transfer of the broad host range plasmid pKJK5 containing a fluorescent marker gene to the natural rhizosphere microbiome obtained from lettuce plants. Transconjugants were sorted by fluorescent protein expression and identified through 16S rRNA gene amplicon sequencing.<br><br>RESULTS AND DISCUSSION: K. variicola EEF15 was able to colonize the lettuce rhizosphere and inhabit its leaf endosphere 7 days past bacterial administration. Fluorescence stereomicroscopy revealed plasmid transfer at a frequency of 10[-3]; cell sorting allowed the selection of the transconjugants. The conjugation rates and the strain's ability to colonize the plant rhizosphere and leaf endosphere make strain EEF15::lacI[q]-pLpp-mCherry-gm[R] with pKJK5::Plac::gfp an interesting candidate to study ARG spread in the agri-food ecosystem. Future studies taking advantage of additional environmental donor strains could provide a comprehensive snapshot of AMR spread in the One Health context.},
}
@article {pmid39266980,
year = {2024},
author = {Wu, H and Dongchen, W and Li, Y and Brown, SE and Wei, S and Lin, C and Mao, Z and Liu, Z},
title = {Mitogenomes comparison of 3 species of Asparagus L shedding light on their functions due to domestication and adaptative evolution.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {857},
pmid = {39266980},
issn = {1471-2164},
support = {202305A0350012//Yunnan Basic Research Program/ ; 202305A0350012//Yunnan Basic Research Program/ ; 202305A0350012//Yunnan Basic Research Program/ ; 202305A0350012//Yunnan Basic Research Program/ ; 202305A0350012//Yunnan Basic Research Program/ ; 32360089//National Natural Science Foundation of China/ ; 32360089//National Natural Science Foundation of China/ ; 202101BD070001-027//Yunnan Agricultural joint Fund-key project/ ; },
mesh = {*Asparagus Plant/genetics ; *Genome, Mitochondrial ; *Phylogeny ; *Domestication ; *Evolution, Molecular ; RNA Editing ; Gene Transfer, Horizontal ; Genome, Chloroplast ; },
abstract = {BACKGROUND: Asparagus L., widely distributed in the old world is a genus under Asparagaceae, Asparagales. The species of the genus were mainly used as vegetables, traditional medicines as well as ornamental plants. However, the evolution and functions of mitochondrial (Mt) genomes (mitogenomes) remains largely unknown. In this study, the typical herbal medicine A. taliensis and ornamental plant A. setaceus were used to assemble and annotate the mitogenomes, and the resulting mitogenomes were further compared with published mitogenome of A. officinalis for the analysis of their functions in the context of domestication and adaptative evolution.<br><br>RESULTS: The mitochondrial genomes of both A. taliensis and A. setaceus were assembled as complete circular ones. The phylogenetic trees based on conserved protein-coding genes of Mt genomes and whole chloroplast (Cp) genomes showed that, the phylogenetic relationship of the sampled 13 species of Asparagus L. were not exactly consistent. The collinear analyses between the nuclear (Nu) and Mt genomes confirmed the existence of mutual horizontal genes transfers (HGTs) between Nu and Mt genomes within these species. Based on RNAseq data, the Mt RNA editing were predicted and atp1 and ccmB RNA editing of A. taliensis were further confirmed by DNA sequencing. Simultaneously homologous search found 5 Nu coding gene families including pentatricopeptide-repeats (PPRs) involved in Mt RNA editing. Finally, the Mt genome variations, gene expressions and mutual HGTs between Nu and Mt were detected with correlation to the growth and developmental phenotypes respectively. The results suggest that, both Mt and Nu genomes co-evolved and maintained the Mt organella replication and energy production through TCA and oxidative phosphorylation .<br><br>CONCLUSION: The assembled and annotated complete mitogenomes of both A. taliensis and A. setaceus provide valuable information for their phylogeny and concerted action of Nu and Mt genomes to maintain the energy production system of Asparagus L. in the context of domestication and adaptation to environmental niches.},
}
@article {pmid39266188,
year = {2024},
author = {Ali, N and Vora, C and Mathuria, A and Kataria, N and Mani, I},
title = {Advances in CRISPR-Cas systems for gut microbiome.},
journal = {Progress in molecular biology and translational science},
volume = {208},
number = {},
pages = {59-81},
doi = {10.1016/bs.pmbts.2024.07.008},
pmid = {39266188},
issn = {1878-0814},
mesh = {*CRISPR-Cas Systems/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; Animals ; Gene Editing ; Probiotics/therapeutic use ; },
abstract = {CRISPR-Cas technology has revolutionized microbiome research by enabling precise genetic manipulation of microbial communities. This review explores its diverse applications in gut microbiome studies, probiotic development, microbiome diagnostics, pathogen targeting, and microbial community engineering. Engineered bacteriophages and conjugative probiotics exemplify CRISPR-Cas's capability for targeted bacterial manipulation, offering promising strategies against antibiotic-resistant infections and other gut-related disorders. CRISPR-Cas systems also enhance probiotic efficacy by improving stress tolerance and colonization in the gastrointestinal tract. CRISPR-based techniques in diagnostics enable early intervention by enabling fast and sensitive pathogen identification. Furthermore, CRISPR-mediated gene editing allows tailored modification of microbial populations, mitigating risks associated with horizontal gene transfer and enhancing environmental and health outcomes. Despite its transformative potential, ethical and regulatory challenges loom large, demanding robust frameworks to guide its responsible application. This chapter highlights CRISPR-Cas's pivotal role in advancing microbiome research toward personalized medicine and microbial therapeutics while emphasizing the imperative of balanced ethical deliberations and comprehensive regulatory oversight.},
}
@article {pmid39266183,
year = {2024},
author = {Mathuria, A and Vora, C and Ali, N and Mani, I},
title = {Advances in CRISPR-Cas systems for human bacterial disease.},
journal = {Progress in molecular biology and translational science},
volume = {208},
number = {},
pages = {19-41},
doi = {10.1016/bs.pmbts.2024.07.013},
pmid = {39266183},
issn = {1878-0814},
mesh = {*CRISPR-Cas Systems/genetics ; Humans ; *Bacterial Infections/microbiology/genetics ; Gene Editing ; Bacteria/genetics ; },
abstract = {Prokaryotic adaptive immune systems called CRISPR-Cas systems have transformed genome editing by allowing for precise genetic alterations through targeted DNA cleavage. This system comprises CRISPR-associated genes and repeat-spacer arrays, which generate RNA molecules that guide the cleavage of invading genetic material. CRISPR-Cas is classified into Class 1 (multi-subunit effectors) and Class 2 (single multi-domain effectors). Its applications span combating antimicrobial resistance (AMR), targeting antibiotic resistance genes (ARGs), resensitizing bacteria to antibiotics, and preventing horizontal gene transfer (HGT). CRISPR-Cas3, for example, effectively degrades plasmids carrying resistance genes, providing a precise method to disarm bacteria. In the context of ESKAPE pathogens, CRISPR technology can resensitize bacteria to antibiotics by targeting specific resistance genes. Furthermore, in tuberculosis (TB) research, CRISPR-based tools enhance diagnostic accuracy and facilitate precise genetic modifications for studying Mycobacterium tuberculosis. CRISPR-based diagnostics, leveraging Cas endonucleases' collateral cleavage activity, offer highly sensitive pathogen detection. These advancements underscore CRISPR's transformative potential in addressing AMR and enhancing infectious disease management.},
}
@article {pmid39264185,
year = {2024},
author = {Magar, S and Kolte, V and Sharma, G and Govindarajan, S},
title = {Exploring pangenomic diversity and CRISPR-Cas evasion potential in jumbo phages: a comparative genomics study.},
journal = {Microbiology spectrum},
volume = {12},
number = {10},
pages = {e0420023},
pmid = {39264185},
issn = {2165-0497},
support = {/WT_/Wellcome Trust/United Kingdom ; //DST-INSPIRE Faculty Grant/ ; IA/E/19/1/504958//Wellcome Trust DBT India Alliance (India Alliance)/ ; CRG/2020/003295//DST | Science and Engineering Research Board (SERB)/ ; },
mesh = {*Genomics ; *Genetic Variation ; *CRISPR-Cas Systems ; *Bacteriophages/genetics ; *Genome, Viral ; Molecular Sequence Annotation ; Viral Proteins/genetics ; Phylogeny ; Genes, Viral ; Gene Regulatory Networks ; *Immune Evasion/genetics ; },
abstract = {UNLABELLED: Jumbo phages are characterized by their remarkably large-sized genome and unique life cycles. Jumbo phages belonging to Chimalliviridae family protect the replicating phage DNA from host immune systems like CRISPR-Cas and restriction-modification system through a phage nucleus structure. Several recent studies have provided new insights into jumbo phage infection biology, but the pan-genome diversity of jumbo phages and their relationship with CRISPR-Cas targeting beyond Chimalliviridae are not well understood. In this study, we used pan-genome analysis to identify orthologous gene families shared among 331 jumbo phages with complete genomes. We show that jumbo phages lack a universally conserved set of core genes but identified seven "soft-core genes" conserved in over 50% of these phages. These genes primarily govern DNA-related activities, such as replication, repair, or nucleotide synthesis. Jumbo phages exhibit a wide array of accessory and unique genes, underscoring their genetic diversity. Phylogenetic analyses of the soft-core genes revealed frequent horizontal gene transfer events between jumbo phages, non-jumbo phages, and occasionally even giant eukaryotic viruses, indicating a polyphyletic evolutionary nature. We categorized jumbo phages into 11 major viral clusters (VCs) spanning 130 sub-clusters, with the majority being multi-genus jumbo phage clusters. Moreover, through the analysis of hallmark genes related to CRISPR-Cas targeting, we predict that many jumbo phages can evade host immune systems using both known and yet-to-be-identified mechanisms. In summary, our study enhances our understanding of jumbo phages, shedding light on their pan-genome diversity and remarkable genome protection capabilities.<br><br>IMPORTANCE: Jumbo phages are large bacterial viruses known for more than 50 years. However, only in recent years, a significant number of complete genome sequences of jumbo phages have become available. In this study, we employed comparative genomic approaches to investigate the genomic diversity and genome protection capabilities of the 331 jumbo phages. Our findings revealed that jumbo phages exhibit high genetic diversity, with only a few genes being relatively conserved across jumbo phages. Interestingly, our data suggest that jumbo phages employ yet-to-be-identified strategies to protect their DNA from the host immune system, such as CRISPR-Cas.},
}
@article {pmid39264161,
year = {2024},
author = {Matsumoto, S and Kishida, K and Nonoyama, S and Sakai, K and Tsuda, M and Nagata, Y and Ohtsubo, Y},
title = {Evolution of the Tn4371 ICE family: traR-mediated coordination of cargo gene upregulation and horizontal transfer.},
journal = {Microbiology spectrum},
volume = {12},
number = {10},
pages = {e0060724},
pmid = {39264161},
issn = {2165-0497},
support = {K-2016-004//Institute for Fermentation, Osaka (IFO)/ ; 19H02865//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22H02233//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22K19124//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 19K15725//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
mesh = {*Gene Transfer, Horizontal ; *DNA Transposable Elements/genetics ; *Gene Expression Regulation, Bacterial ; Bacterial Proteins/genetics/metabolism ; Evolution, Molecular ; Operon ; Up-Regulation ; Conjugation, Genetic ; },
abstract = {ICEKKS102Tn4677 carries a bph operon for the mineralization of polychlorinated biphenyls (PCBs)/biphenyl and belongs to the Tn4371 ICE (integrative and conjugative element) family. In this study, we investigated the role of the traR gene in ICE transfer. The traR gene encodes a LysR-type transcriptional regulator, which is conserved in sequence, positioning, and directional orientation among Tn4371 family ICEs. The traR belongs to the bph operon, and its overexpression on solid medium resulted in modest upregulation of traG (threefold), marked upregulation of xis (80-fold), enhanced ICE excision and, most notably, ICE transfer frequency. We propose the evolutional roles of traR, which upon insertion to its current position, might have connected the cargo gene activation and ICE transfer. This property of ICE, i.e., undergoing transfer under environmental conditions that lead to cargo gene activation, would instantly confer fitness advantages to bacteria newly acquiring this ICE, thereby resulting in efficient dissemination of the Tn4371 family ICEs.IMPORTANCEOnly ICEKKS102Tn4677 is proven to transfer among the widely disseminating Tn4371 family integrative and conjugative elements (ICEs) from β and γ-proteobacteria. We showed that the traR gene in ICEKKS102Tn4677, which is conserved in the ICE family with fixed location and direction, is co-transcribed with the cargo gene and activates ICE transfer. We propose that capturing of traR by an ancestral ICE to the current position established the Tn4371 family of ICEs. Our findings provide insights into the evolutionary processes that led to the widespread distribution of the Tn4371 family of ICEs across bacterial species.},
}
@article {pmid39260133,
year = {2024},
author = {Xu, Q and Xie, M and Yang, X and Liu, X and Ye, L and Chen, K and Chan, EW and Chen, S},
title = {Conjugative transmission of virulence plasmid in Klebsiella pneumoniae mediated by a novel IncN-like plasmid.},
journal = {Microbiological research},
volume = {289},
number = {},
pages = {127896},
doi = {10.1016/j.micres.2024.127896},
pmid = {39260133},
issn = {1618-0623},
mesh = {*Klebsiella pneumoniae/genetics/pathogenicity ; *Plasmids/genetics ; Animals ; *Klebsiella Infections/microbiology/transmission ; Virulence/genetics ; *Conjugation, Genetic ; Mice ; *Virulence Factors/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Interleukin-1beta/genetics ; Phagocytosis ; Disease Models, Animal ; Macrophages/microbiology ; Female ; Humans ; Type IV Secretion Systems/genetics ; },
abstract = {Klebsiella pneumoniae (Kp) is increasingly recognized as a reservoir for a range of antibiotic resistance genes and a pathogen that frequently causes severe infections in both hospital and community settings. In this study, we have identified a novel mechanism of conjugative transfer of a non-conjugative virulence plasmid through the formation of a fusion plasmid between the virulence plasmid and a novel 59,162 bp IncN- plasmid. This plasmid was found to be a multidrug-resistance (MDR) plasmid and carried a T4SS cluster, which greatly facilitated the efficient horizontal transfer of the fusion plasmid between Kp strains. The fused virulence plasmid conferred the resistance of serum killing and macrophage phagocytosis to the transconjugants. Importantly, this plasmid was shown to be essential for Kp virulence in a mouse model. Mechanistic analysis revealed that the virulence factors encoded by this virulence plasmid contributed to resistance to in vivo clearance and induced a high level of proinflammatory cytokine IL-1β, which acts as an inducer for more neutrophil recruitment. The transmission of the fusion plasmid in Kp has the potential to convert it into both MDR and hypervirulent Kp, accelerating its evolution, and posing a serious threat to human health. The findings of this study provide new insights into the rapid evolution of MDR and hypervirulent Kp in recent years.},
}
@article {pmid39258299,
year = {2024},
author = {Song, W and Li, C and Lu, Y and Shen, D and Jia, Y and Huo, Y and Piao, W and Jin, H},
title = {Chlomito: a novel tool for precise elimination of organelle genome contamination from nuclear genome assembly.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1430443},
pmid = {39258299},
issn = {1664-462X},
abstract = {INTRODUCTION: Accurate reference genomes are fundamental to understanding biological evolution, biodiversity, hereditary phenomena and diseases. However, many assembled nuclear chromosomes are often contaminated by organelle genomes, which will mislead bioinformatic analysis, and genomic and transcriptomic data interpretation.<br><br>METHODS: To address this issue, we developed a tool named Chlomito, aiming at precise identification and elimination of organelle genome contamination from nuclear genome assembly. Compared to conventional approaches, Chlomito utilized new metrics, alignment length coverage ratio (ALCR) and sequencing depth ratio (SDR), thereby effectively distinguishing true organelle genome sequences from those transferred into nuclear genomes via horizontal gene transfer (HGT).<br><br>RESULTS: The accuracy of Chlomito was tested using sequencing data from Plum, Mango and Arabidopsis. The results confirmed that Chlomito can accurately detect contigs originating from the organelle genomes, and the identified contigs covered most regions of the organelle reference genomes, demonstrating efficiency and precision of Chlomito. Considering user convenience, we further packaged this method into a Docker image, simplified the data processing workflow.<br><br>DISCUSSION: Overall, Chlomito provides an efficient, accurate and convenient method for identifying and removing contigs derived from organelle genomes in genomic assembly data, contributing to the improvement of genome assembly quality.},
}
@article {pmid39255666,
year = {2024},
author = {Li, Y and Zheng, Q and Lu, Y and Qiao, Y and Guo, H and Ma, Q and Zhou, J and Li, H and Wang, T},
title = {Water temperature disturbance alters the conjugate transfer of antibiotic resistance genes via affecting ROS content and intercellular aggregation.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135762},
doi = {10.1016/j.jhazmat.2024.135762},
pmid = {39255666},
issn = {1873-3336},
mesh = {*Reactive Oxygen Species/metabolism ; *Temperature ; *Plasmids/genetics ; Drug Resistance, Microbial/genetics ; Water/chemistry ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Gene Transfer, Horizontal ; Escherichia coli/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; Cell Membrane Permeability/drug effects ; Water Microbiology ; },
abstract = {Spread of antibiotic resistance genes (ARGs) in aquatic ecosystems poses a significant global challenge to public health. The potential effects of water temperature perturbation induced by specific water environment changes on ARGs transmission are still unclear. The conjugate transfer of plasmid-mediated ARGs under water temperature perturbation was investigated in this study. The conjugate transfer frequency (CTF) was only 7.16 × 10[-7] at a constant water temperature of 5 °C, and it reached 2.18 × 10[-5] at 30 °C. Interestingly, compared to the constant 5 °C, the water temperature perturbations (cooling and warming models between 5-30 °C) significantly promoted the CTF. Intracellular reactive oxygen species was a dominant factor, which not only directly affected the CTF of ARGs, but also functioned indirectly via influencing the cell membrane permeability and cell adhesion. Compared to the constant 5 °C, water temperature perturbations significantly elevated the gene expression associated with intercellular contact, cell membrane permeability, oxidative stress responses, and energy driven force for CTF. Furthermore, based on the mathematical model predictions, the stabilization times of acquiring plasmid maintenance were shortened to 184 h and 190 h under cooling and warming model, respectively, thus the water temperature perturbations promoted the ARGs transmission in natural conditions compared with the constant low temperature conditions.},
}
@article {pmid39254330,
year = {2024},
author = {Lee, E and Priutt, E and Woods, S and Quick, A and King, S and McLellan, LK and Shields, RC},
title = {Genomic analysis of conjugative and chromosomally integrated mobile genetic elements in oral streptococci.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {10},
pages = {e0136024},
pmid = {39254330},
issn = {1098-5336},
support = {R01 DE033403/DE/NIDCR NIH HHS/United States ; R03 DE029882/DE/NIDCR NIH HHS/United States ; R03DE029882//HHS | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; R01DE033403//HHS | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; },
mesh = {*Interspersed Repetitive Sequences ; *Conjugation, Genetic ; *Streptococcus/genetics ; *Genome, Bacterial ; *Mouth/microbiology ; Genomics ; Chromosomes, Bacterial/genetics ; Humans ; },
abstract = {This study aimed to investigate the diversity of conjugative and chromosomally integrated mobile genetic elements (cciMGEs) within six oral streptococci species. cciMGEs, including integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs), are stably maintained on the host cell chromosome; however, under certain conditions, they are able to excise, form extrachromosomal circles, and transfer via a conjugation apparatus. Many cciMGEs encode "cargo" functions that aid survival in new niches and evolve new antimicrobial resistance or virulence properties, whereas others have been shown to influence host bacterial physiology. Here, using a workflow employing preexisting bioinformatics tools, we analyzed 551 genomes for the presence of cciMGEs across six common health- and disease-associated oral streptococci. We identified 486 cciMGEs, 173 of which were ICEs and 233 of which were IMEs. The cciMGEs were diverse in size, cargo genes, and relaxase types. We identified several novel relaxase proteins and a widespread IME carrying a small multidrug resistance transporter. Additionally, we provide evidence that several of the bioinformatically predicted cciMGEs encoded within various Streptococcus mutans strains are capable of excision and circularization, a critical step for cciMGE conjugative transfer. These findings highlight the significance and potential impact of MGEs in shaping the genetic landscape, pathogenicity, and antimicrobial resistance profiles of the oral microbiota.IMPORTANCEOral streptococci are important players in the oral microbiome, influencing both health and disease states within dental bacterial communities. Evolutionary adaptation, shaped in a major part by the horizontal transfer of genes, is essential for their survival in the oral cavity and within new environments. Conjugation is a significant driver of horizontal gene transfer; however, there is limited information regarding this process in oral bacteria. This study utilizes publicly available genome sequences to identify conjugative and chromosomally integrated mobile genetic elements (cciMGEs) across several species of oral streptococci and presents the preliminary characterization of these elements. Our findings significantly enhance our understanding of the mobile genomic landscape of oral streptococci critical for human health, with valuable insights into how cciMGEs might influence the survival and pathogenesis of these bacteria in the oral microbiome.},
}
@article {pmid39253440,
year = {2025},
author = {Frail, S and Steele-Ogus, M and Doenier, J and Moulin, SLY and Braukmann, T and Xu, S and Yeh, E},
title = {Genomes of nitrogen-fixing eukaryotes reveal a non-canonical model of organellogenesis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39253440},
issn = {2692-8205},
support = {S10 OD030441/OD/NIH HHS/United States ; T32 AI007328/AI/NIAID NIH HHS/United States ; T32 GM007276/GM/NIGMS NIH HHS/United States ; },
abstract = {Endosymbiotic gene transfer and import of host-encoded proteins are considered hallmarks of organelles necessary for stable integration of two cells. However, newer endosymbiotic models have challenged the origin and timing of such genetic integration during organellogenesis. Epithemia diatoms contain diazoplasts, obligate endosymbionts that are closely related to recently-described nitrogen-fixing organelles and share similar function as integral cell compartments. We report genomic analyses of two species which are highly divergent but share a common ancestor at the origin of the endosymbiosis. We found minimal evidence of genetic integration in E.clementina: nonfunctional diazoplast-to-nucleus DNA transfers and 6 host-encoded proteins of unknown function in the diazoplast proteome, far fewer than detected in other recently-acquired endosymbionts designated organelles. Epithemia diazoplasts are a valuable counterpoint to existing organellogenesis models, demonstrating that endosymbionts can function as integral compartments absent significant genetic integration. The minimal genetic integration makes diazoplasts valuable blueprints for bioengineering endosymbiotic compartments de novo.},
}
@article {pmid39249569,
year = {2024},
author = {Ruhal, R and Sahu, A and Koujalagi, T and Das, A and Prasanth, H and Kataria, R},
title = {Biofilm-specific determinants of enterococci pathogen.},
journal = {Archives of microbiology},
volume = {206},
number = {10},
pages = {397},
pmid = {39249569},
issn = {1432-072X},
support = {NA//VIT University/ ; NA//VIT University/ ; NA//VIT University/ ; NA//VIT University/ ; NA//VIT University/ ; NA//VIT University/ ; },
mesh = {*Enterococcus/genetics/metabolism ; *Biofilms ; Gene Expression Regulation, Bacterial ; *Gram-Positive Bacterial Infections/epidemiology/microbiology/physiopathology ; Bacterial Adhesion/genetics ; Adhesins, Bacterial/genetics/metabolism ; Polysaccharides, Bacterial/metabolism ; Gene Transfer, Horizontal ; },
abstract = {Amongst all Enterococcus spp., E. faecalis and E. faecium are most known notorious pathogen and their biofilm formation has been associated with endocarditis, oral, urinary tract, and wound infections. Biofilm formation involves a pattern of initial adhesion, microcolony formation, and mature biofilms. The initial adhesion and microcolony formation involve numerous surface adhesins e.g. pili Ebp and polysaccharide Epa. The mature biofilms are maintained by eDNA, It's worth noting that phage-mediated dispersal plays a prominent role. Further, the involvement of peptide pheromones in regulating biofilm maintenance sets it apart from other pathogens and facilitating the horizontal transfer of resistance genes. The role of fsr based regulation by regulating gelE expression is also discussed. Thus, we provide a concise overview of the significant determinants at each stage of Enterococcus spp. biofilm formation. These elements could serve as promising targets for antibiofilm strategies.},
}
@article {pmid39248569,
year = {2024},
author = {Hassan, J and Hinenoya, A and Hatanaka, N and Awasthi, SP and Manjunath, GB and Rahman, N and Yamate, J and Nakamura, S and Motooka, D and Nagita, A and Faruque, SM and Yamasaki, S},
title = {A plasmid-mediated type III secretion system associated with invasiveness and diarrheagenicity of Providencia rustigianii.},
journal = {mBio},
volume = {15},
number = {10},
pages = {e0229724},
pmid = {39248569},
issn = {2150-7511},
support = {20K07483//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
mesh = {*Providencia/genetics/metabolism/pathogenicity ; *Plasmids/genetics ; Humans ; *Type III Secretion Systems/genetics/metabolism ; Animals ; HeLa Cells ; *Bacterial Toxins/genetics/metabolism ; *Enterobacteriaceae Infections/microbiology ; Rabbits ; Diarrhea/microbiology ; Genome, Bacterial ; Whole Genome Sequencing ; Virulence Factors/genetics ; Virulence/genetics ; Conjugation, Genetic ; Gene Transfer, Horizontal ; },
abstract = {We have recently described a clinical isolate of Providencia rustigianii strain JH-1 carrying the genes for cytolethal distending toxin (CDT) in a conjugative plasmid. A cdtB mutant of strain JH-1, which lost CDT activity, was still found to retain invasiveness and diarrheagenicity. The strain was subjected to phenotypic and genetic analyses including whole genome sequencing (WGS) to explore the genetic determinants of the observed invasiveness and diarrheagenic properties. Analysis and annotation of WGS data revealed the presence of two distinct type III secretion systems (T3SS) in strain JH-1, one of which was located on the chromosome designated as cT3SS (3,992,833 bp) and the other on a mega-plasmid designated as pT3SS (168,819 bp). Comparative genomic analysis revealed that cT3SS is generally conserved in Providencia spp. but pT3SS was limited to a subset of Providencia spp., carrying cdt genes. Strain JH-1 was found to invade HeLa cells and induce fluid accumulation with characteristic pathological lesions in rabbit ileal loops. Remarkably, these phenomena were associated with the pT3SS but not cT3SS. The plasmid could be transferred by conjugation from strain JH-1 to other strains of P. rustigianii, Providencia rettgeri, and Escherichia coli with concomitant transfer of these virulence properties. This is the first report of a functional and mobile T3SS in P. rustigianii and its association with invasiveness and diarrheagenicity of this bacterium. These data suggest that P. rustigianii and other CDT-producing Providencia strains might carry T3SS and exert their diarrheagenic effect by exploiting the T3SS nano-machinery.IMPORTANCEThe precise mechanism of virulence of Providencia rustigianii is unclear, although some strains produce cytolethal distending toxin as a putative virulence factor. We have detected the presence of a type III secretion system (T3SS) for the first time on a plasmid in a P. rustigianii strain. Plasmid-mediated T3SS seems to be directly involved in virulence of P. rustigianii and may serve as a means of horizontal transfer of T3SS genes. Our results may have implication in understanding the mechanism of emergence of new pathogenic strains of P. rustigianii.},
}
@article {pmid39248479,
year = {2024},
author = {Glen, KA and Lamont, IL},
title = {Characterization of acquired β-lactamases in Pseudomonas aeruginosa and quantification of their contributions to resistance.},
journal = {Microbiology spectrum},
volume = {12},
number = {10},
pages = {e0069424},
pmid = {39248479},
issn = {2165-0497},
support = {//University of Otago (Te Whare W&#x101;nanga o Ot&#x101;go)/ ; },
mesh = {*Pseudomonas aeruginosa/drug effects/genetics/enzymology ; *beta-Lactamases/genetics/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; *Carbapenems/pharmacology ; *Pseudomonas Infections/microbiology/drug therapy ; *beta-Lactam Resistance/genetics ; Humans ; beta-Lactams/pharmacology ; Bacterial Proteins/genetics/metabolism ; Plasmids/genetics ; Cephalosporins/pharmacology ; },
abstract = {Pseudomonas aeruginosa is a highly problematic opportunistic pathogen that causes a range of different infections. Infections are commonly treated with β-lactam antibiotics, including cephalosporins, monobactams, penicillins, and carbapenems, with carbapenems regarded as antibiotics of last resort. Isolates of P. aeruginosa can contain horizontally acquired bla genes encoding β-lactamase enzymes, but the extent to which these contribute to β-lactam resistance in this species has not been systematically quantified. The overall aim of this research was to address this knowledge gap by quantifying the frequency of β-lactamase-encoding genes in P. aeruginosa and by determining the effects of β-lactamases on susceptibility of P. aeruginosa to β-lactams. Genome analysis showed that β-lactamase-encoding genes are present in 3% of P. aeruginosa but are enriched in carbapenem-resistant isolates (35%). To determine the substrate antibiotics, 10 β-lactamases were expressed from an integrative plasmid in the chromosome of P. aeruginosa reference strain PAO1. The β-lactamases reduced susceptibility to a variety of clinically used antibiotics, including carbapenems (meropenem, imipenem), penicillins (ticarcillin, piperacillin), cephalosporins (ceftazidime, cefepime), and a monobactam (aztreonam). Different enzymes acted on different β-lactams. β-lactamases encoded by the genomes of P. aeruginosa clinical isolates had similar effects to the enzymes expressed in strain PAO1. Genome engineering was used to delete β-lactamase-encoding genes from three carbapenem-resistant clinical isolates and increased susceptibility to substrate β-lactams. Our findings demonstrate that acquired β-lactamases play an important role in β-lactam resistance in P. aeruginosa, identifying substrate antibiotics for a range of enzymes and quantifying their contributions to resistance.IMPORTANCEPseudomonas aeruginosa is an extremely problematic pathogen, with isolates that are resistant to the carbapenem class of β-lactam antibiotics being in critical need of new therapies. Genes encoding β-lactamase enzymes that degrade β-lactam antibiotics can be present in P. aeruginosa, including carbapenem-resistant isolates. Here, we show that β-lactamase genes are over-represented in carbapenem-resistant isolates, indicating their key role in resistance. We also show that different β-lactamases alter susceptibility of P. aeruginosa to different β-lactam antibiotics and quantify the effects of selected enzymes on β-lactam susceptibility. This research significantly advances the understanding of the contributions of acquired β-lactamases to antibiotic resistance, including carbapenem resistance, in P. aeruginosa and by implication in other species. It has potential to expedite development of methods that use whole genome sequencing of infecting bacteria to inform antibiotic treatment, allowing more effective use of antibiotics, and facilitate the development of new antibiotics.},
}
@article {pmid39245329,
year = {2024},
author = {Zhang, F and Li, Z and Liu, X and Li, Z and Lei, Z and Zhao, J and Zhang, Y and Wu, Y and Yang, X and Lu, B},
title = {In-host intra- and inter-species transfer of blaKPC-2 and blaNDM-1 in Serratia marcescens and its local and global epidemiology.},
journal = {International journal of antimicrobial agents},
volume = {64},
number = {5},
pages = {107327},
doi = {10.1016/j.ijantimicag.2024.107327},
pmid = {39245329},
issn = {1872-7913},
mesh = {*Serratia marcescens/genetics/drug effects/isolation &amp; purification ; *beta-Lactamases/genetics ; Humans ; *Serratia Infections/microbiology/epidemiology ; *Gene Transfer, Horizontal ; *Plasmids/genetics ; *Whole Genome Sequencing ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Phylogeny ; Providencia/genetics/drug effects ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {OBJECTIVES: The aim of this study was to investigate interspecies transfer of resistance gene blaNDM-1 and intraspecies transfer of resistance gene blaKPC-2 in Serratia marcescens, and explore the epidemical and evolutionary characteristics of carbapenemase-producing S. marcescens (CPSM) regionally and globally.<br><br>METHODS: Interspecies and intraspecies transfer of blaKPC-2- or blaNDM-1 were identified by antimicrobial susceptibility testing, plasmid conjugation and curing, discovery of transposable units (TUs), outer membrane vesicles (OMVs), qPCR, whole-genome sequencing (WGS) and bioinformatic analysis. The genomic evolution of CPSM strains was explored by cgSNP and maximum-likelihood phylogenetic tree.<br><br>RESULTS: CPSM S50079 strain, co-carrying blaKPC-2 and blaNDM-1 on one plasmid, was isolated from the blood of a patient with acute pancreatitis and could generate TUs carrying either blaKPC-2 or blaNDM-1. The interspecies transfer of blaNDM-1-carrying plasmid from Providencia rettgeri P50213, producing the identical blaNDM-1-carrying TUs, to S. marcescens S50079K, an S50079 variant via plasmid curing, was identified through blaNDM-1-harbouring plasmid conjugation and OMVs transfer. Moreover, the intraspecies transfer of blaKPC-2, mediated by IS26 from plasmid to chromosome in S50079, was also identified. In another patient, who underwent lung transplantation, interspecies transfer of blaNDM-1 carried by IncX3 plasmid was identified among S. marcescens and Citrobacter freundii as well as Enterobacter hormaechei via plasmid transfer. Furthermore, 11 CPSM from 349 non-repetitive S. marcescens strains were identified in the same hospital, and clonal dissemination, with carbapenemase evolution from blaKPC-2 to both blaKPC-2 and blaNDM-1, was found in the 8 CPSM across 4 years. Finally, the analysis of 236 global CPSM from 835 non-repetitive S. marcescens genomes, retrieved from the NCBI database, revealed long-term spread and evolution worldwide, and would cause the convergence of more carbapenemase genes.<br><br>CONCLUSIONS: Interspecies transfer of resistance gene blaNDM-1 and intraspecies transfer of resistance gene blaKPC-2 in CPSM were identified. Nosocomial and global dissemination of CPSM were revealed and more urgent surveillance was acquired.},
}
@article {pmid39243547,
year = {2024},
author = {Hu, RG and Yang, L and Wang, LY and Yang, YL and Li, HJ and Yang, BT and Kang, YH and Liang, ZL and Cong, W},
title = {Unveiling the pathogenic and multidrug-resistant profiles of Vibrio alfacsensis: A potential identified threat in turbot (Scophthalmus maximus) aquaculture.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135729},
doi = {10.1016/j.jhazmat.2024.135729},
pmid = {39243547},
issn = {1873-3336},
mesh = {Animals ; *Flatfishes/microbiology ; *Vibrio/drug effects/genetics/pathogenicity ; *Aquaculture ; *Fish Diseases/microbiology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Vibrio Infections/microbiology/veterinary ; Phylogeny ; Virulence ; Microbial Sensitivity Tests ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Vibrio alfacsensis is traditionally seen as an environmental symbiont within its genus, with no detailedly documented pathogenicity in marine aquaculture to date. This study delves into the largely unexplored pathogenic potential and emerging antibiotic resistance of V. alfacsensis. The VA-1 strain, isolated from recirculating aquaculture system (RAS) effluent of cultured turbot (Scophthalmus maximus), underwent comprehensive analysis including biochemical identification, antibiotic susceptibility testing and reinfection trials. The results confirmed VA-1's pathogenicity and significant multiple antibiotic resistance. VA-1 could induce systemic infection in turbot, with symptoms like kidney enlargement, exhibiting virulence comparable to known Vibrio pathogens, with an LD50 around 2.36 × 10[6] CFU/fish. VA-1's remarkable resistance phenotype (14/22) suggested potential for genetic exchange and resistance factor acquisition in aquaculture environments. Phylogenetic analysis based on 16S rDNA sequences and whole-genome sequencing has firmly placed VA-1 within the V. alfacsensis clade, while genome-wide analysis highlights its similarity and diversity in relation to strains from across the globe. VA-1 contained numerous replicons, indicating the possibility for the spread of resistance and virulence genes. This study suggests V. alfacsensis may acquire and transfer pathogenic and resistant traits through horizontal gene transfer, a likelihood intensified by changing environmental and aquaculture conditions, highlighting the need for vigilant pathogen monitoring and new non-antibiotic treatments.},
}
@article {pmid39243538,
year = {2024},
author = {Lin, L and Li, L and Yang, X and Hou, L and Wu, D and Wang, B and Ma, B and Liao, X and Yan, X and Gad, M and Su, J and Liu, Y and Liu, K and Hu, A},
title = {Unnoticed antimicrobial resistance risk in Tibetan cities unveiled by sewage metagenomic surveillance: Compared to the eastern Chinese cities.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135730},
doi = {10.1016/j.jhazmat.2024.135730},
pmid = {39243538},
issn = {1873-3336},
mesh = {*Sewage/microbiology ; Tibet ; China ; *Cities ; *Metagenomics ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; },
abstract = {Sewage surveillance is a cost-effective tool for assessing antimicrobial resistance (AMR) in urban populations. However, research on sewage AMR in remote areas is still limited. Here, we used shotgun metagenomic sequencing to profile antibiotic resistance genes (ARGs) and ARG-carrying pathogens (APs) across 15 cities in Tibetan Plateau (TP) and the major cities in eastern China. Notable regional disparities in sewage ARG composition were found, with a significantly higher ARG abundance in TP (2.97 copies/cell). A total of 542 and 545 APs were identified in sewage from TP and the East, respectively, while more than 40 % carried mobile genetic elements (MGEs). Moreover, 65 MGEs-carrying APs were identified as World Health Organization (WHO) priority-like bacterial and fungal pathogens. Notably, a fungal zoonotic pathogen, Enterocytozoon bieneusi, was found for the first time to carry a nitroimidazole resistance gene (nimJ). Although distinct in AP compositions, the relative abundances of APs were comparable in these two regions. Furthermore, sewage in TP was found to be comparable to the cities in eastern China in terms of ARG mobility and AMR risks. These findings provide insights into ARGs and APs distribution in Chinese sewage and stress the importance of AMR surveillance and management strategies in remote regions.},
}
@article {pmid39242818,
year = {2024},
author = {Porras, M&#xc1;G and Assié, A and Tietjen, M and Violette, M and Kleiner, M and Gruber-Vodicka, H and Dubilier, N and Leisch, N},
title = {An intranuclear bacterial parasite of deep-sea mussels expresses apoptosis inhibitors acquired from its host.},
journal = {Nature microbiology},
volume = {9},
number = {11},
pages = {2877-2891},
pmid = {39242818},
issn = {2058-5276},
support = {340535//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; Gottfried Wilhelm Leibniz Prize//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Heisenberggrant GR 5028/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; OIA 1934844//National Science Foundation (NSF)/ ; IOS 2003107//National Science Foundation (NSF)/ ; },
mesh = {Animals ; *Phylogeny ; *Apoptosis ; *Gene Transfer, Horizontal ; Bivalvia/microbiology/parasitology ; Cell Nucleus/metabolism ; Transcriptome ; Bacteroidetes/genetics/metabolism ; Apoptosis Regulatory Proteins/genetics/metabolism ; },
abstract = {A limited number of bacteria are able to colonize the nuclei of eukaryotes. 'Candidatus Endonucleobacter' infects the nuclei of deep-sea mussels, where it replicates to ≥80,000 bacteria per nucleus and causes nuclei to swell to 50 times their original size. How these parasites are able to replicate and avoid apoptosis is not known. Dual RNA-sequencing transcriptomes of infected nuclei isolated using laser-capture microdissection revealed that 'Candidatus Endonucleobacter' does not obtain most of its nutrition from nuclear DNA or RNA. Instead, 'Candidatus Endonucleobacter' upregulates genes for importing and digesting sugars, lipids, amino acids and possibly mucin from its host. It likely prevents apoptosis of host cells by upregulating 7-13 inhibitors of apoptosis, proteins not previously seen in bacteria. Comparative phylogenetic analyses revealed that 'Ca. Endonucleobacter' acquired inhibitors of apoptosis through horizontal gene transfer from their hosts. Horizontal gene transfer from eukaryotes to bacteria is assumed to be rare, but may be more common than currently recognized.},
}
@article {pmid39236811,
year = {2024},
author = {Sun, Z and Hong, W and Xue, C and Dong, N},
title = {A comprehensive review of antibiotic resistance gene contamination in agriculture: Challenges and AI-driven solutions.},
journal = {The Science of the total environment},
volume = {953},
number = {},
pages = {175971},
doi = {10.1016/j.scitotenv.2024.175971},
pmid = {39236811},
issn = {1879-1026},
mesh = {*Agriculture/methods ; *Drug Resistance, Microbial/genetics ; Artificial Intelligence ; Anti-Bacterial Agents ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Wastewater/microbiology ; Animals ; },
abstract = {Since their discovery, the prolonged and widespread use of antibiotics in veterinary and agricultural production has led to numerous problems, particularly the emergence and spread of antibiotic-resistant bacteria (ARB). In addition, other anthropogenic factors accelerate the horizontal transfer of antibiotic resistance genes (ARGs) and amplify their impact. In agricultural environments, animals, manure, and wastewater are the vectors of ARGs that facilitate their spread to the environment and humans via animal products, water, and other environmental pathways. Therefore, this review comprehensively analyzed the current status, removal methods, and future directions of ARGs on farms. This article 1) investigates the origins of ARGs on farms, the pathways and mechanisms of their spread to surrounding environments, and various strategies to mitigate their spread; 2) determines the multiple factors influencing the abundance of ARGs on farms, the pathways through which ARGs spread from farms to the environment, and the effects and mechanisms of non-antibiotic factors on the spread of ARGs; 3) explores methods for controlling ARGs in farm wastes; and 4) provides a comprehensive summary and integration of research across various fields, proposing that in modern smart farms, emerging technologies can be integrated through artificial intelligence to control or even eliminate ARGs. Moreover, challenges and future research directions for controlling ARGs on farms are suggested.},
}
@article {pmid39236533,
year = {2024},
author = {Yuan, Q and Li, W and Goh, SG and Chen, SL and Ng, OT and He, Y and Gin, KY},
title = {Genetic traits and transmission of antimicrobial resistance characteristics of cephalosporin resistant Escherichia coli in tropical aquatic environments.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135707},
doi = {10.1016/j.jhazmat.2024.135707},
pmid = {39236533},
issn = {1873-3336},
mesh = {*Escherichia coli/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; Singapore ; Tropical Climate ; Water Microbiology ; Gene Transfer, Horizontal ; Wastewater/microbiology ; Cephalosporins/pharmacology ; Sewage/microbiology ; Drug Resistance, Bacterial/genetics ; Humans ; Cephalosporin Resistance/genetics ; Aquaculture ; },
abstract = {This study investigates the genetic traits and transmission mechanisms of cephalosporin-resistant Escherichia coli in tropical aquatic environments in Singapore. From 2016 to 2020, monthly samples were collected from wastewater treatment plants, marine niches, community sewage, beaches, reservoirs, aquaculture farms, and hospitals, yielding 557 isolates that were analyzed for antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) using genomic methods. Findings reveal significant genotypic similarities between environmental and hospital-derived strains, particularly the pandemic E. coli ST131. Environmental strains exhibited high levels of intrinsic resistance mechanisms, including mutations in porins and efflux pumps, with key ARGs such as CMY-2 and NDM-9 predominantly carried by MGEs, which facilitate horizontal gene transfer. Notably, pathogenic EPEC and EHEC strains were detected in community sewage and aquaculture farms, posing substantial public health risks. This underscores the critical role of these environments as reservoirs for multidrug-resistant pathogens and emphasizes the interconnectedness of human activities and environmental health.},
}
@article {pmid39236354,
year = {2024},
author = {Brdová, D and Ruml, T and Viktorová, J},
title = {Mechanism of staphylococcal resistance to clinically relevant antibiotics.},
journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy},
volume = {77},
number = {},
pages = {101147},
doi = {10.1016/j.drup.2024.101147},
pmid = {39236354},
issn = {1532-2084},
mesh = {*Anti-Bacterial Agents/pharmacology/therapeutic use ; Humans ; *Staphylococcal Infections/drug therapy/microbiology ; *Staphylococcus aureus/drug effects ; Drug Resistance, Bacterial ; Microbial Sensitivity Tests ; Animals ; },
abstract = {Staphylococcus aureus, a notorious pathogen with versatile virulence, poses a significant challenge to current antibiotic treatments due to its ability to develop resistance mechanisms against a variety of clinically relevant antibiotics. In this comprehensive review, we carefully dissect the resistance mechanisms employed by S. aureus against various antibiotics commonly used in clinical settings. The article navigates through intricate molecular pathways, elucidating the mechanisms by which S. aureus evades the therapeutic efficacy of antibiotics, such as β-lactams, vancomycin, daptomycin, linezolid, etc. Each antibiotic is scrutinised for its mechanism of action, impact on bacterial physiology, and the corresponding resistance strategies adopted by S. aureus. By synthesising the knowledge surrounding these resistance mechanisms, this review aims to serve as a comprehensive resource that provides a foundation for the development of innovative therapeutic strategies and alternative treatments for S. aureus infections. Understanding the evolving landscape of antibiotic resistance is imperative for devising effective countermeasures in the battle against this formidable pathogen.},
}
@article {pmid39235659,
year = {2025},
author = {Fu, Y and Fu, Z and Yu, J and Wang, H and Zhang, Y and Liu, M and Wang, X and Yu, W and Han, F},
title = {Biochemical Characterization of Hyaluronate Lyase CpHly8 from an Intestinal Microorganism Clostridium perfringens G1121.},
journal = {Applied biochemistry and biotechnology},
volume = {197},
number = {2},
pages = {771-792},
pmid = {39235659},
issn = {1559-0291},
support = {2022QNLM030003-1//Qingdao Marine Science and Technology Center/ ; ZR2019ZD18//Natural Science Foundation of Shandong Province/ ; 2018YFC0311105//Shandong Province Technology Innovation Guidance Program/ ; 22-3-6-gjxm-5-gx//Science &amp; Technology Development Project of Qingdao/ ; 21-1-6-gjxm-27-gx//Science &amp; Technology Development Project of Qingdao/ ; 20-11-6-64-gx//Science &amp; Technology Development Project of Qingdao/ ; },
mesh = {*Clostridium perfringens/enzymology/genetics ; *Polysaccharide-Lyases/metabolism/genetics/chemistry ; Animals ; *Hyaluronic Acid/metabolism ; Mice ; *Intestines/microbiology ; *Bacterial Proteins/metabolism/chemistry/genetics ; Hydrogen-Ion Concentration ; },
abstract = {Hyaluronic acid (HA) is an important component of extracellular matrices (ECM) and a linear polysaccharide involved in various physiological and pathological processes within the biological system. Several pathogens exploit HA degradation within the extracellular matrix to facilitate infection. While many intestinal microorganisms play significant roles in HA utilization in the human body, there remains a scarcity of related studies. This paper addressed this gap by screening intestinal microorganisms capable of degrading HA, resulting in the isolation of Clostridium perfringens G1121, which had been demonstrated the ability to degrade HA. Subsequent genome sequencing and analysis of C. perfringens G1121 revealed its utilization of the polysaccharide utilization loci of HA (PULHA), which was obtained by horizontal gene transfer. The PULHA contains a sequence encoding a hyaluronic acid-specific degradation enzyme designated CpHly8, belonging to polysaccharide lyase family 8. The specific activity of CpHly8 towards HA was 142.98 U/mg, with the optimum reaction temperature and pH observed at 50℃ and 6.0, respectively. The final product of HA degradation by CpHly8 was unsaturated hyaluronic acid disaccharide. Moreover, subcutaneous diffusion experiments with trypan blue in mice revealed that CpHly8 effectively promoted subcutaneous diffusion and sustained its effects long-term, suggesting its potential application as an adjunct in drug delivery. Overall, our study enriches our understanding of intestinal microbial degradation of HA, provides new evidence for horizontal gene transfer among intestinal microorganisms, and confirms that CpHly8 is a promising candidate for intestinal microbial hyaluronidase.},
}
@article {pmid39235644,
year = {2024},
author = {Jaswal, R and Dubey, H and Kiran, K and Rawal, H and Kumar, G and Rajarammohan, S and Deshmukh, R and Sonah, H and Prasad, P and Bhardwaj, SC and Gupta, N and Sharma, TR},
title = {Identification and functional characterization of the npc-2-like domain containing rust effector protein that suppresses cell death in plants.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {962},
pmid = {39235644},
issn = {1573-4978},
mesh = {*Plant Diseases/microbiology ; *Phylogeny ; *Cell Death ; *Fungal Proteins/metabolism/genetics ; Nicotiana/microbiology/metabolism/genetics ; Basidiomycota/pathogenicity/metabolism/genetics ; Puccinia/pathogenicity/metabolism ; Protein Domains ; Molecular Docking Simulation ; Onions/microbiology/metabolism/genetics ; },
abstract = {The MD-2-related lipid-recognition (ML/Md-2) domain is a lipid/sterol-binding domain that are involved in sterol transfer and innate immunity in eukaryotes. Here we report a genome-wide survey of this family, identifying 84 genes in 30 fungi including plant pathogens. All the studied species were found to have varied ML numbers, and expansion of the family was observed in Rhizophagus irregularis (RI) with 33 genes. The molecular docking studies of these proteins with cholesterol derivatives indicate lipid-binding functional conservation across the animal and fungi kingdom. The phylogenetic studies among eukaryotic ML proteins showed that Puccinia ML members are more closely associated with animal (insect) npc2 proteins than other fungal ML members. One of the candidates from leaf rust fungus Puccinia triticina, Pt5643 was PCR amplified and further characterized using various studies such as qRT-PCR, subcellular localization studies, yeast functional complementation, signal peptide validation, and expression studies. The Pt5643 exhibits the highest expression on the 5th day post-infection (dpi). The confocal microscopy of Pt5643 in onion epidermal cells and N. benthamiana shows its location in the cytoplasm and nucleus. The functional complementation studies of Pt5643 in npc2 mutant yeast showed its functional similarity to the eukaryotic/yeast npc2 gene. Furthermore, the overexpression of Pt5643 also suppressed the BAX, NEP1, and H2O2-induced program cell death in Nicotiana species and yeast. Altogether the present study reports the novel function of ML domain proteins in plant fungal pathogens and their possible role as effector molecules in host defense manipulation.},
}
@article {pmid39235595,
year = {2024},
author = {Xu, R and Huang, C and Yang, B and Wang, S and Zhong, T and Ma, L and Shang, Q and Zhang, M and Chu, Z and Liu, X},
title = {Influence of Two-Dimensional Black Phosphorus on the Horizontal Transfer of Plasmid-Mediated Antibiotic Resistance Genes: Promotion or Inhibition?.},
journal = {Current microbiology},
volume = {81},
number = {10},
pages = {344},
pmid = {39235595},
issn = {1432-0991},
support = {52070063//National Natural Science Foundation of China/ ; 2308085Y38//Science Fund for Distinguished Young Scholars of Anhui Province/ ; 21-22RC30//Hefei University/ ; },
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Phosphorus/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Conjugation, Genetic ; Escherichia coli/genetics/drug effects ; Nanostructures ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial/drug effects ; Bacteria/genetics/drug effects ; },
abstract = {The problem of bacterial resistance caused by antibiotic abuse is seriously detrimental to global human health and ecosystem security. The two-dimensional nanomaterial (2D) such as black phosphorus (BP) is recently expected to become a new bacterial inhibitor and has been widely used in the antibacterial field due to its specific physicochemical properties. Nevertheless, the effects of 2D-BP on the propagation of antibiotic resistance genes (ARGs) in environments and the relevant mechanisms are not clear. Herein, we observed that the sub-inhibitory concentrations of 2D-BP dramatically increased the conjugative transfer of ARGs mediated by the RP4 plasmid up to 2.6-fold at the 125 mg/L exposure level compared with the untreated bacterial cells. Nevertheless, 2D-BP with the inhibitory concentration caused a dramatic decrease in the conjugative frequency. The phenotypic changes revealed that the increase of the conjugative transfer caused by 2D-BP exposure were attributed to the excessive reactive oxygen species and oxidative stress, and increased bacterial cell membrane permeability. The genotypic evidence demonstrated that 2D-BP affecting the horizontal gene transfer of ARGs was probably through the upregulation of mating pair formation genes (trbBp and traF) and DNA transfer and replication genes (trfAp and traJ), as well as the downregulation of global regulatory gene expression (korA, korB, and trbA). In summary, the changes in the functional and regulatory genes in the conjugative transfer contributed to the stimulation of conjugative transfer. This research aims to broaden our comprehension of how nanomaterials influence the dissemination of ARGs by elucidating their effects and mechanisms.},
}
@article {pmid39233522,
year = {2024},
author = {Lee, JH and Tareen, AR and Kim, NH and Jeong, C and Kang, B and Lee, G and Kim, DW and Zahra, R and Lee, SH},
title = {Comparative Genomic Analyses of E. coli ST2178 Strains Originated from Wild Birds in Pakistan.},
journal = {Journal of microbiology and biotechnology},
volume = {34},
number = {10},
pages = {2041-2048},
pmid = {39233522},
issn = {1738-8872},
mesh = {Animals ; Pakistan ; *Phylogeny ; *Escherichia coli/genetics/isolation &amp; purification/classification ; *Birds/microbiology ; *Genome, Bacterial ; *Virulence Factors/genetics ; *Feces/microbiology ; *Plasmids/genetics ; *Escherichia coli Infections/microbiology/veterinary ; *Animals, Wild/microbiology ; *Genomics ; Humans ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences/genetics ; Whole Genome Sequencing ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The emergence and spread of multidrug-resistance (MDR) pathogenic Escherichia coli due to horizontal gene transfer of antibiotic resistance genes (ARGs) and virulence factors (VFs) is a global health concern, particularly in developing countries. While numerous studies have focused on major sequence types (STs), the implication of minor STs in ARG dissemination and their pathogenicity remains crucial. In this study, two E. coli strains (PEC1011 and PEC1012) were isolated from wild bird feces in Pakistan and identified as ST2178 based on their complete genome sequences. To understand this minor ST, 204 genome assemblies of ST2178 were comparatively analyzed with the isolates' genomes. The phylogenetic analyses revealed five subclades of ST2178. Subclade E strains were predominantly isolated from human specimens, whereas subclades A and B strains including strains PEC1011 and PEC1012, respectively, were frequently isolated from animal. Mobile genetic elements (MGEs) exhibited the positive correlation with ARGs but not with VFs in this ST. Plasmid-borne ARGs exhibited higher correlation with plasmid-borne MGEs, indicating the role of diverse mobile plasmid structures in ARG transmission. Subclade E exhibited diverse plasmid-borne ARG repertoires correlated with MGEs, marking it as a critical surveillance target. In the case of VFs, they exhibited phylogeny-dependent profiles. Strain PEC1012 harbored various plasmid-borne ARGs, which are similar with conserved ARG repertoires in subclade A. The presence of unique ARG insertion in pPEC1012 highlights the importance of subclade A in ARG dissemination. This study comprehensively elucidates the landscape of ST2178, identifying critical phylogenetic subclades and their characteristics in ARG and VF occurrence.},
}
@article {pmid39233087,
year = {2024},
author = {Kong, F and Qi, Z and Tong, H and Ren, N and You, S},
title = {Case study on the relationship between transmission of antibiotic resistance genes and microbial community under freeze-thaw cycle on cold-region dairy farm.},
journal = {The Science of the total environment},
volume = {952},
number = {},
pages = {175989},
doi = {10.1016/j.scitotenv.2024.175989},
pmid = {39233087},
issn = {1879-1026},
mesh = {*Soil Microbiology ; *Dairying ; *Drug Resistance, Microbial/genetics ; *Freezing ; *Microbiota/genetics/drug effects ; Farms ; Gene Transfer, Horizontal ; Genes, Bacterial ; China ; Environmental Monitoring ; },
abstract = {Freeze-thaw cycle (FTC) is a naturally occurring phenomenon in high-latitude terrestrial ecosystems, which may exert influence on distribution and evolution of microbial community in the soil. The relationship between transmission of antibiotic resistance genes (ARGs) and microbial community was investigated upon the case study on the soil of cold-region dairy farm under seasonal FTC. The results demonstrated that 37 ARGs underwent decrease in the abundance of blaTEM from 80.4 % for frozen soil to 71.7 % for thawed soil, and that sul2 from 8.8 % for frozen soil to 6.5 % for thawed soil, respectively. Antibiotic deactivation was identified to be closely related to the highest relative abundance of blaTEM, and the spread of sulfonamide resistance genes (SRGs) occurred mainly via target modification. Firmicutes in frozen soil were responsible for dominating the abundance of ARGs by suppressing the native bacteria under starvation effect in cold regions, and then underwent horizontal gene transfer (HGT) among native bacteria through mobile genetic elements (MGEs). The TRB-C (32.6-49.1 %) and tnpA-06 (0.27-7.5 %) were significantly increased in frozen soil, while Int3 (0.67-10.6 %) and tnpA-04 (11.1-19.4 %) were up-regulated in thawed soil. Moreover, the ARGs in frozen soil primarily underwent HGT through MGEs, i.e. TRB-C and tnpA-06, with increased number of Firmicutes serving as carrier. The case study not only demonstrated relationship between transmission of ARGs and microbial community in the soil under practically relevant FTC condition, but also emphasized the importance for formulating better strategies for preventing FTC-induced ARGs in dairy farm in cold regions.},
}
@article {pmid39231787,
year = {2024},
author = {Baqar, Z and Sinwat, N and Prathan, R and Chuanchuen, R},
title = {Meat ducks as carriers of antimicrobial-resistant Escherichia coli harboring transferable R plasmids.},
journal = {Journal of veterinary science},
volume = {25},
number = {5},
pages = {e62},
pmid = {39231787},
issn = {1976-555X},
support = {N42A660897/NRCT/National Research Council of Thailand/Thailand ; },
mesh = {Animals ; *Ducks ; *Escherichia coli/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; Drug Resistance, Bacterial/genetics ; Escherichia coli Infections/veterinary/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Poultry Diseases/microbiology ; Microbial Sensitivity Tests ; R Factors/genetics ; Gene Transfer, Horizontal ; },
abstract = {IMPORTANCE: Antimicrobial resistance (AMR) is a serious public health threat. AMR bacteria and their resistance determinants in food can be transmitted to humans through the food chain and by direct contact and disseminate directly to the environment.<br><br>OBJECTIVE: This study examined the AMR characteristics and transferable R plasmids in Escherichia coli isolated from meat ducks raised in an open-house system.<br><br>METHODS: One hundred seventy-seven (n = 177) commensal E. coli were examined for their antimicrobial susceptibilities and horizontal resistance transfer. The plasmids were examined by PCR-based plasmid replicon typing (PBRT) and plasmid multi-locus sequence typing (pMLST).<br><br>RESULTS: The highest resistance rate was found against ampicillin (AMP, 83.0%) and tetracycline (TET, 81.9%), and most isolates exhibited multidrug resistance (MDR) (86.4%). The R plasmids were conjugally transferred when TET (n = 4), AMP (n = 3), and chloramphenicol (n = 3) were used as a selective pressure. The three isolates transferred resistance genes either in AMP or TET. The blaCTX-M1 gene resided on conjugative plasmids. Five replicon types were identified, of which Inc FrepB was most common in the donors (n = 13, 38.4%) and transconjugants (n = 16, 31.2%). Subtyping F plasmids revealed five distinct replicons combinations, including F47:A-:B- (n = 2), F29:A-:B23 (n = 1), F29:A-:B- (n = 1), F18:A-B:- (n = 1), and F4:A-:B- (n = 1). The chloramphenicol resistance was significantly correlated with the other AMR phenotypes (p < 0.05).<br><br>CONCLUSIONS AND RELEVANCE: The meat ducks harbored MDR E. coli and played an important role in the environmental dissemination of AMR bacteria and its determinants. This confirms AMR as a health issue, highlighting the need for routine AMR monitoring and surveillance of meat ducks.},
}
@article {pmid39226958,
year = {2024},
author = {Cedeño-Muñoz, JS and Aransiola, SA and Reddy, KV and Ranjit, P and Victor-Ekwebelem, MO and Oyedele, OJ and Pérez-Almeida, IB and Maddela, NR and Rodríguez-Díaz, JM},
title = {Antibiotic resistant bacteria and antibiotic resistance genes as contaminants of emerging concern: Occurrences, impacts, mitigations and future guidelines.},
journal = {The Science of the total environment},
volume = {952},
number = {},
pages = {175906},
doi = {10.1016/j.scitotenv.2024.175906},
pmid = {39226958},
issn = {1879-1026},
mesh = {*Anti-Bacterial Agents ; *Bacteria/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Environmental Monitoring ; Environmental Restoration and Remediation/methods ; },
abstract = {Antibiotic resistance, driven by the proliferation of antibiotic resistance genes (ARGs) and antibiotic resistance bacteria (ARBs), has emerged as a pressing global health concern. Antimicrobial resistance is exacerbated by the widespread use of antibiotics in agriculture, aquaculture, and human medicine, leading to their accumulation in various environmental compartments such as soil, water, and sediments. The presence of ARGs in the environment, particularly in municipal water, animal husbandry, and hospital environments, poses significant risks to human health, as they can be transferred to potential human pathogens. Current remediation strategies, including the use of pyroligneous acid, coagulants, advanced oxidation, and bioelectrochemical systems, have shown promising results in reducing ARGs and ARBs from soil and water. However, these methods come with their own set of challenges, such as the need for elevated base levels in UV-activated persulfate and the long residence period required for photocatalysts. The future of combating antibiotic resistance lies in the development of standardized monitoring techniques, global collaboration, and the exploration of innovative remediation methods. Emphasis on combination therapies, advanced oxidation processes, and monitoring horizontal gene transfer can pave the way for a comprehensive approach to mitigate the spread of antibiotic resistance in the environment.},
}
@article {pmid39224035,
year = {2025},
author = {Chopra, A and Bhuvanagiri, G and Natu, K and Chopra, A},
title = {Role of CRISPR-Cas systems in periodontal disease pathogenesis and potential for periodontal therapy: A review.},
journal = {Molecular oral microbiology},
volume = {40},
number = {1},
pages = {1-16},
pmid = {39224035},
issn = {2041-1014},
mesh = {Humans ; *CRISPR-Cas Systems ; *Periodontal Diseases/therapy/microbiology ; *Gene Editing/methods ; Biofilms ; Bacteria/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Transfer, Horizontal ; Virulence/genetics ; Periodontitis/therapy/microbiology ; Genetic Therapy/methods ; },
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPRs) are DNA sequences capable of editing a host genome sequence. CRISPR and its specific CRISPR-associated (Cas) protein complexes have been adapted for various applications. These include activating or inhibiting specific genetic sequences or acting as molecular scissors to cut and modify the host DNA precisely. CRISPR-Cas systems are also naturally present in many oral bacteria, where they aid in nutrition, biofilm formation, inter- and intraspecies communication (quorum sensing), horizontal gene transfer, virulence, inflammation modulation, coinfection, and immune response evasion. It even functions as an adaptive immune system, defending microbes against invading viruses and foreign genetic elements from other bacteria by targeting and degrading their DNA. Recently, CRISPR-Cas systems have been tested as molecular editing tools to manipulate specific genes linked with periodontal disease (such as periodontitis) and as novel methods of delivering antimicrobial agents to overcome antimicrobial resistance. With the rapidly increasing role of CRISPR in treating inflammatory diseases, its application in periodontal disease is also becoming popular. Therefore, this review aims to discuss the different types of CRISPR-Cas in oral microbes and their role in periodontal disease pathogenesis and precision periodontal therapy.},
}
@article {pmid39223450,
year = {2024},
author = {Valerio, F and Martel, C and Stefanescu, C and van Nouhuys, S and Kankare, M and Duplouy, A},
title = {Wolbachia strain diversity in a complex group of sympatric cryptic parasitoid wasp species.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {319},
pmid = {39223450},
issn = {1471-2180},
mesh = {Animals ; *Wolbachia/genetics/classification/isolation &amp; purification ; *Wasps/microbiology ; *Symbiosis ; *Phylogeny ; Sympatry ; Gene Transfer, Horizontal ; Genetic Variation ; Lepidoptera/microbiology/parasitology ; },
abstract = {BACKGROUND: Maternally-inherited symbionts can induce pre-mating and/or post-mating reproductive isolation between sympatric host lineages, and speciation, by modifying host reproductive phenotypes. The large parasitoid wasp genus Cotesia (Braconidae) includes a diversity of cryptic species, each specialized in parasitizing one to few related Lepidoptera host species. Here, we characterized the infection status of an assemblage of 21 Cotesia species from 15 countries by several microbial symbionts, as a first step toward investigating whether symbionts may provide a barrier to gene flow between these parasitoid host lineages.<br><br>RESULTS: The symbiotic microbes Arsenophonus, Cardinium, Microsporidium and Spiroplasma were not detected in the Cotesia wasps. However, the endosymbiotic bacterium Wolbachia was present in at least eight Cotesia species, and hence we concentrated on it upon screening additional DNA extracts and SRAs from NCBI. Some of the closely related Cotesia species carry similar Wolbachia strains, but most Wolbachia strains showed patterns of horizontal transfer between phylogenetically distant host lineages.<br><br>CONCLUSIONS: The lack of co-phylogenetic signal between Wolbachia and Cotesia suggests that the symbiont and hosts have not coevolved to an extent that would drive species divergence between the Cotesia host lineages. However, as the most common facultative symbiont of Cotesia species, Wolbachia may still function as a key-player in the biology of the parasitoid wasps. Its precise role in the evolution of this complex clade of cryptic species remains to be experimentally investigated.},
}
@article {pmid39222343,
year = {2024},
author = {Lyulina, AS and Liu, Z and Good, BH},
title = {Linkage equilibrium between rare mutations.},
journal = {Genetics},
volume = {228},
number = {3},
pages = {},
pmid = {39222343},
issn = {1943-2631},
support = {R35 GM146949/GM/NIGMS NIH HHS/United States ; FG-2021-15708//Alfred P. Sloan Foundation/ ; R35GM146949/GM/NIGMS NIH HHS/United States ; },
mesh = {*Models, Genetic ; *Recombination, Genetic ; *Mutation ; *Selection, Genetic ; Genetic Linkage ; Genetic Drift ; Evolution, Molecular ; Gene Transfer, Horizontal ; },
abstract = {Recombination breaks down genetic linkage by reshuffling existing variants onto new genetic backgrounds. These dynamics are traditionally quantified by examining the correlations between alleles, and how they decay as a function of the recombination rate. However, the magnitudes of these correlations are strongly influenced by other evolutionary forces like natural selection and genetic drift, making it difficult to tease out the effects of recombination. Here, we introduce a theoretical framework for analyzing an alternative family of statistics that measure the homoplasy produced by recombination. We derive analytical expressions that predict how these statistics depend on the rates of recombination and recurrent mutation, the strength of negative selection and genetic drift, and the present-day frequencies of the mutant alleles. We find that the degree of homoplasy can strongly depend on this frequency scale, which reflects the underlying timescales over which these mutations occurred. We show how these scaling properties can be used to isolate the effects of recombination and discuss their implications for the rates of horizontal gene transfer in bacteria.},
}
@article {pmid39221153,
year = {2024},
author = {Belay, WY and Getachew, M and Tegegne, BA and Teffera, ZH and Dagne, A and Zeleke, TK and Abebe, RB and Gedif, AA and Fenta, A and Yirdaw, G and Tilahun, A and Aschale, Y},
title = {Mechanism of antibacterial resistance, strategies and next-generation antimicrobials to contain antimicrobial resistance: a review.},
journal = {Frontiers in pharmacology},
volume = {15},
number = {},
pages = {1444781},
pmid = {39221153},
issn = {1663-9812},
abstract = {Antibacterial drug resistance poses a significant challenge to modern healthcare systems, threatening our ability to effectively treat bacterial infections. This review aims to provide a comprehensive overview of the types and mechanisms of antibacterial drug resistance. To achieve this aim, a thorough literature search was conducted to identify key studies and reviews on antibacterial resistance mechanisms, strategies and next-generation antimicrobials to contain antimicrobial resistance. In this review, types of resistance and major mechanisms of antibacterial resistance with examples including target site modifications, decreased influx, increased efflux pumps, and enzymatic inactivation of antibacterials has been discussed. Moreover, biofilm formation, and horizontal gene transfer methods has also been included. Furthermore, measures (interventions) taken to control antimicrobial resistance and next-generation antimicrobials have been discussed in detail. Overall, this review provides valuable insights into the diverse mechanisms employed by bacteria to resist the effects of antibacterial drugs, with the aim of informing future research and guiding antimicrobial stewardship efforts.},
}
@article {pmid39221073,
year = {2024},
author = {Xie, X and Deng, X and Chen, L and Yuan, J and Chen, H and Wei, C and Liu, X and Wuertz, S and Qiu, G},
title = {Integrated genomics provides insights into the evolution of the polyphosphate accumulation trait of Ca. Accumulibacter.},
journal = {Environmental science and ecotechnology},
volume = {20},
number = {},
pages = {100353},
pmid = {39221073},
issn = {2666-4984},
abstract = {Candidatus Accumulibacter, a prominent polyphosphate-accumulating organism (PAO) in wastewater treatment, plays a crucial role in enhanced biological phosphorus removal (EBPR). The genetic underpinnings of its polyphosphate accumulation capabilities, however, remain largely unknown. Here, we conducted a comprehensive genomic analysis of Ca. Accumulibacter-PAOs and their relatives within the Rhodocyclaceae family, identifying 124 core genes acquired via horizontal gene transfer (HGT) at its least common ancestor. Metatranscriptomic analysis of an enrichment culture of Ca. Accumulibacter revealed active transcription of 44 of these genes during an EBPR cycle, notably including the polyphosphate kinase 2 (PPK2) gene instead of the commonly recognized polyphosphate kinase 1 (PPK1) gene. Intriguingly, the phosphate regulon (Pho) genes showed minimal transcriptions, pointing to a distinctive fact of Pho dysregulation, where PhoU, the phosphate signaling complex protein, was not regulating the high-affinity phosphate transport (Pst) system, resulting in continuous phosphate uptake. To prevent phosphate toxicity, Ca. Accumulibacter utilized the laterally acquired PPK2 to condense phosphate into polyphosphate, resulting in the polyphosphate-accumulating feature. This study provides novel insights into the evolutionary emergence of the polyphosphate-accumulating trait in Ca. Accumulibacter, offering potential advancements in understanding the PAO phenotype in the EBPR process.},
}
@article {pmid39219575,
year = {2024},
author = {He, XY and Chen, JM and Li, ZZ},
title = {Complete organelle genomes of the threatened aquatic species Scheuchzeria palustris (Scheuchzeriaceae): Insights into adaptation and phylogenomic placement.},
journal = {Ecology and evolution},
volume = {14},
number = {9},
pages = {e70248},
pmid = {39219575},
issn = {2045-7758},
abstract = {Scheuchzeria palustris, the only species in the Scheuchzeriaceae family, plays a crucial role in methane production and transportation, influencing the global carbon cycle and maintaining ecosystem stability. However, it is now threatened by human activities and global warming. In this study, we generated new organelle genomes for S. palustris, with the plastome (pt) measuring 158,573 bp and the mitogenome (mt) measuring 420,724 bp. We predicted 296 RNA editing sites in mt protein-coding genes (PCGs) and 142 in pt-PCGs. Notably, abundant RNA editing sites in pt-PCGs likely originated from horizontal gene transfer between the plastome and mitogenome. Additionally, we identified positive selection signals in four mt-PCGs (atp4, ccmB, nad3, and sdh4) and one pt-PCG (rps7), which may contribute to the adaptation of S. palustris to low-temperature and high-altitude environments. Furthermore, we identified 35 mitochondrial plastid DNA (MTPT) segments totaling 58,479 bp, attributed to dispersed repeats near most MTPT. Phylogenetic trees reconstructed from mt- and pt-PCGs showed topologies consistent with the APG IV system. However, the conflicting position of S. palustris can be explained by significant differences in the substitution rates of its mt- and pt-PCGs (p < .001). In conclusion, our study provides vital genomic resources to support future conservation efforts and explores the adaptation mechanisms of S. palustris.},
}
@article {pmid39216666,
year = {2024},
author = {Qiu, T and Shen, L and Guo, Y and Gao, M and Gao, H and Li, Y and Zhao, G and Wang, X},
title = {Impact of aeration rate on the transfer range of antibiotic-resistant plasmids during manure composting.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {361},
number = {},
pages = {124851},
doi = {10.1016/j.envpol.2024.124851},
pmid = {39216666},
issn = {1873-6424},
mesh = {*Manure ; *Plasmids/genetics ; *Composting/methods ; *Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Animals ; Pseudomonas putida/genetics ; Drug Resistance, Microbial/genetics ; },
abstract = {Conjugative plasmids are important vectors of mobile antibiotic resvistance genes (ARGs), facilitating their horizontal transfer within the environment. While composting is recognized as an effective method to reduce antibiotics and ARGs in animal manure, its impact on the bacterial host communities containing antibiotic-resistant plasmids remains unclear. In this study, we investigated the permissiveness of bacterial community during composting when challenged with multidrug-resistant conjugative RP4 plasmids, employing Pseudomonas putida as the donor strain. Ultimately, this represents the first exploration of the effects of aeration rates on the range of RP4 plasmid transfer hosts. Transconjugants were analyzed through fluorescent reporter gene-based fluorescence-activated cell sorting and Illumina sequencing. Overall, aeration rates were found to influence various physicochemical parameters of compost, including temperature, pH, total organic matter, total nitrogen, and potassium. Regarding RP4 plasmid host bacteria, the dominant phylum was determined to shift from Bacteroidetes in the raw material to Proteobacteria in the compost. Notably, a moderate-intensity aeration rate (0.05 L/min/L) was found to be more effective in reducing the diversity and richness of the RP4 plasmid host bacterial community. Following composting, the total percentage of dominant transconjugant-related genera decreased by 66.15-76.62%. Ultimately, this study determined that the aeration rate negatively impacts RP4 plasmid host abundance primarily through alterations to the environmental factors during composting. In summary, these findings enhance our understanding of plasmid host bacterial communities under varying composting aeration rates and offer novel insights into preventing the dissemination of ARGs from animal manure to farmland.},
}
@article {pmid39216410,
year = {2024},
author = {Vissapragada, M and Addala, S and Aggunna, M and Sodasani, M and Grandhi, AVKS and Yedidi, RS},
title = {Leveraging the potential of bacterial lateral gene transfer in boosting the efficacy of an edible probiotic prototype yogurt vaccine for COVID-19.},
journal = {Biochemical and biophysical research communications},
volume = {734},
number = {},
pages = {150622},
doi = {10.1016/j.bbrc.2024.150622},
pmid = {39216410},
issn = {1090-2104},
mesh = {*Probiotics/administration &amp; dosage ; *Yogurt/microbiology ; Humans ; *COVID-19 Vaccines/immunology ; *SARS-CoV-2/immunology/genetics ; *COVID-19/prevention &amp; control ; *Spike Glycoprotein, Coronavirus/immunology/genetics ; Lactobacillus/genetics ; Gene Transfer, Horizontal ; Gastrointestinal Microbiome ; Escherichia coli/genetics ; Animals ; },
abstract = {Administration of coronavirus disease-2019 (COVID-19) vaccines with appropriate booster doses through painful injections under clinical supervision was challenging during the recent COVID-19 pandemic. As an alternative solution, we designed a safer, edible probiotic yogurt vaccine prototype (YoVac) that can be orally consumed by circumventing painful injections and clinical supervision. We hypothesized that YoVac prepared using Lactobacillus carrying an antigen coding gene (donor) can transfer the same to other bacteria (recipients) in the human gut microbiome (hgMb) through lateral gene transfer (LGT) for boosted antigen levels potentially triggering a robust immune response. In this study we confirmed the in vitro LGT efficiency of a plasmid (pRBD-Amp[r]) containing severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) spike protein-receptor binding domain (RBD) coding gene along with an ampicillin-resistance gene (selection marker) from the probiotic Lactobacillus (donor) cultured from homemade yogurt to E. coli and Helicobacter pylori (recipients). Both the donor and recipient bacteria not only exhibited ampicillin-resistance from pRBD-Amp[r] but also expressed RBD protein. Furthermore, Lactobacillus isolated from YoVac consistently showed the expression of RBD protein over a period of one month confirming the shelf life of our prototype stored at 4 °C. Taken together, our in vitro results provide a preliminary basis for the potential in vivo transfer of RBD coding gene from YoVac to other bacterial species in the hgMb through LGT and may potentially boost the vaccine dosage by delegating them.},
}
@article {pmid39216330,
year = {2024},
author = {Fernández-Arévalo, U and Fuchs, J and Boll, M and Díaz, E},
title = {Transcriptional regulation of the anaerobic 3-hydroxybenzoate degradation pathway in Aromatoleum sp. CIB.},
journal = {Microbiological research},
volume = {288},
number = {},
pages = {127882},
doi = {10.1016/j.micres.2024.127882},
pmid = {39216330},
issn = {1618-0623},
mesh = {*Gene Expression Regulation, Bacterial ; Anaerobiosis ; *Hydroxybenzoates/metabolism ; *Multigene Family ; Bacterial Proteins/genetics/metabolism ; Promoter Regions, Genetic ; Metabolic Networks and Pathways/genetics ; Operon ; Transcription, Genetic ; Acyl Coenzyme A/metabolism/genetics ; Transcription Factors/metabolism/genetics ; Lignin/metabolism ; },
abstract = {Phenolic compounds are commonly found in anoxic environments, where they serve as both carbon and energy sources for certain anaerobic bacteria. The anaerobic breakdown of m-cresol, catechol, and certain lignin-derived compounds yields the central intermediate 3-hydroxybenzoate/3-hydroxybenzoyl-CoA. In this study, we have characterized the transcription and regulation of the hbd genes responsible for the anaerobic degradation of 3-hydroxybenzoate in the β-proteobacterium Aromatoleum sp. CIB. The hbd cluster is organized in three catabolic operons and a regulatory hbdR gene that encodes a dimeric transcriptional regulator belonging to the TetR family. HbdR suppresses the activity of the three catabolic promoters (PhbdN, PhbdE and PhbdH) by binding to a conserved palindromic operator box (ATGAATGAN4TCATTCAT). 3-Hydroxybenzoyl-CoA, the initial intermediate of the 3-hydroxybenzoate degradation pathway, along with benzoyl-CoA, serve as effector molecules that bind to HbdR inducing the expression of the hbd genes. Moreover, the hbd genes are subject to additional regulation influenced by the presence of non-aromatic carbon sources (carbon catabolite repression), and their expression is induced in oxygen-deprived conditions by the AcpR transcriptional activator. The prevalence of the hbd cluster among members of the Aromatoleum/Thauera bacterial group, coupled with its association with mobile genetic elements, suggests acquisition through horizontal gene transfer. These findings significantly enhance our understanding of the regulatory mechanisms governing the hbd gene cluster in bacteria, paving the way for further exploration into the anaerobic utilization/valorization of phenolic compounds derived from lignin.},
}
@article {pmid39214976,
year = {2024},
author = {Yi, X and Liang, JL and Wen, P and Jia, P and Feng, SW and Liu, SY and Zhuang, YY and Guo, YQ and Lu, JL and Zhong, SJ and Liao, B and Wang, Z and Shu, WS and Li, JT},
title = {Giant viruses as reservoirs of antibiotic resistance genes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7536},
pmid = {39214976},
issn = {2041-1723},
mesh = {*Phylogeny ; *Giant Viruses/genetics ; *Genome, Viral/genetics ; Drug Resistance, Microbial/genetics ; Bacteriophages/genetics/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; Metagenome/genetics ; Gene Transfer, Horizontal ; Trimethoprim/pharmacology ; Drug Resistance, Bacterial/genetics ; },
abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs; also called giant viruses), constituting the phylum Nucleocytoviricota, can infect a wide range of eukaryotes and exchange genetic material with not only their hosts but also prokaryotes and phages. A few NCLDVs were reported to encode genes conferring resistance to beta‑lactam, trimethoprim, or pyrimethamine, suggesting that they are potential vehicles for the transmission of antibiotic resistance genes (ARGs) in the biome. However, the incidence of ARGs across the phylum Nucleocytoviricota, their evolutionary characteristics, their dissemination potential, and their association with virulence factors remain unexplored. Here, we systematically investigated ARGs of 1416 NCLDV genomes including those of almost all currently available cultured isolates and high-quality metagenome-assembled genomes from diverse habitats across the globe. We reveal that 39.5% of them carry ARGs, which is approximately 37 times higher than that for phage genomes. A total of 12 ARG types are encoded by NCLDVs. Phylogenies of the three most abundant NCLDV-encoded ARGs hint that NCLDVs acquire ARGs from not only eukaryotes but also prokaryotes and phages. Two NCLDV-encoded trimethoprim resistance genes are demonstrated to confer trimethoprim resistance in Escherichia coli. The presence of ARGs in NCLDV genomes is significantly correlated with mobile genetic elements and virulence factors.},
}
@article {pmid39214865,
year = {2024},
author = {Fonseca, DR and Day, LA and Crone, KK and Costa, KC},
title = {An Extracellular, Ca[2+]-Activated Nuclease (EcnA) Mediates Transformation in a Naturally Competent Archaeon.},
journal = {Molecular microbiology},
volume = {122},
number = {4},
pages = {477-490},
doi = {10.1111/mmi.15311},
pmid = {39214865},
issn = {1365-2958},
support = {MCB-2148165//National Science Foundation/ ; },
mesh = {*Methanococcus/genetics/metabolism/enzymology ; *Calcium/metabolism ; *DNA, Single-Stranded/metabolism/genetics ; Archaeal Proteins/metabolism/genetics ; Endonucleases/metabolism/genetics ; Archaea/genetics/metabolism/enzymology ; DNA, Archaeal/genetics/metabolism ; },
abstract = {Transformation, the uptake of DNA directly from the environment, is a major driver of gene flow in microbial populations. In bacteria, DNA uptake requires a nuclease that processes dsDNA to ssDNA, which is subsequently transferred into the cell and incorporated into the genome. However, the process of DNA uptake in archaea is still unknown. Previously, we cataloged genes essential to natural transformation in Methanococcus maripaludis, but few homologs of bacterial transformation-associated genes were identified. Here, we characterize one gene, MMJJ_16440 (named here as ecnA), to be an extracellular nuclease. We show that EcnA is Ca[2+]-activated, present on the cell surface, and essential for transformation. While EcnA can degrade several forms of DNA, the highest activity was observed with ssDNA as a substrate. Activity was also observed with circular dsDNA, suggesting that EcnA is an endonuclease. This is the first biochemical characterization of a transformation-associated protein in a member of the archaeal domain and suggests that both archaeal and bacterial transformation initiate in an analogous fashion.},
}
@article {pmid39214042,
year = {2024},
author = {Li, G and Long, TF and Zhou, SY and Xia, LJ and Gao, A and Wan, L and Diao, XY and He, YZ and Sun, RY and Yang, JT and Tang, SQ and Ren, H and Fang, LX and Liao, XP and Liu, YH and Chen, L and Sun, J},
title = {CRISPR-AMRtracker: A novel toolkit to monitor the antimicrobial resistance gene transfer in fecal microbiota.},
journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy},
volume = {77},
number = {},
pages = {101142},
doi = {10.1016/j.drup.2024.101142},
pmid = {39214042},
issn = {1532-2084},
mesh = {*Feces/microbiology ; Humans ; *CRISPR-Cas Systems/genetics ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Gene Transfer, Horizontal ; *Plasmids/genetics ; Animals ; Bacteria/genetics/drug effects ; RNA, Ribosomal, 16S/genetics ; Microbiota/drug effects/genetics ; Gastrointestinal Microbiome/drug effects/genetics ; Drug Resistance, Microbial/genetics ; },
abstract = {The spread of antibiotic resistance genes (ARGs), particularly those carried on plasmids, poses a major risk to global health. However, the extent and frequency of ARGs transfer in microbial communities among human, animal, and environmental sectors is not well understood due to a lack of effective tracking tools. We have developed a novel fluorescent tracing tool, CRISPR-AMRtracker, to study ARG transfer. It combines CRISPR/Cas9 fluorescence tagging, fluorescence-activated cell sorting, 16S rRNA gene sequencing, and microbial community analysis. CRISPR-AMRtracker integrates a fluorescent tag immediately downstream of ARGs, enabling the tracking of ARG transfer without compromising the host cell's antibiotic susceptibility, fitness, conjugation, and transposition. Notably, our experiments demonstrate that sfGFP-tagged plasmid-borne mcr-1 can transfer across diverse bacterial species within fecal samples. This innovative approach holds the potential to illuminate the dynamics of ARG dissemination and provide valuable insights to shape effective strategies in mitigating the escalating threat of antibiotic resistance.},
}
@article {pmid39213533,
year = {2024},
author = {Zeng, Q and Wu, X and Song, M and Jiang, L and Zeng, Q and Qiu, R and Luo, C},
title = {Opposite Effects of Planting on Antibiotic Resistomes in Rhizosphere Soil with Different Sulfamethoxazole Levels.},
journal = {Journal of agricultural and food chemistry},
volume = {72},
number = {36},
pages = {19957-19965},
doi = {10.1021/acs.jafc.4c04258},
pmid = {39213533},
issn = {1520-5118},
mesh = {*Sulfamethoxazole/pharmacology/metabolism ; *Rhizosphere ; *Soil Microbiology ; *Glycine max/growth &amp; development/metabolism/chemistry/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification/drug effects/growth &amp; development ; Soil/chemistry ; Drug Resistance, Bacterial/genetics ; Plant Roots/microbiology/metabolism/chemistry/growth &amp; development ; Soil Pollutants/metabolism ; },
abstract = {Achieving consensus about the rhizosphere effect on soil antibiotic resistomes is challenging due to the variability in antibiotic concentrations, sources, and the elusory underlying mechanisms. Here, we characterized the antibiotic resistomes in both the rhizosphere and bulk soils of soybean plants grown in environments with varying levels of antibiotic contamination, using sulfamethoxazole (SMX) as a model compound. We also investigated the factors influencing resistome profiles. Soybean cultivation altered the structure of antibiotic-resistant genes (ARGs) and increased their absolute abundance. However, the rhizosphere effect on the relative abundance of ARGs was dependent on SMX concentrations. At low SMX levels, the rhizosphere effect was characterized by the inhibition of antibiotic-resistant bacteria (ARBs) and the promotion of sensitive bacteria. In contrast, at high SMX levels, the rhizosphere promoted the growth of ARBs and facilitated horizontal gene transfer of ARGs. This novel mechanism provides new insights into accurately assessing the rhizosphere effect on soil antibiotic resistomes.},
}
@article {pmid39213158,
year = {2024},
author = {Ma, Y and Kan, A and Johnson, DR},
title = {Metabolic interactions control the transfer and spread of plasmid-encoded antibiotic resistance during surface-associated microbial growth.},
journal = {Cell reports},
volume = {43},
number = {9},
pages = {114653},
doi = {10.1016/j.celrep.2024.114653},
pmid = {39213158},
issn = {2211-1247},
mesh = {*Plasmids/metabolism/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics/metabolism/growth &amp; development ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; },
abstract = {Surface-associated microbial systems are hotspots for the spread of plasmid-encoded antibiotic resistance, but how surface association affects plasmid transfer and proliferation remains unclear. Surface association enables prolonged spatial proximities between different populations, which promotes plasmid transfer between them. However, surface association also fosters strong metabolic interactions between different populations, which can direct their spatial self-organization with consequences for plasmid transfer and proliferation. Here, we hypothesize that metabolic interactions direct the spatial self-organization of different populations and, in turn, regulate the spread of plasmid-encoded antibiotic resistance. We show that resource competition causes populations to spatially segregate, which represses plasmid transfer. In contrast, resource cross-feeding causes populations to spatially intermix, which promotes plasmid transfer. We further show that the spatial positionings that emerge from metabolic interactions determine the proliferation of plasmid recipients. Our results demonstrate that metabolic interactions are important regulators of both the transfer and proliferation of plasmid-encoded antibiotic resistance.},
}
@article {pmid39213152,
year = {2024},
author = {Cordero, M and Jauffred, L},
title = {Following plasmid propagation in complex bacterial communities.},
journal = {Cell reports},
volume = {43},
number = {9},
pages = {114675},
doi = {10.1016/j.celrep.2024.114675},
pmid = {39213152},
issn = {2211-1247},
mesh = {*Plasmids/genetics/metabolism ; *Gene Transfer, Horizontal ; *Bacteria/genetics/metabolism ; Conjugation, Genetic ; },
abstract = {In this issue of Cell Reports, Ma et al.[1] identify causative regulatory links between self-organization in surface-attached bacterial colonies and the rate of horizontal gene transfers (conjugations) and subsequent selection of the newly arising population of recipient bacteria (transconjugants).},
}
@article {pmid39211246,
year = {2024},
author = {Hughes Lago, C and Blackburn, D and Kinder Pavlicek, M and Threadgill, DS},
title = {Comparative Genomic Analysis of Campylobacter rectus and Closely Related Species.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.07.26.605372},
pmid = {39211246},
issn = {2692-8205},
abstract = {Campylobacter rectus is a gram-negative, anaerobic bacterium strongly associated with periodontitis. It also causes various extraoral infections and is linked to adverse pregnancy outcomes in humans and murine models. C. rectus and related oral Campylobacters have been termed "emerging Campylobacter species" because infections by these organisms are likely underreported. Previously, no comparative methods have been used to analyze more than single C. rectus strains and until recently, very few C. rectus genomes have been publicly available. More sequenced genomes and comparative analyses are needed to study the genomic features and pathogenicity of this species. We sequenced eight new C. rectus strains and used comparative methods to identify regions of interest. An emphasis was put on the type III flagellar secretion system (T3SS), type IV secretion system (T4SS), and type VI secretion system (T6SS) because these protein complexes are important for pathogenesis in other Campylobacter species. RAST, BV-BRC, and other bioinformatics tools were used to assemble, annotate, and compare these regions in the genomes. The pan-genome of C. rectus consists of 2670 genes with core and accessory genomes of 1429 and 1241 genes, respectively. All isolates analyzed in this study have T3SS and T6SS hallmark proteins, while five of the isolates are missing a T4SS system. Twenty-one prophage clusters were identified across the panel of isolates, including four that appear intact. Overall, significant genomic islands were found, suggesting regions in the genomes that underwent horizontal gene transfer. Additionally, the high frequency of CRISPR arrays and other repetitive elements has led to genome rearrangements across the strains, including in areas adjacent to secretion system gene clusters. This study describes the substantial diversity present among C. rectus isolates and highlights tools/assays that have been developed to permit functional genomic studies. Additionally, we have expanded the studies on C. showae T4SS since we have two new C. showae genomes to report. We also demonstrate that unlike C. rectus , C showae does not demonstrate evidence of intact T6SS except for the strain CAM. The only strain of sequenced C. massilensis has neither T4SS or T6SS.},
}
@article {pmid39211212,
year = {2024},
author = {Marcarian, HQ and Sivakoses, A and Arias, AM and Ihedioha, O and Bishop, MC and Lee, BR and Bothwell, ALM},
title = {Renal cancer cells acquire immune surface protein through trogocytosis and horizontal gene transfer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.08.07.607036},
pmid = {39211212},
issn = {2692-8205},
abstract = {Trogocytosis is an underappreciated phenomenon that shapes the immune microenvironment surrounding many types of solid tumors. The consequences of membrane-bound proteins being deposited from a donor immune cell to a recipient cancer cell via trogocytosis are still unclear. Here, we report that human clear cell renal carcinoma tumors stably express the lymphoid markers CD45, CD56, CD14, and CD16. Flow cytometry performed on fresh kidney tumors revealed consistent CD45 expression on tumor cells, as well as varying levels of the other markers mentioned previously. These results were consistent with our immunofluorescent analysis, which also revealed colocalization of lymphoid markers with carbonic anhydrase 9 (CAIX), a standard kidney tumor marker. RNA analysis showed a significant upregulation of genes typically associated with immune cells in tumor cells following trogocytosis. Finally, we show evidence of chromosomal DNA being transferred from immune cells to tumor cells during trogocytosis. This horizontal gene transfer has transcriptional consequences in the recipient tumor cell, resulting in a fusion phenotype that expressed both immune and cancer specific proteins. This work demonstrates a novel mechanism by which tumor cell protein expression is altered through the acquisition of surface membrane fragments and genomic DNA from infiltrating lymphocytes. These results alter the way in which we understand tumor-immune cell interactions and may reveal new insights into the mechanisms by which tumors develop. Additionally, further studies into trogocytosis will help push the field towards the next generation of immunotherapies and biomarkers for treating renal cell carcinoma and other types of cancers.},
}
@article {pmid39210455,
year = {2024},
author = {Abdellati, S and Gestels, Z and Laumen, JGE and Van Dijck, C and De Baetselier, I and de Block, T and Van den Bossche, D and Vanbaelen, T and Kanesaka, I and Manoharan-Basil, SS and Kenyon, C},
title = {Antimicrobial susceptibility of commensal Neisseria spp. in parents and their children in Belgium: a cross-sectional survey.},
journal = {FEMS microbiology letters},
volume = {371},
number = {},
pages = {},
doi = {10.1093/femsle/fnae069},
pmid = {39210455},
issn = {1574-6968},
support = {PRESTIP//SOFI-B/ ; },
mesh = {Humans ; Belgium/epidemiology ; *Neisseria/drug effects/isolation &amp; purification/genetics ; Cross-Sectional Studies ; Child ; *Anti-Bacterial Agents/pharmacology ; Female ; Child, Preschool ; *Microbial Sensitivity Tests ; Male ; Adult ; *Parents ; Middle Aged ; Adolescent ; Drug Resistance, Bacterial ; Infant ; Oropharynx/microbiology ; Prevalence ; Young Adult ; },
abstract = {BACKGROUND: commensal Neisseria species are part of the oropharyngeal microbiome and play an important role in nitrate reduction and protecting against colonization by pathogenic bacteria. They do, however, also serve as a reservoir of antimicrobial resistance. Little is known about the prevalence of these species in the general population, how this varies by age and how antimicrobial susceptibility varies between species.<br><br>METHODS: we assessed the prevalence and antimicrobial susceptibility of commensal Neisseria species in the parents (n&#xa0;=&#xa0;38) and children (n&#xa0;=&#xa0;50) of 35 families in Belgium.<br><br>RESULTS: various commensal Neisseria (n&#xa0;=&#xa0;5) could be isolated from the participants. Most abundant were N. subflava and N. mucosa. Neisseria subflava was detected in 77 of 88 (87.5%) individuals and N. mucosa in 64 of 88 (72.7%). Neisseria mucosa was more prevalent in children [41/50 (82%)] than parents [23/38 (60.5%); P&#xa0;<&#xa0;.05], while N. bacilliformis was more prevalent in parents [7/36 (19.4%)] than children [2/50 (4%); P&#xa0;<&#xa0;.05]. Neisseria bacilliformis had high ceftriaxone minimum inhibitory concentrations (MICs; median MIC 0.5&#xa0;mg/l; IQR 0.38-0.75). The ceftriaxone MICs of all Neisseria isolates were higher in the parents than in the children. This could be explained by a higher prevalence of N. bacilliformis in the parents.<br><br>INTERPRETATION: the N. bacilliformis isolates had uniformly high ceftriaxone MICs which warrant further investigation.},
}
@article {pmid39208359,
year = {2024},
author = {Ares-Arroyo, M and Coluzzi, C and Moura de Sousa, JA and Rocha, EPC},
title = {Hijackers, hitchhikers, or co-drivers? The mysteries of mobilizable genetic elements.},
journal = {PLoS biology},
volume = {22},
number = {8},
pages = {e3002796},
pmid = {39208359},
issn = {1545-7885},
mesh = {*Gene Transfer, Horizontal ; Interspersed Repetitive Sequences/genetics ; Bacteria/genetics ; Evolution, Molecular ; Genomic Islands ; Symbiosis/genetics ; Genome, Bacterial ; },
abstract = {Mobile genetic elements shape microbial gene repertoires and populations. Recent results reveal that many, possibly most, microbial mobile genetic elements require helpers to transfer between genomes, which we refer to as Hitcher Genetic Elements (hitchers or HGEs). They may be a large fraction of pathogenicity and resistance genomic islands, whose mechanisms of transfer have remained enigmatic for decades. Together with their helper elements and their bacterial hosts, hitchers form tripartite networks of interactions that evolve rapidly within a parasitism-mutualism continuum. In this emerging view of microbial genomes as communities of mobile genetic elements many questions arise. Which elements are being moved, by whom, and how? How often are hitchers costly hyper-parasites or beneficial mutualists? What is the evolutionary origin of hitchers? Are there key advantages associated with hitchers' lifestyle that justify their unexpected abundance? And why are hitchers systematically smaller than their helpers? In this essay, we start answering these questions and point ways ahead for understanding the principles, origin, mechanisms, and impact of hitchers in bacterial ecology and evolution.},
}
@article {pmid39207571,
year = {2024},
author = {Smiatek, J},
title = {Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning.},
journal = {Journal of molecular evolution},
volume = {92},
number = {6},
pages = {703-719},
pmid = {39207571},
issn = {1432-1432},
mesh = {*Evolution, Molecular ; *Thermodynamics ; *Entropy ; *Mutation ; Models, Genetic ; Learning/physiology ; },
abstract = {We present a non-equilibrium thermodynamics approach to the multilevel theory of learning for the study of molecular evolution. This approach allows us to study the explicit time dependence of molecular evolutionary processes and their impact on entropy production. Interpreting the mathematical expressions, we can show that two main contributions affect entropy production of molecular evolution processes which can be identified as mutation and gene transfer effects. Accordingly, our results show that the optimal adaptation of organisms to external conditions in the context of evolutionary processes is driven by principles of minimum entropy production. Such results can also be interpreted as the basis of some previous postulates of the theory of learning. Although our macroscopic approach requires certain simplifications, it allows us to interpret molecular evolutionary processes using thermodynamic descriptions with reference to well-known biological processes.},
}
@article {pmid39207102,
year = {2024},
author = {Zhang, W and Fan, Y and Deng, W and Chen, Y and Wang, S and Kang, S and Steenwyk, JL and Xiang, M and Liu, X},
title = {Characterization of genome-wide phylogenetic conflict uncovers evolutionary modes of carnivorous fungi.},
journal = {mBio},
volume = {15},
number = {10},
pages = {e0213324},
pmid = {39207102},
issn = {2150-7511},
support = {32020103001//MOST | National Natural Science Foundation of China (NSFC)/ ; 32200009//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Phylogeny ; *Genome, Fungal ; *Evolution, Molecular ; *Ascomycota/genetics/classification ; Animals ; Biological Evolution ; Nematoda/genetics/microbiology ; },
abstract = {Mass extinction has often paved the way for rapid evolutionary radiation, resulting in the emergence of diverse taxa within specific lineages. The emergence and diversification of carnivorous nematode-trapping fungi (NTF) in Ascomycota have been linked to the Permian-Triassic (PT) extinction, but the processes underlying NTF radiation remain unclear. We conducted phylogenomic analyses using 23 genomes that represent three NTF lineages, each employing distinct nematode traps-mechanical traps (Drechslerella spp.), three-dimensional (3D) adhesive traps (Arthrobotrys spp.), and two-dimensional (2D) adhesive traps (Dactylellina spp.), and the genome of one non-NTF species as the outgroup. These analyses revealed multiple mechanisms that likely contributed to the tempo of the NTF evolution and rapid radiation. The species tree of NTFs based on 2,944 single-copy orthologous genes suggested that Drechslerella emerged earlier than Arthrobotrys and Dactylellina. Extensive genome-wide phylogenetic discordance was observed, mainly due to incomplete lineage sorting (ILS) between lineages. Two modes of non-vertical evolution (introgression and horizontal gene transfer) also contributed to phylogenetic discordance. The ILS genes that are associated with hyphal growth and trap morphogenesis (e.g., those associated with the cell membrane system and polarized cell division) exhibited signs of positive selection.IMPORTANCEBy conducting a comprehensive phylogenomic analysis of 23 genomes across three NTF lineages, the research reveals how diverse evolutionary mechanisms, including ILS and non-vertical evolution (introgression and horizontal gene transfer), contribute to the swift diversification of NTFs. These findings highlight the complex evolutionary dynamics that drive the rapid radiation of NTFs, providing valuable insights into the processes underlying their diversity and adaptation.},
}
@article {pmid39206372,
year = {2024},
author = {Kirk, A and Stavrinides, J},
title = {Distribution and comparative genomic analysis of antimicrobial gene clusters found in Pantoea.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1416674},
pmid = {39206372},
issn = {1664-302X},
abstract = {Members of the bacterial genus Pantoea produce a variety of antimicrobial products that are effective against plant, animal, and human pathogens. To date, little is known about the distribution and evolutionary history of these clusters. We surveyed the public databases for the 12 currently known antibiotic biosynthetic gene clusters found across Pantoea strains to determine their distribution. We show that some clusters, namely pantocin B, PNP-3, and PNP-4 are found strictly in Pantoea, while agglomerin, andrimid, AGA, dapdiamide, herbicolin, PNP-1, PNP-2, PNP-5, and pantocin A, are more broadly distributed in distantly related genera within Vibrionaceae, Pectobacteriaceae, Yersiniaceae, Morganellaceae, and Hafniaceae. We evaluated the evolutionary history of these gene clusters relative to a cpn60-based species tree, considering the flanking regions of each cluster, %GC, and presence of mobile genetic elements, and identified potential occurrences of horizontal gene transfer. Lastly, we also describe the biosynthetic gene cluster of pantocin B in the strain Pantoea agglomerans Eh318 more than 20 years after this antibiotic was first described.},
}
@article {pmid39203510,
year = {2024},
author = {Lv, N and Ni, J and Fang, S and Liu, Y and Wan, S and Sun, C and Li, J and Zhou, A},
title = {Potential Convergence to Accommodate Pathogenicity Determinants and Antibiotic Resistance Revealed in Salmonella Mbandaka.},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
pmid = {39203510},
issn = {2076-2607},
support = {32260032//National Natural Science Foundation of China/ ; 32370143//National Natural Science Foundation of China/ ; 31800118//National Natural Science Foundation of China/ ; jxsq2019101054//Double Thousand Talents Plan of Jiangxi/ ; },
abstract = {Salmonella species are causal pathogens instrumental in human food-borne diseases. The pandemic survey related to multidrug resistant (MDR) Salmonella genomics enables the prevention and control of their dissemination. Currently, serotype Mbandaka is notorious as a multiple host-adapted non-typhoid Salmonella. However, its epidemic and MDR properties are still obscure, especially its genetic determinants accounting for virulence and MD resistance. Here, we aim to characterize the genetic features of a strain SMEH pertaining to Salmonella Mbandaka (S. Mbandaka), isolated from the patient's hydropericardium, using cell infections, a mouse model, antibiotic susceptibility test and comparative genomics. The antibiotic susceptibility testing showed that it could tolerate four antibiotics, including chloramphenicol, tetracycline, fisiopen and doxycycline by Kirby-Bauer (K-B) testing interpreted according to the Clinical and Laboratory Standards Institute (CLSI). Both the reproducibility in RAW 264.7 macrophages and invasion ability to infect HeLa cells with strain SMEH were higher than those of S. Typhimurium strain 14028S. In contrast, its attenuated virulence was determined in the survival assay using a mouse model. As a result, the candidate genetic determinants responsible for antimicrobial resistance, colonization/adaptability and their transferability were comparatively investigated, such as bacterial secretion systems and pathogenicity islands (SPI-1, SPI-2 and SPI-6). Moreover, collective efforts were made to reveal a potential role of the plasmid architectures in S. Mbandaka as the genetic reservoir to transfer or accommodate drug-resistance genes. Our findings highlight the essentiality of antibiotic resistance and risk assessment in S. Mbandaka. In addition, genomic surveillance is an efficient method to detect pathogens and monitor drug resistance. The genetic determinants accounting for virulence and antimicrobial resistance underscore the increasing clinical challenge of emerging MDR Mbandaka isolates, and provide insights into their prevention and treatment.},
}
@article {pmid39201699,
year = {2024},
author = {Li, H and Liang, T and Liu, Y and Wang, P and Wang, S and Zhao, M and Zhang, Y},
title = {Exploring Mitochondrial Heterogeneity and Evolutionary Dynamics in Thelephora ganbajun through Population Genomics.},
journal = {International journal of molecular sciences},
volume = {25},
number = {16},
pages = {},
pmid = {39201699},
issn = {1422-0067},
support = {31870009//National Natural Science Foundation of China/ ; YNWR-QNBJ-2018-355//Top Young Talents Program of the Ten Thousand Talents Plan in Yunnan Province/ ; 2021KF009//YNCUB/ ; },
mesh = {*Genome, Mitochondrial ; *Evolution, Molecular ; Phylogeny ; Introns/genetics ; Mitochondria/genetics ; Basidiomycota/genetics ; DNA, Mitochondrial/genetics ; Genomics/methods ; Gene Transfer, Horizontal ; },
abstract = {Limited exploration in fungal mitochondrial genetics has uncovered diverse inheritance modes. The mitochondrial genomes are inherited uniparentally in the majority of sexual eukaryotes, our discovery of persistent mitochondrial heterogeneity within the natural population of the basidiomycete fungus Thelephora ganbajun represents a significant advance in understanding mitochondrial inheritance and evolution in eukaryotes. Here, we present a comprehensive analysis by sequencing and assembling the complete mitogenomes of 40 samples exhibiting diverse cox1 heterogeneity patterns from various geographical origins. Additionally, we identified heterogeneous variants in the nad5 gene, which, similar to cox1, displayed variability across multiple copies. Notably, our study reveals a distinct prevalence of introns and homing endonucleases in these heterogeneous genes. Furthermore, we detected potential instances of horizontal gene transfer involving homing endonucleases. Population genomic analyses underscore regional variations in mitochondrial genome composition among natural samples exhibiting heterogeneity. Thus, polymorphisms in heterogeneous genes, introns, and homing endonucleases significantly influence mitochondrial structure, structural variation, and evolutionary dynamics in this species. This study contributes valuable insights into mitochondrial genome architecture, population dynamics, and the evolutionary implications of mitochondrial heterogeneity in sexual eukaryotes.},
}
@article {pmid39200594,
year = {2024},
author = {Habibi, N and Uddin, S and Behbehani, M and Mustafa, AS and Al-Fouzan, W and Al-Sarawi, HA and Safar, H and Alatar, F and Al Sawan, RMZ},
title = {Aerosol-Mediated Spread of Antibiotic Resistance Genes: Biomonitoring Indoor and Outdoor Environments.},
journal = {International journal of environmental research and public health},
volume = {21},
number = {8},
pages = {},
pmid = {39200594},
issn = {1660-4601},
mesh = {*Aerosols/analysis ; *Gene Transfer, Horizontal ; Humans ; Biological Monitoring ; Drug Resistance, Microbial/genetics ; Air Microbiology ; Air Pollution, Indoor/analysis ; Environmental Monitoring ; Anti-Bacterial Agents/analysis ; Drug Resistance, Bacterial/genetics ; },
abstract = {Antimicrobial resistance (AMR) has emerged as a conspicuous global public health threat. The World Health Organization (WHO) has launched the "One-Health" approach, which encourages the assessment of antibiotic resistance genes (ARGs) within an environment to constrain and alleviate the development of AMR. The prolonged use and overuse of antibiotics in treating human and veterinary illnesses, and the inability of wastewater treatment plants to remove them have resulted in elevated concentrations of these metabolites in the surroundings. Microbes residing within these settings acquire resistance under selective pressure and circulate between the air-land interface. Initial evidence on the indoor environments of wastewater treatment plants, hospitals, and livestock-rearing facilities as channels of AMR has been documented. Long- and short-range transport in a downwind direction disseminate aerosols within urban communities. Inhalation of such aerosols poses a considerable occupational and public health risk. The horizontal gene transfer (HGT) is another plausible route of AMR spread. The characterization of ARGs in the atmosphere therefore calls for cutting-edge research. In the present review, we provide a succinct summary of the studies that demonstrated aerosols as a media of AMR transport in the atmosphere, strengthening the need to biomonitor these pernicious pollutants. This review will be a useful resource for environmental researchers, healthcare practitioners, and policymakers to issue related health advisories.},
}
@article {pmid39200027,
year = {2024},
author = {Milani, G and Cortimiglia, C and Belloso Daza, MV and Greco, E and Bassi, D and Cocconcelli, PS},
title = {Microplastic-Mediated Transfer of Tetracycline Resistance: Unveiling the Role of Mussels in Marine Ecosystems.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {8},
pages = {},
pmid = {39200027},
issn = {2079-6382},
support = {PE00000003//Italian Ministry of University and Research funded by the European Union - NextGenerationEU/ ; },
abstract = {The global threat of antimicrobial resistance (AMR) is exacerbated by the mobilization of antimicrobial resistance genes (ARGs) occurring in different environmental niches, including seawater. Marine environments serve as reservoirs for resistant bacteria and ARGs, further complicated by the ubiquity of microplastics (MPs). MPs can adsorb pollutants and promote bacterial biofilm formation, creating conditions favorable to the dissemination of ARGs. This study explores the dynamics of ARG transfer in the marine bivalve Mytilus galloprovincialis within a seawater model, focusing on the influence of polyethylene MPs on the mobilization of the Tn916-carrying tetM gene and plasmid-encoded ermB. Experiments revealed that biofilm formation on MPs by Enterococcus faecium and Listeria monocytogenes facilitated the transfer of the tetM resistance gene, but not the ermB gene. Furthermore, the presence of MPs significantly increased the conjugation frequency of tetM within mussels, indicating that MPs enhance the potential for ARG mobilization in marine environments. These findings highlight the role of MPs and marine organisms in ARG spread, underscoring the ecological and public health implications.},
}
@article {pmid39199982,
year = {2024},
author = {Yao, Y and Imirzalioglu, C and Falgenhauer, L and Falgenhauer, J and Heinmüller, P and , and Domann, E and Chakraborty, T},
title = {Plasmid-Mediated Spread of Carbapenem Resistance in Enterobacterales: A Three-Year Genome-Based Survey.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {8},
pages = {},
pmid = {39199982},
issn = {2079-6382},
abstract = {The worldwide emergence and dissemination of carbapenem-resistant Gram-negative bacteria (CRGNB) is a challenging problem of antimicrobial resistance today. Outbreaks with CRGNB have severe consequences for both the affected healthcare settings as well as the patients with infection. Thus, bloodstream infections caused by metallo-ß-lactamase-producing Enterobacterales can often have clinical implications, resulting in high mortality rates due to delays in administering effective treatment and the limited availability of treatment options. The overall threat of CRGNB is substantial because carbapenems are used to treat infections caused by ESBL-producing Enterobacterales which also exist with high frequency within the same geographical regions. A genome-based surveillance of 589 CRGNB from 61 hospitals across the federal state Hesse in Germany was implemented using next-generation sequencing (NGS) technology to obtain a high-resolution landscape of carbapenem-resistant isolates over a three-year period (2017-2019). The study examined all reportable CRGNB isolates submitted by participating hospitals. This included isolates carrying known carbapenemases (435) together with carbapenem-resistant non-carbapenemase producers (154). Predominant carbapenemase producers included Klebsiella pneumoniae, Escherichia coli, Citrobacter freundii and Acinetobacter baumannii. Over 80% of 375 carbapenem-resistant determinants including KPC-, NDM-, VIM- and OXA-48-like ones detected in 520 Enterobacterales were plasmid-encoded, and half of these were dominated by a few incompatibility (Inc) types, viz., IncN, IncL/M, IncFII and IncF(K). Our results revealed that plasmids play an extraordinary role in the dissemination of carbapenem resistance in the heterogeneous CRGNB population. The plasmids were also associated with several multispecies dissemination events and local outbreaks throughout the study period, indicating the substantial role of horizontal gene transfer in carbapenemase spread. Furthermore, due to vertical and horizontal plasmid transfer, this can have an impact on implant-associated infections and is therefore important for antibiotic-loaded bone cement and drug-containing devices in orthopedic surgery. Future genomic surveillance projects should increase their focus on plasmid characterization.},
}
@article {pmid39198891,
year = {2024},
author = {Tian, F and Wainaina, JM and Howard-Varona, C and Domínguez-Huerta, G and Bolduc, B and Gazitúa, MC and Smith, G and Gittrich, MR and Zablocki, O and Cronin, DR and Eveillard, D and Hallam, SJ and Sullivan, MB},
title = {Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {159},
pmid = {39198891},
issn = {2049-2618},
support = {T32 GM141955/GM/NIGMS NIH HHS/United States ; ABI#1759874, ABI#2149505, OCE#1536989, OCE#1829831, and OCE#2019589//National Science Foundation/ ; #3790//Gordon and Betty Moore Foundation Investigator Award/ ; },
mesh = {*Oceans and Seas ; *Seawater/virology/microbiology ; Metagenomics ; Bacteria/genetics/classification/metabolism ; Viruses/genetics/classification/isolation &amp; purification ; Prokaryotic Cells/metabolism/virology ; Metagenome ; Metabolic Networks and Pathways/genetics ; Gene Transfer, Horizontal ; Phosphatidylethanolamines/metabolism ; },
abstract = {BACKGROUND: Prokaryotic microbes have impacted marine biogeochemical cycles for billions of years. Viruses also impact these cycles, through lysis, horizontal gene transfer, and encoding and expressing genes that contribute to metabolic reprogramming of prokaryotic cells. While this impact is difficult to quantify in nature, we hypothesized that it can be examined by surveying virus-encoded auxiliary metabolic genes (AMGs) and assessing their ecological context.<br><br>RESULTS: We systematically developed a global ocean AMG catalog by integrating previously described and newly identified AMGs and then placed this catalog into ecological and metabolic contexts relevant to ocean biogeochemistry. From 7.6 terabases of Tara Oceans paired prokaryote- and virus-enriched metagenomic sequence data, we increased known ocean virus populations to 579,904 (up 16%). From these virus populations, we then conservatively identified 86,913 AMGs that grouped into 22,779 sequence-based gene clusters, 7248 (~&#x2009;32%) of which were not previously reported. Using our catalog and modeled data from mock communities, we estimate that&#x2009;~&#x2009;19% of ocean virus populations carry at least one AMG. To understand AMGs in their metabolic context, we identified 340 metabolic pathways encoded by ocean microbes and showed that AMGs map to 128 of them. Furthermore, we identified metabolic "hot spots" targeted by virus AMGs, including nine pathways where most steps (&#x2265;&#x2009;0.75) were AMG-targeted (involved in carbohydrate, amino acid, fatty acid, and nucleotide metabolism), as well as other pathways where virus-encoded AMGs outnumbered cellular homologs (involved in lipid A phosphates, phosphatidylethanolamine, creatine biosynthesis, phosphoribosylamine-glycine ligase, and carbamoyl-phosphate synthase pathways).<br><br>CONCLUSIONS: Together, this systematically curated, global ocean AMG catalog and analyses provide a valuable resource and foundational observations to understand the role of viruses in modulating global ocean metabolisms and their biogeochemical implications. Video Abstract.},
}
@article {pmid39198572,
year = {2024},
author = {Sastre-Dominguez, J and DelaFuente, J and Toribio-Celestino, L and Herencias, C and Herrador-Gómez, P and Costas, C and Hernández-García, M and Cantón, R and Rodríguez-Beltrán, J and Santos-Lopez, A and San Millan, A},
title = {Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria.},
journal = {Nature ecology &amp; evolution},
volume = {8},
number = {11},
pages = {2097-2112},
pmid = {39198572},
issn = {2397-334X},
support = {PI23/01945//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; CD21/00115//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; PI21/01363//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; 101077809-HorizonGT//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; CP20/00154//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; 895671-REPLAY//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 757440-PLASREVOLUTION//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; LCF/BQ/PR22/11920001//"la Caixa" Foundation (Caixa Foundation)/ ; Research Grant 2022//European Society of Clinical Microbiology and Infectious Diseases (ESCMID)/ ; PI19/00749//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; 757440/ERC_/European Research Council/International ; },
mesh = {*Plasmids/genetics ; *DNA Transposable Elements/genetics ; *Enterobacteriaceae/genetics/physiology ; Adaptation, Physiological/genetics ; Enterobacteriaceae Infections/microbiology ; Humans ; Gene Transfer, Horizontal ; },
abstract = {Plasmids are extrachromosomal genetic elements commonly found in bacteria. They are known to fuel bacterial evolution through horizontal gene transfer, and recent analyses indicate that they can also promote intragenomic adaptations. However, the role of plasmids as catalysts of bacterial evolution beyond horizontal gene transfer is poorly explored. In this study, we investigated the impact of a widespread conjugative plasmid, pOXA-48, on the evolution of several multidrug-resistant clinical enterobacteria. Combining experimental and within-patient evolution analyses, we unveiled that plasmid pOXA-48 promotes bacterial evolution through the transposition of plasmid-encoded insertion sequence 1 (IS1) elements. Specifically, IS1-mediated gene inactivation expedites the adaptation rate of clinical strains in vitro and fosters within-patient adaptation in the gut microbiota. We deciphered the mechanism underlying the plasmid-mediated surge in IS1 transposition, revealing a negative feedback loop regulated by the genomic copy number of IS1. Given the overrepresentation of IS elements in bacterial plasmids, our findings suggest that plasmid-mediated IS1 transposition represents a crucial mechanism for swift bacterial adaptation.},
}
@article {pmid39198281,
year = {2024},
author = {He, Z and Smets, BF and Dechesne, A},
title = {Mating Assay: Plating Below a Cell Density Threshold is Required for Unbiased Estimation of Plasmid Conjugation Frequency of RP4 Transfer Between E. coli Strains.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {109},
pmid = {39198281},
issn = {1432-184X},
support = {0236-00022B//Innovationsfonden/ ; 0236-00022B//Innovationsfonden/ ; 0236-00022B//Innovationsfonden/ ; PhD Scholarship//Sino-Danish Center/ ; PhD Scholarship//Sino-Danish Center/ ; },
mesh = {*Escherichia coli/genetics ; *Conjugation, Genetic ; *Plasmids/genetics ; Gene Transfer, Horizontal ; },
abstract = {Mating assays are common laboratory experiments for measuring the conjugation frequency, i.e. efficiency at which a plasmid transfers from a population of donor cells to a population of recipient cells. Selective plating remains a widely used quantification method to enumerate transconjugants at the end of such assays. However, conjugation frequencies may be inaccurately estimated because plasmid transfer can occur on transconjugant-selective plates rather than only during the intended mating duration. We investigated the influence of cell density on this phenomenon. We conducted mating experiments with IncPα plasmid RP4 harbored in Escherichia coli at a fixed cell density and mating conditions, inoculated a serial dilution of the mating mixture on transconjugant-selective plates or in transconjugant-selective broth, and compared the results to a model of cell-to-cell distance distribution. Our findings suggest that irrespective of the mating mode (liquid vs solid), the enumeration of transconjugants becomes significantly biased if the plated cell density exceeds 28 Colony Forming Unit (CFU)/mm[2] (or 1.68•10[5] CFU/standard 9 cm Petri dish). This threshold is determined with a 95% confidence interval of ± 4 CFU/mm[2] (± 2.46•10[4] CFU/standard 9 cm Petri dish). Liquid mating assays were more sensitive to this bias because the conjugation frequency of RP4 is several orders of magnitude lower in suspension compared to surface mating. Therefore, if selective plating is used, we recommend to plate at this density threshold and that negative controls are performed where donors and recipients are briefly mixed before plating at the same dilutions as for the actual mating assay. As an alternative, a liquid enumeration method can be utilized to increase the signal-to-noise ratio and allow for more accurate enumeration of transconjugants.},
}
@article {pmid39194517,
year = {2024},
author = {Yang, X and Liu, Z and Zhang, Y and Shi, X and Wu, Z},
title = {Dinoflagellate-Bacteria Interactions: Physiology, Ecology, and Evolution.},
journal = {Biology},
volume = {13},
number = {8},
pages = {},
pmid = {39194517},
issn = {2079-7737},
support = {42106093 and 41976130//National Natural Science Foundation of China/ ; 2022T150706//China Postdoctoral Science Foundation/ ; GPCGD223103FG015F//Comprehensive Protection and Utilization Program for the Coastal Zone of Guangdong 534 Province (Revision)/ ; DD20230460, DD20230107, and DD20242792//Marine Geological Survey 535 Program of China Geological Survey/ ; },
abstract = {Dinoflagellates and heterotrophic bacteria are two major micro-organism groups within marine ecosystems. Their coexistence has led to a co-evolutionary relationship characterized by intricate interactions that not only alter their individual behaviors but also exert a significant influence on the broader biogeochemical cycles. Our review commenced with an analysis of bacterial populations, both free-living and adherent to dinoflagellate surfaces. Members of Alphaproteobacteria, Gammaproteobacteria, and the Cytophaga-Flavobacterium-Bacteroides group are repeatedly found to be associated with dinoflagellates, with representation by relatively few genera, such as Methylophaga, Marinobacter, and Alteromonas. These bacterial taxa engage with dinoflagellates in a limited capacity, involving nutrient exchange, the secretion of pathogenic substances, or participation in chemical production. Furthermore, the genomic evolution of dinoflagellates has been profoundly impacted by the horizontal gene transfer from bacteria. The integration of bacterial genes into dinoflagellates has been instrumental in defining their biological characteristics and nutritional strategies. This review aims to elucidate the nuanced interactions between dinoflagellates and their associated bacteria, offering a detailed perspective on their complex relationship.},
}
@article {pmid39194203,
year = {2024},
author = {Allain, M and Morel-Journel, T and Condamine, B and Gibeaux, B and Gachet, B and Gschwind, R and Denamur, E and Landraud, L},
title = {IncC plasmid genome rearrangements influence the vertical and horizontal transmission tradeoff in Escherichia coli.},
journal = {Antimicrobial agents and chemotherapy},
volume = {68},
number = {10},
pages = {e0055424},
pmid = {39194203},
issn = {1098-6596},
support = {DEQ20161136698//Fondation pour la Recherche M&#xe9;dicale (FRM)/ ; },
mesh = {*Plasmids/genetics ; *Escherichia coli/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; *Conjugation, Genetic ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Escherichia coli Infections/microbiology/transmission ; },
abstract = {It has been shown that an evolutionary tradeoff between vertical (host growth rate) and horizontal (plasmid conjugation) transmissions contributes to global plasmid fitness. As conjugative IncC plasmids are important for the spread of multidrug resistance (MDR), in a broad range of bacterial hosts, we investigated vertical and horizontal transmissions of two multidrug-resistant IncC plasmids according to their backbones and MDR-region rearrangements, upon plasmid entry into a new host. We observed plasmid genome deletions after conjugation in three diverse natural Escherichia coli clinical strains, varying from null to high number depending on the plasmid, all occurring in the MDR region. The plasmid burden on bacterial fitness depended more on the strain background than on the structure of the MDR region, with deletions appearing to have no impact. Besides, we observed an increase in plasmid transfer rate, from ancestral host to new clinical recipient strains, when the IncC plasmid was rearranged. Finally, using a second set of conjugation experiments, we investigated the evolutionary tradeoff of the IncC plasmid during the critical period of plasmid establishment in E. coli K-12, by correlating the transfer rates of deleted or non-deleted IncC plasmids and their costs on the recipient strain. Plasmid deletions strongly improved conjugation efficiency with no negative growth effect. Our findings indicate that the flexibility of the MDR-region of the IncC plasmids can promote their dissemination, and provide diverse opportunities to capture new resistance genes. In a broader view, they suggest that the vertical-horizontal transmission tradeoff can be manipulated by the plasmid to improve its fitness.},
}
@article {pmid39193949,
year = {2024},
author = {Kim, HJ and Koo, SH and Choi, Q},
title = {Horizontal Gene Transfer of blaNDM-5 Among Three Different Enterobacteriaceae Species Isolated from a Single Patient.},
journal = {Clinical laboratory},
volume = {70},
number = {8},
pages = {},
doi = {10.7754/Clin.Lab.2024.240309},
pmid = {39193949},
issn = {1433-6510},
mesh = {Humans ; *Gene Transfer, Horizontal ; *Microbial Sensitivity Tests ; *beta-Lactamases/genetics ; *Enterobacteriaceae/genetics/drug effects/isolation &amp; purification ; *Anti-Bacterial Agents/pharmacology ; *Plasmids/genetics ; Enterobacteriaceae Infections/microbiology/diagnosis/drug therapy ; Whole Genome Sequencing ; Escherichia coli/genetics/drug effects/isolation &amp; purification ; Klebsiella oxytoca/genetics/isolation &amp; purification/drug effects ; Citrobacter/genetics/isolation &amp; purification/drug effects ; },
abstract = {BACKGROUND: In this study, Escherichia coli, Klebsiella oxytoca, and Citrobacter amalonaticus carrying blaNDM-5 were isolated from a single patient.<br><br>METHODS: The antibiotic susceptibility of the isolates was evaluated by using E-test and agar dilution methods, and blaNDM-5 was identified in genomic and plasmid DNA by using polymerase chain reaction and sequencing. Whole genome sequencing and de novo assembly were used for species characterization, resistance gene identification, and plasmid analysis.<br><br>RESULTS: All three species had identical plasmids, which were similar to pEC463-NDM5, a plasmid harboring blaNDM-5. Transconjugation experiments confirmed the horizontal gene transfer of blaNDM-5, highlighting the need for a close monitoring of Enterobacteriaceae species harboring this gene.<br><br>CONCLUSIONS: This study conclusively demonstrates the propensity for horizontal gene transfer of blaNDM-5 among Enterobacteriaceae species, underlining the importance of vigilant monitoring to combat antibiotic resistance.},
}
@article {pmid39191402,
year = {2024},
author = {Aoun, N and Georgoulis, SJ and Avalos, JK and Grulla, KJ and Miqueo, K and Tom, C and Lowe-Power, TM},
title = {A pangenomic atlas reveals eco-evolutionary dynamics that shape type VI secretion systems in plant-pathogenic Ralstonia.},
journal = {mBio},
volume = {15},
number = {10},
pages = {e0032324},
pmid = {39191402},
issn = {2150-7511},
support = {Hatch #1023861,Award# 1030618//USDA | National Institute of Food and Agriculture (NIFA)/ ; //Hellman Foundation (The Hellman Foundation)/ ; },
mesh = {*Type VI Secretion Systems/genetics/metabolism ; *Phylogeny ; *Genome, Bacterial ; *Ralstonia solanacearum/genetics/metabolism ; *Evolution, Molecular ; Plant Diseases/microbiology ; Bacterial Toxins/genetics/metabolism ; Burkholderiaceae/genetics/metabolism/classification ; Multigene Family ; Ralstonia/genetics/metabolism ; Genomics ; Gene Transfer, Horizontal ; },
abstract = {Soilborne Ralstonia solanacearum species complex (RSSC) pathogens disrupt microbial communities as they invade roots and fatally wilt plants. RSSC pathogens secrete antimicrobial toxins using a type VI secretion system (T6SS). To investigate how evolution and ecology have shaped the T6SS of these bacterial pathogens, we analyzed the T6SS gene content and architecture across the RSSC and their evolutionary relatives. Our analysis reveals that two ecologically similar Burkholderiaceae taxa, xylem-pathogenic RSSC and Paracidovorax, have convergently evolved to wield large arsenals of T6SS toxins. To understand the mechanisms underlying genomic enrichment of T6SS toxins, we compiled an atlas of 1,066 auxiliary T6SS toxin clusters ("aux" clusters) across 99 high-quality RSSC genomes. We classified 25 types of aux clusters with toxins that predominantly target lipids, nucleic acids, or unknown cellular substrates. The aux clusters were located in diverse genetic neighborhoods and had complex phylogenetic distributions, suggesting frequent horizontal gene flow. Phages and other mobile genetic elements account for most of the aux cluster acquisition on the chromosome but very little on the megaplasmid. Nevertheless, RSSC genomes were more enriched in aux clusters on the megaplasmid. Although the single, ancestral T6SS was broadly conserved in the RSSC, the T6SS has been convergently lost in atypical, non-soilborne lineages. Overall, our data suggest dynamic interplay between the lifestyle of RSSC lineages and the evolution of T6SSes with robust arsenals of toxins. This pangenomic atlas poises the RSSC as an emerging, tractable model to understand the role of the T6SS in shaping pathogen populations.IMPORTANCEWe explored the eco-evolutionary dynamics that shape the inter-microbial warfare mechanisms of a globally significant plant pathogen, the Ralstonia solanacearum species complex. We discovered that most Ralstonia wilt pathogens have evolved extensive and diverse repertoires of type VI secretion system-associated antimicrobial toxins. These expansive toxin arsenals potentially enhance the ability of Ralstonia pathogens to invade plant microbiomes, enabling them to rapidly colonize and kill their host plants. We devised a classification system to categorize the Ralstonia toxins. Interestingly, many of the toxin gene clusters are encoded on mobile genetic elements, including prophages, which may be mutualistic symbionts that enhance the inter-microbial competitiveness of Ralstonia wilt pathogens. Moreover, our findings suggest that the convergent loss of this multi-gene trait contributes to genome reduction in two vector-transmitted lineages of Ralstonia pathogens. Our findings demonstrate that the interplay between microbial ecology and pathogen lifestyle shapes the evolution of a genetically complex antimicrobial weapon.},
}
@article {pmid39191296,
year = {2024},
author = {Xiao, Y and Qin, Y and Jiang, X and Gao, P},
title = {Effects of polypropylene microplastics on digestion performance, microbial community, and antibiotic resistance during microbial anaerobic digestion.},
journal = {Bioresource technology},
volume = {411},
number = {},
pages = {131358},
doi = {10.1016/j.biortech.2024.131358},
pmid = {39191296},
issn = {1873-2976},
mesh = {*Polypropylenes ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; *Microplastics ; Bioreactors ; Methane/metabolism ; Biodegradation, Environmental ; Bacteria/drug effects/genetics/metabolism ; },
abstract = {As an emerging pollutant, microplastics (MPs) have attracted increasing attention worldwide. The effects of polypropylene (PP) MPs on digestion performance, behaviors of dominant microbial communities, antibiotic resistance genes (ARGs) and mobile genetic elements in microbial anaerobic digesters were investigated. The results showed that the addition of PP-MPs to digesters led to an increase in methane production of 10.8% when 300 particles/g TSS of PP-MPs was introduced compared with that in digester not treated with PP-MPs. This increase was attributed to the enrichment of acetogens such as Syntrophobacter (42.0%), Syntrophorhabdus (27.0%), and Syntrophomonas (10.6%), and methanogens including Methanobacterium and Methanosaeta. tetX was highly enriched due to PP-MP exposure, whereas parC exhibited the greatest increase (35.5% - 222.7%). Horizontal gene transfer via ISCR1 and intI1 genes might play an important role in the spread of ARGs. Overall, these findings provide comprehensive insight into the ecological dynamics of PP-MPs during microbial anaerobic digestion.},
}
@article {pmid39191191,
year = {2024},
author = {Middendorf, PS and Zomer, AL and Bergval, IL and Jacobs-Reitsma, WF and den Besten, HMW and Abee, T},
title = {Host associations of Campylobacter jejuni and Campylobacter coli isolates carrying the L-fucose or d-glucose utilization cluster.},
journal = {International journal of food microbiology},
volume = {425},
number = {},
pages = {110855},
doi = {10.1016/j.ijfoodmicro.2024.110855},
pmid = {39191191},
issn = {1879-3460},
mesh = {*Campylobacter coli/genetics/isolation &amp; purification/metabolism ; *Campylobacter jejuni/genetics/metabolism/isolation &amp; purification ; *Glucose/metabolism ; Humans ; *Fucose/metabolism ; Genome, Bacterial ; Gene Transfer, Horizontal ; Campylobacter Infections/microbiology/veterinary ; Multigene Family ; Finland ; Netherlands ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Campylobacter was considered asaccharolytic, but is now known to carry saccharide metabolization pathways for L-fucose and d-glucose. We hypothesized that these clusters are beneficial for Campylobacter niche adaptation and may help establish human infection. We investigated the distribution of d-glucose and L-fucose clusters among ∼9600 C. jejuni and C. coli genomes of different isolation sources in the Netherlands, the United Kingdom, the United States of America and Finland. The L-fucose utilization cluster was integrated at the same location in all C. jejuni and C. coli genomes, and was flanked by the genes rpoB, rpoC, rspL, repsG and fusA, which are associated with functions in transcription as well as translation and in acquired drug resistance. In contrast, the flanking regions of the d-glucose utilization cluster were variable among the isolates, and integration sites were located within one of the three different 16S23S ribosomal RNA areas of the C. jejuni and C. coli genomes. In addition, we investigated whether acquisition of the L-fucose utilization cluster could be due to horizontal gene transfer between the two species and found three isolates for which this was the case: one C. jejuni isolate carrying a C. coli L-fucose cluster, and two C. coli isolates which carried a C. jejuni L-fucose cluster. Furthermore, L-fucose utilization cluster alignments revealed multiple frameshift mutations, most of which were commonly found in the non-essential genes for L-fucose metabolism, namely, Cj0484 and Cj0489. These findings support our hypothesis that the L-fucose cluster was integrated multiple times across the C. coli/C. jejuni phylogeny. Notably, association analysis using the C. jejuni isolates from the Netherlands showed a significant correlation between human C. jejuni isolates and C. jejuni isolates carrying the L-fucose utilization cluster. This correlation was even stronger when the Dutch isolates were combined with the isolates from the UK, the USA and Finland. No such correlations were observed for C. coli or for the d-glucose cluster for both species. This research provides insight into the spread and host associations of the L-fucose and d-glucose utilization clusters in C. jejuni and C. coli, and the potential benefits in human infection and/or proliferation in humans, conceivably after transmission from any reservoir.},
}
@article {pmid39191006,
year = {2024},
author = {Zhao, H and Sun, Y and Cao, X and Waigi, MG and Liu, J},
title = {Effects and mechanisms of chlormequat on horizontal transfer of antibiotic resistance genes through plasmid-mediated conjugation in agro-ecosystems.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135639},
doi = {10.1016/j.jhazmat.2024.135639},
pmid = {39191006},
issn = {1873-3336},
mesh = {*Plasmids/genetics ; *Oryza/microbiology/growth &amp; development/drug effects/genetics ; *Gene Transfer, Horizontal ; *Conjugation, Genetic ; *Escherichia coli/genetics/drug effects ; *Pseudomonas/genetics/drug effects/metabolism ; Pseudomonas putida/genetics/drug effects/metabolism ; Genes, Bacterial/drug effects ; Anti-Bacterial Agents/pharmacology ; Agriculture ; Drug Resistance, Bacterial/genetics/drug effects ; Drug Resistance, Microbial/genetics ; },
abstract = {Chlormequat (CCC) is widely used in agricultural production to increase the crop yield. However, the effects of CCC on transfer of ARGs in agricultural system are still unclear. In this study, using E.coli DH5α (carrying RP4 plasmid with Amp[R], Tet[R], Kan[R]) as the donor bacterium, E.coli HB101, endophytic Pseudomonas sp. Ph6 or rhizosphere Pseudomonas putida KT2440 as the recipient strain, three conjugative systems were designed to investigate the effects of CCC on ARG transfer. Meanwhile, hydroponics experiments were designed to study the ARG spread in the rice-nutrient solution system after CCC application. The results showed that CCC significantly promoted the RP4 conjugation by expanding cell membrane permeability and improving the relative transcription levels of trfAp, trbBp, traA and traL genes in RP4. Furthermore, the conjugation frequency between E. coli and Pseudomonas was much higher than that between E. coli cells. Compared with spraying foliage with 2500 mg·L[-1] of CCC, soaking seeds with 250 mg·L[-1] of CCC was more beneficial to the colonization of ARB in rice, and also increased the abundance of ARGs in rice cultivation system. These results remind that the use of CCC in agricultural production might promote the ARG transmission in agro-ecosystems; however, foliage spraying with 2500 mg·L[-1] of CCC could control its spread.},
}
@article {pmid39190937,
year = {2024},
author = {Wen, AX and Herman, C},
title = {Horizontal gene transfer and beyond: the delivery of biological matter by bacterial membrane vesicles to host and bacterial cells.},
journal = {Current opinion in microbiology},
volume = {81},
number = {},
pages = {102525},
pmid = {39190937},
issn = {1879-0364},
support = {DP1 AI152073/AI/NIAID NIH HHS/United States ; },
mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/metabolism ; *Extracellular Vesicles/metabolism ; Cell Membrane/metabolism ; },
abstract = {Membrane vesicles (MVs) are produced in all domains of life. In eukaryotes, extracellular vesicles have been shown to mediate the horizontal transfer of biological material between cells [1]. Therefore, bacterial MVs are also thought to mediate horizontal material transfer to host cells and other bacteria, especially in the context of cell stress. In this review, we discuss the mechanisms of bacterial MV production, evidence that their contents can be trafficked to host cells and other bacteria, and the biological relevance of horizontal material transfer by bacterial MVs.},
}
@article {pmid39190025,
year = {2024},
author = {Alav, I and Pordelkhaki, P and Rodriguez-Navarro, J and Neo, O and Kessler, C and Awodipe, RJ and Cliffe, P and Pulavan, N and Marton, HL and Gibbons, S and Buckner, MMC},
title = {Natural products from food sources can alter the spread of antimicrobial resistance plasmids in Enterobacterales.},
journal = {Microbiology (Reading, England)},
volume = {170},
number = {8},
pages = {},
pmid = {39190025},
issn = {1465-2080},
mesh = {*Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; *Klebsiella pneumoniae/drug effects/genetics ; *Escherichia coli/genetics/drug effects ; *beta-Lactamases/genetics/metabolism ; *Biological Products/pharmacology ; Drug Resistance, Bacterial/genetics ; Conjugation, Genetic ; Bacterial Proteins/genetics/metabolism ; Enterobacteriaceae/drug effects/genetics ; Microbial Sensitivity Tests ; Food Microbiology ; Gene Transfer, Horizontal ; },
abstract = {Antimicrobial resistance (AMR) poses a significant threat to global public health. Notably, resistance to carbapenem and extended-spectrum β-lactam antibiotics in Gram-negative bacteria is a major impediment to treating infections. Genes responsible for antibiotic resistance are frequently carried on plasmids, which can transfer between bacteria. Therefore, exploring strategies to prevent this transfer and the prevalence of AMR plasmids is timely and pertinent. Here, we show that certain natural product extracts and associated pure compounds can reduce the conjugation of AMR plasmids into new bacterial hosts. Using our established high-throughput fluorescence-based flow cytometry assay, we found that the natural products were more active in reducing transmission of the IncK extended-spectrum β-lactamase-encoding plasmid pCT in Escherichia coli EC958c, compared to Klebsiella pneumoniae Ecl8 carrying the IncFII carbapenemase-encoding plasmid pKpQIL. The exception was the natural product rottlerin, also active in K. pneumoniae. In classical conjugation assays, rottlerin also reduced the conjugation frequency of the IncFII bla NDM-1 carrying plasmid pCPE16_3 from a clinical K. pneumoniae isolate. Our data indicate that the natural products tested here, in their current molecular structure, reduced conjugation by a small amount, which is unlikely to achieve a large-scale reduction in AMR in bacterial populations. However, certain natural products like rottlerin could provide a foundation for further research into compounds with effective anti-plasmid activity.},
}
@article {pmid39189989,
year = {2024},
author = {Brewer, TE and Wagner, A},
title = {Horizontal Gene Transfer of a key Translation Factor and its Role in Polyproline Proteome Evolution.},
journal = {Molecular biology and evolution},
volume = {41},
number = {9},
pages = {},
pmid = {39189989},
issn = {1537-1719},
mesh = {*Gene Transfer, Horizontal ; *Peptide Elongation Factors/genetics/metabolism ; *Evolution, Molecular ; *Peptides/metabolism/genetics ; *Proteome ; Bacteria/genetics/metabolism ; Phylogeny ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Prolines cause ribosomes to stall during translation due to their rigid structure. This phenomenon occurs in all domains of life and is exacerbated at polyproline motifs. Such stalling can be eased by the elongation factor P (EF-P) in bacteria. We discovered a potential connection between the loss of ancestral EF-P, the appearance of horizontally transferred EF-P variants, and genomic signs of EF-P dysfunction. Horizontal transfer of the efp gene has occurred several times among bacteria and is associated with the loss of highly conserved polyproline motifs. In this study, we pinpoint cases of horizontal EF-P transfer among a diverse set of bacteria and examine genomic features associated with these events in the phyla Thermotogota and Planctomycetes. In these phyla, horizontal EF-P transfer is also associated with the loss of entire polyproline motif-containing proteins, whose expression is likely dependent on EF-P. In particular, three proteases (Lon, ClpC, and FtsH) and three tRNA synthetases (ValS, IleS1, and IleS2) appear highly sensitive to EF-P transfer. The conserved polyproline motifs within these proteins all reside within close proximity to ATP-binding-regions, some of which are crucial for their function. Our work shows that an ancient EF-P dysfunction has left genomic traces that persist to this day, although it remains unclear whether this dysfunction was strictly due to loss of ancestral EF-P or was related to the appearance of an exogenous variant. The latter possibility would imply that the process of "domesticating" a horizontally transferred efp gene can perturb the overall function of EF-P.},
}
@article {pmid39189956,
year = {2024},
author = {Zheng, X and Huang, L},
title = {Diverse non-canonical electron bifurcating [FeFe]-hydrogenases of separate evolutionary origins in Hydrogenedentota.},
journal = {mSystems},
volume = {9},
number = {9},
pages = {e0099924},
pmid = {39189956},
issn = {2379-5077},
support = {SQ2021QZKK0302//Ministry of Science and Technology of the People's Republic of China (MOST)/ ; XDB42000000//CAS | Bureau of Development and Planning, Chinese Academy of Sciences (Bureau of Development and Planning, CAS)/ ; 42376238//MOST | National Natural Science Foundation of China (NSFC)/ ; 32393970//MOST | National Natural Science Foundation of China (NSFC)/ ; 91751000//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Hydrogenase/genetics/metabolism/chemistry ; *Phylogeny ; *Evolution, Molecular ; *Iron-Sulfur Proteins/genetics/metabolism ; Bacterial Proteins/genetics/metabolism/chemistry ; Bacteria/genetics/enzymology ; Genome, Bacterial ; Hydrogen/metabolism ; Gene Transfer, Horizontal ; },
abstract = {UNLABELLED: Hydrogenedentota, a globally distributed bacterial phylum-level lineage, is poorly understood. Here, we established a comprehensive genomic catalog of Hydrogenedentota, including a total of seven clades (or families) with 179 genomes, and explored the metabolic potential and evolutionary history of these organisms. We show that a single genome, especially those belonging to Clade 6, often encodes multiple hydrogenases with genomes in Clade 2, which rarely encode hydrogenases being the exception. Notably, most members of Hydrogenedentota contain a group A3 [FeFe]-hydrogenase (BfuABC) with a non-canonical electron bifurcation mechanism, in addition to substrate-level phosphorylation and electron transport-linked phosphorylation pathways, in energy conservation. Furthermore, we show that BfuABC from Hydrogenedentota fall into five sub-types. Phylogenetic analysis reveals five independent routes for the evolution of BfuABC homologs in Hydrogenedentota. We speculate that the five sub-types of BfuABC might be acquired from Bacillota (synonym Firmicutes) through separate horizontal gene transfer events. These data shed light on the diversity and evolution of bifurcating [FeFe]-hydrogenases and provide insight into the strategy of Hydrogenedentota to adapt to survival in various habitats.<br><br>IMPORTANCE: The phylum Hydrogenedentota is widely distributed in various environments. However, their physiology, ecology, and evolutionary history remain unknown, primarily due to the limited availability of the genomes and the lack of cultured representatives of the phylum. Our results have increased the knowledge of the genetic and metabolic diversity of these organisms and shed light on their diverse energy conservation strategies, especially those involving electron bifurcation with a non-canonical mechanism, which are likely responsible for their wide distribution. Besides, the organization and phylogenetic relationships of gene clusters coding for BfuABC in Hydrogenedentota provide valuable clues to the evolutionary history of group A3 electron bifurcating [FeFe]-hydrogenases.},
}
@article {pmid39189770,
year = {2024},
author = {Kopejtka, K and Tomasch, J and Shivaramu, S and Saini, MK and Kaftan, D and Koblížek, M},
title = {Minimal transcriptional regulation of horizontally transferred photosynthesis genes in phototrophic bacterium Gemmatimonas phototrophica.},
journal = {mSystems},
volume = {9},
number = {9},
pages = {e0070624},
pmid = {39189770},
issn = {2379-5077},
support = {GX19-28778X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky (GA&#x10c;R)/ ; CZ.02.01.01/00/22_008/0004624//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; },
mesh = {*Gene Transfer, Horizontal ; *Photosynthesis/genetics ; *Gene Expression Regulation, Bacterial/radiation effects ; Light ; Bacterial Proteins/genetics/metabolism ; Transcriptome ; },
abstract = {UNLABELLED: The first phototrophic member of the bacterial phylum Gemmatimonadota, Gemmatimonas phototrophica AP64[T], received all its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Here, we investigated how these acquired genes, which are tightly controlled by oxygen and light in the ancestor, are integrated into the regulatory system of its new host. G. phototrophica grew well under aerobic and semiaerobic conditions, with almost no difference in gene expression. Under aerobic conditions, the growth of G. phototrophica was optimal at 80 µmol photon m[-2] s[-1], while higher light intensities had an inhibitory effect. The transcriptome showed only a minimal response to the dark-light shift at optimal light intensity, while the exposure to a higher light intensity (200 µmol photon m[-2] s[-1]) induced already stronger but still transient changes in gene expression. Interestingly, a singlet oxygen defense was not activated under any conditions tested. Our results indicate that G. phototrophica possesses neither the oxygen-dependent repression of photosynthesis genes known from purple bacteria nor the light-dependent repression described in aerobic anoxygenic phototrophs. Instead, G. phototrophica has evolved as a low-light species preferring reduced oxygen concentrations. Under these conditions, the bacterium can safely employ its photoheterotrophic metabolism without the need for complex regulatory mechanisms.<br><br>IMPORTANCE: Horizontal gene transfer is one of the main mechanisms by which bacteria acquire new genes. However, it represents only the first step as the transferred genes have also to be functionally and regulatory integrated into the recipient's cellular machinery. Gemmatimonas phototrophica, a member of bacterial phylum Gemmatimonadota, acquired its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Thus, it represents a unique natural experiment, in which the entire package of photosynthesis genes was transplanted into a distant host. We show that G. phototrophica lacks the regulation of photosynthesis gene expressions in response to oxygen concentration and light intensity that are common in purple bacteria. This restricts its growth to low-light habitats with reduced oxygen. Understanding the regulation of horizontally transferred genes is important not only for microbial evolution but also for synthetic biology and the engineering of novel organisms, as these rely on the successful integration of foreign genes.},
}
@article {pmid39189747,
year = {2024},
author = {Duchin Rapp, Y and Lipsman, V and Yuda, L and Kublanov, IV and Matsliyah, D and Segev, E},
title = {Algal exudates promote conjugation in marine Roseobacters.},
journal = {mBio},
volume = {15},
number = {10},
pages = {e0106224},
pmid = {39189747},
issn = {2150-7511},
mesh = {*Roseobacter/metabolism/genetics ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; Plasmids/genetics ; Aquatic Organisms/genetics/metabolism ; Type IV Secretion Systems/metabolism/genetics ; Seawater/microbiology ; },
abstract = {UNLABELLED: Horizontal gene transfer (HGT) is a pivotal mechanism driving bacterial evolution, conferring adaptability within dynamic marine ecosystems. Among HGT mechanisms, conjugation mediated by type IV secretion systems (T4SSs) plays a central role in the ecological success of marine bacteria. However, the conditions promoting conjugation events in the marine environment are not well-understood. Roseobacters, abundant marine bacteria commonly associated with algae, possess a multitude of T4SSs. Many Roseobacters are heterotrophic bacteria that rely on algal secreted compounds to support their growth. These compounds attract bacteria, facilitating colonization and attachment to algal cells. Algae and their metabolites bring bacteria into close proximity, potentially promoting bacterial HGT. Investigation across various Roseobacters revealed that algal exudates indeed enhance plasmid transfer through conjugation. While algal exudates do not influence the transcription of bacterial conjugative machinery genes, they promote bacterial attachment, potentially stabilizing proximity and facilitating HGT. Notably, under conditions where attachment is less advantageous, the impact of algal exudates on conjugation is reduced. These findings suggest that algae enhance bacterial conjugation primarily by fostering attachment and highlight the importance of studying bacterial HGT within the context of algal-bacterial interactions.<br><br>IMPORTANCE: This study explores how algal-bacterial interactions influence horizontal gene transfer (HGT) among marine bacteria. HGT, a key driver of bacterial evolution, is facilitated by conjugation mediated by type IV secretion systems (T4SSs). Through investigating Roseobacters, abundant marine bacteria often found to be associated with algae, the study reveals that algal exudates enhance plasmid transfer via conjugation. This enhancement is attributed to the promotion of bacterial attachment by algal compounds, emphasizing the role of algal-bacterial interactions in shaping genetic exchange within dynamic marine ecosystems. Understanding these mechanisms is crucial for elucidating bacterial adaptability and evolution in the marine environment.},
}
@article {pmid39189727,
year = {2024},
author = {Xu, Y and Liu, B and Jiao, N and Liu, J and Chen, F},
title = {New evidence supports the prophage origin of RcGTA.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {9},
pages = {e0043424},
pmid = {39189727},
issn = {1098-5336},
support = {2020ZLYS04//Department of Science and Technology of Shandong Province ()/ ; 2018YFA0605800//Ministry of Science and Technology of the People's Republic of China (MOST)/ ; },
mesh = {*Prophages/genetics ; Rhodobacter capsulatus/virology/genetics ; Gene Transfer, Horizontal ; Genome, Viral ; Phylogeny ; Evolution, Molecular ; Methylobacterium/virology/genetics ; },
abstract = {Gene transfer agents (GTAs) are phage-like entities that package and transfer random host genome fragments between prokaryotes. RcGTA, produced by Rhodobacter capsulatus, is hypothesized to originate from a prophage ancestor. Most of the evidence supporting this hypothesis came from the finding of RcGTA-like genes in phages. More than 75% of the RcGTA genes have a phage homolog. However, only a few RcGTA homologs have been identified in a (pro)phage genome, leaving the hypothesis that GTAs evolved from prophages through gene loss with only weak evidence. We herein report the discovery of an inducible prophage (vB_MseS-P1) from a Mesorhizobium sediminum strain that contains the largest number (12) of RcGTA homologs found in a phage genome to date. We also identified three putative prophages and two prophage remnants harboring 12-14 RcGTA homologs in a Methylobacterium nodulans strain. The protein remote homology detection also revealed more RcGTA homologs from other phages than we previously thought. Moreover, the head-tail gene architecture of these newly discovered prophage-related elements closely resembles that of RcGTA. Furthermore, vB_MseS-P1 virions have structural proteins similar to RcGTA particles. Close phylogenetic relationships between certain prophage genes and RcGTA-like genes in Alphaproteobacteria further support the shared ancestry between RcGTA and prophages. Our findings provide new relatively direct evidence of the origin of RcGTA from a prophage progenitor.IMPORTANCEGTAs are important genetic elements in certain groups of bacteria and contribute to the genetic diversification, evolution, and ecological adaptation of bacteria. RcGTA, a common type of GTA, is known to package and transfer random fragments of the bacterial genome to recipient cells. However, the origin of RcGTA is still elusive. It has been hypothesized that RcGTA evolved from a prophage ancestor through gene loss. However, the few RcGTA homologs identified in a (pro)phage genome leave the hypothesis lacking direct evidence. This study uncovers the presence of a large number of RcGTA homologs in an inducible prophage and several putative prophages. The similar head-tail gene architecture and structural protein compositions of these newly discovered prophage-related elements and RcGTA further demonstrate an unprecedentedly observed close evolutionary relationship between prophages and RcGTA. Together, our findings provide more direct evidence supporting the origin of RcGTA from prophage.},
}
@article {pmid39187833,
year = {2024},
author = {Yutin, N and Tolstoy, I and Mutz, P and Wolf, YI and Krupovic, M and Koonin, EV},
title = {DNA polymerase swapping in Caudoviricetes bacteriophages.},
journal = {Virology journal},
volume = {21},
number = {1},
pages = {200},
pmid = {39187833},
issn = {1743-422X},
support = {/LM/NLM NIH HHS/United States ; },
mesh = {*DNA-Directed DNA Polymerase/genetics ; *Phylogeny ; *Viral Proteins/genetics/metabolism ; Evolution, Molecular ; Genome, Viral ; Caudovirales/genetics/classification ; DNA, Viral/genetics ; Bacteriophages/genetics/enzymology/classification ; DNA Replication ; },
abstract = {BACKGROUND: Viruses with double-stranded (ds) DNA genomes in the realm Duplodnaviria share a conserved structural gene module but show a broad range of variation in their repertoires of DNA replication proteins. Some of the duplodnaviruses encode (nearly) complete replication systems whereas others lack (almost) all genes required for replication, relying on the host replication machinery. DNA polymerases (DNAPs) comprise the centerpiece of the DNA replication apparatus. The replicative DNAPs are classified into 4 unrelated or distantly related families (A-D), with the protein structures and sequences within each family being, generally, highly conserved. More than half of the duplodnaviruses encode a DNAP of family A, B or C. We showed previously that multiple pairs of closely related viruses in the order Crassvirales encode DNAPs of different families.<br><br>METHODS: Groups of phages in which DNAP swapping likely occurred were identified as subtrees of a defined depth in a comprehensive evolutionary tree of tailed bacteriophages that included phages with DNAPs of different families. The DNAP swaps were validated by constrained tree analysis that was performed on phylogenetic tree of large terminase subunits, and the phage genomes encoding swapped DNAPs were aligned using Mauve. The structures of the discovered unusual DNAPs were predicted using AlphaFold2.<br><br>RESULTS: We identified four additional groups of tailed phages in the class Caudoviricetes in which the DNAPs apparently were swapped on multiple occasions, with replacements occurring both between families A and B, or A and C, or between distinct subfamilies within the same family. The DNAP swapping always occurs "in situ", without changes in the organization of the surrounding genes. In several cases, the DNAP gene is the only region of substantial divergence between closely related phage genomes, whereas in others, the swap apparently involved neighboring genes encoding other proteins involved in phage genome replication. In addition, we identified two previously undetected, highly divergent groups of family A DNAPs that are encoded in some phage genomes along with the main DNAP implicated in genome replication.<br><br>CONCLUSIONS: Replacement of the DNAP gene by one encoding a DNAP of a different family occurred on many independent occasions during the evolution of different families of tailed phages, in some cases, resulting in very closely related phages encoding unrelated DNAPs. DNAP swapping was likely driven by selection for avoidance of host antiphage mechanisms targeting the phage DNAP that remain to be identified, and/or by selection against replicon incompatibility.},
}
@article {pmid39186748,
year = {2024},
author = {Pradel, N and Bartoli, M and Koenen, M and Bale, N and Neumann-Schaal, M and Spröer, C and Bunk, B and Rohde, M and Pester, M and Spring, S},
title = {Description and genome analysis of a novel archaeon isolated from a syntrophic pyrite-forming enrichment culture and reclassification of Methanospirillum hungatei strains GP1 and SK as Methanospirillum purgamenti sp. nov.},
journal = {PloS one},
volume = {19},
number = {8},
pages = {e0308405},
pmid = {39186748},
issn = {1932-6203},
mesh = {*Methanospirillum/genetics/metabolism ; *Phylogeny ; *Genome, Archaeal ; Sulfides/metabolism ; Iron/metabolism ; RNA, Ribosomal, 16S/genetics ; Methane/metabolism ; },
abstract = {The archaeal isolate J.3.6.1-F.2.7.3T was obtained from an anaerobic enrichment culture, where it may play an important role in methane production during pyrite formation. The new isolate formed a species-level clade with Methanospirillum hungatei strains GP1 and SK, which is separate from the type strain JF-1T. Cultivation-independent surveys indicate the occurrence of this phylogenetic group in sediments and anaerobic digesters. The abundance of this clade appears to be negatively affected by high nitrogen loads, indicating a sensitivity to certain nitrogen compounds that is not known in M. hungatei JF-1T. The relatively large core genome of this Methanospirillum clade is indicative of niche specialization and efficient control of horizontal gene transfer. Genes for nitrogenase and F420-dependent secondary alcohol dehydrogenase contribute to the metabolic versatility of this lineage. Characteristics of the new isolate such as the ability to utilize 2-propanol as an electron donor or the requirement for acetate as a carbon source are found also in the strains GP1 and SK, but not in the type strain M. hungatei JF-1T. Based on the genomic differences to related species, a new species within the genus Methanospirillum is proposed with the name M. purgamenti sp. nov. The determined phenotypic characteristics support this proposal and indicate a metabolic adaptation to a separate ecological niche.},
}
@article {pmid39184916,
year = {2024},
author = {Han, H and He, T and Wu, Y and He, T and Zhou, W},
title = {Multidimensional analysis of tumor stem cells: from biological properties, metabolic adaptations to immune escape mechanisms.},
journal = {Frontiers in cell and developmental biology},
volume = {12},
number = {},
pages = {1441081},
pmid = {39184916},
issn = {2296-634X},
abstract = {As a key factor in tumorigenesis, progression, recurrence and metastasis, the biological properties, metabolic adaptations and immune escape mechanisms of CSCs are the focus of current oncological research. CSCs possess self-renewal, multidirectional differentiation and tumorigenicity, and their mechanisms of action can be elucidated by the clonal evolution, hierarchical model and the dynamic CSCs model, of which the dynamic model is widely recognized due to its better explanation of the function and origin of CSCs. The origin hypothesis of CSCs involves cell-cell fusion, horizontal gene transfer, genomic instability and microenvironmental regulation, which together shape the diversity of CSCs. In terms of classification, CSCs include primary CSCs (pri-CSCs), precancerous stem cells (pre-CSCs), migratory CSCs (mig-CSCs), and chemo-radiotherapy-resistant CSCs (cr-CSCs and rr-CSCs), with each type playing a specific role in tumor progression. Surface markers of CSCs, such as CD24, CD34, CD44, CD90, CD133, CD166, EpCAM, and LGR5, offer the possibility of identifying, isolating, and targeting CSCs, but the instability and heterogeneity of their expression increase the difficulty of treatment. CSCs have adapted to their survival needs through metabolic reprogramming, showing the ability to flexibly switch between glycolysis and oxidative phosphorylation (OXPHOS), as well as adjustments to amino acid and lipid metabolism. The Warburg effect typifies their metabolic profiles, and altered glutamine and fatty acid metabolism further contributes to the rapid proliferation and survival of CSCs. CSCs are able to maintain their stemness by regulating the metabolic networks to maintain their stemness characteristics, enhance antioxidant defences, and adapt to therapeutic stress. Immune escape is another strategy for CSCs to maintain their survival, and CSCs can effectively evade immune surveillance through mechanisms such as up-regulating PD-L1 expression and promoting the formation of an immunosuppressive microenvironment. Together, these properties reveal the multidimensional complexity of CSCs, underscoring the importance of a deeper understanding of the biology of CSCs for the development of more effective tumor therapeutic strategies. In the future, therapies targeting CSCs will focus on precise identification of surface markers, intervention of metabolic pathways, and overcoming immune escape, with the aim of improving the relevance and efficacy of cancer treatments, and ultimately improving patient prognosis.},
}
@article {pmid39184814,
year = {2024},
author = {Chen, N and Li, Y and Liang, X and Qin, K and Zhang, Y and Wang, J and Wu, Q and Gupta, TB and Ding, Y},
title = {Bacterial extracellular vesicle: A non-negligible component in biofilm life cycle and challenges in biofilm treatments.},
journal = {Biofilm},
volume = {8},
number = {},
pages = {100216},
pmid = {39184814},
issn = {2590-2075},
abstract = {Bacterial biofilms, especially those formed by pathogens, have been increasingly impacting human health. Bacterial extracellular vesicle (bEV), a kind of spherical membranous structure released by bacteria, has not only been reported to be a component of the biofilm matrix but also plays a non-negligible role in the biofilm life cycle. Nevertheless, a comprehensive overview of the bEVs functions in biofilms remains elusive. In this review, we summarize the biogenesis and distinctive features characterizing bEVs, and consolidate the current literature on their functions and proposed mechanisms in the biofilm life cycle. Furthermore, we emphasize the formidable challenges associated with vesicle interference in biofilm treatments. The primary objective of this review is to raise awareness regarding the functions of bEVs in the biofilm life cycle and lay the groundwork for the development of novel therapeutic strategies to control or even eliminate bacterial biofilms.},
}
@article {pmid39182428,
year = {2024},
author = {Ando, S and Tanaka, R and Ito, H},
title = {Activity examination of plant Mg-dechelatase and its bacterial homolog in plants and in vitro.},
journal = {Plant physiology and biochemistry : PPB},
volume = {215},
number = {},
pages = {109073},
doi = {10.1016/j.plaphy.2024.109073},
pmid = {39182428},
issn = {1873-2690},
mesh = {*Bacterial Proteins/metabolism/genetics ; Chlorophyll/metabolism ; Plant Proteins/metabolism/genetics ; Chlorophyll A/metabolism ; Nicotiana/genetics/metabolism ; },
abstract = {Chlorophyll a serves as a photosynthetic pigment in plants. Its degradation is initiated by the extraction of the central Mg by the Mg-dechelatase enzyme, which is encoded by Stay-Green (SGR). Plant SGR is believed to be derived from bacterial SGR homolog obtained through horizontal gene transfer into photosynthetic eukaryotes. However, it is not known how the bacterial SGR homolog was modified to function in plants. To assess its adaptation mechanism in plants, a bacterial SGR homolog derived from the Anaerolineae bacterium SM23_63 was introduced into plants. It was found that the bacterial SGR homolog metabolized chlorophyll in plants. However, its chlorophyll catabolic activity was lower than that of plant SGR. Recombinant proteins of the bacterial SGR homolog exhibited higher activity than those of the plant SGR. The reduced chlorophyll catabolic activity of bacterial SGR homologs in plants may be associated with low hydrophobicity of the entrance to the catalytic site compared to that of plant SGR. This hinders the enzyme access to chlorophyll, which is localized in hydrophobic environments. This study offers insights into the molecular changes underlying the optimization of enzyme function.},
}
@article {pmid39180708,
year = {2024},
author = {Witt, ASA and Carvalho, JVRP and Serafim, MSM and Arias, NEC and Rodrigues, RAL and Abrahão, JS},
title = {The GC% landscape of the Nucleocytoviricota.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {55},
number = {4},
pages = {3373-3387},
pmid = {39180708},
issn = {1678-4405},
support = {88882.348380/2010-1//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 405249/2022-5//Ministry of Science and Technology/ ; 406441/2022-7//Ministry of Science and Technology/ ; },
mesh = {Base Composition ; *Genome, Viral ; Phylogeny ; Evolution, Molecular ; Gene Transfer, Horizontal ; },
abstract = {Genomic studies on sequence composition employ various approaches, such as calculating the proportion of guanine and cytosine within a given sequence (GC% content), which can shed light on various aspects of the organism's biology. In this context, GC% can provide insights into virus-host relationships and evolution. Here, we present a comprehensive gene-by-gene analysis of 61 representatives belonging to the phylum Nucleocytoviricota, which comprises viruses with the largest genomes known in the virosphere. Parameters were evaluated not only based on the average GC% of a given viral species compared to the entire phylum but also considering gene position and phylogenetic history. Our results reveal that while some families exhibit similar GC% among their representatives (e.g., Marseilleviridae), others such as Poxviridae, Phycodnaviridae, and Mimiviridae have members with discrepant GC% values, likely reflecting adaptation to specific biological cycles and hosts. Interestingly, certain genes located at terminal regions or within specific genomic clusters show GC% values distinct from the average, suggesting recent acquisition or unique evolutionary pressures. Horizontal gene transfer and the presence of potential paralogs were also assessed in genes with the most discrepant GC% values, indicating multiple evolutionary histories. Taken together, to the best of our knowledge, this study represents the first global and gene-by-gene analysis of GC% distribution and profiles within genomes of Nucleocytoviricota members, highlighting their diversity and identifying potential new targets for future studies.},
}
@article {pmid39179660,
year = {2024},
author = {Wang, S and Sun, S and Wang, Q and Chen, H and Guo, Y and Cai, M and Yin, Y and Ma, S and Wang, H},
title = {PathoTracker: an online analytical metagenomic platform for Klebsiella pneumoniae feature identification and outbreak alerting.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1038},
pmid = {39179660},
issn = {2399-3642},
support = {32141001//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81991533//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Klebsiella pneumoniae/genetics/isolation &amp; purification ; *Metagenomics/methods ; Humans ; *Disease Outbreaks ; *Klebsiella Infections/microbiology/epidemiology/diagnosis ; *Phylogeny ; China/epidemiology ; Nanopore Sequencing/methods ; Databases, Genetic ; Genome, Bacterial ; },
abstract = {Clinical metagenomics (CMg) Nanopore sequencing can facilitate infectious disease diagnosis. In China, sub-lineages ST11-KL64 and ST11-KL47 Carbapenem-resistant Klebsiella pneumoniae (CRKP) are widely prevalent. We propose PathoTracker, a specially compiled database and arranged method for strain feature identification in CMg samples and CRKP traceability. A database targeting high-prevalence horizontal gene transfer in CRKP strains and a ST11-only database for distinguishing two sub-lineages in China were created. To make the database user-friendly, facilitate immediate downstream strain feature identification from raw Nanopore metagenomic data, and avoid the need for phylogenetic analysis from scratch, we developed data analysis methods. The methods included pre-performed phylogenetic analysis, gene-isolate-cluster index and multilevel pan-genome database and reduced storage space by 10-fold and random-access memory by 52-fold compared with normal methods. PathoTracker can provide accurate and fast strain-level analysis for CMg data after 1 h Nanopore sequencing, allowing early warning of outbreaks. A user-friendly page (http://PathoTracker.pku.edu.cn/) was developed to facilitate online analysis, including strain-level feature, species identifications and phylogenetic analyses. PathoTracker proposed in this study will aid in the downstream analysis of CMg.},
}
@article {pmid39176446,
year = {2024},
author = {Ahmed, M and Kayal, E and Lavrov, DV},
title = {Mitochondrial DNA of the Demosponge Acanthella acuta: Linear Architecture and Other Unique Features.},
journal = {Genome biology and evolution},
volume = {16},
number = {8},
pages = {},
pmid = {39176446},
issn = {1759-6653},
mesh = {*DNA, Mitochondrial/genetics ; Animals ; *Phylogeny ; *Introns ; *Open Reading Frames ; *Porifera/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; },
abstract = {While Acanthella acuta Schmidt 1862, a common demosponge found in the Mediterranean Sea and Atlantic Ocean, is morphologically similar to other sponges, its mitochondrial DNA (mtDNA) is unique within the class. In contrast to all other studied demosponges, the mtDNA of A. acuta is inferred to be linear and displays several unusual features such as inverted terminal repeats, group II introns in three mitochondrial genes, and two unique open reading frames (ORFs): one of which (ORF1535) combines a DNA polymerase domain with a DNA-directed RNA polymerase domain, while the second bears no discernible similarity to any reported sequences. The group II intron within the cox2 gene is the first such intron reported in an animal. Our phylogenetic analyses indicate that the cox1 intron is related to similar introns found in other demosponges, while the cox2 intron is likely not of animal origin. The two domains found within ORF1535 do not share a common origin and, along with the cox2 intron, were likely acquired by horizontal gene transfer. The findings of this paper open new avenues of exploration in the understanding of mtDNA linearization within Metazoa.},
}
@article {pmid39174812,
year = {2024},
author = {Döcker, J and Linz, S and Wicke, K},
title = {Bounding the Softwired Parsimony Score of a Phylogenetic Network.},
journal = {Bulletin of mathematical biology},
volume = {86},
number = {10},
pages = {121},
pmid = {39174812},
issn = {1522-9602},
support = {XXXX//Marsden Fund/ ; },
mesh = {*Phylogeny ; *Models, Genetic ; *Mathematical Concepts ; Algorithms ; Evolution, Molecular ; Sequence Alignment/statistics &amp; numerical data ; },
abstract = {In comparison to phylogenetic trees, phylogenetic networks are more suitable to represent complex evolutionary histories of species whose past includes reticulation such as hybridisation or lateral gene transfer. However, the reconstruction of phylogenetic networks remains challenging and computationally expensive due to their intricate structural properties. For example, the small parsimony problem that is solvable in polynomial time for phylogenetic trees, becomes NP-hard on phylogenetic networks under softwired and parental parsimony, even for a single binary character and structurally constrained networks. To calculate the parsimony score of a phylogenetic network N, these two parsimony notions consider different exponential-size sets of phylogenetic trees that can be extracted from N and infer the minimum parsimony score over all trees in the set. In this paper, we ask: What is the maximum difference between the parsimony score of any phylogenetic tree that is contained in the set of considered trees and a phylogenetic tree whose parsimony score equates to the parsimony score of N? Given a gap-free sequence alignment of multi-state characters and a rooted binary level-k phylogenetic network, we use the novel concept of an informative blob to show that this difference is bounded by k + 1 times the softwired parsimony score of N. In particular, the difference is independent of the alignment length and the number of character states. We show that an analogous bound can be obtained for the softwired parsimony score of semi-directed networks, while under parental parsimony on the other hand, such a bound does not hold.},
}
@article {pmid39173632,
year = {2024},
author = {Yang, XY and Shen, Z and Wang, C and Nakanishi, K and Fu, TM},
title = {DdmDE eliminates plasmid invasion by DNA-guided DNA targeting.},
journal = {Cell},
volume = {187},
number = {19},
pages = {5253-5266.e16},
pmid = {39173632},
issn = {1097-4172},
support = {R01 GM124320/GM/NIGMS NIH HHS/United States ; R01 GM138997/GM/NIGMS NIH HHS/United States ; },
mesh = {*Bacterial Proteins/metabolism/genetics ; DNA/metabolism ; DNA Helicases/metabolism ; DNA, Bacterial/metabolism/genetics ; Escherichia coli/genetics/metabolism ; *Gene Transfer, Horizontal ; Models, Molecular ; *Plasmids/metabolism/genetics ; },
abstract = {Horizontal gene transfer is a key driver of bacterial evolution, but it also presents severe risks to bacteria by introducing invasive mobile genetic elements. To counter these threats, bacteria have developed various defense systems, including prokaryotic Argonautes (pAgos) and the DNA defense module DdmDE system. Through biochemical analysis, structural determination, and in vivo plasmid clearance assays, we elucidate the assembly and activation mechanisms of DdmDE, which eliminates small, multicopy plasmids. We demonstrate that DdmE, a pAgo-like protein, acts as a catalytically inactive, DNA-guided, DNA-targeting defense module. In the presence of guide DNA, DdmE targets plasmids and recruits a dimeric DdmD, which contains nuclease and helicase domains. Upon binding to DNA substrates, DdmD transitions from an autoinhibited dimer to an active monomer, which then translocates along and cleaves the plasmids. Together, our findings reveal the intricate mechanisms underlying DdmDE-mediated plasmid clearance, offering fundamental insights into bacterial defense systems against plasmid invasions.},
}
@article {pmid39173362,
year = {2024},
author = {Zhang, Y and Zuo, S and Zheng, Q and Yu, G and Wang, Y},
title = {Removal of antibiotic resistant bacteria and antibiotic resistance genes by an electrochemically driven UV/chlorine process for decentralized water treatment.},
journal = {Water research},
volume = {265},
number = {},
pages = {122298},
doi = {10.1016/j.watres.2024.122298},
pmid = {39173362},
issn = {1879-2448},
mesh = {*Water Purification/methods ; *Ultraviolet Rays ; *Chlorine/chemistry/pharmacology ; Escherichia coli/drug effects/genetics ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology/chemistry ; Bacteria ; Drug Resistance, Bacterial/genetics ; },
abstract = {The UV/chlorine (UV/Cl2) process is a developing advanced oxidation process and can efficiently remove antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). However, the transportation and storage of chlorine solutions limit the application of the UV/Cl2 process, especially for decentralized water treatment. To overcome the limitation, an electrochemically driven UV/Cl2 process (E-UV/Cl2) where Cl2 can be electrochemically produced in situ from anodic oxidation of chloride (Cl[-]) ubiquitously present in various water matrices was evaluated in this study. >5-log inactivation of the ARB (E. coli) was achieved within 5 s of the E-UV/Cl2 process, and no photoreactivation of the ARB was observed after the treatment. In addition to the ARB, intracellular and extracellular ARGs (tetA, sul1, sul2, and ermB) could be effectively degraded (e.g., log(C0/C) > 4 for i-ARGs) within 5 min of the E-UV/Cl2 process. Atomic force microscopy showed that the most of the i-ARGs were interrupted into short fragments (< 30 nm) during the E-UV/Cl2 process, which can thus effectively prevent the self-repair of i-ARGs and the horizontal gene transfer. Modelling results showed that the abatement efficiencies of i-ARG correlated positively with the exposures of •OH, Cl2[-]•, and ClO• during the E-UV/Cl2 process. Due to the short treatment time (5 min) required for ARB and ARG removal, insignificant concentrations of trihalomethanes (THMs) were generated during of the E-UV/Cl2 process, and the energy consumption (EEO) of ARG removal was ∼0.20‒0.27 kWh/m[3]-log, which is generally comparable to that of the UV/Cl2 process (0.18-0.23 kWh/m[3]-log). These results demonstrate that the E-UV/Cl2 process can provide a feasible and attractive alternative to the UV/Cl2 process for ARB and ARG removal in decentralized water treatment system.},
}
@article {pmid39172952,
year = {2024},
author = {Zhou, W and Karan, KR and Gu, W and Klein, HU and Sturm, G and De Jager, PL and Bennett, DA and Hirano, M and Picard, M and Mills, RE},
title = {Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts.},
journal = {PLoS biology},
volume = {22},
number = {8},
pages = {e3002723},
pmid = {39172952},
issn = {1545-7885},
support = {P30 AG072975/AG/NIA NIH HHS/United States ; U01 AG046152/AG/NIA NIH HHS/United States ; R01 AG066828/AG/NIA NIH HHS/United States ; U01 AG061356/AG/NIA NIH HHS/United States ; R01 AG017917/AG/NIA NIH HHS/United States ; P30 AG010161/AG/NIA NIH HHS/United States ; R21 HG011493/HG/NHGRI NIH HHS/United States ; P30 AG072931/AG/NIA NIH HHS/United States ; R01 AG015819/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Fibroblasts/metabolism ; *Brain/metabolism ; Male ; Female ; Cell Nucleus/metabolism ; Middle Aged ; Adult ; Aged ; Longevity/genetics ; Aging/physiology/genetics ; },
abstract = {The transfer of mitochondrial DNA into the nuclear genomes of eukaryotes (Numts) has been linked to lifespan in nonhuman species and recently demonstrated to occur in rare instances from one human generation to the next. Here, we investigated numtogenesis dynamics in humans in 2 ways. First, we quantified Numts in 1,187 postmortem brain and blood samples from different individuals. Compared to circulating immune cells (n = 389), postmitotic brain tissue (n = 798) contained more Numts, consistent with their potential somatic accumulation. Within brain samples, we observed a 5.5-fold enrichment of somatic Numt insertions in the dorsolateral prefrontal cortex (DLPFC) compared to cerebellum samples, suggesting that brain Numts arose spontaneously during development or across the lifespan. Moreover, an increase in the number of brain Numts was linked to earlier mortality. The brains of individuals with no cognitive impairment (NCI) who died at younger ages carried approximately 2 more Numts per decade of life lost than those who lived longer. Second, we tested the dynamic transfer of Numts using a repeated-measures whole-genome sequencing design in a human fibroblast model that recapitulates several molecular hallmarks of aging. These longitudinal experiments revealed a gradual accumulation of 1 Numt every ~13 days. Numtogenesis was independent of large-scale genomic instability and unlikely driven by cell clonality. Targeted pharmacological perturbations including chronic glucocorticoid signaling or impairing mitochondrial oxidative phosphorylation (OxPhos) only modestly increased the rate of numtogenesis, whereas patient-derived SURF1-mutant cells exhibiting mtDNA instability accumulated Numts 4.7-fold faster than healthy donors. Combined, our data document spontaneous numtogenesis in human cells and demonstrate an association between brain cortical somatic Numts and human lifespan. These findings open the possibility that mito-nuclear horizontal gene transfer among human postmitotic tissues produces functionally relevant human Numts over timescales shorter than previously assumed.},
}
@article {pmid39172793,
year = {2024},
author = {Chen, X and Wang, M and Luo, L and Liu, X and An, L and Nie, Y and Wu, XL},
title = {The evolution of autonomy from two cooperative specialists in fluctuating environments.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {35},
pages = {e2317182121},
pmid = {39172793},
issn = {1091-6490},
support = {2018YFA0902100//MOST | National Key Research and Development Program of China (NKPs)/ ; 91951204//Data Center of Management Science, National Natural Science Foundation of China - Peking University (DCMS, NSFC-PKU)/ ; },
mesh = {*Naphthalenes/metabolism ; Gene Transfer, Horizontal ; Biological Evolution ; Symbiosis ; Microbial Consortia/genetics/physiology ; Genotype ; },
abstract = {From microbes to humans, organisms perform numerous tasks for their survival, including food acquisition, migration, and reproduction. A complex biological task can be performed by either an autonomous organism or by cooperation among several specialized organisms. However, it remains unclear how autonomy and cooperation evolutionarily switch. Specifically, it remains unclear whether and how cooperative specialists can repair deleted genes through direct genetic exchange, thereby regaining metabolic autonomy. Here, we address this question by experimentally evolving a mutualistic microbial consortium composed of two specialists that cooperatively degrade naphthalene. We observed that autonomous genotypes capable of performing the entire naphthalene degradation pathway evolved from two cooperative specialists and dominated the community. This evolutionary transition was driven by the horizontal gene transfer (HGT) between the two specialists. However, this evolution was exclusively observed in the fluctuating environment alternately supplied with naphthalene and pyruvate, where mutualism and competition between the two specialists alternated. The naphthalene-supplied environment exerted selective pressure that favors the expansion of autonomous genotypes. The pyruvate-supplied environment promoted the coexistence and cell density of the cooperative specialists, thereby increasing the likelihood of HGT. Using a mathematical model, we quantitatively demonstrate that environmental fluctuations facilitate the evolution of autonomy through HGT when the relative growth rate and carrying capacity of the cooperative specialists allow enhanced coexistence and higher cell density in the competitive environment. Together, our results demonstrate that cooperative specialists can repair deleted genes through a direct genetic exchange under specific conditions, thereby regaining metabolic autonomy.},
}
@article {pmid39168346,
year = {2024},
author = {Li, J and Li, C and Han, Y and Yang, J and Hu, Y and Xu, H and Zhou, Y and Zuo, J and Tang, Y and Lei, C and Li, C and Wang, H},
title = {Bacterial membrane vesicles from swine farm microbial communities harboring and safeguarding diverse functional genes promoting horizontal gene transfer.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175639},
doi = {10.1016/j.scitotenv.2024.175639},
pmid = {39168346},
issn = {1879-1026},
mesh = {*Gene Transfer, Horizontal ; Animals ; Swine ; Farms ; Microbiota ; Bacteria/genetics ; Feces/microbiology ; Drug Resistance, Microbial/genetics ; Wastewater/microbiology ; Drug Resistance, Bacterial/genetics ; Soil Microbiology ; Genes, Bacterial ; },
abstract = {Antibiotic resistance (AMR) poses a significant global health challenge, with swine farms recognized as major reservoirs of antibiotic resistance genes (ARGs). Recently, bacterial membrane vesicles (BMVs) have emerged as novel carriers mediating horizontal gene transfer. However, little is known about the ARGs carried by BMVs in swine farm environments and their transfer potential. This study investigated the distribution, sources, and microbiological origins of BMVs in three key microbial habitats of swine farms (feces, soil, and fecal wastewater), along with the ARGs and mobile genetic elements (MGEs) they harbor. Characterization of BMVs revealed particle sizes ranging from 20 to 500 nm and concentrations from 10[8] to 10[12] particles/g, containing DNA and proteins. Metagenomic sequencing identified BMVs predominantly composed of members of the Proteobacteria phyla, including Pseudomonadaceae, Moraxellaceae, and Enterobacteriaceae, carrying diverse functional genes encompassing resistance to 14 common antibiotics and 74,340 virulence genes. Notably, multidrug resistance, tetracycline, and chloramphenicol resistance genes were particularly abundant. Furthermore, BMVs harbored various MGEs, primarily plasmids, and demonstrated the ability to protect their DNA cargo from degradation and facilitate horizontal gene transfer, including the transmission of resistance genes. In conclusion, this study reveals widespread presence of BMVs carrying ARGs and potential virulence genes in swine farm feces, soil, and fecal wastewater. These findings not only provide new insights into the role of extracellular DNA in the environment but also highlight concerns regarding the gene transfer potential mediated by BMVs and associated health risks.},
}
@article {pmid39167960,
year = {2024},
author = {Nasu, T and Maeda, S},
title = {Escherichia coli persisters in biofilm can perform horizontal gene transfer by transformation.},
journal = {Biochemical and biophysical research communications},
volume = {738},
number = {},
pages = {150549},
doi = {10.1016/j.bbrc.2024.150549},
pmid = {39167960},
issn = {1090-2104},
mesh = {*Biofilms/drug effects/growth &amp; development ; *Escherichia coli/genetics/drug effects ; *Gene Transfer, Horizontal ; *Plasmids/genetics ; *Transformation, Bacterial ; Ampicillin/pharmacology ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics/drug effects ; },
abstract = {Persisters represent a subset of cells that exhibit transient tolerance to antimicrobials. These persisters can withstand sudden exposure to antimicrobials, even as the majority of normal cells perish. In this study, we have demonstrated the capacity of ampicillin-tolerant and alkali-tolerant persisters to execute horizontal gene transfer via in situ transformation within biofilms. Air-solid biofilms, comprising two Escherichia coli populations each with a distinct plasmid, were formed on agar media. They were treated with lethal doses of ampicillin or NaOH for 24 h, followed by a 1-min glass-ball roll. This process led to a high frequency of horizontal plasmid transfer (10[-7]-10[-6] per cell) from dead cells to surviving persisters within the biofilms. Plasmid transfer was DNase-sensitive and also occurred by adding purified plasmid DNA to plasmid-free biofilms, demonstrating a transformation mechanism. This marks the first evidence of persisters' novel ability for horizontal gene transfer, via transformation.},
}
@article {pmid39166873,
year = {2024},
author = {Kwan, S-Y and Sabotta, CM and Cruz, LR and Wong, MC and Ajami, NJ and McCormick, JB and Fisher-Hoch, SP and Beretta, L},
title = {Gut phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes.},
journal = {mSystems},
volume = {9},
number = {9},
pages = {e0043424},
pmid = {39166873},
issn = {2379-5077},
support = {P50 CA217674/CA/NCI NIH HHS/United States ; UL1 TR000371/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; Male ; Female ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics ; Middle Aged ; *Virome/genetics ; *Mexican Americans ; *Fatty Liver/genetics ; Cross-Sectional Studies ; Adult ; Diabetes Mellitus ; Feces/microbiology/virology ; Aged ; },
abstract = {Mexican Americans are disproportionally affected by metabolic dysfunction-associated steatotic liver disease (MASLD), which often co-occurs with diabetes. Despite extensive evidence on the causative role of the gut microbiome in MASLD, studies determining the involvement of the gut phageome are scarce. In this cross-sectional study, we characterized the gut phageome in Mexican Americans of South Texas by stool shotgun metagenomic sequencing of 340 subjects, concurrently screened for liver steatosis by transient elastography. Inter-individual variations in the phageome were associated with gender, country of birth, diabetes, and liver steatosis. The phage signatures for diabetes and liver steatosis were subsequently determined. Enrichment of Inoviridae was associated with both diabetes and liver steatosis. Diabetes was further associated with the enrichment of predominantly temperate Escherichia phages, some of which possessed virulence factors. Liver steatosis was associated with the depletion of Lactococcus phages r1t and BK5-T, and enrichment of the globally prevalent Crassvirales phages, including members of genus cluster IX (Burzaovirus coli, Burzaovirus faecalis) and VI (Kahnovirus oralis). The Lactococcus phages showed strong correlations and co-occurrence with Lactococcus lactis, while the Crassvirales phages, B. coli, B. faecalis, and UAG-readthrough crAss clade correlated and co-occurred with Prevotella copri. In conclusion, we identified the gut phageome signatures for two closely linked metabolic diseases with significant global burden. These phage signatures may have utility in risk modeling and disease prevention in this high-risk population, and identification of potential bacterial targets for phage therapy.IMPORTANCEPhages influence human health and disease by shaping the gut bacterial community. Using stool samples from a high-risk Mexican American population, we provide insights into the gut phageome changes associated with diabetes and liver steatosis, two closely linked metabolic diseases with significant global burden. Common to both diseases was an enrichment of Inoviridae, a group of phages that infect bacterial hosts chronically without lysis, allowing them to significantly influence bacterial growth, virulence, motility, biofilm formation, and horizontal gene transfer. Diabetes was additionally associated with the enrichment of Escherichia coli-infecting phages, some of which contained virulence factors. Liver steatosis was additionally associated with the depletion of Lactococcus lactis-infecting phages, and enrichment of Crassvirales phages, a group of virulent phages with high global prevalence and persistence across generations. These phageome signatures may have utility in risk modeling, as well as identify potential bacterial targets for phage therapy.},
}
@article {pmid39166856,
year = {2024},
author = {Karpenko, A and Shelenkov, A and Manzeniuk, I and Kulikova, N and Gevorgyan, A and Mikhaylova, Y and Akimkin, V},
title = {Whole genome analysis of multidrug-resistant Escherichia coli isolate collected from drinking water in Armenia revealed the plasmid-borne mcr-1.1-mediated colistin resistance.},
journal = {Microbiology spectrum},
volume = {12},
number = {10},
pages = {e0075124},
pmid = {39166856},
issn = {2165-0497},
support = {075-15-2019-1666//Ministry of Science and Higher Education of the Russian Federation (Minobrnauki of Russia)/ ; },
mesh = {*Escherichia coli/genetics/drug effects/isolation &amp; purification ; *Drug Resistance, Multiple, Bacterial/genetics ; *Plasmids/genetics ; *Colistin/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Whole Genome Sequencing ; *Escherichia coli Proteins/genetics ; *Drinking Water/microbiology ; Humans ; Armenia ; Microbial Sensitivity Tests ; Genome, Bacterial/genetics ; Escherichia coli Infections/microbiology/veterinary ; Water Microbiology ; },
abstract = {UNLABELLED: The rate of polymyxin-resistant Enterobacteriaceae, as well as human and animal infections caused by them, is increasing worldwide, posing a high epidemiological threat since colistin represents a last-resort antibiotic to treat complicated infections. The study of environmental niches, in particular, aquatic ecosystems in terms of genome analysis of inhabiting antimicrobial-resistant (AMR) microorganisms as reservoirs of acquired resistance determinants (AMR genes), represents a specific concern from a One Health approach. Here, we present a phenotypic AMR analysis and molecular characterization of Escherichia coli isolate found in municipal drinking water after an accident in the water supply system of a residential building in Armenia in 2021. CrieF1144 E. coli isolate was resistant to ampicillin, ampicillin/sulbactam, cefuroxime, ciprofloxacin, levofloxacin, trimethoprim/sulfamethoxazole, colistin, and tigecycline, whereas whole genome sequencing (WGS) revealed blaTEM-1B, tet(A), and a combination of dfrA14 with sul1 resistance determinants, which corresponds well with phenotypic resistance above. Moreover, the multidrug-resistant isolate studied harbored mcr-1.1 gene on a conjugative 251 Kb IncHI2 plasmid, whose structure was determined using hybrid short- and long-reads assembly. CrieF1141_p1 plasmid carried all antimicrobial resistance genes revealed in the isolate and did not harbor any virulence determinants, so it could contribute to the spread of AMR genes in the bacterial population. Two copies of ISApl1 transposase-encoding element, which is likely to mediate mcr-1.1 gene mobilization, were revealed surrounding this gene in a plasmid.<br><br>IMPORTANCE: Evolutionary patterns of Escherichia coli show that they usually develop into highly pathogenic forms by acquiring fitness advantages such as antimicrobial resistance (AMR) and various virulence factors through horizontal gene transfer mediated by mobile elements. This has led to high prevalence of multidrug-resistant (MDR) strains, which highlights the relevancy of enhanced surveillance to monitor and prevent transmission of the MDR bacteria to human and animal populations. However, the limited number of reports regarding the whole genome sequencing (WGS) investigation of MDR E. coli strains isolated from drinking water and harboring mcr genes hampers the adoption of a comprehensive approach to address the relationship between environmental E. coli populations and human and veterinary infections. Our results highlight the relevance of analyzing the environment, especially water, as a part of the surveillance programs to understand the origins and dissemination of antimicrobial resistance within the One Health concept.},
}
@article {pmid39166427,
year = {2024},
author = {Wu, JJ and Deng, QW and Qiu, YY and Liu, C and Lin, CF and Ru, YL and Sun, Y and Lai, J and Liu, LX and Shen, XX and Pan, R and Zhao, YP},
title = {Post-transfer adaptation of HGT-acquired genes and contribution to guanine metabolic diversification in land plants.},
journal = {The New phytologist},
volume = {244},
number = {2},
pages = {694-707},
doi = {10.1111/nph.20040},
pmid = {39166427},
issn = {1469-8137},
support = {32071484//National Natural Science Foundation of China/ ; 32200231//National Natural Science Foundation of China/ ; 32371691//National Natural Science Foundation of China/ ; LZ21C030003//Natural Science Foundation of Zhejiang Province/ ; LZ23C020002//Natural Science Foundation of Zhejiang Province/ ; LR23C140001//Natural Science Foundation of Zhejiang Province/ ; 2023000CC0010//Beijing Life Science Academy/ ; 226-2023-00021//Fundamental Research Funds for the Central Universities/ ; 2022YFD1401600//National Key Research and Development Program of China/ ; },
mesh = {*Gene Transfer, Horizontal ; *Embryophyta/genetics ; *Introns/genetics ; *Genes, Plant ; *Guanine/metabolism ; Phylogeny ; Adaptation, Physiological/genetics ; Genome, Plant ; Evolution, Molecular ; },
abstract = {Horizontal gene transfer (HGT) is a major driving force in the evolution of prokaryotic and eukaryotic genomes. Despite recent advances in distribution and ecological importance, the extensive pattern, especially in seed plants, and post-transfer adaptation of HGT-acquired genes in land plants remain elusive. We systematically identified 1150 foreign genes in 522 land plant genomes that were likely acquired via at least 322 distinct transfers from nonplant donors and confirmed that recent HGT events were unevenly distributed between seedless and seed plants. HGT-acquired genes evolved to be more similar to native genes in terms of average intron length due to intron gains, and HGT-acquired genes containing introns exhibited higher expression levels than those lacking introns, suggesting that intron gains may be involved in the post-transfer adaptation of HGT in land plants. Functional validation of bacteria-derived gene GuaD in mosses and gymnosperms revealed that the invasion of foreign genes introduced a novel bypass of guanine degradation and resulted in the loss of native pathway genes in some gymnosperms, eventually shaping three major types of guanine metabolism in land plants. We conclude that HGT has played a critical role in land plant evolution.},
}
@article {pmid39165128,
year = {2024},
author = {Trost, K and Knopp, MR and Wimmer, JLE and Tria, FDK and Martin, WF},
title = {A universal and constant rate of gene content change traces pangenome flux to LUCA.},
journal = {FEMS microbiology letters},
volume = {371},
number = {},
pages = {},
pmid = {39165128},
issn = {1574-6968},
support = {101018894/ERC_/European Research Council/International ; 101018894/ERC_/European Research Council/International ; },
mesh = {*Bacteria/genetics/classification ; *Genome, Bacterial ; *Archaea/genetics/classification ; *Evolution, Molecular ; *Genome, Archaeal ; Gene Transfer, Horizontal ; Phylogeny ; },
abstract = {Prokaryotic genomes constantly undergo gene flux via lateral gene transfer, generating a pangenome structure consisting of a conserved core genome surrounded by a more variable accessory genome shell. Over time, flux generates change in genome content. Here, we measure and compare the rate of genome flux for 5655 prokaryotic genomes as a function of amino acid sequence divergence in 36 universally distributed proteins of the informational core (IC). We find a clock of gene content change. The long-term average rate of gene content flux is remarkably constant across all higher prokaryotic taxa sampled, whereby the size of the accessory genome-the proportion of the genome harboring gene content difference for genome pairs-varies across taxa. The proportion of species-level accessory genes per genome, varies from 0% (Chlamydia) to 30%-33% (Alphaproteobacteria, Gammaproteobacteria, and Clostridia). A clock-like rate of gene content change across all prokaryotic taxa sampled suggest that pangenome structure is a general feature of prokaryotic genomes and that it has been in existence since the divergence of bacteria and archaea.},
}
@article {pmid39163267,
year = {2024},
author = {Kloub, L and Gosselin, S and Graf, J and Gogarten, JP and Bansal, MS},
title = {Investigating Additive and Replacing Horizontal Gene Transfers Using Phylogenies and Whole Genomes.},
journal = {Genome biology and evolution},
volume = {16},
number = {9},
pages = {},
pmid = {39163267},
issn = {1759-6653},
support = {1616514//National Science Foundation/ ; 8082-32000-006-00-D//United States Department of Agriculture/ ; },
mesh = {*Gene Transfer, Horizontal ; *Phylogeny ; *Genome, Bacterial ; Aeromonas/genetics ; Evolution, Molecular ; },
abstract = {Horizontal gene transfer (HGT) is fundamental to microbial evolution and adaptation. When a gene is horizontally transferred, it may either add itself as a new gene to the recipient genome (possibly displacing nonhomologous genes) or replace an existing homologous gene. Currently, studies do not usually distinguish between "additive" and "replacing" HGTs, and their relative frequencies, integration mechanisms, and specific roles in microbial evolution are poorly understood. In this work, we develop a novel computational framework for large-scale classification of HGTs as either additive or replacing. Our framework leverages recently developed phylogenetic approaches for HGT detection and classifies HGTs inferred between terminal edges based on gene orderings along genomes and phylogenetic relationships between the microbial species under consideration. The resulting method, called DART, is highly customizable and scalable and can classify a large fraction of inferred HGTs with high confidence and statistical support. Our application of DART to a large dataset of thousands of gene families from 103 Aeromonas genomes provides insights into the relative frequencies, functional biases, and integration mechanisms of additive and replacing HGTs. Among other results, we find that (i) the relative frequency of additive HGT increases with increasing phylogenetic distance, (ii) replacing HGT dominates at shorter phylogenetic distances, (iii) additive and replacing HGTs have strikingly different functional profiles, (iv) homologous recombination in flanking regions of a novel gene may be a frequent integration mechanism for additive HGT, and (v) phages and mobile genetic elements likely play an important role in facilitating additive HGT.},
}
@article {pmid39162532,
year = {2024},
author = {Ito, Y and Hashimoto, Y and Suzuki, M and Kaneko, N and Yoshida, M and Nakayama, H and Tomita, H},
title = {The emergence of metronidazole-resistant Prevotella bivia harboring nimK gene in Japan.},
journal = {Microbiology spectrum},
volume = {12},
number = {10},
pages = {e0056224},
pmid = {39162532},
issn = {2165-0497},
support = {21KA1004,24KA1005//Japanese Ministry of Health, Labor and Welfare/ ; JP23fk0108604,JP24fk0108665//Japan Agency for Medical Research and Development (AMED)/ ; 22K07067//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; JP23gm1610003,JP23fk0108665,JP23wm0225029//Japan Agency for Medical Research and Development (AMED)/ ; 22K16368//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; },
mesh = {*Prevotella/genetics/drug effects/isolation &amp; purification ; *Metronidazole/pharmacology ; Humans ; Female ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; Japan ; *Drug Resistance, Bacterial/genetics ; *Bacteroidaceae Infections/microbiology ; Whole Genome Sequencing ; Aged ; Bacterial Proteins/genetics/metabolism ; DNA Transposable Elements/genetics ; Genome, Bacterial/genetics ; Interspersed Repetitive Sequences/genetics ; },
abstract = {UNLABELLED: We present the identification and characterization of the complete genome of metronidazole (MTZ)-resistant Prevotella bivia strain TOH-2715 [minimum inhibitory concentration (MIC): 8 mg/L], isolated from the urine of an elderly Japanese woman, as well as details of its mobile genetic elements (MGEs) containing antimicrobial resistance (AMR) genes and its relationship with other bacterial species determined using whole-genome sequencing (WGS) data. TOH-2715 possessed two chromosomes with putative MGEs containing AMR genes. Two AMR-related MGE regions were present in chromosome 2. MGE-region 1 (7,821 bp) included Tn6456, where nimK was located, and MGE-region 2 (58.8 Kbp) included the integrative and conjugative element (ICE), where tet(Q) and ermF were located. The genetic structure of the ICE of TOH-2715 was similar to that of CTnDOT-family transposons, where ermF and tet(Q) are located. A search of public databases revealed that nimK was present in Prevotella spp., including P. bivia, and was partially composed of a Tn6456-like element lacking the efflux transporter gene qacE and the Crp/Fnr family transcriptional regulator gene in some cases. Core ICE gene analysis showed that ICEs similar to that of TOH-2715 were present in Prevotella spp. and Bacteroides spp., suggesting horizontal gene transfer among anaerobes. This is the report of WGS analysis of an MTZ-resistant clinical strain of P. bivia (TOH-2715) with Tn6456 encoding nimK. Other submitted genomes have described the presence of nimK, but none of them have described MTZ resistance. Additionally, we described putative MGE regions containing the AMR gene within the genus Prevotella and among anaerobes, raising concerns about the future spread of nimK among anaerobes.<br><br>IMPORTANCE: Metronidazole (MTZ) is an important antimicrobial agent in anaerobic infections and is widely used in clinical settings. The rate of MTZ resistance in anaerobic bacteria has been increasing in recent years, and the nim gene (nitro-imidazole reductase) is one of the resistance mechanisms. Prevotella bivia is found in humans in the urinary tract and vagina and is known to cause infections in some cases. One of the nim genes, nimK, has recently been discovered in this species of bacteria, but there are no reports of antimicrobial resistance (AMR)-related regions in its whole genome level. In this study, we analyzed the AMR region of nimK-positive P. bivia derived from clinical specimens based on comparisons with other anaerobic genomes. P. bivia was found to be engaged in horizontal gene transfer with other anaerobic bacteria, and the future spread of the nimK gene is a concern.},
}
@article {pmid39162515,
year = {2024},
author = {Wang, Z and Hülpüsch, C and Foesel, B and Traidl-Hoffmann, C and Reiger, M and Schloter, M},
title = {Genomic and functional divergence of Staphylococcus aureus strains from atopic dermatitis patients and healthy individuals: insights from global and local scales.},
journal = {Microbiology spectrum},
volume = {12},
number = {10},
pages = {e0057124},
pmid = {39162515},
issn = {2165-0497},
support = {//Helmholtz Munich Internal Funding/ ; },
mesh = {*Dermatitis, Atopic/microbiology/genetics ; *Staphylococcus aureus/genetics/classification/isolation &amp; purification ; Humans ; *Skin/microbiology ; Staphylococcal Infections/microbiology ; Genome, Bacterial/genetics ; Genomics ; Genetic Variation ; Phylogeny ; Gene Transfer, Horizontal ; Bacteriocins/genetics/metabolism ; },
abstract = {Atopic dermatitis (AD) is the most common chronic inflammatory skin disease worldwide and is characterized by a complex interplay with skin microbiota, with Staphylococcus aureus often abnormally more abundant in AD patients than in healthy individuals (HE). S. aureus harbors diverse strains with varied genetic compositions and functionalities, which exhibit differential connections with the severity of AD. However, the differences in S. aureus strains between AD and HE remain unclear, with most variations seen at a specific geographic level, implying spontaneous adaptations rather than systematic distinctions. This study presents genomic and functional differences between these S. aureus strains from AD and HE on both global and local levels. We observed reduced gene content diversity but increased functional variation in the global AD-associated strains. Two additional AD-dominant clusters emerged, with Cluster 1 enriched in transposases and Cluster 2 showcasing genes linked to adaptability and antibiotic resistance. Particularly, robust evidence illustrates that the lantibiotic operon of S. aureus, involved in the biosynthesis of lantibiotics, was acquired via horizontal gene transfer from environmental bacteria. Comparisons of the gene abundance profiles in functional categories also indicate limited zoonotic potential between human and animal isolates. Local analysis mirrored global gene diversity but showed distinct functional variations between AD and HE strains. Overall, this research provides foundational insights into the genomic evolution, adaptability, and antibiotic resistance of S. aureus, with significant implications for clinical microbiology.IMPORTANCEOur study uncovers significant genomic variations in Staphylococcus aureus strains associated with atopic dermatitis. We observed adaptive evolution tailored to the disease microenvironment, characterized by a smaller pan-genome than strains from healthy skin both on the global and local levels. Key functional categories driving strain diversification include "replication and repair" and "transporters," with transposases being pivotal. Interestingly, the local strains predominantly featured metal-related genes, whereas global ones emphasized antimicrobial resistances, signifying scale-dependent diversification nuances. We also pinpointed horizontal gene transfer events, indicating interactions between human-associated and environmental bacteria. These insights expand our comprehension of S. aureus's genetic adaptation in atopic dermatitis, yielding valuable implications for clinical approaches.},
}
@article {pmid39159726,
year = {2024},
author = {Zhang, Y and Wang, N and Wan, J and Jousset, A and Jiang, G and Wang, X and Wei, Z and Xu, Y and Shen, Q},
title = {Exploring the antibiotic resistance genes removal dynamics in chicken manure by composting.},
journal = {Bioresource technology},
volume = {410},
number = {},
pages = {131309},
doi = {10.1016/j.biortech.2024.131309},
pmid = {39159726},
issn = {1873-2976},
mesh = {Animals ; *Manure/microbiology ; *Chickens ; *Composting ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Bacteria/genetics/drug effects ; Microbiota/drug effects ; Gene Transfer, Horizontal ; },
abstract = {Prolonged antibiotic usage in livestock farming leads to the accumulation of antibiotic resistance genes in animal manure. Composting has been shown as an effective way of removing antibiotic resistance from manures, but the specific mechanisms remain unclear. This study used time-series sampling and metagenomics to analyse the resistome types and their bacterial hosts in chicken manures. Composting significantly altered the physicochemical properties and microbiome composition, reduced antibiotic resistance genes by 65.71 %, mobile genetic elements by 68.15 % and horizontal gene transfer frequency. Source tracking revealed that Firmicutes, Actinobacteria, and Proteobacteria are the major bacterial hosts involved in the resistome and gene transfer events. Composting reduces the resistome risk by targeting pathogens such as Staphylococcus aureus. Structural equation modelling confirmed that composting reduces resistome risk by changing pH and pathogen abundance. This study demonstrates that composting is an effective strategy for mitigating resistome risk in chicken manure, thereby supporting the One Health initiative.},
}
@article {pmid39158311,
year = {2024},
author = {Liu, H and Zheng, L and Fan, H and Pang, J},
title = {Genomic analysis of antibiotic resistance genes and mobile genetic elements in eight strains of nontyphoid Salmonella.},
journal = {mSystems},
volume = {9},
number = {9},
pages = {e0058624},
pmid = {39158311},
issn = {2379-5077},
support = {2022-JSYZ-13//The Second Phase of Jinshan Medical Personnel Training Program/ ; KFQM-27//Rehabilitation Medicine Talent Leading Program/ ; },
mesh = {Humans ; *Salmonella/genetics/drug effects/isolation &amp; purification ; *Interspersed Repetitive Sequences/genetics ; *Salmonella Infections/microbiology/epidemiology ; Anti-Bacterial Agents/pharmacology ; China/epidemiology ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Plasmids/genetics ; Genomics ; Feces/microbiology ; },
abstract = {UNLABELLED: Nontyphoidal Salmonella (NTS) is the main etiological agent of human nontyphoidal salmonellosis. The aim of this study was to analyze the epidemiological characteristics and horizontal transfer mechanisms of antimicrobial resistance (AMR) genes from eight strains of NTS detected in Zhenjiang City, Jiangsu Province, China. Fecal samples from outpatients with food-borne diarrhea were collected in 2022. The NTS isolates were identified, and their susceptibility was tested with the Vitek 2 Compact system. The genomes of the NTS isolates were sequenced with the Illumina NovaSeq platform and Oxford Nanopore Technologies platform. The AMR genes and mobile genetic elements (MGEs) were predicted with the relevant open access resources. Eight strains of NTS were isolated from 153 specimens, and Salmonella Typhimurium ST19 was the most prevalent serotype. The AMR gene with the highest detection rate was AAC(6')-Iaa (10.5%) followed by TEM-1 (7.9%), sul2 (6.6%), and tet(A) (5.3%). Eleven MGEs carrying 34 AMR genes were identified on the chromosomes of 3 of the 8 NTS, including 3 resistance islands, 6 composite transposons (Tns), and 2 integrons. Eighteen plasmids carrying 40 AMR genes were detected in the 8 NTS strains, including 6 mobilizable plasmids, 3 conjugative plasmids, and 9 nontransferable plasmids, 7 of which carried 10 composite Tns and 3 integrons. This study provided a theoretical basis, from a genetic perspective, for the prevention and control of NTS resistance in Zhenjiang City.<br><br>IMPORTANCE: Human nontyphoidal salmonellosis is one of the common causes of bacterial food-borne illnesses, with significant social and economic impacts, especially those caused by invasive multidrug-resistant nontyphoidal Salmonella, which entails high morbidity and mortality. Antimicrobial resistance is mainly mediated by drug resistance genes, and mobile genetic elements play key roles in the capture, accumulation, and dissemination of antimicrobial resistance genes. Therefore, it is necessary to study the epidemiological characteristics and horizontal transfer mechanisms of antimicrobial resistance genes of nontyphoidal Salmonella to prevent the spread of multidrug-resistant nontyphoidal Salmonella.},
}
@article {pmid39158272,
year = {2024},
author = {Upreti, C and Kumar, P and Durso, LM and Palmer, KL},
title = {CRISPR-Cas inhibits plasmid transfer and immunizes bacteria against antibiotic resistance acquisition in manure.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {9},
pages = {e0087624},
pmid = {39158272},
issn = {1098-5336},
support = {R01 AI116610/AI/NIAID NIH HHS/United States ; 58-3042-8-012//U.S. Department of Agriculture (USDA)/ ; R01AI116610//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {*Plasmids/genetics ; *Enterococcus faecalis/genetics/drug effects ; *CRISPR-Cas Systems ; Animals ; *Manure/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal ; Humans ; Swine ; Cattle ; },
abstract = {The horizontal transfer of antibiotic resistance genes among bacteria is a pressing global issue. The bacterial defense system clustered regularly interspaced short palindromic repeats (CRISPR)-Cas acts as a barrier to the spread of antibiotic resistance plasmids, and CRISPR-Cas-based antimicrobials can be effective to selectively deplete antibiotic-resistant bacteria. While significant surveillance efforts monitor the spread of antibiotic-resistant bacteria in the clinical context, a major, often overlooked aspect of the issue is resistance emergence in agriculture. Farm animals are commonly treated with antibiotics, and antibiotic resistance in agriculture is on the rise. Yet, CRISPR-Cas efficacy has not been investigated in this setting. Here, we evaluate the prevalence of CRISPR-Cas in agricultural Enterococcus faecalis strains and its antiplasmid efficacy in an agricultural niche: manure. Analyzing 1,986 E. faecalis genomes from human and animal hosts, we show that the prevalence of CRISPR-Cas subtypes is similar between clinical and agricultural E. faecalis strains. Using plasmid conjugation assays, we found that CRISPR-Cas is a significant barrier against resistance plasmid transfer in manure. Finally, we used a CRISPR-based antimicrobial approach to cure resistant E. faecalis of erythromycin resistance, but this was limited by delivery efficiency of the CRISPR antimicrobial in manure. However, immunization of bacteria against resistance gene acquisition in manure was highly effective. Together, our results show that E. faecalis CRISPR-Cas is prevalent and effective in an agricultural setting and has the potential to be utilized for depleting antibiotic-resistant populations. Our work has broad implications for tackling antibiotic resistance in the increasingly relevant agricultural setting, in line with a One Health approach.IMPORTANCEAntibiotic resistance is a growing global health crisis in human and veterinary medicine. Previous work has shown technologies based on CRISPR-Cas-a bacterial defense system-to be effective in tackling antibiotic resistance. Here we test if CRISPR-Cas is present and effective in agricultural niches, specifically in the ubiquitously present bacterium, Enterococcus faecalis. We show that CRISPR-Cas is both prevalent and functional in manure and has the potential to be used to specifically kill bacteria carrying antibiotic resistance genes. This study demonstrates the utility of CRISPR-Cas-based strategies for control of antibiotic resistance in agricultural settings.},
}
@article {pmid39158107,
year = {2024},
author = {Ming, Y and Abdullah Al, M and Zhang, D and Zhu, W and Liu, H and Cai, L and Yu, X and Wu, K and Niu, M and Zeng, Q and He, Z and Yan, Q},
title = {Insights into the evolutionary and ecological adaption strategies of nirS- and nirK-type denitrifying communities.},
journal = {Molecular ecology},
volume = {33},
number = {18},
pages = {e17507},
doi = {10.1111/mec.17507},
pmid = {39158107},
issn = {1365-294X},
support = {SML2020SP004//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2021SP203//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2023SP205//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 42377111//National Natural Science Foundation of China/ ; //Ocean Negative Carbon Emissions (ONCE) Program/ ; },
mesh = {*Denitrification/genetics ; *Nitrite Reductases/genetics ; China ; *Phylogeny ; *Metagenome/genetics ; Lakes/microbiology ; Bioreactors/microbiology ; Gene Transfer, Horizontal ; Microbiota/genetics ; Metagenomics ; Geologic Sediments/microbiology ; Bacteria/genetics/classification/metabolism ; Nitrogen/metabolism ; Adaptation, Physiological/genetics ; },
abstract = {Denitrification is a crucial process in the global nitrogen cycle, in which two functionally equivalent genes, nirS and nirK, catalyse the critical reaction and are usually used as marker genes. The nirK gene can function independently, whereas nirS requires additional genes to encode nitrite reductase and is more sensitive to environmental factors than nirK. However, the ecological differentiation mechanisms of those denitrifying microbial communities and their adaptation strategies to environmental stresses remain unclear. Here, we conducted metagenomic analysis for sediments and bioreactor samples from Lake Donghu, China. We found that nirS-type denitrifying communities had a significantly lower horizontal gene transfer frequency than that of nirK-type denitrifying communities, and nirS gene phylogeny was more congruent with taxonomy than that of nirK gene. Metabolic reconstruction of metagenome-assembled genomes further revealed that nirS-type denitrifying communities have robust metabolic systems for energy conservation, enabling them to survive under environmental stresses. Nevertheless, nirK-type denitrifying communities seemed to adapt to oxygen-limited environments with the ability to utilize various carbon and nitrogen compounds. Thus, this study provides novel insights into the ecological differentiation mechanism of nirS and nirK-type denitrifying communities, as well as the regulation of the global nitrogen cycle and greenhouse gas emissions.},
}
@article {pmid39153565,
year = {2024},
author = {Yang, C and Yan, S and Zhang, B and Yao, X and Mo, J and Rehman, F and Guo, J},
title = {Spatiotemporal distribution of the planktonic microbiome and antibiotic resistance genes in a typical urban river contaminated by macrolide antibiotics.},
journal = {Environmental research},
volume = {262},
number = {Pt 1},
pages = {119808},
doi = {10.1016/j.envres.2024.119808},
pmid = {39153565},
issn = {1096-0953},
mesh = {*Rivers/microbiology/chemistry ; *Microbiota/drug effects ; *Macrolides/analysis ; *Anti-Bacterial Agents/pharmacology/analysis ; *Plankton/drug effects/genetics ; *Drug Resistance, Microbial/genetics ; *Water Pollutants, Chemical/analysis ; Environmental Monitoring ; Genes, Bacterial ; Bacteria/genetics/drug effects/classification ; },
abstract = {The widespread application of macrolide antibiotics has caused antibiotic resistance pollution, threatening the river ecological health. In this study, five macrolide antibiotics (azithromycin, clarithromycin, roxithromycin, erythromycin, and anhydro erythromycin A) were monitored in the Zao River across three hydrological periods (April, July, and December). Simultaneously, the changes in antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and planktonic bacterial communities were determined using metagenomic sequencing. A clear pollution gradient was observed for azithromycin and roxithromycin, with the concentrations in the dry season surpassing those in other seasons. The highest concentration was observed for azithromycin (1.36 μg/L). The abundance of MLS resistance genes increased along the Zao River during the dry season, whereas the opposite trend was obtained during the wet season. A significant correlation between the levels of MLS resistance genes and macrolide antibiotics was identified during the dry season. Notably, compared with the reference site, the abundance of transposase in the effluent from wastewater treatment plants (WWTPs) was significantly elevated in both dry and wet seasons, whereas the abundance of insertion sequences (IS) and plasmids declined during the dry season. The exposure to wastewater containing macrolide antibiotics altered the diversity of planktonic bacterial communities. The bacterial host for ARGs appeared to be Pseudomonas, primarily associated with multidrug subtypes. Moreover, the ARG subtypes were highly correlated with MGEs (transposase and istA). The partial least-squares path model (PLS-PM) demonstrated a positive correlation between the abundance of MGEs and ARGs, indicating the significance of horizontal gene transfer (HGT) in the dissemination of ARGs within the Zao River. Environmental variables, such as TN and NO3[-]-N, were significantly correlated with the abundance of MGEs, ARGs, and bacteria. Collectively, our findings could provide insights into the shift patterns of the microbiome and ARGs across the contamination gradient of AZI and ROX in the river.},
}
@article {pmid39153075,
year = {2024},
author = {Panickar, A and Manoharan, A and Anbarasu, A and Ramaiah, S},
title = {Respiratory tract infections: an update on the complexity of bacterial diversity, therapeutic interventions and breakthroughs.},
journal = {Archives of microbiology},
volume = {206},
number = {9},
pages = {382},
pmid = {39153075},
issn = {1432-072X},
support = {IRIS ID: 2021-11889//Indian Council of Medical Research/ ; },
mesh = {*Respiratory Tract Infections/microbiology/drug therapy ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/genetics/drug effects/classification ; Drug Resistance, Bacterial ; Bacterial Infections/microbiology/drug therapy ; Virulence ; },
abstract = {Respiratory tract infections (RTIs) have a significant impact on global health, especially among children and the elderly. The key bacterial pathogens Streptococcus pneumoniae, Haemophilus influenzae, Klebsiella pneumoniae, Staphylococcus aureus and non-fermenting Gram Negative bacteria such as Acinetobacter baumannii and Pseudomonas aeruginosa are most commonly associated with RTIs. These bacterial pathogens have evolved a diverse array of resistance mechanisms through horizontal gene transfer, often mediated by mobile genetic elements and environmental acquisition. Treatment failures are primarily due to antimicrobial resistance and inadequate bacterial engagement, which necessitates the development of alternative treatment strategies. To overcome this, our review mainly focuses on different virulence mechanisms and their resulting pathogenicity, highlighting different therapeutic interventions to combat resistance. To prevent the antimicrobial resistance crisis, we also focused on leveraging the application of artificial intelligence and machine learning to manage RTIs. Integrative approaches combining mechanistic insights are crucial for addressing the global challenge of antimicrobial resistance in respiratory infections.},
}
@article {pmid39149034,
year = {2024},
author = {Kadkhoda, H and Gholizadeh, P and Samadi Kafil, H and Ghotaslou, R and Pirzadeh, T and Ahangarzadeh Rezaee, M and Nabizadeh, E and Feizi, H and Aghazadeh, M},
title = {Role of CRISPR-Cas systems and anti-CRISPR proteins in bacterial antibiotic resistance.},
journal = {Heliyon},
volume = {10},
number = {14},
pages = {e34692},
pmid = {39149034},
issn = {2405-8440},
abstract = {The emergence and development of antibiotic resistance in bacteria is a serious threat to global public health. Antibiotic resistance genes (ARGs) are often located on mobile genetic elements (MGEs). They can be transferred among bacteria by horizontal gene transfer (HGT), leading to the spread of drug-resistant strains and antibiotic treatment failure. CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated genes) is one of the many strategies bacteria have developed under long-term selection pressure to restrict the HGT. CRISPR-Cas systems exist in about half of bacterial genomes and play a significant role in limiting the spread of antibiotic resistance. On the other hand, bacteriophages and other MGEs encode a wide range of anti-CRISPR proteins (Acrs) to counteract the immunity of the CRISPR-Cas system. The Acrs could decrease the CRISPR-Cas system's activity against phages and facilitate the acquisition of ARGs and virulence traits for bacteria. This review aimed to assess the relationship between the CRISPR-Cas systems and Acrs with bacterial antibiotic resistance. We also highlighted the CRISPR technology and Acrs to control and prevent antibacterial resistance. The CRISPR-Cas system can target nucleic acid sequences with high accuracy and reliability; therefore, it has become a novel gene editing and gene therapy tool to prevent the spread of antibiotic resistance. CRISPR-based approaches may pave the way for developing smart antibiotics, which could eliminate multidrug-resistant (MDR) bacteria and distinguish between pathogenic and beneficial microorganisms. Additionally, the engineered anti-CRISPR gene-containing phages in combination with antibiotics could be used as a cutting-edge treatment approach to reduce antibiotic resistance.},
}
@article {pmid39148687,
year = {2024},
author = {Santos, AJDC and Dias, RS and da Silva, CHM and Vidigal, PMP and de Sousa, MP and da Silva, CC and de Paula, SO},
title = {Genomic analysis of Oceanotoga teriensis strain UFV_LIMV02, a multidrug-resistant thermophilic bacterium isolated from an offshore oil reservoir.},
journal = {Access microbiology},
volume = {6},
number = {8},
pages = {},
pmid = {39148687},
issn = {2516-8290},
abstract = {Bacteria of the species Oceanotoga teriensis belong to the family Petrotogaceae, are Gram-negative bacilli, are moderately thermophilic and are included in the group of thiosulfate-reducing bacteria, being capable of significantly accelerating corrosion in metallic structures. However, no in-depth study on the genome, antibiotic resistance and mobile elements has been carried out so far. In this work, the isolation, phenotypic and genotypic characterization of the multi-resistant O. teriensis UFV_LIMV02 strain was carried out, from water samples from an offshore oil extraction platform in Rio de Janeiro (Brazil). We determined that the isolate has a genome of 2 812 778 bp in size, with 26 % GC content, organized into 34 contigs. Genomic annotation using Rapid Annotation using Subsystem Technology revealed the presence of genes related to resistance to antibiotics and heavy metals. By evaluating the antimicrobial resistance of the isolate using the disc diffusion technique, resistance was verified for the classes of antibiotics, beta-lactams, fluoroquinolones, aminoglycosides, sulfonamides, lincosamides and rifamycins, a total of 14 antibiotics. The search for genomic islands, prophages and defence systems against phage infection revealed the presence of five genomic islands in its genome, containing genes related to resistance to heavy metals and antibiotics, most of which are efflux pumps and several transposases. No prophage was found in its genome; however, nine different defence systems against phage infection were detected. When analysing the clustered regularly interspaced short palindromic repeat (CRISPR) systems, four CRISPR arrays, classified as types I-B and III-B, with 272 spacers, can provide the strain with immunity to different mobile genetic elements and bacteriophage infection. The results found in this study show that the isolate UFV_LIVM02 is an environmental bacterium, resistant to different classes of antibiotics, and that the proteins encoded by the predicted genomic islands may be associated with the development of greater resistance to antibiotics and heavy metals. They provide evidence that environmental bacteria found in offshore oil exploration residues may pose a risk for the spread of antibiotic resistance genes. More comprehensive studies on the microbial community present in oil waste are needed to assess the risks of horizontal gene transfer.},
}
@article {pmid39147525,
year = {2024},
author = {Wu, Q and Li, W and Kwok, LY and Lv, H and Sun, J and Sun, Z},
title = {Regional variation and adaptive evolution in Bifidobacterium pseudocatenulatum: Insights into genomic and functional diversity in human gut.},
journal = {Food research international (Ottawa, Ont.)},
volume = {192},
number = {},
pages = {114840},
doi = {10.1016/j.foodres.2024.114840},
pmid = {39147525},
issn = {1873-7145},
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Phylogeny ; *Genome, Bacterial ; *Bifidobacterium pseudocatenulatum/genetics/metabolism ; Genetic Variation ; Genomics ; Diet ; },
abstract = {Bifidobacterium pseudocatenulatum is a prevalent gut microbe in humans of all ages and plays a crucial role in host health. However, its adaptive evolutionary characteristics remain poorly understood. This study analyzed the genome of 247 B. pseudocatenulatum isolates from Chinese, Vietnamese, Japanese and other region populations using population genomics and functional genomics. Our findings revealed high genetic heterogeneity and regional clustering within B. pseudocatenulatum isolates. Significant differences were observed in genome characteristics, phylogeny, and functional genes. Specifically, Chinese and Vietnamese isolates exhibited a higher abundance of genes involved in the metabolism of plant-derived carbohydrates (GH13, GH43, and GH5 enzyme families), aligning with the predominantly vegetable-, wheat- and fruit-based diets of these populations. Additionally, we found widespread transmission of antibiotic resistance genes (tetO and tetW) through mobile genetic elements, such as genomic islands (GIs), resulting in substantial intra-regional differences. Our findings highlight distinct adaptive evolution in B. pseudocatenulatum driven by gene specialization, possibly in response to regional variations in diet and lifestyle. This study sheds light on bifidobacteria colonization mechanisms in the host gut. IMPORTANCE: Gut microbiota, as a key link in the gut-brain axis, helps to maintain the health of the organism, among which, Bifidobacterium pseudocatenulatum (B. pseudocatenulatum) is an important constituent member of the gut microbiota, which plays an important role in maintaining the balance of gut microbiota. The probiotic properties of B. pseudocatenulatum have been widely elaborated, and in order to excavate its evolutionary features at the genomic level, here we focused on the genetic background and evolutionary mechanism of the B. pseudocatenulatum genomes isolated from the intestinal tracts of different populations. Ultimately, based on the phylogenetic tree, we found that B. pseudocatenulatum has high genetic diversity and regional clustering phenomenon, in which plant-derived carbohydrate metabolism genes (GH13, GH43, GH5) showed significant regional differences, and this genetic differentiation drove the adaptive evolution, which likely shaped by diet and lifestyle.},
}
@article {pmid39144201,
year = {2024},
author = {Pramanik, S and Sil, AK},
title = {Anti-foam cell activity of metabolites of a bacterium isolated from yogurt.},
journal = {Food science and biotechnology},
volume = {33},
number = {11},
pages = {2597-2610},
pmid = {39144201},
issn = {2092-6456},
abstract = {UNLABELLED: Existing literature documents the beneficial effects of probiotics against atherosclerosis, a major cause of human death. However, it suffers from a serious limitation due to horizontal gene transfer. Therefore, currently, efforts are targeted to examine the beneficial effects of metabolites obtained from probiotics. In this context, the current study isolated a bacterium from yogurt and investigated the effect of its metabolites on foam cell formation, a key event for developing atherosclerosis. Results showed that the cell-free conditioned medium (CM) of this isolate and di-chloro methane extract of CM (CME) not only prevented the formation but also reduced the level of preformed foam cells. To understand the mechanism, the GC-MS study revealed the presence of compounds known to exert anti-atherogenic activities like anti-oxidant, anti-NF-κB, and lipolytic activities. Consistently, CME exhibited substantial anti-oxidant and anti-NF-κB activity. In conclusion, metabolites of this bacterium have anti-atherogenic activities and thus have therapeutic potential.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-023-01515-7.},
}
@article {pmid39141729,
year = {2024},
author = {Lai, S and Wang, H and Bork, P and Chen, WH and Zhao, XM},
title = {Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts.},
journal = {Science advances},
volume = {10},
number = {33},
pages = {eadn3316},
pmid = {39141729},
issn = {2375-2548},
mesh = {*Bacteriophages/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/virology/genetics ; *Gene Transfer, Horizontal ; Metagenomics/methods ; Genetic Variation ; Virome/genetics ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; },
abstract = {Genetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here, we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By using virome-enriched long-read metagenomic sequencing across 91 individuals, we identified a total of 14,438 nonredundant phage SVs and revealed their prevalence within the human gut phageome. These SVs are mainly enriched in genes involved in recombination, DNA methylation, and antibiotic resistance. Notably, a substantial fraction of phage SV sequences share close homology with bacterial fragments, with most SVs enriched for horizontal gene transfer (HGT) mechanism. Further investigations showed that these SV sequences were genetic exchanged between specific phage-bacteria pairs, particularly between phages and their respective bacterial hosts. Temperate phages exhibit a higher frequency of genetic exchange with bacterial chromosomes and then virulent phages. Collectively, our findings provide insights into the genetic landscape of the human gut phageome.},
}
@article {pmid39141706,
year = {2024},
author = {Souque, C and González Ojeda, I and Baym, M},
title = {From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance.},
journal = {Annual review of microbiology},
volume = {78},
number = {1},
pages = {361-382},
doi = {10.1146/annurev-micro-041522-102707},
pmid = {39141706},
issn = {1545-3251},
support = {T32 GM008313/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; *Evolution, Molecular ; *Drug Resistance, Bacterial/genetics ; Bacterial Infections/microbiology/drug therapy ; },
abstract = {Tackling the challenge created by antibiotic resistance requires understanding the mechanisms behind its evolution. Like any evolutionary process, the evolution of antimicrobial resistance (AMR) is driven by the underlying variation in a bacterial population and the selective pressures acting upon it. Importantly, both selection and variation will depend on the scale at which resistance evolution is considered (from evolution within a single patient to the host population level). While laboratory experiments have generated fundamental insights into the mechanisms underlying antibiotic resistance evolution, the technological advances in whole genome sequencing now allow us to probe antibiotic resistance evolution beyond the lab and directly record it in individual patients and host populations. Here we review the evolutionary forces driving antibiotic resistance at each of these scales, highlight gaps in our current understanding of AMR evolution, and discuss future steps toward evolution-guided interventions.},
}
@article {pmid39141562,
year = {2024},
author = {Karan, J and Mandal, S and Khan, G and Arya, H and Samhita, L},
title = {Enhanced Extraction of Low-Molecular Weight DNA from Wastewater for Comprehensive Assessment of Antimicrobial Resistance.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {209},
pages = {},
doi = {10.3791/66899},
pmid = {39141562},
issn = {1940-087X},
mesh = {*Wastewater/microbiology/chemistry ; Polyethylene Glycols/chemistry ; Molecular Weight ; DNA, Bacterial/genetics/isolation &amp; purification ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; },
abstract = {Environmental surveillance is recognized as an important tool for assessing public health in the post-pandemic era. Water, in particular wastewater, has emerged as the source of choice to sample pathogen burdens in the environment. Wastewater from open drains and community water treatment plants is a reservoir of both pathogens and antimicrobial resistance (AMR) genes, and frequently comes in contact with humans. While there are many methods of tracking AMR from water, isolating good-quality DNA at high yields from heterogeneous samples remains a challenge. To compensate, sample volumes often need to be high, creating practical constraints. Additionally, environmental DNA is frequently fragmented, and the sources of AMR (plasmids, phages, linear DNA) consist of low-molecular-weight DNA. Yet, few extraction processes have focused on methods for high-yield extraction of linear and low-molecular-weight DNA. Here, a simple method for high-yield linear DNA extraction from small volumes of wastewater using the precipitation properties of polyethylene glycol (PEG) is reported. This study makes a case for increasing overall DNA yields from water samples collected for metagenomic analyses by enriching the proportion of linear DNA. In addition, enhancing low-molecular-weight DNA overcomes the current problem of under-sampling environmental AMR due to a focus on high-molecular-weight and intracellular DNA. This method is expected to be particularly useful when extracellular DNA exists but at low concentrations, such as with effluents from treatment plants. It should also enhance the environmental sampling of AMR gene fragments that spread through horizontal gene transfer.},
}
@article {pmid39139006,
year = {2024},
author = {Rao, Y and Wang, Y and Zhang, H and Wang, Y and He, Q and Yuan, X and Guo, J and Chen, H},
title = {A Strategy of Killing Two Birds With One Stone for Blocking Drug Resistance Spread With Engineered Bdellovibrio bacteriovorus.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {36},
number = {41},
pages = {e2406910},
doi = {10.1002/adma.202406910},
pmid = {39139006},
issn = {1521-4095},
support = {21935008//National Natural Science Foundation of China/ ; SKJY2021042//Livelihood Technology Project of Suzhou/ ; 23KJA150008//Jiangsu Province Higher Education Natural Science Research Major Project/ ; //Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; },
mesh = {*Bdellovibrio bacteriovorus ; *Anti-Bacterial Agents/pharmacology/chemistry ; Pseudomonas aeruginosa/drug effects ; Biofilms/drug effects ; Cerium/chemistry/pharmacology ; Drug Resistance, Bacterial/drug effects ; Animals ; Kanamycin/pharmacology ; Dopamine/metabolism ; Polymers/chemistry/pharmacology ; Plasmids/metabolism/genetics ; DNA Cleavage/drug effects ; Indoles ; },
abstract = {Drug-resistant pathogens significantly threaten human health and life. Simply killing drug-resistant pathogens cannot effectively eliminate their threat since the drug-resistant genes (DRGs) released from dead drug-resistant pathogens are difficult to eliminate and can further spread via horizontal gene transfer, leading to the spread of drug resistance. The development of antibacterial materials with sterilization and DRGs cleavage activities is highly crucial. Herein, a living system, Ce-PEA@Bdello, is fabricated with bacterial killing and DRGs cleavage activities for blocking bacterial drug resistance dissemination by engineered Bdellovibrio bacteriovorus (Bdello). Ce-PEA@Bdello is obtained by engineering Bdello with dopamine and a multinuclear cerium (IV) complex. Ce-PEA@Bdello can penetrate and eliminate kanamycin-resistant P. aeruginosa (Kan[R]) biofilms via the synergistic effect of predatory Bdello and photothermal polydopamine under near-infrared light. Additionally, the DNase-mimicking ability of Ce-PEA@Bdello endows it with genome and plasmid DNA cleavage ability. An in vivo study reveals that Ce-PEA@Bdello can eliminate P. aeruginosa (Kan[R]) and cleave DRGs in scald/burn infected wounds to block the spread of drug resistance and accelerate wound healing. This bioactive system constructed from natural living materials offers a promising means for blocking the spread of drug resistance.},
}
@article {pmid39138294,
year = {2024},
author = {York, A},
title = {Targeting the spread of antimicrobial resistance plasmids.},
journal = {Nature reviews. Microbiology},
volume = {22},
number = {10},
pages = {595},
pmid = {39138294},
issn = {1740-1534},
mesh = {*Plasmids/genetics ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Bacteria/drug effects/genetics ; Gene Transfer, Horizontal ; },
}
@article {pmid39135654,
year = {2024},
author = {Winter, M and Vos, M and Buckling, A and Johnsen, PJ and Harms, K},
title = {Effect of chemotherapeutic agents on natural transformation frequency in Acinetobacter baylyi.},
journal = {Access microbiology},
volume = {6},
number = {7},
pages = {},
pmid = {39135654},
issn = {2516-8290},
abstract = {Natural transformation is the ability of a bacterial cell to take up extracellular DNA which is subsequently available for recombination into the chromosome (or maintenance as an extrachromosomal element). Like other mechanisms of horizontal gene transfer, natural transformation is a significant driver for the dissemination of antimicrobial resistance. Recent studies have shown that many pharmaceutical compounds such as antidepressants and anti-inflammatory drugs can upregulate transformation frequency in the model species Acinetobacter baylyi. Chemotherapeutic compounds have been shown to increase the abundance of antimicrobial resistance genes and increase colonization rates of potentially pathogenic bacteria in patient gastrointestinal tracts, indicating an increased risk of infection and providing a pool of pathogenicity or resistance genes for transformable commensal bacteria. We here test for the effect of six cancer chemotherapeutic compounds on A. baylyi natural transformation frequency, finding two compounds, docetaxel and daunorubicin, to significantly decrease transformation frequency, and daunorubicin to also decrease growth rate significantly. Enhancing our understanding of the effect of chemotherapeutic compounds on the frequency of natural transformation could aid in preventing the horizontal spread of antimicrobial resistance genes.},
}
@article {pmid39132438,
year = {2024},
author = {Liu, H and Fan, S and Zhang, X and Yuan, Y and Zhong, W and Wang, L and Wang, C and Zhou, Z and Zhang, S and Geng, Y and Peng, G and Wang, Y and Zhang, K and Yan, Q and Luo, Y and Shi, K and Zhong, Z},
title = {Antibiotic-resistant characteristics and horizontal gene transfer ability analysis of extended-spectrum β-lactamase-producing Escherichia coli isolated from giant pandas.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1394814},
pmid = {39132438},
issn = {2297-1769},
abstract = {Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) is regarded as one of the most important priority pathogens within the One Health interface. However, few studies have investigated the occurrence of ESBL-EC in giant pandas, along with their antibiotic-resistant characteristics and horizontal gene transfer abilities. In this study, we successfully identified 12 ESBL-EC strains (8.33%, 12/144) out of 144 E. coli strains which isolated from giant pandas. We further detected antibiotic resistance genes (ARGs), virulence-associated genes (VAGs) and mobile genetic elements (MGEs) among the 12 ESBL-EC strains, and the results showed that 13 ARGs and 11 VAGs were detected, of which bla CTX-M (100.00%, 12/12, with 5 variants observed) and papA (83.33%, 10/12) were the most prevalent, respectively. And ISEcp1 (66.67%, 8/12) and IS26 (66.67%, 8/12) were the predominant MGEs. Furthermore, horizontal gene transfer ability analysis of the 12 ESBL-EC showed that all bla CTX-M genes could be transferred by conjugative plasmids, indicating high horizontal gene transfer ability. In addition, ARGs of rmtB and sul2, VAGs of papA, fimC and ompT, MGEs of ISEcp1 and IS26 were all found to be co-transferred with bla CTX-M. Phylogenetic analysis clustered these ESBL-EC strains into group B2 (75.00%, 9/12), D (16.67%, 2/12), and B1 (8.33%, 1/12), and 10 sequence types (STs) were identified among 12 ESBL-EC (including ST48, ST127, ST206, ST354, ST648, ST1706, and four new STs). Our present study showed that ESBL-EC strains from captive giant pandas are reservoirs of ARGs, VAGs and MGEs that can co-transfer with bla CTX-M via plasmids. Transmissible ESBL-EC strains with high diversity of resistance and virulence elements are a potential threat to humans, animals and surrounding environment.},
}
@article {pmid39128935,
year = {2024},
author = {Wang, W and Ge, Q and Wen, J and Zhang, H and Guo, Y and Li, Z and Xu, Y and Ji, D and Chen, C and Guo, L and Xu, M and Shi, C and Fan, G and Xie, C},
title = {Horizontal gene transfer and symbiotic microorganisms regulate the adaptive evolution of intertidal algae, Porphyra sense lato.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {976},
pmid = {39128935},
issn = {2399-3642},
support = {42176117//National Natural Science Foundation of China (National Science Foundation of China)/ ; U21A20265//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32100514//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Gene Transfer, Horizontal ; *Symbiosis/genetics ; *Porphyra/microbiology/genetics ; Adaptation, Physiological/genetics ; Phylogeny ; Biological Evolution ; },
abstract = {Intertidal algae may adapt to environmental challenges by acquiring genes from other organisms and relying on symbiotic microorganisms. Here, we obtained a symbiont-free and chromosome-level genome of Pyropia haitanensis (47.2 Mb), a type of intertidal algae, by using multiple symbiont screening methods. We identified 286 horizontal gene transfer (HGT) genes, 251 of which harbored transposable elements (TEs), reflecting the importance of TEs for facilitating the transfer of genes into P. haitanensis. Notably, the bulked segregant analysis revealed that two HGT genes, sirohydrochlorin ferrochelatase and peptide-methionine (R)-S-oxide reductase, play a significant role in the adaptation of P. haitanensis to heat stress. Besides, we found Pseudomonas, Actinobacteria, and Bacteroidetes are the major taxa among the symbiotic bacteria of P. haitanensis (nearly 50% of the HGT gene donors). Among of them, a heat-tolerant actinobacterial strain (Saccharothrix sp.) was isolated and revealed to be associated with the heat tolerance of P. haitanensis through its regulatory effects on the genes involved in proline synthesis (proC), redox homeostasis (ggt), and protein folding (HSP20). These findings contribute to our understanding of the adaptive evolution of intertidal algae, expanding our knowledge of the HGT genes and symbiotic microorganisms to enhance their resilience and survival in challenging intertidal environments.},
}
@article {pmid39127705,
year = {2024},
author = {Park, H and Bulzu, PA and Shabarova, T and Kavagutti, VS and Ghai, R and Kasalický, V and Jezberová, J},
title = {Uncovering the genomic basis of symbiotic interactions and niche adaptations in freshwater picocyanobacteria.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {150},
pmid = {39127705},
issn = {2049-2618},
support = {20&#x2011;12496X//Grantov&#xe1; Agentura Cesk&#xe9; Republiky (GA&#x10c;R)/ ; 20&#x2011;12496X//Grantov&#xe1; Agentura Cesk&#xe9; Republiky (GA&#x10c;R)/ ; 23-05081S//Grantov&#xe1; Agentura Cesk&#xe9; Republiky (GA&#x10c;R)/ ; 19-23261S//Grantov&#xe1; Agentura Cesk&#xe9; Republiky (GA&#x10c;R)/ ; 20&#x2011;12496X//Grantov&#xe1; Agentura Cesk&#xe9; Republiky (GA&#x10c;R)/ ; 19-23261S//Grantov&#xe1; Agentura Cesk&#xe9; Republiky (GA&#x10c;R)/ ; 19-23261S//Grantov&#xe1; Agentura Cesk&#xe9; Republiky (GA&#x10c;R)/ ; },
mesh = {*Symbiosis ; *Fresh Water/microbiology ; *Genome, Bacterial ; *Phylogeny ; *Cyanobacteria/genetics/classification ; Adaptation, Physiological/genetics ; Europe ; Ecosystem ; Gene Transfer, Horizontal ; Genomics ; },
abstract = {BACKGROUND: Picocyanobacteria from the genera Prochlorococcus, Synechococcus, and Cyanobium are the most widespread photosynthetic organisms in aquatic ecosystems. However, their freshwater populations remain poorly explored, due to uneven and insufficient sampling across diverse inland waterbodies.<br><br>RESULTS: In this study, we present 170 high-quality genomes of freshwater picocyanobacteria from non-axenic cultures collected across Central Europe. In addition, we recovered 33 genomes of their potential symbiotic partners affiliated with four genera, Pseudomonas, Mesorhizobium, Acidovorax, and Hydrogenophaga. The genomic basis of symbiotic interactions involved heterotrophs benefiting from picocyanobacteria-derived nutrients while providing detoxification of ROS. The global abundance patterns of picocyanobacteria revealed ecologically significant ecotypes, associated with trophic status, temperature, and pH as key environmental factors. The adaptation of picocyanobacteria in (hyper-)eutrophic waterbodies could be attributed to their colonial lifestyles and CRISPR-Cas systems. The prevailing CRISPR-Cas subtypes in picocyanobacteria were I-G and I-E, which appear to have been acquired through horizontal gene transfer from other bacterial phyla.<br><br>CONCLUSIONS: Our findings provide novel insights into the population diversity, ecology, and evolutionary strategies of the most widespread photoautotrophs within freshwater ecosystems. Video Abstract.},
}
@article {pmid39125965,
year = {2024},
author = {Sadowska-Bartosz, I and Bartosz, G},
title = {Antioxidant Defense in the Toughest Animals on the Earth: Its Contribution to the Extreme Resistance of Tardigrades.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
pmid = {39125965},
issn = {1422-0067},
mesh = {Animals ; *Tardigrada/metabolism/genetics ; *Antioxidants/metabolism ; Oxidative Stress ; Earth, Planet ; Trehalose/metabolism ; },
abstract = {Tardigrades are unique among animals in their resistance to dehydration, mainly due to anhydrobiosis and tun formation. They are also very resistant to high-energy radiation, low and high temperatures, low and high pressure, and various chemical agents, Interestingly, they are resistant to ionizing radiation both in the hydrated and dehydrated states to a similar extent. They are able to survive in the cosmic space. Apparently, many mechanisms contribute to the resistance of tardigrades to harmful factors, including the presence of trehalose (though not common to all tardigrades), heat shock proteins, late embryogenesis-abundant proteins, tardigrade-unique proteins, DNA repair proteins, proteins directly protecting DNA (Dsup and TDR1), and efficient antioxidant system. Antioxidant enzymes and small-molecular-weight antioxidants are an important element in the tardigrade resistance. The levels and activities of many antioxidant proteins is elevated by anhydrobiosis and UV radiation; one explanation for their induction during dehydration is provided by the theory of "preparation for oxidative stress", which occurs during rehydration. Genes coding for some antioxidant proteins are expanded in tardigrades; some genes (especially those coding for catalases) were hypothesized to be of bacterial origin, acquired by horizontal gene transfer. An interesting antioxidant protein found in tardigrades is the new Mn-dependent peroxidase.},
}
@article {pmid39125866,
year = {2024},
author = {Cheng, X and Liu, X and Jordan, KW and Yu, J and Whitworth, RJ and Park, Y and Chen, MS},
title = {Frequent Acquisition of Glycoside Hydrolase Family 32 (GH32) Genes from Bacteria via Horizontal Gene Transfer Drives Adaptation of Invertebrates to Diverse Sources of Food and Living Habitats.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
pmid = {39125866},
issn = {1422-0067},
mesh = {*Gene Transfer, Horizontal ; *Glycoside Hydrolases/genetics/metabolism ; Animals ; *Bacteria/genetics/enzymology ; *Phylogeny ; Invertebrates/genetics ; Adaptation, Physiological/genetics ; Ecosystem ; Evolution, Molecular ; },
abstract = {Glycoside hydrolases (GHs, also called glycosidases) catalyze the hydrolysis of glycosidic bonds in polysaccharides. Numerous GH genes have been identified from various organisms and are classified into 188 families, abbreviated GH1 to GH188. Enzymes in the GH32 family hydrolyze fructans, which are present in approximately 15% of flowering plants and are widespread across microorganisms. GH32 genes are rarely found in animals, as fructans are not a typical carbohydrate source utilized in animals. Here, we report the discovery of 242 GH32 genes identified in 84 animal species, ranging from nematodes to crabs. Genetic analyses of these genes indicated that the GH32 genes in various animals were derived from different bacteria via multiple, independent horizontal gene transfer events. The GH32 genes in animals appear functional based on the highly conserved catalytic blades and triads in the active center despite the overall low (35-60%) sequence similarities among the predicted proteins. The acquisition of GH32 genes by animals may have a profound impact on sugar metabolism for the recipient organisms. Our results together with previous reports suggest that the acquired GH32 enzymes may not only serve as digestive enzymes, but also may serve as effectors for manipulating host plants, and as metabolic enzymes in the non-digestive tissues of certain animals. Our results provide a foundation for future studies on the significance of horizontally transferred GH32 genes in animals. The information reported here enriches our knowledge of horizontal gene transfer, GH32 functions, and animal-plant interactions, which may result in practical applications. For example, developing crops via targeted engineering that inhibits GH32 enzymes could aid in the plant's resistance to animal pests.},
}
@article {pmid39125715,
year = {2024},
author = {Bucka-Kolendo, J and Kiousi, DE and Dekowska, A and Mikołajczuk-Szczyrba, A and Karadedos, DM and Michael, P and Galanis, A and Sokołowska, B},
title = {Exploration of Alicyclobacillus spp. Genome in Search of Antibiotic Resistance.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
pmid = {39125715},
issn = {1422-0067},
mesh = {*Alicyclobacillus/genetics/drug effects ; *Genome, Bacterial ; *Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Guaiacol/pharmacology/analogs &amp; derivatives ; },
abstract = {The study investigates the antibiotic resistance (AR) profiles and genetic determinants in three strains of guaiacol-producing Alicyclobacillus spp. isolated from orchard soil and pears. Their phenotypic characteristics, such as spore formation; resistance to different factors, including drugs or disinfectants; or production of off-flavor compounds, can affect the taste and aroma of spoiled products. Food and beverages are potential vectors for the transfer of antibiotic resistance genes, which is a growing health concern; thus, microorganisms in food and beverages should not be a potential source of drug resistance to consumers. Whole-genome sequencing (WGS) was utilized to identify antibiotic resistance genes, metabolic pathways, and elements associated with guaiacol and halophenol production. Minimum inhibitory concentration (MIC) testing revealed that all strains were susceptible to eight out of nine tested antibiotics (ampicillin, gentamycin, kanamycin, streptomycin, clindamycin, tetracycline, chloramphenicol, and vancomycin) but exhibited high resistance to erythromycin. Analysis indicated that the erythromycin resistance gene, ribosomal RNA small subunit methyltransferase A (RsmA), was intrinsic and likely acquired through horizontal gene transfer (HGT). The comprehensive genomic analysis provides insights into the molecular mechanisms of antibiotic resistance in Alicyclobacillus spp., highlighting the potential risk of these bacteria as vectors for antibiotic resistance genes in the food chain. This study expands the understanding of the genetic makeup of these spoilage bacteria and their role in antimicrobial resistance dissemination.},
}
@article {pmid39122691,
year = {2024},
author = {Williams, SK and Jerlström Hultqvist, J and Eglit, Y and Salas-Leiva, DE and Curtis, B and Orr, RJS and Stairs, CW and Atalay, TN and MacMillan, N and Simpson, AGB and Roger, AJ},
title = {Extreme mitochondrial reduction in a novel group of free-living metamonads.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6805},
pmid = {39122691},
issn = {2041-1723},
support = {FRN-142349//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; },
mesh = {*Mitochondria/metabolism/genetics ; *Phylogeny ; *Proteome/metabolism/genetics ; Transcriptome ; Eukaryota/genetics/metabolism/classification ; Gene Transfer, Horizontal ; Iron-Sulfur Proteins/metabolism/genetics ; },
abstract = {Metamonads are a diverse group of heterotrophic microbial eukaryotes adapted to living in hypoxic environments. All metamonads but one harbour metabolically altered 'mitochondrion-related organelles' (MROs) with reduced functions, however the degree of reduction varies. Here, we generate high-quality draft genomes, transcriptomes, and predicted proteomes for five recently discovered free-living metamonads. Phylogenomic analyses placed these organisms in a group we name the 'BaSk' (Barthelonids+Skoliomonads) clade, a deeply branching sister group to the Fornicata, a phylum that includes parasitic and free-living flagellates. Bioinformatic analyses of gene models shows that these organisms are predicted to have extremely reduced MRO proteomes in comparison to other free-living metamonads. Loss of the mitochondrial iron-sulfur cluster assembly system in some organisms in this group appears to be linked to the acquisition in their common ancestral lineage of a SUF-like minimal system Fe/S cluster pathway by lateral gene transfer. One of the isolates, Skoliomonas litria, appears to have lost all other known MRO pathways. No proteins were confidently assigned to the predicted MRO proteome of this organism suggesting that the organelle has been lost. The extreme mitochondrial reduction observed within this free-living anaerobic protistan clade demonstrates that mitochondrial functions may be completely lost even in free-living organisms.},
}
@article {pmid39121985,
year = {2024},
author = {Yan, Y and Lu, H and Liang, X and Xu, T and Yan, S and Yu, Y and Wang, Y},
title = {The virulence plasmid associated with AHPND in shrimp appears to have originated from Vibrio owensii through a process of homologous recombination of parental plasmids and the transposable insertion of two large fragments.},
journal = {Journal of invertebrate pathology},
volume = {206},
number = {},
pages = {108173},
doi = {10.1016/j.jip.2024.108173},
pmid = {39121985},
issn = {1096-0805},
mesh = {*Vibrio/genetics/pathogenicity ; Animals ; *Plasmids/genetics ; Virulence/genetics ; *Penaeidae/microbiology ; *Homologous Recombination ; Vibrio Infections/veterinary/microbiology ; Phylogeny ; DNA Transposable Elements ; },
abstract = {Acute hepatopancreatic necrosis disease (AHPND) is a highly contagious and lethal disease of shrimp caused by Vibrio strains carrying the virulence plasmid (pAHPND) containing the pirAB virulence genes. Through analysis of plasmid sequence similarity, clustering, and phylogeny, a horizontal transfer element similar to IS91 was discovered within the pAHPND plasmid. Additionally, two distinct clades of plasmids related to pAHPND (designated as pAHPND-r1 and pAHPND-r2) were identified, which may serve as potential parental plasmids for pAHPND. The available evidence, including the difference in G+C content between the plasmid and its host, codon usage preference, and plasmid recombination event prediction, suggests that the formation of the pAHPND plasmid in the Vibrio owensii strain was likely due to the synergistic effect of the recombinase RecA and the associated proteins RecBCD on the pAHPND-r1 and pAHPND-r2, resulting in the recombination and formation of the precursor plasmid for pAHPND (pre-pAHPND). The emergence of pAHPND was found to be a result of successive insertions of the horizontal transfer elements of pirAB-Tn903 and IS91-like segment, which led to the deletion of one third of the pre-pAHPND. This plasmid was then able to spread horizontally to other Vibrio strains, contributing to the epidemics of AHPND. These findings shed light on previously unknown mechanisms involved in the emergence of pAHPND and improve our understanding of the disease's spread.},
}
@article {pmid39119206,
year = {2024},
author = {Zaer-Anaqz, Z and Khakvar, R and Mohammadi, SA and Bannazadeh Baghi, H and Koolivand, D},
title = {Physicochemical Characterization of Novel Bacteriophages of Pseudomonas syringe from Northwest Iran.},
journal = {PHAGE (New Rochelle, N.Y.)},
volume = {5},
number = {2},
pages = {99-106},
pmid = {39119206},
issn = {2641-6549},
abstract = {Bacterial canker, caused by Pseudomonas syringae, is a devastating disease of stone fruit trees worldwide. The bacterium has a broad host range and a high capacity for adaptation and dissemination, owing to its high mutation rate and horizontal gene transfer. Traditional control methods based on copper compounds and antibiotics have resulted in the development of resistance in the bacterial population. Thus, alternative approaches are needed, such as phage therapy. This study aimed to characterize the physicochemical and biological properties of novel Pseudomonas syringae pv. syringae (Pss)-specific phages isolated from the soils of northwestern Iran. Seventy-five phage isolates were obtained, and their host range was determined against various bacterial pathogens. Five phages exhibiting the highest lytic activity against Pss and a narrow host range were selected for subsequent analysis. The stability of the selected phages was assessed under different conditions such as ultraviolet irradiation, temperature, pH, NaCl concentration, and chloroform exposure. The selected phages demonstrated significant effectiveness in vivo, exerting substantial suppression on the population of Pss. This reduction was observed for both individual phages and when the phages were utilized as a mixture. The findings indicate that phages have the potential to be used as biocontrol agents in agriculture.},
}
@article {pmid39119203,
year = {2024},
author = {Delesalle, VA and Ankeriasniemi, RE and Lewis, CM and Mody, JM and Roy, AM and Sarvis, WA and Vo, DD and Walsh, AE and Zappia, RJ},
title = {Introducing Casbah, Kronus, and MmasiCarm, Members of the Mycobacteriophage Subcluster B3.},
journal = {PHAGE (New Rochelle, N.Y.)},
volume = {5},
number = {2},
pages = {84-90},
pmid = {39119203},
issn = {2641-6549},
abstract = {BACKGROUND: As part of a large science education effort, bacteriophages that lyse Mycobacterium smegmatis mc[2]155 continue to be discovered.<br><br>MATERIALS AND METHODS: Phages were isolated from soil samples from urban sites in the Northeastern United States. Their genomes were sequenced, assembled, and bioinformatically compared.<br><br>RESULTS: Three lytic siphoviruses belonging to subcluster B3 with high similarity to each other and other B3 mycobacteriophages were isolated. These phages contain double-stranded DNA genomes (68,754 to 69,495 bp) with high GC content (67.4-67.5%) and 102-104 putative protein coding genes. Notable features include a HicA-like toxin and 33 genes exclusive to subcluster B3. One phage had an intein in its terminase sequence.<br><br>CONCLUSIONS: Genomic analyses of these phages provide insights into genome evolution and horizontal gene transfer (HGT). The networks for HGT are apparently vast and gene specific. Interestingly, a number of genes are found in both B3 and Gordonia DR phages.},
}
@article {pmid39117207,
year = {2024},
author = {Erler, T and Droop, F and Lübbert, C and Knobloch, JK and Carlsen, L and Papan, C and Schwanz, T and Zweigner, J and Dengler, J and Hoffmann, M and Mutters, NT and Savin, M},
title = {Analysing carbapenemases in hospital wastewater: Insights from intracellular and extracellular DNA using qPCR and digital PCR.},
journal = {The Science of the total environment},
volume = {950},
number = {},
pages = {175344},
doi = {10.1016/j.scitotenv.2024.175344},
pmid = {39117207},
issn = {1879-1026},
mesh = {*Wastewater/microbiology ; *beta-Lactamases/genetics ; *Real-Time Polymerase Chain Reaction ; *Bacterial Proteins/genetics ; DNA, Bacterial ; Germany ; Environmental Monitoring/methods ; Hospitals ; Polymerase Chain Reaction/methods ; },
abstract = {The widespread dissemination of carbapenem-resistant bacteria in wastewater systems, particularly from clinical sources, poses a significant public health risk. This study assessed the concentrations and distributions of extracellular DNA (exDNA) and intracellular DNA (iDNA) harboring carbapenemase genes in wastewater from six tertiary care hospitals in Germany. We collected a total of 36 samples, comprising six biological replicates from each hospital, and analysed them using quantitative real-time PCR (qPCR) and digital PCR (dPCR). The analysis targeted seven carbapenemase genes: blaNDM, blaKPC, blaIMP, blaVIM, blaOXA-23-like, blaOXA-48-like, and blaOXA-58-like across both DNA fractions. Our results revealed significant variability in the concentrations of exDNA and iDNA across the sampling sites, with iDNA typically present at higher concentrations. Using NanoDrop One spectrophotometry and the Qubit dsDNA kit, exDNA concentrations ranged from 2.7 to 7.7 ng/mL, while Qubit recorded lower values between 1.1 and 4.0 ng/mL. Conversely, iDNA concentrations were markedly higher, spanning from 42.3 to 191.7 ng/mL with NanoDrop and 12.0 to 46.5 ng/mL with Qubit, highlighting the variability between DNA types and quantification methods. Despite its lower concentrations, exDNA comprised up to 18.2 % of total DNA, highlighting its potential role in the horizontal transfer of antimicrobial resistance genes (ARGs). The study detected target ARGs in both DNA fractions at all sites, with notable differences in their concentrations; iDNA consistently exhibited higher levels of ARGs, with the highest concentrations reaching 10.57 ± 0.20 log gene copies per liter (GC/L) for blaVIM in iDNA and 6.96 ± 0.72 log GC/L for blaIMP in exDNA. dPCR demonstrated greater sensitivity than qPCR, especially effective for detecting low-abundance targets like blaOXA-23-like in the exDNA fraction. Additionally, qPCR's susceptibility to inhibition and contamination emphasizes the superior robustness of dPCR. This research highlights the need for improved monitoring and the implementation of advanced treatment technologies to mitigate ARG dissemination in wastewater.},
}
@article {pmid39113256,
year = {2024},
author = {Hossain, AKMZ and Chowdhury, AMMA},
title = {Understanding the Evolution and Transmission Dynamics of Antibiotic Resistance Genes: A Comprehensive Review.},
journal = {Journal of basic microbiology},
volume = {64},
number = {10},
pages = {e2400259},
doi = {10.1002/jobm.202400259},
pmid = {39113256},
issn = {1521-4028},
mesh = {*Gene Transfer, Horizontal ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Bacteria/genetics/drug effects ; *Evolution, Molecular ; Bangladesh ; Plasmids/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Bacterial Infections/microbiology/drug therapy/transmission ; Public Health ; },
abstract = {Antibiotic resistance poses a formidable challenge to global public health, necessitating comprehensive understanding and strategic interventions. This review explores the evolution and transmission dynamics of antibiotic resistance genes, with a focus on Bangladesh. The indiscriminate use of antibiotics, compounded by substandard formulations and clinical misdiagnosis, fuels the emergence and spread of resistance in the country. Studies reveal high resistance rates among common pathogens, emphasizing the urgent need for targeted interventions and rational antibiotic use. Molecular assessments uncover a diverse array of antibiotic resistance genes in environmental reservoirs, highlighting the complex interplay between human activities and resistance dissemination. Horizontal gene transfer mechanisms, particularly plasmid-mediated conjugation, facilitate the exchange of resistance determinants among bacterial populations, driving the evolution of multidrug-resistant strains. The review discusses clinical implications, emphasizing the interconnectedness of environmental and clinical settings in resistance dynamics. Furthermore, bioinformatic and experimental evidence elucidates novel mechanisms of resistance gene transfer, underscoring the dynamic nature of resistance evolution. In conclusion, combating antibiotic resistance requires a multifaceted approach, integrating surveillance, stewardship, and innovative research to preserve the efficacy of antimicrobial agents and safeguard public health.},
}
@article {pmid39107250,
year = {2024},
author = {Barragan, AC and Latorre, SM and Malmgren, A and Harant, A and Win, J and Sugihara, Y and Burbano, HA and Kamoun, S and Langner, T},
title = {Multiple Horizontal Mini-chromosome Transfers Drive Genome Evolution of Clonal Blast Fungus Lineages.},
journal = {Molecular biology and evolution},
volume = {41},
number = {8},
pages = {},
pmid = {39107250},
issn = {1537-1719},
support = {//Gatsby Charitable Foundation/ ; UKRI-BBSRC//UK Research and Innovation Biotechnology and Biological Sciences Research Council/ ; /ERC_/European Research Council/International ; 743165//BLASTOFF/ ; 101077853//PANDEMIC/ ; RSWF\R1\191011//Royal Society/ ; },
mesh = {*Gene Transfer, Horizontal ; *Evolution, Molecular ; Chromosomes, Fungal/genetics ; Ascomycota/genetics ; Plant Diseases/microbiology ; Genome, Fungal ; },
abstract = {Crop disease pandemics are often driven by asexually reproducing clonal lineages of plant pathogens that reproduce asexually. How these clonal pathogens continuously adapt to their hosts despite harboring limited genetic variation, and in absence of sexual recombination remains elusive. Here, we reveal multiple instances of horizontal chromosome transfer within pandemic clonal lineages of the blast fungus Magnaporthe (Syn. Pyricularia) oryzae. We identified a horizontally transferred 1.2Mb accessory mini-chromosome which is remarkably conserved between M. oryzae isolates from both the rice blast fungus lineage and the lineage infecting Indian goosegrass (Eleusine indica), a wild grass that often grows in the proximity of cultivated cereal crops. Furthermore, we show that this mini-chromosome was horizontally acquired by clonal rice blast isolates through at least nine distinct transfer events over the past three centuries. These findings establish horizontal mini-chromosome transfer as a mechanism facilitating genetic exchange among different host-associated blast fungus lineages. We propose that blast fungus populations infecting wild grasses act as genetic reservoirs that drive genome evolution of pandemic clonal lineages that afflict cereal crops.},
}
@article {pmid39106433,
year = {2024},
author = {Tan, Y and Aravind, L and Zhang, D},
title = {Genomic Underpinnings of Cytoplasmic Incompatibility: CIF Gene-Neighborhood Diversification Through Extensive Lateral Transfers and Recombination in Wolbachia.},
journal = {Genome biology and evolution},
volume = {16},
number = {8},
pages = {},
pmid = {39106433},
issn = {1759-6653},
support = {//Saint Louis University/ ; //Intramural Research Program of the NIH/ ; /LM/NLM NIH HHS/United States ; },
mesh = {*Wolbachia/genetics ; *Gene Transfer, Horizontal ; *Recombination, Genetic ; Evolution, Molecular ; Phylogeny ; Genome, Bacterial ; Cytoplasm/genetics ; Animals ; Bacterial Proteins/genetics ; },
abstract = {Cytoplasmic incompatibility (CI), a non-Mendelian genetic phenomenon, involves the manipulation of host reproduction by Wolbachia, a maternally transmitted alphaproteobacterium. The underlying mechanism is centered around the CI Factor (CIF) system governed by two genes, cifA and cifB, where cifB induces embryonic lethality, and cifA counteracts it. Recent investigations have unveiled intriguing facets of this system, including diverse cifB variants, prophage association in specific strains, copy number variation, and rapid component divergence, hinting at a complex evolutionary history. We utilized comparative genomics to systematically classify CIF systems, analyze their locus structure and domain architectures, and reconstruct their diversification and evolutionary trajectories. Our new classification identifies ten distinct CIF types, featuring not just versions present in Wolbachia, but also other intracellular bacteria, and eukaryotic hosts. Significantly, our analysis of CIF loci reveals remarkable variability in gene composition and organization, encompassing an array of diverse endonucleases, variable toxin domains, deubiquitinating peptidases (DUBs), prophages, and transposons. We present compelling evidence that the components within the loci have been diversifying their sequences and domain architectures through extensive, independent lateral transfers and interlocus recombination involving gene conversion. The association with diverse transposons and prophages, coupled with selective pressures from host immunity, likely underpins the emergence of CIF loci as recombination hotspots. Our investigation also posits the origin of CifB-REase domains from mobile elements akin to CR (Crinkler-RHS-type) effectors and Tribolium Medea1 factor, which is linked to another non-Mendelian genetic phenomenon. This comprehensive genomic analysis offers novel insights into the molecular evolution and genomic foundations of Wolbachia-mediated host reproductive control.},
}
@article {pmid39103341,
year = {2024},
author = {Hu, K and Chou, CW and Wilke, CO and Finkelstein, IJ},
title = {Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6653},
pmid = {39103341},
issn = {2041-1723},
support = {R01 GM124141/GM/NIGMS NIH HHS/United States ; R01GM088344//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01 GM088344/GM/NIGMS NIH HHS/United States ; F-1808//Welch Foundation/ ; R01GM124141//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*DNA Transposable Elements/genetics ; *Escherichia coli/genetics/metabolism ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; *Gene Transfer, Horizontal ; *CRISPR-Associated Proteins/metabolism/genetics ; Escherichia coli Proteins/genetics/metabolism ; },
abstract = {CASTs use both CRISPR-associated proteins and Tn7-family transposons for RNA-guided vertical and horizontal transmission. CASTs encode minimal CRISPR arrays but can't acquire new spacers. Here, we report that CASTs can co-opt defense-associated CRISPR arrays for horizontal transmission. A bioinformatic analysis shows that CASTs co-occur with defense-associated CRISPR systems, with the highest prevalence for type I-B and type V CAST sub-types. Using an E. coli quantitative transposition assay and in vitro reconstitution, we show that CASTs can use CRISPR RNAs from these defense systems. A high-resolution structure of the type I-F CAST-Cascade in complex with a type III-B CRISPR RNA reveals that Cas6 recognizes direct repeats via sequence-independent π - π interactions. In addition to using heterologous CRISPR arrays, type V CASTs can also transpose via an unguided mechanism, even when the S15 co-factor is over-expressed. Over-expressing S15 and the trans-activating CRISPR RNA or a single guide RNA reduces, but does not abrogate, off-target integration for type V CASTs. Our findings suggest that some CASTs may exploit defense-associated CRISPR arrays and that this fact must be considered when porting CASTs to heterologous bacterial hosts. More broadly, this work will guide further efforts to engineer the activity and specificity of CASTs for gene editing applications.},
}
@article {pmid39103039,
year = {2024},
author = {Zhang, H and Xu, L and Hou, X and Li, Y and Niu, L and Zhang, J and Wang, X},
title = {Ketoprofen promotes the conjugative transfer of antibiotic resistance among antibiotic resistant bacteria in natural aqueous environments.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {360},
number = {},
pages = {124676},
doi = {10.1016/j.envpol.2024.124676},
pmid = {39103039},
issn = {1873-6424},
mesh = {*Ketoprofen/pharmacology ; *Gene Transfer, Horizontal ; Conjugation, Genetic ; Escherichia coli/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Water Pollutants, Chemical/toxicity ; Anti-Inflammatory Agents, Non-Steroidal/pharmacology ; },
abstract = {The emergence and spread of antibiotic resistance in the environment pose a serious threat to global public health. It is acknowledged that non-antibiotic stresses, including disinfectants, pharmaceuticals and organic pollutants, play a crucial role in horizontal transmission of antibiotic resistance genes (ARGs). Despite the widespread presence of non-steroidal anti-inflammatory drugs (NSAIDs), notably in surface water, their contributions to the transfer of ARGs have not been systematically explored. Furthermore, previous studies have primarily concentrated on model strains to investigate whether contaminants promote the conjugative transfer of ARGs, leaving the mechanisms of ARG transmission among antibiotic resistant bacteria in natural aqueous environments under the selective pressures of non-antibiotic contaminants remains unclear. In this study, the Escherichia coli (E. coli) K12 carrying RP4 plasmid was used as the donor strain, indigenous strain Aeromonas veronii containing rifampicin resistance genes in Taihu Lake, and E. coli HB101 were used as receptor strains to establish inter-genus and intra-genus conjugative transfer systems, examining the conjugative transfer frequency under the stress of ketoprofen. The results indicated that ketoprofen accelerated the environmental spread of ARGs through several mechanisms. Ketoprofen promoted cell-to-cell contact by increasing cell surface hydrophobicity and reducing cell surface charge, thereby mitigating cell-to-cell repulsion. Furthermore, ketoprofen induced increased levels of reactive oxygen species (ROS) production, activated the DNA damage-induced response (SOS), and enhanced cell membrane permeability, facilitating ARG transmission in intra-genus and inter-genus systems. The upregulation of outer membrane proteins, oxidative stress, SOS response, mating pair formation (Mpf) system, and DNA transfer and replication (Dtr) system related genes, as well as the inhibition of global regulatory genes, all contributed to higher transfer efficiency under ketoprofen treatment. These findings served as an early warning for a comprehensive assessment of the roles of NSAIDs in the spread of antibiotic resistance in natural aqueous environments.},
}
@article {pmid39102038,
year = {2024},
author = {Olanrewaju, OS and Molale-Tom, LG and Bezuidenhout, CC},
title = {Genomic diversity, antibiotic resistance, and virulence in South African Enterococcus faecalis and Enterococcus lactis isolates.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {40},
number = {10},
pages = {289},
pmid = {39102038},
issn = {1573-0972},
mesh = {South Africa ; *Genome, Bacterial ; *Enterococcus faecalis/genetics/drug effects/pathogenicity/isolation &amp; purification ; Virulence/genetics ; *Genetic Variation ; *Anti-Bacterial Agents/pharmacology ; *Virulence Factors/genetics ; Humans ; Drug Resistance, Bacterial/genetics ; Genomic Islands/genetics ; Gram-Positive Bacterial Infections/microbiology ; Enterococcus/genetics/drug effects/pathogenicity/isolation &amp; purification/classification ; Phylogeny ; Gene Transfer, Horizontal ; Genomics ; Microbial Sensitivity Tests ; },
abstract = {This study presents the empirical findings of an in-depth genomic analysis of Enterococcus faecalis and Enterococcus lactis isolates from South Africa. It offers valuable insights into their genetic characteristics and their significant implications for public health. The study uncovers nuanced variations in the gene content of these isolates, despite their similar GC contents, providing a comprehensive view of the evolutionary diversity within the species. Genomic islands are identified, particularly in E. faecalis, emphasizing its propensity for horizontal gene transfer and genetic diversity, especially in terms of antibiotic resistance genes. Pangenome analysis reveals the existence of a core genome, accounting for a modest proportion of the total genes, with 2157 core genes, 1164 shell genes, and 4638 cloud genes out of 7959 genes in 52 South African E. faecalis genomes (2 from this study, 49 south Africa genomes downloaded from NCBI, and E. faecalis reference genome). Detecting large-scale genomic rearrangements, including chromosomal inversions, underscores the dynamic nature of bacterial genomes and their role in generating genetic diversity. The study uncovers an array of antibiotic resistance genes, with trimethoprim, tetracycline, glycopeptide, and multidrug resistance genes prevalent, raising concerns about the effectiveness of antibiotic treatment. Virulence gene profiling unveils a diverse repertoire of factors contributing to pathogenicity, encompassing adhesion, biofilm formation, stress resistance, and tissue damage. These empirical findings provide indispensable insights into these bacteria's genomic dynamics, antibiotic resistance mechanisms, and virulence potential, underlining the pressing need to address antibiotic resistance and implement robust control measures.},
}
@article {pmid39101807,
year = {2024},
author = {Dhurve, G and Behera, SR and Kodetham, G and Siddavattam, D},
title = {Outer membrane vesicles of Acinetobacter baumannii DS002 carry circular DNA similar to bovine meat and milk factors (BMMFs) and SPHINX 2.36 and probably play a role in interdomain lateral gene transfer.},
journal = {Microbiology spectrum},
volume = {12},
number = {9},
pages = {e0081724},
pmid = {39101807},
issn = {2165-0497},
mesh = {Animals ; Mice ; *Plasmids/genetics ; *Acinetobacter baumannii/genetics/metabolism ; Cattle ; *Gene Transfer, Horizontal ; *DNA, Circular/genetics/metabolism ; Bacterial Outer Membrane/metabolism ; Female ; Bacteriophages/genetics/physiology ; Meat/microbiology ; Milk/microbiology ; Acinetobacter Infections/microbiology ; Extracellular Vesicles/metabolism ; Mice, Inbred BALB C ; DNA, Bacterial/genetics ; },
abstract = {UNLABELLED: The discovery of Replication Competent Circular DNA molecules in mammalian cells and tissues is being linked to debilitating diseases, such as multiple sclerosis (MS), bovine spongiform encephalopathy (BSE), and colorectal cancer (CRC). These circular DNA molecules, otherwise known as bovine meat and milk factors (BMMFs) and Slow Progressive Hidden INfections of variable (X) latency (SPHINX), bear significant (80%) sequence similarity with the plasmids of Acinetobacter baumannii strains. Nanostructures, such as bacterial outer membrane vesicles (OMVs) serve as vehicles for transporting biomolecular cargo and have the potential to facilitate interkingdom lateral mobility of DNA. Strengthening the proposed hypothesis, this study demonstrates that OMVs derived from A. baumannii DS002 carrying four plasmids and genome (pTS236) of phage, AbDs1, successfully reached different parts of the body, including the central nervous system, following the injection of fluorescein isothiocyanate (FITC)-labeled OMVs into experimental mice. Out of the four OMV-associated plasmids, three (pTS4586, pTS9900, and pTS134338) were identified within the lumen, and the fourth one (pTS11291) was found on the surface of OMVs. In addition to the indigenous plasmids, the phage-encoded protein, Orf96, anchored on the surface of the OMVs by establishing a strong interaction with the OMV-associated porin, OmpA. Intriguingly, a subset of labeled OMVs, when incubated with Neuro2A cells, translocated across the membrane and reached to the cytoplasmic space of the cells. Collectively, the experimental evidence presented herein underscores the promising potential of OMVs as vehicles for delivering molecular cargo containing plasmids and phage genomes to diverse mammalian tissues and cells.<br><br>IMPORTANCE: Several independent studies have demonstrated the existence of replication competent circular DNA molecules of bacterial and viral origin in mammalian cells and tissues. However, studies about their origin and lateral mobility to mammalian cells are scarce. Our work describes the existence of circular DNA, similar to that of DNA molecules identified in mammalian cells, OMVs derived from soil isolate of A. baumannii DS002. Furthermore, the work also provides visual evidence that demonstrates the passage of labeled OMVs to different organs of experimental mice within hours after intravenously administering OMVs into experimental mice. Some of the labeled OMVs have even crossed the membrane of Neuro2A, suggesting the existence of interkingdom horizontal mobility between bacteria and mammals.},
}
@article {pmid39101574,
year = {2024},
author = {Rappaport, HB and Oliverio, AM},
title = {Lessons from Extremophiles: Functional Adaptations and Genomic Innovations across the Eukaryotic Tree of Life.},
journal = {Genome biology and evolution},
volume = {16},
number = {8},
pages = {},
pmid = {39101574},
issn = {1759-6653},
mesh = {Adaptation, Physiological/genetics ; *Eukaryota/genetics ; Evolution, Molecular ; *Extremophiles/genetics ; Genome ; Genomics ; Phylogeny ; },
abstract = {From hydrothermal vents, to glaciers, to deserts, research in extreme environments has reshaped our understanding of how and where life can persist. Contained within the genomes of extremophilic organisms are the blueprints for a toolkit to tackle the multitude of challenges of survival in inhospitable environments. As new sequencing technologies have rapidly developed, so too has our understanding of the molecular and genomic mechanisms that have facilitated the success of extremophiles. Although eukaryotic extremophiles remain relatively understudied compared to bacteria and archaea, an increasing number of studies have begun to leverage 'omics tools to shed light on eukaryotic life in harsh conditions. In this perspective paper, we highlight a diverse breadth of research on extremophilic lineages across the eukaryotic tree of life, from microbes to macrobes, that are collectively reshaping our understanding of molecular innovations at life's extremes. These studies are not only advancing our understanding of evolution and biological processes but are also offering a valuable roadmap on how emerging technologies can be applied to identify cellular mechanisms of adaptation to cope with life in stressful conditions, including high and low temperatures, limited water availability, and heavy metal habitats. We shed light on patterns of molecular and organismal adaptation across the eukaryotic tree of life and discuss a few promising research directions, including investigations into the role of horizontal gene transfer in eukaryotic extremophiles and the importance of increasing phylogenetic diversity of model systems.},
}
@article {pmid39100236,
year = {2024},
author = {Bhattacharya, A and Aluquin, A and Kennedy, DA},
title = {Exceptions to the rule: When does resistance evolution not undermine antibiotic therapy in human bacterial infections?.},
journal = {Evolution letters},
volume = {8},
number = {4},
pages = {478-493},
pmid = {39100236},
issn = {2056-3744},
support = {R01 GM140459/GM/NIGMS NIH HHS/United States ; },
abstract = {The use of antibiotics to treat bacterial infections often imposes strong selection for antibiotic resistance. However, the prevalence of antibiotic resistance varies greatly across different combinations of pathogens and drugs. What underlies this variation? Systematic reviews, meta-analyses, and literature surveys capable of integrating data across many studies have tried to answer this question, but the vast majority of these studies have focused only on cases where resistance is common or problematic. Yet much could presumably be learned from the cases where resistance is infrequent or absent. Here we conducted a literature survey and a systematic review to study the evolution of antibiotic resistance across a wide range of pathogen-by-drug combinations (57 pathogens and 53 antibiotics from 15 drug classes). Using Akaike information criterion-based model selection and model-averaged parameter estimation we explored 14 different factors posited to be associated with resistance evolution. We find that the most robust predictors of high resistance are nosocomial transmission (i.e., hospital-acquired pathogens) and indirect transmission (e.g., vector-, water-, air-, or vehicle-borne pathogens). While the former was to be expected based on prior studies, the positive correlation between high resistance frequencies and indirect transmission is, to our knowledge, a novel insight. The most robust predictor of low resistance is zoonosis from wild animal reservoirs. We also found partial support that resistance was associated with pathogen type, horizontal gene transfer, commensalism, and human-to-human transmission. We did not find support for correlations between resistance and environmental reservoirs, mechanisms of drug action, and global drug use. This work explores the relative explanatory power of various pathogen and drug factors on resistance evolution, which is necessary to identify priority targets of stewardship efforts to slow the spread of drug-resistant pathogens.},
}
@article {pmid39100235,
year = {2024},
author = {Ciach, MA and Pawłowska, J and Górecki, P and Muszewska, A},
title = {The interkingdom horizontal gene transfer in 44 early diverging fungi boosted their metabolic, adaptive, and immune capabilities.},
journal = {Evolution letters},
volume = {8},
number = {4},
pages = {526-538},
pmid = {39100235},
issn = {2056-3744},
abstract = {Numerous studies have been devoted to individual cases of horizontally acquired genes in fungi. It has been shown that such genes expand the hosts' metabolic capabilities and contribute to their adaptations as parasites or symbionts. Some studies have provided an extensive characterization of the horizontal gene transfer (HGT) in Dikarya. However, in the early diverging fungi (EDF), a similar characterization is still missing. In order to fill this gap, we have designed a computational pipeline to obtain a statistical sample of reliable HGT events with a low false discovery rate. We have analyzed 44 EDF proteomes and identified 829 xenologs in fungi ranging from Chytridiomycota to Mucoromycota. We have identified several patterns and statistical properties of EDF HGT. We show that HGT is driven by bursts of gene exchange and duplication, resulting in highly divergent numbers and molecular properties of xenologs between fungal lineages. Ancestrally aquatic fungi are generally more likely to acquire foreign genetic material than terrestrial ones. Endosymbiotic bacteria can be a source of useful xenologs, as exemplified by NOD-like receptors transferred to Mortierellomycota. Closely related fungi have similar rates of intronization of xenologs. Posttransfer gene fusions and losses of protein domains are common and may influence the encoded proteins' functions. We argue that there is no universal approach for HGT identification and inter- and intra-kingdom transfers require tailored identification methods. Our results help to better understand how and to what extent HGT has shaped the metabolic, adaptive, and immune capabilities of fungi.},
}
@article {pmid39098155,
year = {2024},
author = {Wang, H and Gao, J and Ren, H and Zhao, Y and Wang, Y and An, J and Chen, H and Wang, Q},
title = {Whatever does not kill them makes them stronger: Using quaternary ammonia antimicrobials to alleviate the inhibition of ammonia oxidation under perfluorooctanoic acid stress.},
journal = {Water research},
volume = {263},
number = {},
pages = {122171},
doi = {10.1016/j.watres.2024.122171},
pmid = {39098155},
issn = {1879-2448},
mesh = {*Ammonia/metabolism ; *Fluorocarbons ; *Caprylates/pharmacology ; *Oxidation-Reduction ; Sewage ; Anti-Infective Agents/pharmacology ; Water Pollutants, Chemical ; Bacteria/metabolism/drug effects ; Nitrification ; },
abstract = {Perfluorooctanoic acid (PFOA), benzalkyl dimethylammonium compounds (BAC) and antibiotic resistance genes (ARGs) have negative effects on biological sewage treatment. The performance of nitrification systems under stress of PFOA (0.1-5 mg/L) or/and BAC (0.2-10 mg/L) was explored during 84-day experiments using four sequencing batch reactors, in this study. Low (0.1 mg/L) concentration PFOA had a positive influence on ammonia removal, while medium and high (2 and 5 mg/L) concentrations PFOA caused severe inhibition. Meanwhile, PFOA stress resulted in the enrichment of ARGs in water (w-ARGs). BAC (0-10 mg/L) had no obvious influence on ammonia removal. However, BAC promoted the reduction of ARGs and the bacterial community was the main participator (48.07%) for the spread of ARGs. Interestingly, the joint stress of PFOA and BAC increased the ammonia-oxidizing bacteria (AOB) activity from 5.81 ± 0.19 and 6.05 ± 0.79 mg N/(g MLSS·h) to 7.09 ± 0.87 and 7.23 ± 0.29 mg N/(g MLSS·h) in medium and high concentrations, compared to single stress of PFOA, which was observed for the first time. BAC could reduce bioavailability of PFOA through competitive adsorption and decreasing sludge hydrophobicity by the lower β-Sheet and α-Helix in tightly bound protein. Furthermore, the joint stress of PFOA and BAC was able to intensify the proliferation of w-ARGs and extracellular ARGs in sludge, and developed the most active horizontal gene transfer mediated by intl1 compared to single stress of PFOA or BAC. The batch tests verified the detoxification capacity of BAC on nitrification under 2.5 mg/L PFOA (48 h exposing), and the maximum alleviation of AOB activity was achieved at BAC and PFOA mass ratio of 2:1. In summary, BAC could be used to alleviate the inhibition of PFOA on ammonia oxidation, providing an efficient and sustainable approach in wastewater treatment.},
}
@article {pmid39096995,
year = {2024},
author = {Tian, J and Xu, L and Sun, JQ},
title = {Taxonomic characterization and comparative genomic analysis of a novel Devosia species revealed that phenolic acid-degrading traits are ubiquitous in the Devosia genus.},
journal = {Environmental research},
volume = {261},
number = {},
pages = {119724},
doi = {10.1016/j.envres.2024.119724},
pmid = {39096995},
issn = {1096-0953},
mesh = {*Hydroxybenzoates/metabolism ; Hyphomicrobiaceae/genetics/metabolism ; Soil Microbiology ; Genome, Bacterial ; Genomics ; Phylogeny ; Rhizosphere ; Biodegradation, Environmental ; },
abstract = {Phenolic acids (PAs) are widely distributed allelochemicals in various environments. To better understand the fate of PAs in environments, a halotolerant PAs-degrading bacterium (named strain RR2S18[T]) isolated from rhizosphere soil was identified as a novel species of Devosia, named Devosia rhizosphaerae sp. nov. The strain initially degraded PAs into central ring-fission intermediates (protocatechuic acid) using the CoA-dependent non-β-oxidation pathway. The produced ring-fission intermediates were then consecutively degraded by an ortho-cleavage reaction and the β-ketoadipic acid pathway. A comparative genomics analysis of 62 Devosia strains revealed that PAs-degrading genes were ubiquitous in their genomes, indicating that PAs degradation is universal among members of this genus. The analysis also suggested that the genes involved in CoA-dependent non-β-oxidation are inherent to Devosia strains, while those involved in ring-fission and β-ketoadipic acid pathways were obtained by horizontal gene transfer.},
}
@article {pmid39096644,
year = {2024},
author = {Wu, Q and Wu, GG and Pan, KN and Wang, XP and Li, HY and Tian, Z and Jin, RC and Fan, NS},
title = {Beta-blocker drives the conjugative transfer of multidrug resistance genes in pure and complex biological systems.},
journal = {Journal of hazardous materials},
volume = {477},
number = {},
pages = {135403},
doi = {10.1016/j.jhazmat.2024.135403},
pmid = {39096644},
issn = {1873-3336},
mesh = {*Metoprolol ; *Plasmids/genetics ; *Conjugation, Genetic/drug effects ; Drug Resistance, Multiple, Bacterial/genetics/drug effects ; Adrenergic beta-Antagonists/pharmacology ; Gene Transfer, Horizontal ; Bacteria/genetics/drug effects/metabolism ; Anti-Bacterial Agents/pharmacology ; Genes, MDR/genetics ; Microbiota/drug effects ; },
abstract = {Drug resistance poses a high risk to human health. Extensive use of non-antibiotic drugs contributes to antibiotic resistance genes (ARGs) transfer. However, how they affect the spread of broad-host plasmids in complex biological systems remains unknown. This study investigated the effect of metoprolol on the transfer frequency and host range of ARGs in both intrageneric and intergeneric pure culture systems, as well as in anammox microbiome. The results showed that environmental concentrations of metoprolol significantly promoted the intrageneric and intergeneric conjugative transfer. Initially, metoprolol induced excessive oxidative stress, resulting in high cell membrane permeability and bacterial SOS response. Meanwhile, more pili formation increased the adhesion and contact between bacteria, and the abundance of conjugation-related genes also increased significantly. Activation of the electron transport chain provided more ATP for this energy-consuming process. The underlying mechanism was further verified in the complex anammox conjugative system. Metoprolol induced the enrichment of ARGs and mobile genetic elements. The enhanced bacterial interaction and energy generation facilitated the high conjugative transfer frequency of ARGs. In addition, plasmid-borne ARGs tended to transfer to opportunistic pathogens. This work raises public concerns about the health and ecological risks of non-antibiotic drugs.},
}
@article {pmid39095425,
year = {2024},
author = {Landa, CR and Ariza-Mateos, A and Briones, C and Perales, C and Wagner, A and Domingo, E and Gómez, J},
title = {Adapting the rhizome concept to an extended definition of viral quasispecies and the implications for molecular evolution.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {17914},
pmid = {39095425},
issn = {2045-2322},
mesh = {*Rhizome/virology ; *Evolution, Molecular ; *Quasispecies/genetics ; *Phylogeny ; RNA Viruses/genetics/classification ; Gene Transfer, Horizontal ; Mutation ; Genome, Viral ; },
abstract = {The rhizome concept proposed by Gilles Deleuze and Félix Guattari offers a novel perspective on the organization and interdependence of complex constellations of heterogeneous entities, their mapping and their ruptures. The emphasis of the present study is placed on the dynamics of contacts and communication among such entities that arise from experimentation, without any favored hierarchy or origin. When applied to biological evolution, the rhizome concept integrates all types of heterogeneity resulting from "symbiotic" relationships among living beings (or their genomic material), horizontal genetic transfer, recombination and mutation, and breaks away from the approach that gives rise to the phylogenetic tree of life. It has already been applied to describe the dynamics and evolution of RNA viruses. Thus, here we introduce a novel framework for the interpretation the viral quasispecies concept, which explains the evolution of RNA virus populations as the result of dynamic interconnections and multifaceted interdependence between highly heterogeneous viral sequences and its inherently heterogeneous host cells. The rhizome network perspective underlines even further the medical implications of the broad mutant spectra of viruses that are in constant flow, given the multiple pathways they have available for fitness loss and gain.},
}
@article {pmid39095161,
year = {2025},
author = {Guo, Z and Tang, X and Wang, W and Luo, Z and Zeng, Y and Zhou, N and Yu, Z and Wang, D and Song, B and Zhou, C and Xiong, W},
title = {The photo-based treatment technology simultaneously removes resistant bacteria and resistant genes from wastewater.},
journal = {Journal of environmental sciences (China)},
volume = {148},
number = {},
pages = {243-262},
doi = {10.1016/j.jes.2024.01.005},
pmid = {39095161},
issn = {1001-0742},
mesh = {*Wastewater/chemistry ; *Waste Disposal, Fluid/methods ; Bacteria ; Disinfection/methods ; Drug Resistance, Bacterial/genetics ; Ultraviolet Rays ; Water Purification/methods ; },
abstract = {Because of the recent widespread usage of antibiotics, the acquisition and dissemination of antibiotic-resistance genes (ARGs) were prevalent in the majority of habitats. Generally, the biological wastewater treatment processes used in wastewater treatment plants have a limited efficiencies of antibiotics resistant bacteria (ARB) disinfection and ARGs degradation and even promote the proliferation of ARGs. Problematically, ARB and ARGs in effluent pose potential risks if they are not further treated. Photocatalytic oxidation is considered a promising disinfection technology, where the photocatalytic process generates many free radicals that enhance the interaction between light and deoxyribonucleic acid (DNA) for ARB elimination and subsequent degradation of ARGs. This review aims to illustrate the progress of photocatalytic oxidation technology for removing antibiotics resistant (AR) from wastewater in recent years. We discuss the sources and transfer of ARGs in wastewater. The overall removal efficiencies of ultraviolet radiation (UV)/chlorination, UV/ozone, UV/H2O2, and UV/sulfate-radical based system for ARB and ARGs, as well as the experimental parameters and removal mechanisms, are systematically discussed. The contribution of photocatalytic materials based on TiO2 and g-C3N4 to the inactivation of ARB and degradation of ARGs is highlighted, producing many free radicals to attack ARB and ARGs while effectively limiting the horizontal gene transfer (HGT) in wastewater. Finally, based on the reviewed studies, future research directions are proposed to realize specific photocatalytic oxidation technology applications and overcome current challenges.},
}
@article {pmid39093595,
year = {2024},
author = {Wu, J and Meng, L and Gaïa, M and Hikida, H and Okazaki, Y and Endo, H and Ogata, H},
title = {Gene Transfer Among Viruses Substantially Contributes to Gene Gain of Giant Viruses.},
journal = {Molecular biology and evolution},
volume = {41},
number = {8},
pages = {},
pmid = {39093595},
issn = {1537-1719},
support = {18H02279//JSPS/KAKENHI/ ; JPMJSP2110//JST SPRING/ ; 2022-26//Institute for Chemical Research, Kyoto University/ ; },
mesh = {*Gene Transfer, Horizontal ; *Giant Viruses/genetics ; Evolution, Molecular ; Phylogeny ; Genome, Viral ; Gene Duplication ; },
abstract = {The phylum Nucleocytoviricota comprises a diverse group of double-stranded DNA viruses that display a wide range of gene repertoires. Although these gene repertoires determine the characteristics of individual viruses, the evolutionary processes that have shaped the gene repertoires of extant viruses since their common ancestor are poorly characterized. In this study, we aimed to address this gap in knowledge by using amalgamated likelihood estimation, a probabilistic tree reconciliation method that infers evolutionary scenarios by distinguishing origination, gene duplications, virus-to-virus horizontal gene transfer (vHGT), and gene losses. We analyzed over 4,700 gene families from 195 genomes spanning all known viral orders. The evolutionary reconstruction suggests a history of extensive gene gains and losses during the evolution of these viruses, notably with vHGT contributing to gene gains at a comparable level to duplications and originations. The vHGT frequently occurred between phylogenetically closely related viruses, as well as between distantly related viruses with an overlapping host range. We observed a pattern of massive gene duplications that followed vHGTs for gene families that was potentially related to host range control and virus-host arms race. These results suggest that vHGT represents a previously overlooked, yet important, evolutionary force that integrates the evolutionary paths of multiple viruses and affects shaping of Nucleocytoviricota virus gene repertoires.},
}
@article {pmid39089095,
year = {2024},
author = {Zhuang, M and Yan, W and Xiong, Y and Wu, Z and Cao, Y and Sanganyado, E and Siame, BA and Chen, L and Kashi, Y and Leung, KY},
title = {Horizontal plasmid transfer promotes antibiotic resistance in selected bacteria in Chinese frog farms.},
journal = {Environment international},
volume = {190},
number = {},
pages = {108905},
doi = {10.1016/j.envint.2024.108905},
pmid = {39089095},
issn = {1873-6750},
mesh = {Animals ; *Plasmids/genetics ; China ; *Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Farms ; Drug Resistance, Bacterial/genetics ; Rana catesbeiana/microbiology/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/genetics ; },
abstract = {The emergence and dissemination of antibiotic resistance genes (ARGs) in the ecosystem are global public health concerns. One Health emphasizes the interconnectivity between different habitats and seeks to optimize animal, human, and environmental health. However, information on the dissemination of antibiotic resistance genes (ARGs) within complex microbiomes in natural habitats is scarce. We investigated the prevalence of antibiotic resistant bacteria (ARB) and the spread of ARGs in intensive bullfrog (Rana catesbeiana) farms in the Shantou area of China. Antibiotic susceptibilities of 361 strains, combined with microbiome analyses, revealed Escherichia coli, Edwardsiella tarda, Citrobacter and Klebsiella sp. as prevalent multidrug resistant bacteria on these farms. Whole genome sequencing of 95 ARB identified 250 large plasmids that harbored a wide range of ARGs. Plasmid sequences and sediment metagenomes revealed an abundance of tetA, sul1, and aph(3″)-Ib ARGs. Notably, antibiotic resistance (against 15 antibiotics) highly correlated with plasmid-borne rather than chromosome-borne ARGs. Based on sequence similarities, most plasmids (62%) fell into 32 distinct groups, indicating a potential for horizontal plasmid transfer (HPT) within the frog farm microbiome. HPT was confirmed in inter- and intra-species conjugation experiments. Furthermore, identical mobile ARGs, flanked by mobile genetic elements (MGEs), were found in different locations on the same plasmid, or on different plasmids residing in the same or different hosts. Our results suggest a synergy between MGEs and HPT to facilitate ARGs dissemination in frog farms. Mining public databases retrieved similar plasmids from different bacterial species found in other environmental niches globally. Our findings underscore the importance of HPT in mediating the spread of ARGs in frog farms and other microbiomes of the ecosystem.},
}
@article {pmid39086116,
year = {2024},
author = {Yang, Q and Li, L and Zhao, G and Cui, Q and Gong, X and Ying, L and Yang, T and Fu, M and Shen, Z},
title = {Characterization of a multiresistance optrA- and lsa(E)-harbouring unconventional circularizable structure in Streptococcus suis.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {79},
number = {10},
pages = {2528-2533},
doi = {10.1093/jac/dkae250},
pmid = {39086116},
issn = {1460-2091},
support = {2022YFC2303900//National Key Research and Development Program of China/ ; 32141001//National Natural Science Foundation of China/ ; },
mesh = {*Streptococcus suis/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Microbial Sensitivity Tests ; *Multigene Family ; *Conjugation, Genetic/genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genomic Islands/genetics ; Lincosamides/pharmacology ; Pleuromutilins ; Diterpenes/pharmacology ; Polycyclic Compounds ; Streptococcal Infections/microbiology ; Genes, Bacterial ; Streptogramin A/pharmacology ; },
abstract = {OBJECTIVES: To identify novel genetic elements facilitating the horizontal transfer of the oxazolidinone/phenicol resistance gene optrA and the pleuromutilin-lincosamide-streptogramin A resistance gene lsa(E) in Streptococcus suis.<br><br>METHODS: The complete genomes of S. suis HB18 and two transconjugants were obtained using both the Illumina and Nanopore platforms. MICs were determined by broth microdilution. Inverse PCR was performed to identify circular forms of the novel unconventional circularizable structure (UCS), genomic island (GI) and integrative and conjugative element (ICE). Conjugation experiments assessed the transferability of optrA and lsa(E) genes in S. suis.<br><br>RESULTS: S. suis HB18 carried a multiresistance gene cluster optrA-lsa(E)-lnu(B)-aphA-aadE-spw. This gene cluster, flanked by intact and truncated erm(B) in the same orientation, resided on a novel ICESsuHB18. Inverse PCR revealed the existence of a novel UCS, named UCS-optrA&#x200a;+&#x200a;lsa(E), which could excise the gene cluster optrA-lsa(E)-lnu(B)-aphA-aadE-spw and one copy of erm(B) from ICESsuHB18. Two transconjugants with different characteristics were obtained. In transconjugant T-JH-GI, UCS-optrA&#x200a;+&#x200a;lsa(E) excised from ICESsuHB18 inserted into the erm(B)-positive GI, designated GISsuHB18, generating the novel GISsuHB18-1. Meanwhile, in T-JH-ICE, genetic rearrangement events occurred in ICESsuHB18 and GISsuHB18, forming the novel ICESsuHB18-1.<br><br>CONCLUSIONS: This is the first report demonstrating the functionally active UCS-optrA&#x200a;+&#x200a;lsa(E) excising from ICESsuHB18 and inserting into the erm(B)-positive GISsuHB18 during the conjugation process. The location of optrA and lsa(E) on a multiresistance UCS enhances its persistence and dissemination.},
}
@article {pmid39082809,
year = {2024},
author = {Kanno, K and Kuriki, R and Yasuno, Y and Shinada, T and Ito, T and Hemmi, H},
title = {Archaeal mevalonate pathway in the uncultured bacterium Candidatus Promineifilum breve belonging to the phylum Chloroflexota.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {8},
pages = {e0110624},
pmid = {39082809},
issn = {1098-5336},
support = {18K19170,19H04651, 20H02899, 23K18109, 23H02126.//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
mesh = {*Mevalonic Acid/metabolism ; Archaea/genetics/metabolism/classification/enzymology ; Chloroflexi/genetics/metabolism/enzymology/classification ; Metabolic Networks and Pathways/genetics ; Phylogeny ; Escherichia coli/genetics/metabolism ; },
abstract = {The archaeal mevalonate pathway is a recently discovered modified version of the eukaryotic mevalonate pathway. This pathway is widely conserved in archaea, except for some archaeal lineages possessing the eukaryotic or other modified mevalonate pathways. Although the pathway seems almost exclusive to the domain Archaea, the whole set of homologous genes of the pathway is found in the metagenome-assembled genome sequence of an uncultivated bacterium, Candidatus Promineifilum breve, of the phylum Chloroflexota. To prove the existence of the archaea-specific pathway in the domain Bacteria, we confirmed the activities of the enzymes specific to the pathway, phosphomevalonate dehydratase and anhydromevalonate phosphate decarboxylase, because only these two enzymes are absent in closely related Chloroflexota bacteria that possess a different type of modified mevalonate pathway. The activity of anhydromevalonate phosphate decarboxylase was evaluated by carotenoid production via the archaeal mevalonate pathway reconstituted in Escherichia coli cells, whereas that of phosphomevalonate dehydratase was confirmed by an in vitro assay using the recombinant enzyme after purification and iron-sulfur cluster reconstruction. Phylogenetic analyses of some mevalonate pathway-related enzymes suggest an evolutionary route for the archaeal mevalonate pathway in Candidatus P. breve, which probably involves horizontal gene transfer events.IMPORTANCEThe recent discovery of various modified mevalonate pathways in microorganisms, such as archaea and Chloroflexota bacteria, has shed light on the complexity of the evolution of metabolic pathways, including those involved in primary metabolism. The fact that the archaeal mevalonate pathway, which is almost exclusive to the domain Archaea, exists in a Chloroflexota bacterium provides valuable insights into the molecular evolution of the mevalonate pathways and associated enzymes. Putative genes probably involved in the archaeal mevalonate pathway have also been found in the metagenome-assembled genomes of Chloroflexota bacteria. Such genes can contribute to metabolic engineering for the bioproduction of valuable isoprenoids because the archaeal mevalonate pathway is known to be an energy-saving metabolic pathway that consumes less ATP than other mevalonate pathways do.},
}
@article {pmid39080678,
year = {2024},
author = {Rajput, M and Pandey, M and Dixit, R and Shukla, VK},
title = {Is cross-species horizontal gene transfer responsible for gallbladder carcinogenesis.},
journal = {World journal of surgical oncology},
volume = {22},
number = {1},
pages = {201},
pmid = {39080678},
issn = {1477-7819},
mesh = {Humans ; *Gene Transfer, Horizontal ; *Gallbladder Neoplasms/genetics/pathology/virology ; Carcinogenesis/genetics ; RNA, Antisense/genetics ; Gene Expression Regulation, Neoplastic ; Transcriptome ; },
abstract = {BACKGROUND: Cross-species horizontal gene transfer (HGT) involves the transfer of genetic material between different species of organisms. In recent years, mounting evidence has emerged that cross-species HGT does take place and may play a role in the development and progression of diseases.<br><br>METHODS: Transcriptomic data obtained from patients with gallbladder cancer (GBC)&#xa0;was assessed for the differential expression of antisense RNAs (asRNAs). The Basic Local Alignment Search Tool (BLAST) was used for&#xa0;cross-species analysis with viral, bacterial, fungal, and ancient human genomes to elucidate the evolutionary cross species origins of these differential asRNAs. Functional enrichment analysis and text mining were conducted and a network of asRNAs targeting mRNAs was constructed to understand the function of differential asRNAs better.<br><br>RESULTS: A total of 17 differentially expressed antisense RNAs (asRNAs) were identified in gallbladder cancer tissue&#xa0;compared to that of normal gallbladder. BLAST analysis of 15 of these asRNAs (AFAP1-AS1, HMGA2-AS1, MNX1-AS1, SLC2A1-AS1, BBOX1-AS1, ELFN1-AS1, TRPM2-AS, DNAH17-AS1, DCST1-AS1, VPS9D1-AS1, MIR1-1HG-AS1, HAND2-AS1, PGM5P4-AS1, PGM5P3-AS1, and MAGI2-AS) showed varying degree of similarities with bacterial and viral genomes, except for UNC5B-AS1 and SOX21-AS1, which were conserved during evolution. Two of these 15&#xa0;asRNAs, (VPS9D1-AS1 and SLC2A1-AS1) exhibited a high degree of similarity with viral genomes (Chikungunya virus, Human immunodeficiency virus 1, Stealth virus 1, and Zika virus) and bacterial genomes including (Staphylococcus sp., Bradyrhizobium sp., Pasteurella multocida sp., and, Klebsiella pneumoniae sp.), indicating potential HGT during evolution.<br><br>CONCLUSION: The results provide novel evidence supporting the hypothesis that differentially expressed asRNAs in GBC exhibit varying sequence similarity with bacterial, viral, and ancient human genomes, indicating a potential shared evolutionary origin. These non-coding genes are enriched with methylation and were found to be associated with cancer-related pathways, including the P53 and PI3K-AKT signaling pathways, suggesting their possible involvement in tumor development.},
}
@article {pmid39079455,
year = {2025},
author = {Russell, SL and Penunuri, G and Condon, C},
title = {Diverse genetic conflicts mediated by molecular mimicry and computational approaches to detect them.},
journal = {Seminars in cell &amp; developmental biology},
volume = {165},
number = {},
pages = {1-12},
doi = {10.1016/j.semcdb.2024.07.001},
pmid = {39079455},
issn = {1096-3634},
support = {R00 GM135583/GM/NIGMS NIH HHS/United States ; T32 HG012344/HG/NHGRI NIH HHS/United States ; },
mesh = {*Molecular Mimicry/genetics ; Humans ; Animals ; Computational Biology/methods ; },
abstract = {In genetic conflicts between intergenomic and selfish elements, driver and killer elements achieve biased survival, replication, or transmission over sensitive and targeted elements through a wide range of molecular mechanisms, including mimicry. Driving mechanisms manifest at all organismal levels, from the biased propagation of individual genes, as demonstrated by transposable elements, to the biased transmission of genomes, as illustrated by viruses, to the biased transmission of cell lineages, as in cancer. Targeted genomes are vulnerable to molecular mimicry through the conserved motifs they use for their own signaling and regulation. Mimicking these motifs enables an intergenomic or selfish element to control core target processes, and can occur at the sequence, structure, or functional level. Molecular mimicry was first appreciated as an important phenomenon more than twenty years ago. Modern genomics technologies, databases, and machine learning approaches offer tremendous potential to study the distribution of molecular mimicry across genetic conflicts in nature. Here, we explore the theoretical expectations for molecular mimicry between conflicting genomes, the trends in molecular mimicry mechanisms across known genetic conflicts, and outline how new examples can be gleaned from population genomic datasets. We discuss how mimics involving short sequence-based motifs or gene duplications can evolve convergently from new mutations. Whereas, processes that involve divergent domains or fully-folded structures occur among genomes by horizontal gene transfer. These trends are largely based on a small number of organisms and should be reevaluated in a general, phylogenetically independent framework. Currently, publicly available databases can be mined for genotypes driving non-Mendelian inheritance patterns, epistatic interactions, and convergent protein structures. A subset of these conflicting elements may be molecular mimics. We propose approaches for detecting genetic conflict and molecular mimicry from these datasets.},
}
@article {pmid39078126,
year = {2024},
author = {Ai, C and Cui, P and Liu, C and Wu, J and Xu, Y and Liang, X and Yang, Q and Tang, X and Zhou, S and Liao, H and Friman, V-P},
title = {Viral and thermal lysis facilitates transmission of antibiotic resistance genes during composting.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {8},
pages = {e0069524},
pmid = {39078126},
issn = {1098-5336},
mesh = {*Composting ; Gene Transfer, Horizontal ; Manure/microbiology/virology ; Soil Microbiology ; Bacteria/genetics/drug effects ; Animals ; Metagenome ; Cattle ; Hot Temperature ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; Microbiota ; Bacteriophages/genetics/physiology ; },
abstract = {UNLABELLED: While the distribution of extracellular ARGs (eARGs) in the environment has been widely reported, the factors governing their release remain poorly understood. Here, we combined multi-omics and direct experimentation to test whether the release and transmission of eARGs are associated with viral lysis and heat during cow manure composting. Our results reveal that the proportion of eARGs increased 2.7-fold during composting, despite a significant and concomitant reduction in intracellular ARG abundances. This relative increase of eARGs was driven by composting temperature and viral lysis of ARG-carrying bacteria based on metagenome-assembled genome (MAG) analysis. Notably, thermal lysis of mesophilic bacteria carrying ARGs was a key factor in releasing eARGs at the thermophilic phase, while viral lysis played a relatively stronger role during the non-thermal phase of composting. Furthermore, MAG-based tracking of ARGs in combination with direct transformation experiments demonstrated that eARGs released during composting pose a potential transmission risk. Our study provides bioinformatic and experimental evidence of the undiscovered role of temperature and viral lysis in co-driving the spread of ARGs in compost microbiomes via the horizontal transfer of environmentally released DNA.<br><br>IMPORTANCE: The spread of antibiotic resistance genes (ARGs) is a critical global health concern. Understanding the factors influencing the release of extracellular ARGs (eARGs) is essential for developing effective strategies. In this study, we investigated the association between viral lysis, heat, and eARG release during composting. Our findings revealed a substantial increase in eARGs despite reduced intracellular ARG abundance. Composting temperature and viral lysis were identified as key drivers, with thermal lysis predominant during the thermophilic phase and viral lysis during non-thermal phases. Moreover, eARGs released during composting posed a transmission risk through horizontal gene transfer. This study highlights the significance of temperature and phage lysis in ARG spread, providing valuable insights for mitigating antibiotic resistance threats.},
}
@article {pmid39073917,
year = {2024},
author = {Gao, L and Liu, L and Lv, AP and Fu, L and Lian, ZH and Nunoura, T and Hedlund, BP and Xu, QY and Wu, D and Yang, J and Ali, M and Li, MM and Liu, YH and Antunes, A and Jiang, HC and Cheng, L and Jiao, JY and Li, WJ and Fang, BZ},
title = {Reversed oxidative TCA (roTCA) for carbon fixation by an Acidimicrobiia strain from a saline lake.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39073917},
issn = {1751-7370},
support = {2022B0202110001//Key-Area Research and Development Program of Guangdong Province/ ; 92251302//National Natural Science Foundation of China/ ; 2022D01A154//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2021FY100900//National Science and Technology Fundamental Resources Investigation Program of China/ ; 2022xjkk1200//Third Xinjiang Scientific Expedition Program/ ; },
mesh = {*Lakes/microbiology ; *Carbon Cycle ; *Phylogeny ; Oxidation-Reduction ; Citric Acid Cycle ; Chemoautotrophic Growth ; },
abstract = {Acidimicrobiia are widely distributed in nature and suggested to be autotrophic via the Calvin-Benson-Bassham (CBB) cycle. However, direct evidence of chemolithoautotrophy in Acidimicrobiia is lacking. Here, we report a chemolithoautotrophic enrichment from a saline lake, and the subsequent isolation and characterization of a chemolithoautotroph, Salinilacustristhrix flava EGI L10123T, which belongs to a new Acidimicrobiia family. Although strain EGI L10123T is autotrophic, neither its genome nor Acidimicrobiia metagenome-assembled genomes from the enrichment culture encode genes necessary for the CBB cycle. Instead, genomic, transcriptomic, enzymatic, and stable-isotope probing data hinted at the activity of the reversed oxidative TCA (roTCA) coupled with the oxidation of sulfide as the electron donor. Phylogenetic analysis and ancestral character reconstructions of Acidimicrobiia suggested that the essential CBB gene rbcL was acquired through multiple horizontal gene transfer events from diverse microbial taxa. In contrast, genes responsible for sulfide- or hydrogen-dependent roTCA carbon fixation were already present in the last common ancestor of extant Acidimicrobiia. These findings imply the possibility of roTCA carbon fixation in Acidimicrobiia and the ecological importance of Acidimicrobiia. Further research in the future is necessary to confirm whether these characteristics are truly widespread across the clade.},
}
@article {pmid39073766,
year = {2024},
author = {González-Pinto, L and Alonso-García, I and Blanco-Martín, T and Camacho-Zamora, P and Fraile-Ribot, PA and Outeda-García, M and Lasarte-Monterrubio, C and Guijarro-Sánchez, P and Maceiras, R and Moya, B and Juan, C and Vázquez-Ucha, JC and Beceiro, A and Oliver, A and Bou, G and Arca-Suárez, J},
title = {Impact of chromosomally encoded resistance mechanisms and transferable β-lactamases on the activity of cefiderocol and innovative β-lactam/β-lactamase inhibitor combinations against Pseudomonas aeruginosa.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {79},
number = {10},
pages = {2591-2597},
pmid = {39073766},
issn = {1460-2091},
support = {//European Union/ ; //Merck Sharp &amp; Dohme/ ; //Investigator Initiated Studies Program/ ; CB21/13/00055//Centro de Investigaci&#xf3;n Biom&#xe9;dica en Red de Enfermedades Infecciosas/ ; //Spanish Network of Research in Infectious Diseases/ ; //National Plan for Scientific Research, Development and Technological Innovation 2013-2016/ ; //ISCIII-General Subdirection of Assessment and Promotion of the Research-European Regional Development Fund/ ; //Axencia Galega de Innovaci&#xf3;n/ ; IN607D2021/12//Conseller&#xed;a de Innovaci&#xf3;n, Conseller&#xed;a de Econom&#xed;a, Emprego e Industria/ ; PI21/00704//ISCIII/ ; CM21/00076//R&#xed;o Hortega program/ ; IN606B-2022/009//Xunta de Galicia/ ; JR21/00026//Juan Rod&#xe9;s program/ ; },
mesh = {*Pseudomonas aeruginosa/drug effects/genetics/enzymology ; *Cephalosporins/pharmacology ; *Microbial Sensitivity Tests ; *beta-Lactamase Inhibitors/pharmacology ; *beta-Lactamases/genetics/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Azabicyclo Compounds/pharmacology ; *Drug Combinations ; *Cefiderocol ; Cyclooctanes/pharmacology ; Tazobactam/pharmacology ; beta-Lactams/pharmacology ; Humans ; beta-Lactam Resistance/genetics ; Ceftazidime/pharmacology ; Pseudomonas Infections/microbiology/drug therapy ; Gene Transfer, Horizontal ; Chromosomes, Bacterial/genetics ; },
abstract = {OBJECTIVES: We aimed to compare the stability of the newly developed β-lactams (cefiderocol) and β-lactam/β-lactamase inhibitor combinations (ceftazidime/avibactam, ceftolozane/tazobactam, aztreonam/avibactam, cefepime/taniborbactam, cefepime/zidebactam, imipenem/relebactam, meropenem/vaborbactam, meropenem/nacubactam and meropenem/xeruborbactam) against the most clinically relevant mechanisms of mutational and transferable β-lactam resistance in Pseudomonas aeruginosa.<br><br>METHODS: We screened a collection of 61 P. aeruginosa PAO1 derivatives. Eighteen isolates displayed the most relevant mechanisms of mutational resistance to &#x3b2;-lactams. The other 43 constructs expressed transferable &#x3b2;-lactamases from genes cloned in pUCP-24. MICs were determined by reference broth microdilution.<br><br>RESULTS: Cefiderocol and imipenem/relebactam exhibited excellent in vitro activity against all of the mutational resistance mechanisms studied. Aztreonam/avibactam, cefepime/taniborbactam, cefepime/zidebactam, meropenem/vaborbactam, meropenem/nacubactam and meropenem/xeruborbactam proved to be more vulnerable to mutational events, especially to overexpression of efflux operons. The agents exhibiting the widest spectrum of activity against transferable &#x3b2;-lactamases were aztreonam/avibactam and cefepime/zidebactam, followed by cefepime/taniborbactam, cefiderocol, meropenem/xeruborbactam and meropenem/nacubactam. However, some MBLs, particularly NDM enzymes, may affect their activity. Combined production of certain enzymes (e.g. NDM-1) with increased MexAB-OprM-mediated efflux and OprD deficiency results in resistance to almost all agents tested, including last options such as aztreonam/avibactam and cefiderocol.<br><br>CONCLUSIONS: Cefiderocol and new &#x3b2;-lactam/&#x3b2;-lactamase inhibitor combinations show promising and complementary in vitro activity against mutational and transferable P. aeruginosa &#x3b2;-lactam resistance. However, the combined effects of efflux pumps, OprD deficiency and efficient &#x3b2;-lactamases could still result in the loss of all therapeutic options. Resistance surveillance, judicious use of new agents and continued drug development efforts are encouraged.},
}
@article {pmid39071422,
year = {2024},
author = {Robinson, LR and McDevitt, CJ and Regan, MR and Quail, SL and Wadsworth, CB},
title = {In vitro evolution of ciprofloxacin resistance in Neisseria commensals and derived mutation population dynamics in natural Neisseria populations.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39071422},
issn = {2692-8205},
support = {R15 AI174182/AI/NIAID NIH HHS/United States ; },
abstract = {Commensal Neisseria are members of a healthy human oropharyngeal microbiome; however, they also serve as a reservoir of antimicrobial resistance for their pathogenic relatives. Despite their known importance as sources of novel genetic variation for pathogens, we still do not understand the full suite of resistance mutations commensal species can harbor. Here, we use in vitro selection to assess the mutations that emerge in response to ciprofloxacin selection in commensal Neisseria by passaging 4 replicates of 4 different species in the presence of a selective antibiotic gradient for 20 days; then categorized derived mutations with whole genome sequencing. 10/16 selected cells lines across the 4 species evolved ciprofloxacin resistance (≥ 1 ug/ml); with resistance-contributing mutations primarily emerging in DNA gyrase subunit A and B (gyrA and gyrB), topoisomerase IV subunits C and E (parC and parE), and the multiple transferable efflux pump repressor (mtrR). Of note, these derived mutations appeared in the same loci responsible for ciprofloxacin reduced susceptibility in the pathogenic Neisseria, suggesting conserved mechanisms of resistance across the genus. Additionally, we tested for zoliflodacin cross-resistance in evolved strain lines and found 6 lineages with elevated zoliflodacin minimum inhibitory concentrations. Finally, to interrogate the likelihood of experimentally derived mutations emerging and contributing to resistance in natural Neisseria, we used a population-based approach and identified GyrA 91I as a substitution circulating within commensal Neisseria populations and ParC 85C in a single gonococcal isolate. Small clusters of gonococcal isolates had commensal-like alleles at parC and parE, indicating recent cross-species recombination events.},
}
@article {pmid39071318,
year = {2024},
author = {Sloan, DB and Broz, AK and Kuster, SA and Muthye, V and Peñafiel-Ayala, A and Marron, JR and Lavrov, DV and Brieba, LG},
title = {Expansion of the MutS Gene Family in Plants.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39071318},
issn = {2692-8205},
support = {R35 GM148134/GM/NIGMS NIH HHS/United States ; T32 GM132057/GM/NIGMS NIH HHS/United States ; },
abstract = {The MutS gene family is distributed across the tree of life and is involved in recombination, DNA repair, and protein translation. Multiple evolutionary processes have expanded the set of MutS genes in plants relative to other eukaryotes. Here, we investigate the origins and functions of these plant-specific genes. Land plants, green algae, red algae, and glaucophytes share cyanobacterial-like MutS1 and MutS2 genes that presumably were gained via plastid endosymbiotic gene transfer. MutS1 was subsequently lost in some taxa, including seed plants, whereas MutS2 was duplicated in Viridiplantae (i.e., land plants and green algae) with widespread retention of both resulting paralogs. Viridiplantae also have two anciently duplicated copies of the eukaryotic MSH6 gene (i.e., MSH6 and MSH7) and acquired MSH1 via horizontal gene transfer - potentially from a nucleocytovirus. Despite sharing the same name, "plant MSH1" is not directly related to the gene known as MSH1 in some fungi and animals, which may be an ancestral eukaryotic gene acquired via mitochondrial endosymbiosis and subsequently lost in most eukaryotic lineages. There has been substantial progress in understanding the functions of MSH1 and MSH6/MSH7 in plants, but the roles of the cyanobacterial-like MutS1 and MutS2 genes remain uncharacterized. Known functions of bacterial homologs and predicted protein structures, including fusions to diverse nuclease domains, provide hypotheses about potential molecular mechanisms. Because most plant-specific MutS proteins are targeted to the mitochondria and/or plastids, the expansion of this family appears to have played a large role in shaping plant organelle genetics.},
}
@article {pmid39071313,
year = {2024},
author = {Yang, XY and Shen, Z and Wang, C and Nakanishi, K and Fu, TM},
title = {DdmDE eliminates plasmid invasion by DNA-guided DNA targeting.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.07.20.604412},
pmid = {39071313},
issn = {2692-8205},
abstract = {Horizontal gene transfer is a key driver of bacterial evolution, but it also presents severe risks to bacteria by introducing invasive mobile genetic elements. To counter these threats, bacteria have developed various defense systems, including prokaryotic Argonautes (pAgo) and the D NA D efense M odule DdmDE system. Through biochemical analysis, structural determination, and in vivo plasmid clearance assays, we elucidate the assembly and activation mechanisms of DdmDE, which eliminates small, multicopy plasmids. We demonstrate that DdmE, a pAgo-like protein, acts as a catalytically inactive, DNA-guided, DNA-targeting defense module. In the presence of guide DNA, DdmE targets plasmids and recruits a dimeric DdmD, which contains nuclease and helicase domains. Upon binding to DNA substrates, DdmD transitions from an autoinhibited dimer to an active monomer, which then translocates along and cleaves the plasmids. Together, our findings reveal the intricate mechanisms underlying DdmDE-mediated plasmid clearance, offering fundamental insights into bacterial defense systems against plasmid invasions.},
}
@article {pmid39067739,
year = {2024},
author = {Chen, X and Song, X and Liang, Y and Wang, F and Pan, C and Wei, Z},
title = {Evaluation of the potential horizontal gene transfer ability during chicken manure and pig manure composting.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {360},
number = {},
pages = {124621},
doi = {10.1016/j.envpol.2024.124621},
pmid = {39067739},
issn = {1873-6424},
mesh = {Animals ; *Manure ; *Chickens ; *Composting ; Swine ; *Gene Transfer, Horizontal ; Bacteria/genetics ; Soil Microbiology ; },
abstract = {Resistance genes have been identified as emerging pollutants due to their ability to rapidly spread in the environment through horizontal gene transfer (HGT). Microbial community serves as the pivotal factor influencing the frequency of HGT during manure composting. However, the characteristics of HGT in microbial community from different types of manure were unclear. Therefore, this study aimed to evaluate the potential risk of HGT in bacterial community through the co-composting of chicken manure and pig manure in different proportions. The experimental results showed that the abundance of sulfonamide antibiotic resistance genes and integrase genes was higher during pig manure composting than those during chicken manure composting. In addition, the addition of pig manure also increased resistance genes abundance during chicken manure composting. These results suggested that the potential HGT risk was greater during pig manure composting. Furthermore, microbial analysis of co-composting suggested that bacterial community of pig manure was more competitive and adaptable than that of chicken manure. Ultimately, statistical analysis indicated that compared to chicken manure composting, the potential ability of HGT was greater during pig manure composting. This study provided the vital theoretical support and scientific guidance for mitigating the HGT risk during manure composting.},
}
@article {pmid39067603,
year = {2024},
author = {Liu, M and Kasuga, I},
title = {Impact of chlorine disinfection on intracellular and extracellular antimicrobial resistance genes in wastewater treatment and water reclamation.},
journal = {The Science of the total environment},
volume = {949},
number = {},
pages = {175046},
doi = {10.1016/j.scitotenv.2024.175046},
pmid = {39067603},
issn = {1879-1026},
mesh = {*Chlorine ; *Wastewater/microbiology ; *Waste Disposal, Fluid/methods ; *Disinfection/methods ; Disinfectants ; Genes, Bacterial ; Water Purification/methods ; Drug Resistance, Bacterial/genetics ; Bacteria/drug effects/genetics ; Drug Resistance, Microbial/genetics ; },
abstract = {Wastewater treatment plants and water reclamation facilities are reservoirs of antimicrobial resistance genes (ARGs). These ARGs are not limited solely to intracellular DNA (inARGs) but include extracellular DNA (exARGs) present in wastewater. The release of exARGs from cells can be exacerbated by treatment processes, including chlorine disinfection, which disrupts bacterial cells. Given the potential for exARGs to drive horizontal gene transfer and contribute to the proliferation of antimicrobial resistance, it is imperative to recognize these fractions as emerging environmental pollutants. In this study, we conducted a comprehensive year-long assessment of both inARGs and exARGs, further differentiating between dissolved exARGs (Dis_exARGs) and exARGs adsorbed onto particulate matter (Ads_exARGs), within a full-scale wastewater treatment and water reclamation facility. The results revealed that Ads_exARGs comprised up to 30 % of the total ARGs in raw sewage with high biomass content. Generally, treatments at low and high doses of chlorine increased the abundance of Dis_exARGs and Ads_exARGs. The fate of ARG levels that varied depending on the type of ARGs suggested variations in the susceptibility of the host bacteria to chlorination. Moreover, co-occurrence of several potential opportunistic pathogenic bacteria and ARGs were observed. Therefore, we propose higher doses of chlorination as a prerequisite for the effective removal of inARGs and exARGs.},
}
@article {pmid39066295,
year = {2024},
author = {Li, W and Tahiri, N},
title = {Host-Virus Cophylogenetic Trajectories: Investigating Molecular Relationships between Coronaviruses and Bat Hosts.},
journal = {Viruses},
volume = {16},
number = {7},
pages = {},
pmid = {39066295},
issn = {1999-4915},
support = {326911//Fonds de recherche du Qu&#xe9;bec/ ; RGPIN-2022-04322//Natural Sciences and Engineering Research Council/ ; },
mesh = {*Chiroptera/virology ; Animals ; *Phylogeny ; *Coronavirus/genetics/classification/physiology ; Evolution, Molecular ; Host-Pathogen Interactions/genetics ; Spike Glycoprotein, Coronavirus/genetics/metabolism ; Host Specificity ; Coronavirus Infections/virology ; },
abstract = {Bats, with their virus tolerance, social behaviors, and mobility, are reservoirs for emerging viruses, including coronaviruses (CoVs) known for genetic flexibility. Studying the cophylogenetic link between bats and CoVs provides vital insights into transmission dynamics and host adaptation. Prior research has yielded valuable insights into phenomena such as host switching, cospeciation, and other dynamics concerning the interaction between CoVs and bats. Nonetheless, a distinct gap exists in the current literature concerning a comparative cophylogenetic analysis focused on elucidating the contributions of sequence fragments to the co-evolution between hosts and viruses. In this study, we analyzed the cophylogenetic patterns of 69 host-virus connections. Among the 69 host-virus links examined, 47 showed significant cophylogeny based on ParaFit and PACo analyses, affirming strong associations. Focusing on two proteins, ORF1ab and spike, we conducted a comparative analysis of host and CoV phylogenies. For ORF1ab, the specific window ranged in multiple sequence alignment (positions 520-680, 770-870, 2930-3070, and 4910-5080) exhibited the lowest Robinson-Foulds (RF) distance (i.e., 84.62%), emphasizing its higher contribution in the cophylogenetic association. Similarly, within the spike region, distinct window ranges (positions 0-140, 60-180, 100-410, 360-550, and 630-730) displayed the lowest RF distance at 88.46%. Our analysis identified six recombination regions within ORF1ab (positions 360-1390, 550-1610, 680-1680, 700-1710, 2060-3090, and 2130-3250), and four within the spike protein (positions 10-510, 50-560, 170-710, and 230-730). The convergence of minimal RF distance regions with combination regions robustly affirms the pivotal role of recombination in viral adaptation to host selection pressures. Furthermore, horizontal gene transfer reveals prominent instances of partial gene transfer events, occurring not only among variants within the same host species but also crossing host species boundaries. This suggests a more intricate pattern of genetic exchange. By employing a multifaceted approach, our comprehensive strategy offers a nuanced understanding of the intricate interactions that govern the co-evolutionary dynamics between bat hosts and CoVs. This deeper insight enhances our comprehension of viral evolution and adaptation mechanisms, shedding light on the broader dynamics that propel viral diversity.},
}
@article {pmid39061350,
year = {2024},
author = {Drane, K and Sheehan, M and Whelan, A and Ariel, E and Kinobe, R},
title = {The Role of Wastewater Treatment Plants in Dissemination of Antibiotic Resistance: Source, Measurement, Removal and Risk Assessment.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {39061350},
issn = {2079-6382},
support = {2256.95982.2331//Townsville City Council, Townsville Australia/ ; },
abstract = {Antibiotic Resistance Genes (ARGs) are contaminants of emerging concern with marked potential to impact public and environmental health. This review focusses on factors that influence the presence, abundance, and dissemination of ARGs within Wastewater Treatment Plants (WWTPs) and associated effluents. Antibiotic-Resistant Bacteria (ARB) and ARGs have been detected in the influent and the effluent of WWTPs worldwide. Different levels of wastewater treatment (primary, secondary, and tertiary) show different degrees of removal efficiency of ARGs, with further differences being observed when ARGs are captured as intracellular or extracellular forms. Furthermore, routinely used molecular methodologies such as quantitative polymerase chain reaction or whole genome sequencing may also vary in resistome identification and in quantifying ARG removal efficiencies from WWTP effluents. Additionally, we provide an overview of the One Health risk assessment framework, as well as future strategies on how WWTPs can be assessed for environmental and public health impact.},
}
@article {pmid39061343,
year = {2024},
author = {Fahy, S and O'Connor, JA and Sleator, RD and Lucey, B},
title = {From Species to Genes: A New Diagnostic Paradigm.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {39061343},
issn = {2079-6382},
abstract = {Molecular diagnostics has the potential to revolutionise the field of clinical microbiology. Microbial identification and nomenclature have, for too long, been restricted to phenotypic characterisation. However, this species-level view fails to wholly account for genetic heterogeneity, a result of lateral gene transfer, mediated primarily by mobile genetic elements. This genetic promiscuity has helped to drive virulence development, stress adaptation, and antimicrobial resistance in several important bacterial pathogens, complicating their detection and frustrating our ability to control them. We argue that, as clinical microbiologists at the front line, we must embrace the molecular technologies that allow us to focus specifically on the genetic elements that cause disease rather than the bacterial species that express them. This review focuses on the evolution of microbial taxonomy since the introduction of molecular sequencing, the role of mobile genetic elements in antimicrobial resistance, the current and emerging assays in clinical laboratories, and the comparison of phenotypic versus genotypic analyses. In essence, it is time now to refocus from species to genes as part of a new diagnostic paradigm.},
}
@article {pmid39061274,
year = {2024},
author = {Ghazawi, A and Anes, F and Mouftah, S and Elbediwi, M and Baig, A and Alketbi, M and Almazrouei, F and Alhashmi, M and Alzarooni, N and Manzoor, A and Habib, I and Strepis, N and Nabi, A and Khan, M},
title = {Genomic Study of High-Risk Clones of Enterobacter hormaechei Collected from Tertiary Hospitals in the United Arab Emirates.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {39061274},
issn = {2079-6382},
support = {G00004620 and G00004164//United Arab Emirates University/ ; },
abstract = {Enterobacter hormaechei has emerged as a significant pathogen within healthcare settings due to its ability to develop multidrug resistance (MDR) and survive in hospital environments. This study presents a genome-based analysis of carbapenem-resistant Enterobacter hormaechei isolates from two major hospitals in the United Arab Emirates. Eight isolates were subjected to whole-genome sequencing (WGS), revealing extensive resistance profiles including the blaNDM-1, blaOXA-48, and blaVIM-4 genes. Notably, one isolate belonging to ST171 harbored dual carbapenemase genes, while five isolates exhibited colistin resistance without mcr genes. The presence of the type VI secretion system (T6SS), various adhesins, and virulence genes contributes to the virulence and competitive advantage of the pathogen. Additionally, our isolates (87.5%) possessed ampC β-lactamase genes, predominantly blaACT genes. The genomic context of blaNDM-1, surrounded by other resistance genes and mobile genetic elements, highlights the role of horizontal gene transfer (HGT) in the spread of resistance. Our findings highlight the need for rigorous surveillance, strategic antibiotic stewardship, and hospital-based WGS to manage and mitigate the spread of these highly resistant and virulent pathogens. Accurate identification and monitoring of Enterobacter cloacae complex (ECC) species and their resistance mechanisms are crucial for effective infection control and treatment strategies.},
}
@article {pmid39060998,
year = {2024},
author = {Seth-Smith, H and Bommana, S and Dean, D and Read, TD and Marti, H},
title = {Chlamydia suis undergoes interclade recombination promoting Tet-island exchange.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {724},
pmid = {39060998},
issn = {1471-2164},
support = {323530_177579//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Chlamydia/genetics ; *Recombination, Genetic ; *Phylogeny ; *Tetracycline Resistance/genetics ; *Genomic Islands ; Animals ; Swine ; Gene Transfer, Horizontal ; Genome, Bacterial ; },
abstract = {BACKGROUND: The obligate intracellular bacterial family Chlamydiaceae comprises a number of different species that cause disease in various vertebrate hosts including humans. Chlamydia suis, primarily found in the gastrointestinal tract of pigs, is the only species of the Chlamydiaceae family to have naturally gained tetracycline resistance (TetR), through a genomic island (Tet-island), integrated into the middle of chromosomal invasin-like gene inv. Previous studies have hypothesised that the uptake of the Tet-island from a host outside the Chlamydiaceae family was a unique event, followed by spread among C. suis through homologous recombination. In vitro recombination studies have shown that Tet-island exchange between C. suis strains is possible. Our aim in this study was to gain a deeper understanding of the interclade recombination of the Tet-island, among currently circulating C. suis field strains compared to in vitro-generated recombinants, using published whole genome sequences of C. suis field strains (n = 35) and in vitro-generated recombinants (n = 63).<br><br>RESULTS: We found that the phylogeny of inv better reflected the phylogeny of the Tet-island than that of the whole genome, supporting recombination rather than site-specific insertion as the means of transfer. There were considerable differences between the distribution of recombinations within in vitro-generated strains compared to that within the field strains. These differences are likely because in vitro-generated recombinants were selected for a tetracycline and rifamycin/rifampicin resistant background, leading to the largest peak of recombination across the Tet-island. Finally, we found that interclade recombinations across the Tet-island were more variable in length downstream of the Tet-island than upstream.<br><br>CONCLUSIONS: Our study supports the hypothesis that the occurrence of TetR strains in both clades of C. suis came about through interclade recombination after a single ancestral horizontal gene transfer event.},
}
@article {pmid39058093,
year = {2024},
author = {Peñil-Celis, A and Tagg, KA and Webb, HE and Redondo-Salvo, S and Francois Watkins, L and Vielva, L and Griffin, C and Kim, JY and Folster, JP and Garcillan-Barcia, MP and de la Cruz, F},
title = {Mobile genetic elements define the non-random structure of the Salmonella enterica serovar Typhi pangenome.},
journal = {mSystems},
volume = {9},
number = {8},
pages = {e0036524},
pmid = {39058093},
issn = {2379-5077},
support = {PID2020-117923GB-I00 MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovaci&#xf3;n (MCIN)/ ; PID2020-117923GB-I00 MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovaci&#xf3;n (MCIN)/ ; Contracts No. 75D30119C06679 and 75D30121C11978//HHS | Centers for Disease Control and Prevention (CDC)/ ; DI-17-09164//Ministerio de Econom&#xed;a y Competitividad (MEC)/ ; },
mesh = {*Salmonella typhi/genetics ; *Genome, Bacterial/genetics ; *Interspersed Repetitive Sequences/genetics ; Plasmids/genetics ; Evolution, Molecular ; Humans ; Phylogeny ; Typhoid Fever/microbiology/epidemiology ; },
abstract = {Bacterial relatedness measured using select chromosomal loci forms the basis of public health genomic surveillance. While approximating vertical evolution through this approach has proven exceptionally valuable for understanding pathogen dynamics, it excludes a fundamental dimension of bacterial evolution-horizontal gene transfer. Incorporating the accessory genome is the logical remediation and has recently shown promise in expanding epidemiological resolution for enteric pathogens. Employing k-mer-based Jaccard index analysis, and a novel genome length distance metric, we computed pangenome (i.e., core and accessory) relatedness for the globally important pathogen Salmonella enterica serotype Typhi (Typhi), and graphically express both vertical (homology-by-descent) and horizontal (homology-by-admixture) evolutionary relationships in a reticulate network of over 2,200 U.S. Typhi genomes. This analysis revealed non-random structure in the Typhi pangenome that is driven predominantly by the gain and loss of mobile genetic elements, confirming and expanding upon known epidemiological patterns, revealing novel plasmid dynamics, and identifying avenues for further genomic epidemiological exploration. With an eye to public health application, this work adds important biological context to the rapidly improving ways of analyzing bacterial genetic data and demonstrates the value of the accessory genome to infer pathogen epidemiology and evolution.IMPORTANCEGiven bacterial evolution occurs in both vertical and horizontal dimensions, inclusion of both core and accessory genetic material (i.e., the pangenome) is a logical step toward a more thorough understanding of pathogen dynamics. With an eye to public, and indeed, global health relevance, we couple contemporary tools for genomic analysis with decades of research on mobile genetic elements to demonstrate the value of the pangenome, known and unknown, annotated, and hypothetical, for stratification of Salmonella enterica serovar Typhi (Typhi) populations. We confirm and expand upon what is known about Typhi epidemiology, plasmids, and antimicrobial resistance dynamics, and offer new avenues of exploration to further deduce Typhi ecology and evolution, and ultimately to reduce the incidence of human disease.},
}
@article {pmid39056664,
year = {2024},
author = {Aguirre-Carvajal, K and Munteanu, CR and Armijos-Jaramillo, V},
title = {Database Bias in the Detection of Interdomain Horizontal Gene Transfer Events in Pezizomycotina.},
journal = {Biology},
volume = {13},
number = {7},
pages = {},
pmid = {39056664},
issn = {2079-7737},
support = {PRG.BIO.23.14.01//Universidad de Las Am&#xe9;ricas/ ; },
abstract = {Horizontal gene transfer (HGT) is a widely acknowledged phenomenon in prokaryotes for generating genetic diversity. However, the impact of this process in eukaryotes, particularly interdomain HGT, is a topic of debate. Although there have been observed biases in interdomain HGT detection, little exploration has been conducted on the effects of imbalanced databases. In our study, we conducted experiments to assess how different databases affect the detection of interdomain HGT using proteomes from the Pezizomycotina fungal subphylum as our focus group. Our objective was to simulate the database imbalance commonly found in public biological databases, where bacterial and eukaryotic sequences are unevenly represented, and demonstrate that an increase in uploaded eukaryotic sequences leads to a decrease in predicted HGTs. For our experiments, four databases with varying proportions of eukaryotic sequences but consistent proportions of bacterial sequences were utilized. We observed a significant reduction in detected interdomain HGT candidates as the proportion of eukaryotes increased within the database. Our data suggest that the imbalance in databases bias the interdomain HGT detection and highlights challenges associated with confirming the presence of interdomain HGT among Pezizomycotina fungi and potentially other groups within Eukarya.},
}
@article {pmid39053184,
year = {2024},
author = {Checcucci, A and Buscaroli, E and Modesto, M and Luise, D and Blasioli, S and Scarafile, D and Di Vito, M and Bugli, F and Trevisi, P and Braschi, I and Mattarelli, P},
title = {The swine waste resistome: Spreading and transfer of antibiotic resistance genes in Escherichia coli strains and the associated microbial communities.},
journal = {Ecotoxicology and environmental safety},
volume = {283},
number = {},
pages = {116774},
doi = {10.1016/j.ecoenv.2024.116774},
pmid = {39053184},
issn = {1090-2414},
mesh = {Animals ; *Escherichia coli/genetics/drug effects ; Swine ; *Manure/microbiology ; *Gene Transfer, Horizontal ; *Integrons/genetics ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Microbiota/drug effects ; Drug Resistance, Microbial/genetics ; },
abstract = {The overuse of antimicrobials in livestock farming has led to the development of resistant bacteria and the spread of antibiotic-resistant genes (ARGs) among animals. When manure containing these antibiotics is applied to agricultural fields, it creates a selective pressure that promotes the acquisition of ARGs by bacteria, primarily through horizontal gene transfer. Most research on ARGs focuses on their role in clinical antibiotic resistance and their transfer from environmental sources to bacteria associated with humans, such as Escherichia coli. The study investigates the spread of antibiotic-resistant genes (ARGs) through class 1 integrons in 27 Escherichia coli strains from pig manure. It focuses on six common ARGs (ermB, cmlA, floR, qnrS, tetA, and TEM) and the class 1 integron gene, assessing their prevalence in manure samples from three pig farms. The study found correlations and anticorrelations among these genes, indicating a predisposition of the integron in spreading certain ARGs. Specifically, cmlA and tetA genes were positively correlated with each other and negatively with int1, suggesting they are not transferred via Int1. Farm B had the highest int1 counts and a higher abundance of the TEM gene, but lower levels of cmlA and tetA genes. The results underscore the complexity of predicting ARG spread in agricultural environments and the associated health risks to humans through the food chain. The study's results offer valuable insights into the antibiotic-resistant genes (ARGs) profile in swine livestock, potentially aiding in the development of methods to trace ARGs in the environment.},
}
@article {pmid39052705,
year = {2024},
author = {Wan, Y and Myall, AC and Boonyasiri, A and Bolt, F and Ledda, A and Mookerjee, S and Weiße, AY and Getino, M and Turton, JF and Abbas, H and Prakapaite, R and Sabnis, A and Abdolrasouli, A and Malpartida-Cardenas, K and Miglietta, L and Donaldson, H and Gilchrist, M and Hopkins, KL and Ellington, MJ and Otter, JA and Larrouy-Maumus, G and Edwards, AM and Rodriguez-Manzano, J and Didelot, X and Barahona, M and Holmes, AH and Jauneikaite, E and Davies, F},
title = {Integrated Analysis of Patient Networks and Plasmid Genomes to Investigate a Regional, Multispecies Outbreak of Carbapenemase-Producing Enterobacterales Carrying Both blaIMP and mcr-9 Genes.},
journal = {The Journal of infectious diseases},
volume = {230},
number = {1},
pages = {e159-e170},
pmid = {39052705},
issn = {1537-6613},
support = {MRF-145-0004-TPG-AVISO/MRF/MRF/United Kingdom ; PSN109//Imperial College London/ ; //National Institute for Health Research/ ; //Imperial Health Charity/ ; EP/N014529///EPSRC Centre for Mathematics of Precision Healthcare/ ; M683//Stoneygate Trust/ ; /WT_/Wellcome Trust/United Kingdom ; //UK Health Security Agency/ ; //Imperial Biomedical Research Centre/ ; MR/T005254/1/MRC_/Medical Research Council/United Kingdom ; //NIHR Health Protection Research Unit/ ; //NIHR Health Protection Research Unit in Genomics and Enabling Data/ ; //Faculty of Medicine, Siriraj Hospital, Mahidol University/ ; NIHR200915//University of Oxford/ ; //Rosetrees Trust/ ; },
mesh = {Humans ; *Plasmids/genetics ; *beta-Lactamases/genetics ; *Enterobacteriaceae Infections/epidemiology/microbiology/transmission ; *Disease Outbreaks ; *Bacterial Proteins/genetics ; London/epidemiology ; Anti-Bacterial Agents/pharmacology ; Phylogeny ; Genome, Bacterial ; Male ; Female ; Middle Aged ; Microbial Sensitivity Tests ; Adult ; Enterobacteriaceae/genetics/drug effects ; Aged ; Carbapenem-Resistant Enterobacteriaceae/genetics/isolation &amp; purification ; Colistin/pharmacology ; },
abstract = {BACKGROUND: Carbapenemase-producing Enterobacterales (CPE) are challenging in healthcare, with resistance to multiple classes of antibiotics. This study describes the emergence of imipenemase (IMP)-encoding CPE among diverse Enterobacterales species between 2016 and 2019 across a London regional network.<br><br>METHODS: We performed a network analysis of patient pathways, using electronic health records, to identify contacts between IMP-encoding CPE-positive patients. Genomes of IMP-encoding CPE isolates were overlaid with patient contacts to imply potential transmission events.<br><br>RESULTS: Genomic analysis of 84 Enterobacterales isolates revealed diverse species (predominantly Klebsiella spp, Enterobacter spp, and Escherichia coli); 86% (72 of 84) harbored an IncHI2 plasmid carrying blaIMP and colistin resistance gene mcr-9 (68 of 72). Phylogenetic analysis of IncHI2 plasmids identified 3 lineages showing significant association with patient contacts and movements between 4 hospital sites and across medical specialties, which was missed in initial investigations.<br><br>CONCLUSIONS: Combined, our patient network and plasmid analyses demonstrate an interspecies, plasmid-mediated outbreak of blaIMPCPE, which remained unidentified during standard investigations. With DNA sequencing and multimodal data incorporation, the outbreak investigation approach proposed here provides a framework for real-time identification of key factors causing pathogen spread. Plasmid-level outbreak analysis reveals that resistance spread may be wider than suspected, allowing more interventions to stop transmission within hospital networks.SummaryThis was an investigation, using integrated pathway networks and genomics methods, of the emergence of imipenemase-encoding carbapenemase-producing Enterobacterales among diverse Enterobacterales species between 2016 and 2019 in patients across a London regional hospital network, which was missed on routine investigations.},
}
@article {pmid39052112,
year = {2024},
author = {Li, H and Liu, B and Li, M and Shen, M},
title = {Livestock and poultry breeding farms as a fixed and underestimated source of antibiotic resistance genes.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {37},
pages = {49916-49931},
pmid = {39052112},
issn = {1614-7499},
mesh = {Animals ; *Poultry ; *Livestock ; *Drug Resistance, Microbial/genetics ; *Farms ; Anti-Bacterial Agents/pharmacology ; Animal Husbandry ; Drug Resistance, Bacterial/genetics ; },
abstract = {The excessive use of antibiotics, disinfectants, and drugs in livestock and poultry breeding has resulted in a rise in the presence of antibiotic resistance genes (ARGs). Antibiotic-resistant bacteria (ARB) and ARGs have been widely found in animal feces, farm wastewater, and farm air. ARGs can not only spread across media through adsorption and migration, but also transfer resistance across bacterial genera through horizontal gene transfer. Livestock breeding has become a fixed and unavoidable source of ARGs in the environment. Existing technologies for controlling ARGs, such as composting, disinfection, and sewage treatment, are not efficient in removing ARB and ARGs from waste. Furthermore, the remaining ARGs still possess a strong capacity for dissemination. At present, antibiotics used in animal husbandry are difficult to replace in a short period of time. The growth and potential risks of resistance genes in livestock and poultry breeding sources in the receiving environment are not yet clear. In this paper, we summarize the current situation of ARGs in the livestock and poultry breeding environment. We also explain the key environmental processes, main influencing factors, and corresponding ecological risks associated with ARGs in this environment. The advantages and disadvantages of current technologies for the removal of ARGs are primarily discussed. There is a particular emphasis on clarifying the spatiotemporal evolution patterns and environmental process mechanisms of ARGs, as well as highlighting the importance and urgency of developing efficient pollution control technologies.},
}
@article {pmid39052074,
year = {2024},
author = {Allman, ES and Baños, H and Garrote-Lopez, M and Rhodes, JA},
title = {Identifiability of Level-1 Species Networks from Gene Tree Quartets.},
journal = {Bulletin of mathematical biology},
volume = {86},
number = {9},
pages = {110},
pmid = {39052074},
issn = {1522-9602},
support = {P20 GM103395/GM/NIGMS NIH HHS/United States ; DMS-2331660//National Science Foundation/ ; P20GM103395//Foundation for the National Institutes of Health/ ; DMS-2051760//National Science Foundation/ ; },
mesh = {*Phylogeny ; *Mathematical Concepts ; *Models, Genetic ; *Gene Transfer, Horizontal ; Evolution, Molecular ; Genetic Speciation ; Gene Regulatory Networks ; Computer Simulation ; Hybridization, Genetic ; },
abstract = {When hybridization or other forms of lateral gene transfer have occurred, evolutionary relationships of species are better represented by phylogenetic networks than by trees. While inference of such networks remains challenging, several recently proposed methods are based on quartet concordance factors-the probabilities that a tree relating a gene sampled from the species displays the possible 4-taxon relationships. Building on earlier results, we investigate what level-1 network features are identifiable from concordance factors under the network multispecies coalescent model. We obtain results on both topological features of the network, and numerical parameters, uncovering a number of failures of identifiability related to 3-cycles in the network. Addressing these identifiability issues is essential for designing statistically consistent inference methods.},
}
@article {pmid39047887,
year = {2024},
author = {Wu, X and Jia, W and Fang, Z and Sun, H and Wang, G and Liu, L and Zheng, M and Chen, G},
title = {Cyanobacteria mediate the dissemination of bacterial antibiotic resistance through conjugal transfer.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {359},
number = {},
pages = {124592},
doi = {10.1016/j.envpol.2024.124592},
pmid = {39047887},
issn = {1873-6424},
mesh = {*Drug Resistance, Bacterial/genetics ; *Microcystis/genetics ; *Gene Transfer, Horizontal ; *Cyanobacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Genes, Bacterial ; Bacteria/genetics/drug effects ; },
abstract = {Cyanobacterial blooms are expanding world-wide in freshwater and marine environments, and can cause serious ecological and environmental issues, which also contribute to the spread of antibiotic resistance genes (ARGs). However, the mechanistic understanding of cyanobacteria-mediated resistance dynamics is not fully elucidated yet. We selected Microcystis aeruginosa as a model cyanobacteria to illustrate how cyanobacteria mediate the evolution and transfer processes of bacterial antibiotic resistance. The results show that the presence of cyanobacteria significantly decreased the abundance of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) by 3%-99% and 2%-18%, respectively. In addition, it clearly altered bacterial community structure, with the dominant genera evolving from Acinetobacter (27%) and Enterobacter (42%) to Porphyrobacter (59%). The abundance of ARGs positively correlated with Proteobacteria and Firmicutes, rather than Cyanobacteria, and Bacteroidetes. In the presence of cyanobacteria, the transfer events of bacterial resistance genes via conjugation were found to decrease by 10%-89% (p < 0.05). Surprisingly, we found an extradentary high transfer frequency (about 0.1) for the ARGs via plasmid conjugation from the bacteria into M. aeruginosa population. It confirmed the role of cyanobacterial population as the competent hosts to facilitate ARGs spreading. Our findings provide valuable information on the risk evaluation of ARGs caused by cyanobacterial blooms in aquatic environments, key for the protection and assessment of aquatic environmental quality.},
}
@article {pmid39044460,
year = {2024},
author = {Roulet, ME and Ceriotti, LF and Gatica-Soria, L and Sanchez-Puerta, MV},
title = {Horizontally transferred mitochondrial DNA tracts become circular by microhomology-mediated repair pathways.},
journal = {The New phytologist},
volume = {243},
number = {6},
pages = {2442-2456},
doi = {10.1111/nph.19984},
pmid = {39044460},
issn = {1469-8137},
support = {PICT2020-01018//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; 06/A092-T1//Secretar&#xed;a de Investigaci&#xf3;n, Internacionales y Posgrado, Universidad Nacional de Cuyo/ ; },
mesh = {*Gene Transfer, Horizontal ; *DNA, Mitochondrial/genetics ; *Phylogeny ; *DNA, Circular/genetics ; DNA Repair/genetics ; Genome, Mitochondrial/genetics ; },
abstract = {The holoparasitic plant Lophophytum mirabile exhibits remarkable levels of mitochondrial horizontal gene transfer (HGT). Gathering comparative data from other individuals and host plants can provide insights into the HGT process. We sequenced the mitochondrial genome (mtDNA) from individuals of two species of Lophophytum and from mimosoid hosts. We applied a stringent phylogenomic approach to elucidate the origin of the whole mtDNAs, estimate the timing of the transfers, and understand the molecular mechanisms involved. Ancestral and recent HGT events replaced and enlarged the multichromosomal mtDNA of Lophophytum spp., with the foreign DNA ascending to 74%. A total of 14 foreign mitochondrial chromosomes originated from continuous regions in the host mtDNA flanked by short direct repeats. These foreign tracts are circularized by microhomology-mediated repair pathways and replicate independently until they are lost or they eventually recombine with other chromosomes. The foreign noncoding chromosomes are variably present in the population and likely evolve by genetic drift. We present the 'circle-mediated HGT' model in which foreign mitochondrial DNA tracts become circular and are maintained as plasmid-like molecules. This model challenges the conventional belief that foreign DNA must be integrated into the recipient genome for successful HGT.},
}
@article {pmid39042422,
year = {2024},
author = {Alves, J and Dry, I and White, JH and Dryden, DTF and Lynskey, NN},
title = {Generation of tools for expression and purification of the phage-encoded Type I restriction enzyme inhibitor, Ocr.},
journal = {Microbiology (Reading, England)},
volume = {170},
number = {7},
pages = {},
pmid = {39042422},
issn = {1465-2080},
mesh = {*Recombinant Proteins/genetics/metabolism/isolation &amp; purification ; Viral Proteins/genetics/metabolism ; Bacteriophages/genetics/enzymology ; Streptococcus pyogenes/genetics/enzymology/metabolism ; Transformation, Bacterial ; Deoxyribonucleases, Type I Site-Specific/metabolism/genetics ; Gene Expression ; Escherichia coli/genetics/metabolism ; },
abstract = {DNA manipulation is an essential tool in molecular microbiology research that is dependent on the ability of bacteria to take up and preserve foreign DNA by horizontal gene transfer. This process can be significantly impaired by the activity of bacterial restriction modification systems; bacterial operons comprising paired enzymatic activities that protectively methylate host DNA, while cleaving incoming unmodified foreign DNA. Ocr is a phage-encoded protein that inhibits Type I restriction modification systems, the addition of which significantly improves bacterial transformation efficiency. We recently established an improved and highly efficient transformation protocol for the important human pathogen group A Streptococcus using commercially available recombinant Ocr protein, manufacture of which has since been discontinued. In order to ensure the continued availability of Ocr protein within the research community, we have generated tools and methods for in-house Ocr production and validated the activity of the purified recombinant protein.},
}
@article {pmid39039821,
year = {2024},
author = {Bohl, V and Mogk, A},
title = {When the going gets tough, the tough get going-Novel bacterial AAA+ disaggregases provide extreme heat resistance.},
journal = {Environmental microbiology},
volume = {26},
number = {7},
pages = {e16677},
doi = {10.1111/1462-2920.16677},
pmid = {39039821},
issn = {1462-2920},
support = {MO970/7-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Bacterial Proteins/metabolism/genetics ; HSP70 Heat-Shock Proteins/metabolism/genetics ; Thermotolerance ; Hot Temperature ; Bacteria/genetics/metabolism ; Endopeptidase Clp/metabolism/genetics ; Heat-Shock Proteins/metabolism/genetics ; Heat-Shock Response ; },
abstract = {Heat stress can lead to protein misfolding and aggregation, potentially causing cell death due to the loss of essential proteins. Bacteria, being particularly exposed to environmental stress, are equipped with disaggregases that rescue these aggregated proteins. The bacterial Hsp70 chaperone DnaK and the ATPase associated with diverse cellular activities protein ClpB form the canonical disaggregase in bacteria. While this combination operates effectively during physiological heat stress, it is ineffective against massive aggregation caused by temperature-based sterilization protocols used in the food industry and clinics. This leaves bacteria unprotected against these thermal processes. However, bacteria that can withstand extreme, man-made stress conditions have emerged. These bacteria possess novel ATPase associated with diverse cellular activities disaggregases, ClpG and ClpL, which are key players in extreme heat resistance. These disaggregases, present in selected Gram-negative or Gram-positive bacteria, respectively, function superiorly by exhibiting increased thermal stability and enhanced threading power compared to DnaK/ClpB. This enables ClpG and ClpL to operate at extreme temperatures and process large and tight protein aggregates, thereby contributing to heat resistance. The genes for ClpG and ClpL are often encoded on mobile genomic islands or conjugative plasmids, allowing for their rapid spread among bacteria via horizontal gene transfer. This threatens the efficiency of sterilization protocols. In this review, we describe the various bacterial disaggregases identified to date, characterizing their commonalities and the specific features that enable these novel disaggregases to provide stress protection against extreme stress conditions.},
}
@article {pmid39039101,
year = {2024},
author = {Brown, CL and Maile-Moskowitz, A and Lopatkin, AJ and Xia, K and Logan, LK and Davis, BC and Zhang, L and Vikesland, PJ and Pruden, A},
title = {Author Correction: Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6166},
doi = {10.1038/s41467-024-50577-6},
pmid = {39039101},
issn = {2041-1723},
}
@article {pmid39038713,
year = {2024},
author = {Sun, B and Bai, Z and Li, R and Song, M and Zhang, J and Wang, J and Zhuang, X},
title = {Efficient elimination of antibiotic resistome in livestock manure by semi-permeable membrane covered hyperthermophilic composting.},
journal = {Bioresource technology},
volume = {407},
number = {},
pages = {131134},
doi = {10.1016/j.biortech.2024.131134},
pmid = {39038713},
issn = {1873-2976},
mesh = {*Manure/microbiology ; *Composting/methods ; Animals ; *Membranes, Artificial ; *Drug Resistance, Microbial/genetics ; *Livestock ; Chickens ; Anti-Bacterial Agents/pharmacology ; Permeability ; Interspersed Repetitive Sequences ; },
abstract = {Livestock manure is a hotspot for antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and an important contributor to antibiotic resistance in non-clinical settings. This study investigated the effectiveness and potential mechanisms of a novel composting technology, semi-permeable membrane covered hyperthermophilic composting (smHTC), in removal of ARGs and MGEs in chicken manure. Results showed that smHTC was more efficient in removal of ARGs and MGEs (92% and 93%) compared to conventional thermophilic composting (cTC) (76% and 92%). The efficient removal in smHTC is attributed to direct or indirect negative effects caused by the high temperature, including reducing the involvement of bio-available heavy metals (HMs) in co-selection processes of antibiotic resistance, decreasing the bacterial abundance and diversity, suppressing the horizontal gene transfer and killing potential ARGs hosts. Overall, smHTC can efficiently remove the resistome in livestock manure, reducing the risk to crops and humans from ARGs residues in compost products.},
}
@article {pmid39038196,
year = {2024},
author = {Mori, BA and Coutu, C and Erlandson, MA and Hegedus, DD},
title = {Exploring the contribution of the salivary gland and midgut to digestion in the swede midge (Contarinia nasturtii) through a genomics-guided approach.},
journal = {Archives of insect biochemistry and physiology},
volume = {116},
number = {3},
pages = {e22135},
doi = {10.1002/arch.22135},
pmid = {39038196},
issn = {1520-6327},
support = {//Alberta Canola Producers Commission/ ; //Alberta Barley Commission/ ; //Alberta Wheat Commission/ ; 545088//NSERC Industrial Research Chair/ ; RGPIN-2021-02479//NSERC/ ; //Agriculture &amp; Agri-Food Canada Genomics Research and Development Initiative/ ; //Alberta Pulse Growers Commission/ ; },
mesh = {Animals ; *Salivary Glands/metabolism/enzymology ; *Larva/genetics/metabolism/growth &amp; development ; *Diptera/genetics/enzymology/metabolism ; Transcriptome ; Digestion ; Genomics ; Gastrointestinal Tract/metabolism ; Insect Proteins/metabolism/genetics ; },
abstract = {The larvae of Contarinia nasturtii (Kieffer) (Diptera: Cecidomyiidae), the swede midge, targets the meristem of brassica crops where they induce the formation of galls and disrupt seed and vegetable production. Previously, we examined the salivary gland transcriptome of newly-hatched first instar larvae as they penetrated the host and initiated gall formation. Here we examine the salivary gland and midgut transcriptome of third instar larvae and provide evidence for cooperative nutrient acquisition beginning with secretion of enzymes and feeding facilitators followed by gastrointestinal digestion. Sucrose, presumably obtained from the phloem, appeared to be a major nutrient source as several α-glucosidases (sucrases, maltases) and β-fructofuranosidases (invertases) were identified. Genes encoding β-fructofuranosidases/invertases were among the most highly expressed in both tissues and represented two distinct gene families that may have originated via horizontal gene transfer from bacteria. The importance of the phloem as a nutrient source is underscored by the expression of genes encoding regucalcin and ARMET (arginine-rich mutated in early stages of tumor) which interfere with calcium signalling and prevent sieve tube occlusion. Lipids, proteins, and starch appear to serve as a secondary nutrient sources. Genes encoding enzymes involved in the detoxification of glucosinolates (myrosinases, arylsulfatases, and glutathione-S-transferases) were expressed indicative of Brassicaceae host specialization. The midgut expressed simple peritrophins and mucins typical of those found in Type II peritrophic matrices, the first such description for a gall midge.},
}
@article {pmid39038013,
year = {2024},
author = {Berg, A and Berntsson, RP and Barandun, J},
title = {Nematocida displodere mechanosensitive ion channel of small conductance 2 assembles into a unique 6-channel super-structure in vitro.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0301951},
pmid = {39038013},
issn = {1932-6203},
mesh = {*Ion Channels/metabolism/chemistry/genetics ; *Cryoelectron Microscopy ; Animals ; Caenorhabditis elegans/metabolism/genetics ; Microsporidia/metabolism/genetics ; Mechanotransduction, Cellular ; },
abstract = {Mechanosensitive ion channels play an essential role in reacting to environmental signals and sustaining cell integrity by facilitating ion flux across membranes. For obligate intracellular pathogens like microsporidia, adapting to changes in the host environment is crucial for survival and propagation. Despite representing a eukaryote of extreme genome reduction, microsporidia have expanded the gene family of mechanosensitive ion channels of small conductance (mscS) through repeated gene duplication and horizontal gene transfer. All microsporidian genomes characterized to date contain mscS genes of both eukaryotic and bacterial origin. Here, we investigated the cryo-electron microscopy structure of the bacterially derived mechanosensitive ion channel of small conductance 2 (MscS2) from Nematocida displodere, an intracellular pathogen of Caenorhabditis elegans. MscS2 is the most compact MscS-like channel known and assembles into a unique superstructure in vitro with six heptameric MscS2 channels. Individual MscS2 channels are oriented in a heterogeneous manner to one another, resembling an asymmetric, flexible six-way cross joint. Finally, we show that microsporidian MscS2 still forms a heptameric membrane channel, however the extreme compaction suggests a potential new function of this MscS-like protein.},
}
@article {pmid39037483,
year = {2024},
author = {de Carvalho, A and Giambiagi-deMarval, M and Rossi, CC},
title = {Mammaliicoccus sciuri's Pan-Immune System and the Dynamics of Horizontal Gene Transfer Among Staphylococcaceae: a One-Health CRISPR Tale.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {62},
number = {9},
pages = {775-784},
pmid = {39037483},
issn = {1976-3794},
support = {408564/2023-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 304839/2022-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; E-26/010.000172/2016; 010.00128/2016; E-26.210.875/2016//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 101056/2018; 001463/2019; 211.554/2019; 201.071/2020//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 200.895/2021//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; E-26/204.925/2022//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; APQ-03498-22//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; 23038.002486/2018-26//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
mesh = {*Gene Transfer, Horizontal ; *CRISPR-Cas Systems ; Humans ; Animals ; *One Health ; Genome, Bacterial ; Virulence/genetics ; Phylogeny ; },
abstract = {Recently emancipated from the Staphylococcus genus due to genomic differences, Mammaliicoccus sciuri, previously classified as an occasional pathogen, emerges as a significant player in the landscape of resistance gene dissemination among Staphylococcaceae. Despite its classification, its role remained enigmatic. In this study, we delved into the genomic repertoire of M. sciuri to unravel its contribution to resistance and virulence gene transfer in the context of One Health. Through comprehensive analysis of publicly available genomes, we unveiled a diverse pan-immune system adept at defending against exogenous genetic elements, yet concurrently fostering horizontal gene transfer (HGT). Specifically, exploration of CRISPR-Cas systems, with spacer sequences as molecular signatures, elucidated a global dissemination pattern spanning environmental, animal, and human hosts. Notably, we identified the integration of CRISPR-Cas systems within SCCmecs (Staphylococcal Cassette Chromosome mec), harboring key genes associated with pathogenicity and resistance, especially the methicillin resistance gene mecA, suggesting a strategic adaptation to outcompete other mobile genetic elements. Our findings underscored M. sciuri's active engagement in HGT dynamics and evolutionary trajectories within Staphylococcaceae, emphasizing its central role in shaping microbial communities and highlighting the significance of understanding its implications in the One Health framework, an interdisciplinary approach that recognizes the interconnectedness of human, animal, and environmental health to address global health challenges.},
}
@article {pmid39035534,
year = {2024},
author = {Gheorghe-Barbu, I and Surleac, M and Barbu, IC and Paraschiv, S and Bănică, LM and Rotaru, LI and Vrâncianu, CO and Niță Lazăr, M and Oțelea, D and Chifiriuc, MC},
title = {Decoding the resistome, virulome and mobilome of clinical versus aquatic Acinetobacter baumannii in southern Romania.},
journal = {Heliyon},
volume = {10},
number = {13},
pages = {e33372},
pmid = {39035534},
issn = {2405-8440},
abstract = {Acinetobacter baumannii, a notorious opportunistic pathogen, presents a formidable challenge in both clinical and environmental fields due to its resilience and ability to acquire resistance. This study undertook a comprehensive analysis of 183 A. baumannii isolates collected between 2019 and 2022 from intra-hospital infections (IHI), hospital sewages (Hs), wastewater treatment plants (WWTP), and adjacent river waters from two Southern cities, focusing on their resistome, virulome, and mobilome through isolation on chromogenic media, identification by MALDI-TOF-MS and antibiotic susceptibility testing by disk diffusion) followed by genotypic characterization [Whole Genome Sequencing (WGS), 3rd generation sequencing through the MinION (ONT) platform, pangenome description, and respectively horizontal gene transfer through conjugation assays]. Our findings reveal significant genomic plasticity and the prevalence of high-risk international clones, underlining the potential of these isolates to act as reservoirs for antibiotic resistance genes (ARGs) that could be dynamically exchanged between clinical and environmental settings through mobile genetic elements (MGEs) such as the pMAL1 plasmids and the critical role of WWTPs in the persistence and spread of A. baumannii. Moreover, our study presents the first report of the co-occurrence of bla OXA-23 and bla OXA-72 in A. baumannii ST2 clone. Thus, our research underscores the necessity for integrated surveillance and targeted interventions across healthcare and environmental sectors to mitigate the risk posed by this adaptable pathogen.},
}
@article {pmid39030691,
year = {2024},
author = {Gan, D and Lin, Z and Zeng, L and Deng, H and Walsh, TR and Zhou, S and Yang, QE},
title = {Housefly gut microbiomes as a reservoir and facilitator for the spread of antibiotic resistance.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39030691},
issn = {1751-7370},
support = {//Science Foundation of Fujian Province/ ; //Outstanding Young Research Talents Program of Fujian Agriculture and Forestry University/ ; //National Science Foundation of China/ ; //National Key R&amp;D Program of China/ ; },
mesh = {*Houseflies/microbiology ; *Gastrointestinal Microbiome ; Animals ; *Plasmids/genetics ; Escherichia coli/genetics/drug effects ; RNA, Ribosomal, 16S/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; },
abstract = {Arthropods, such as houseflies, play a significant role in the dissemination of antimicrobial resistance (AMR); however, their impact has often been overlooked in comparison to other AMR vectors. Understanding the contribution of arthropods to the spread of AMR is critical for implementing robust policies to mitigate the spread of AMR across One Health sectors, affecting animals and environmental habitats as well as humans. In this study, we investigated the in situ transfer of a gfp-labelled AMR plasmid (IncA/C carrying an mcr-8 gene, pA/C_MCR-8) in the gut microbiota of houseflies (Musca domestica) by applying single-cell sorting, 16S rRNA gene amplicon sequencing and whole-genome sequencing. Our findings demonstrate that the pA/C_MCR-8-positive Escherichia coli donor strain is capable of colonizing the gut microbiome of houseflies and persists in the housefly intestine for 5 days; however, no transfer was detectable above the detection threshold of 10-5 per cell. The conjugative plasmid pA/C_MCR-8 demonstrated a high transfer frequency ranging from 4.1 × 10-3 to 5.0 × 10-3 per cell in vitro and exhibited transfer across various bacterial phyla, primarily encompassing Pseudomonadota and Bacillota. Phylogenic analysis has revealed that Providencia stuartii, a human opportunistic pathogen, is a notable recipient of pA/C_MCR-8. The conjugation assays further revealed that newly formed P. stuartii transconjugants readily transfer pA/C_MCR-8 to other clinically relevant pathogens (e.g. Klebsiella pneumoniae). Our findings indicate the potential transfer of AMR plasmids from houseflies to human opportunistic pathogens and further support the adoption of a One Health approach in developing infection control policies that address AMR across clinical settings.},
}
@article {pmid39030685,
year = {2024},
author = {Echeveste Medrano, MJ and Leu, AO and Pabst, M and Lin, Y and McIlroy, SJ and Tyson, GW and van Ede, J and Sánchez-Andrea, I and Jetten, MSM and Jansen, R and Welte, CU},
title = {Osmoregulation in freshwater anaerobic methane-oxidizing archaea under salt stress.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39030685},
issn = {1751-7370},
support = {VI.Vidi.223.012//NWO-VIDI/ ; FT190100211//Australian Research Council/ ; 854088//ERC/ ; 024.002.002//NWO/ ; },
mesh = {*Methane/metabolism ; *Fresh Water/microbiology ; Anaerobiosis ; *Archaea/metabolism/genetics/classification ; *Salt Stress ; *Phylogeny ; *Osmoregulation ; Oxidation-Reduction ; },
abstract = {Climate change-driven sea level rise threatens freshwater ecosystems and elicits salinity stress in microbiomes. Methane emissions in these systems are largely mitigated by methane-oxidizing microorganisms. Here, we characterized the physiological and metabolic response of freshwater methanotrophic archaea to salt stress. In our microcosm experiments, inhibition of methanotrophic archaea started at 1%. However, during gradual increase of salt up to 3% in a reactor over 12 weeks, the culture continued to oxidize methane. Using gene expression profiles and metabolomics, we identified a pathway for salt-stress response that produces the osmolyte of anaerobic methanotrophic archaea: N(ε)-acetyl-β-L-lysine. An extensive phylogenomic analysis on N(ε)-acetyl-β-L-lysine-producing enzymes revealed that they are widespread across both bacteria and archaea, indicating a potential horizontal gene transfer and a link to BORG extrachromosomal elements. Physicochemical analysis of bioreactor biomass further indicated the presence of sialic acids and the consumption of intracellular polyhydroxyalkanoates in anaerobic methanotrophs during salt stress.},
}
@article {pmid39029947,
year = {2024},
author = {Azizpour, A and Balaji, A and Treangen, TJ and Segarra, S},
title = {Graph-based self-supervised learning for repeat detection in metagenomic assembly.},
journal = {Genome research},
volume = {34},
number = {9},
pages = {1468-1476},
pmid = {39029947},
issn = {1549-5469},
mesh = {*Metagenomics/methods ; *Supervised Machine Learning ; Repetitive Sequences, Nucleic Acid ; Neural Networks, Computer ; Sequence Analysis, DNA/methods ; Algorithms ; Metagenome ; },
abstract = {Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, in which genome dynamics such as horizontal gene transfer, gene duplication, and gene loss/gain complicate accurate genome assembly from metagenomic communities. Detecting repeats is a crucial first step in overcoming these challenges. To address this issue, we propose GraSSRep, a novel approach that leverages the assembly graph's structure through graph neural networks (GNNs) within a self-supervised learning framework to classify DNA sequences into repetitive and nonrepetitive categories. Specifically, we frame this problem as a node classification task within a metagenomic assembly graph. In a self-supervised fashion, we rely on a high-precision (but low-recall) heuristic to generate pseudolabels for a small proportion of the nodes. We then use those pseudolabels to train a GNN embedding and a random forest classifier to propagate the labels to the remaining nodes. In this way, GraSSRep combines sequencing features with predefined and learned graph features to achieve state-of-the-art performance in repeat detection. We evaluate our method using simulated and synthetic metagenomic data sets. The results on the simulated data highlight GraSSRep's robustness to repeat attributes, demonstrating its effectiveness in handling the complexity of repeated sequences. Additionally, experiments with synthetic metagenomic data sets reveal that incorporating the graph structure and the GNN enhances the detection performance. Finally, in comparative analyses, GraSSRep outperforms existing repeat detection tools with respect to precision and recall.},
}
@article {pmid39028534,
year = {2024},
author = {da Rosa, EEB and Kremer, FS},
title = {The mobilome landscape of biocide-resistance in Brazilian ESKAPE isolates.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {55},
number = {4},
pages = {3603-3616},
pmid = {39028534},
issn = {1678-4405},
support = {Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
mesh = {*Disinfectants/pharmacology ; Brazil ; Humans ; *Drug Resistance, Bacterial/genetics ; Genome, Bacterial ; Computational Biology ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Whole Genome Sequencing ; *Bacteria/drug effects/genetics/isolation &amp; purification ; },
abstract = {The increasing frequency of antibiotic-resistant bacteria is a constant threat to global human health. Therefore, the pathogens of the ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Enterobacter spp.) are among the most relevant causes of hospital infections responsible for millions of deaths every year. However, little has been explored about the danger of microorganisms resistant to biocides such as antiseptics and disinfectants. Widely used in domestic, industrial, and hospital environments, these substances reach the environment and can cause selective pressure for resistance genes and induce cross-resistance to antibiotics, further aggravating the problem. Therefore, it is necessary to use innovative and efficient strategies to monitor the spread of genes related to resistance to biocides. Whole genome sequencing and bioinformatics analysis aiming to search for sequences encoding resistance mechanisms are essential to help monitor and combat these pathogens. Thus, this work describes the construction of a bioinformatics tool that integrates different databases to identify gene sequences that may confer some resistance advantage about biocides. Furthermore, the tool analyzed all the genomes of Brazilian ESKAPE isolates deposited at NCBI and found a series of different genes related to resistance to benzalkonium chloride, chlorhexidine, and triclosan, which were the focus of this work. As a result, the presence of resistance genes was identified in different types of biological samples, environments, and hosts. Regarding mobile genetic elements (MGEs), around 52% of isolates containing genes related to resistance to these compounds had their genes identified in plasmids, and 48.7% in prophages. These data show that resistance to biocides can be a silent, underestimated danger spreading across different environments and, therefore, requires greater attention.},
}
@article {pmid39025839,
year = {2024},
author = {Nowell, RW and Rodriguez, F and Hecox-Lea, BJ and Mark Welch, DB and Arkhipova, IR and Barraclough, TG and Wilson, CG},
title = {Bdelloid rotifers deploy horizontally acquired biosynthetic genes against a fungal pathogen.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {5787},
pmid = {39025839},
issn = {2041-1723},
support = {R01GM111917//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; NE/M01651X/1//RCUK | Natural Environment Research Council (NERC)/ ; R21AG046899//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; NE/J01933X/1//RCUK | Natural Environment Research Council (NERC)/ ; R01 GM111917/GM/NIGMS NIH HHS/United States ; R21 AG046899/AG/NIA NIH HHS/United States ; LTF-733-2010//European Molecular Biology Organization (EMBO)/ ; NE/S010866/1//RCUK | Natural Environment Research Council (NERC)/ ; },
mesh = {*Gene Transfer, Horizontal ; Animals ; *Rotifera/genetics/metabolism ; Biosynthetic Pathways/genetics ; Peptide Synthases/genetics/metabolism ; Polyketides/metabolism ; Phylogeny ; Multigene Family ; },
abstract = {Coevolutionary antagonism generates relentless selection that can favour genetic exchange, including transfer of antibiotic synthesis and resistance genes among bacteria, and sexual recombination of disease resistance alleles in eukaryotes. We report an unusual link between biological conflict and DNA transfer in bdelloid rotifers, microscopic animals whose genomes show elevated levels of horizontal gene transfer from non-metazoan taxa. When rotifers were challenged with a fungal pathogen, horizontally acquired genes were over twice as likely to be upregulated as other genes - a stronger enrichment than observed for abiotic stressors. Among hundreds of upregulated genes, the most markedly overrepresented were clusters resembling bacterial polyketide and nonribosomal peptide synthetases that produce antibiotics. Upregulation of these clusters in a pathogen-resistant rotifer species was nearly ten times stronger than in a susceptible species. By acquiring, domesticating, and expressing non-metazoan biosynthetic pathways, bdelloids may have evolved to resist natural enemies using antimicrobial mechanisms absent from other animals.},
}
@article {pmid39021167,
year = {2024},
author = {Barcan, AS and Barcan, RA and Vamanu, E},
title = {Genomic Insights into Bacterial Antimicrobial Resistance Transmission and Mitigation Strategies.},
journal = {Current pharmaceutical biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113892010304596240629102419},
pmid = {39021167},
issn = {1873-4316},
abstract = {The rapid emergence and global spread of antimicrobial resistance in recent years have raised significant concerns about the future of modern medicine. Superbugs and multidrugresistant bacteria have become endemic in many parts of the world, raising the specter of untreatable infections. The overuse and misuse of antimicrobials over the past 80 years have undoubtedly contributed to the development of antimicrobial resistance, placing immense pressure on healthcare systems worldwide. Nonetheless, the molecular mechanisms underlying antimicrobial resistance in bacteria have existed since ancient times. Some of these mechanisms and processes have served as the precursors of current resistance determinants, highlighting the ongoing arms race between bacteria and their antimicrobial adversaries. Moreover, the environment harbors many putative resistance genes, yet we cannot still predict which of these genes will emerge and manifest as pathogenic resistance phenotypes. The presence of antibiotics in natural habitats, even at sub-inhibitory concentrations, may provide selective pressures that favor the emergence of novel antimicrobial resistance apparatus and, thus, underscores the need for a comprehensive understanding of the factors driving the persistence and spread of antimicrobial resistance. As the development of antimicrobial strategies that evade resistance is urgently needed, a clear perception of these critical factors could ultimately pave the way for the design of innovative therapeutic targets.},
}
@article {pmid39012117,
year = {2024},
author = {Zalewska, M and Błażejewska, A and Gawor, J and Adamska, D and Goryca, K and Szeląg, M and Kalinowski, P and Popowska, M},
title = {A newly identified IncY plasmid from multi-drug-resistant Escherichia coli isolated from dairy cattle feces in Poland.},
journal = {Microbiology spectrum},
volume = {12},
number = {8},
pages = {e0087724},
pmid = {39012117},
issn = {2165-0497},
support = {2017/25/Z/NZ7/03026//National Science Centre, Poland/ ; },
mesh = {Animals ; Cattle ; *Plasmids/genetics ; *Escherichia coli/genetics/drug effects/isolation &amp; purification ; *Drug Resistance, Multiple, Bacterial/genetics ; Poland ; *Anti-Bacterial Agents/pharmacology ; *Feces/microbiology ; *Gene Transfer, Horizontal ; Whole Genome Sequencing ; Escherichia coli Infections/microbiology/veterinary ; Microbial Sensitivity Tests ; },
abstract = {UNLABELLED: Comprehensive whole-genome sequencing was performed on two multi-drug-resistant Escherichia coli strains isolated from cattle manure from a typical dairy farm in Poland in 2020. The identified strains are resistant to beta-lactams, aminoglycosides, tetracyclines, trimethoprim/sulfamethoxazole, and fluoroquinolones. The complete sequences of the harbored plasmids revealed antibiotic-resistance genes located within many mobile genetic elements (e.g., insertional sequences or transposons) and genes facilitating conjugal transfer or promoting horizontal gene transfer. These plasmids are hitherto undescribed. Similar plasmids have been identified, but not in Poland. The identified plasmids carried resistance genes, including the tetracycline resistance gene tet(A), aph family aminoglycoside resistance genes aph(3″)-lb and aph (6)-ld, beta-lactam resistance genes blaTEM-1 and blaCTX-M-15, sulfonamide resistance gene sul2, fluoroquinolone resistance gene qnrS1, and the trimethoprim resistance gene dfrA14. The characterized resistance plasmids were categorized into the IncY incompatibility group, indicating a high possibility for dissemination among the Enterobacteriaceae. While similar plasmids (99% identity) have been found in environmental and clinical samples, none have been identified in farm animals. These findings are significant within the One Health framework, as they underline the potential for antimicrobial-resistant E. coli from livestock and food sources to be transmitted to humans and vice versa. It highlights the need for careful monitoring and strategies to limit the spread of antibiotic resistance in the One Health approach.<br><br>IMPORTANCE: This study reveals the identification of new strains of antibiotic-resistant Escherichia coli in cattle manure from a dairy farm in Poland, offering critical insights into the spread of drug resistance. Through whole-genome sequencing, researchers discovered novel plasmids within these bacteria, which carry genes resistant to multiple antibiotics. These findings are particularly alarming, as these plasmids can transfer between different bacterial species, potentially escalating the spread of antibiotic resistance. This research underscores the vital connection between the health of humans, animals, and the environment, emphasizing the concept of One Health. It points to the critical need for global vigilance and strategies to curb the proliferation of antibiotic resistance. By showcasing the presence of these strains and their advanced resistance mechanisms, the study calls for enhanced surveillance and preventive actions in both agricultural practices and healthcare settings to address the imminent challenge of antibiotic-resistant bacteria.},
}
@article {pmid39012101,
year = {2024},
author = {Duran-Bedolla, J and Téllez-Sosa, J and Bocanegra-Ibarias, P and Schilmann, A and Bravo-Romero, S and Reyna-Flores, F and Villa-Reyes, T and Barrios-Camacho, H},
title = {Citrobacter spp. and Enterobacter spp. as reservoirs of carbapenemase blaNDM and blaKPC resistance genes in hospital wastewater.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {8},
pages = {e0116524},
pmid = {39012101},
issn = {1098-5336},
support = {001//CONAGUA/ ; },
mesh = {*Wastewater/microbiology ; *beta-Lactamases/genetics ; *Bacterial Proteins/genetics ; *Hospitals ; *Citrobacter/genetics/enzymology/drug effects/isolation &amp; purification ; *Enterobacter/genetics/drug effects/isolation &amp; purification/enzymology ; Anti-Bacterial Agents/pharmacology ; Mexico ; },
abstract = {UNLABELLED: Antibiotic resistance has emerged as a global threat to public health, generating a growing interest in investigating the presence of antibiotic-resistant bacteria in environments influenced by anthropogenic activities. Wastewater treatment plants in hospital serve as significant reservoirs of antimicrobial-resistant bacteria, where a favorable environment is established, promoting the proliferation and transfer of resistance genes among different bacterial species. In our study, we isolated a total of 243 strains from 5 hospital wastewater sites in Mexico, belonging to 21 distinct Gram-negative bacterial species. The presence of β-lactamase was detected in 46.9% (114/243) of the isolates, which belonging to the Enterobacteriaceae family. We identified a total of 169 β-lactamase genes; blaTEM in 33.1%, blaCTX-M in 25.4%, blaKPC in 25.4%, blaNDM 8.8%, blaSHV in 5.3%, and blaOXA-48 in 1.1% distributed in 12 different bacteria species. Among the 114 of the isolates, 50.8% were found to harbor at least one carbapenemase and were discharged into the environment. The carbapenemase blaKPC was found in six Citrobacter spp. and E. coli, while blaNDM was detected in two distinct Enterobacter spp. and E. coli. Notably, blaNDM-1 was identified in a 110 Kb IncFII conjugative plasmid in E. cloacae, E. xiangfangensis, and E. coli within the same hospital wastewater. In conclusion, hospital wastewater showed the presence of Enterobacteriaceae carrying a high frequency of carbapenemase blaKPC and blaNDM. We propose that hospital wastewater serves as reservoirs for resistance mechanism within bacterial communities and creates an optimal environment for the exchange of this resistance mechanism among different bacterial strains.<br><br>IMPORTANCE: The significance of this study lies in its findings regarding the prevalence and diversity of antibiotic-resistant bacteria and genes identified in hospital wastewater in Mexico. The research underscores the urgent need for enhanced surveillance and prevention strategies to tackle the escalating challenge of antibiotic resistance, particularly evident through the elevated frequencies of carbapenemase genes such as blaKPC and blaNDM within the Enterobacteriaceae family. Moreover, the identification of these resistance genes on conjugative plasmids highlights the potential for widespread transmission via horizontal gene transfer. Understanding the mechanisms of antibiotic resistance in hospital wastewater is crucial for developing targeted interventions aimed at reducing transmission, thereby safeguarding public health and preserving the efficacy of antimicrobial therapies.},
}
@article {pmid39011898,
year = {2024},
author = {Yuan, W and Yu, J and Li, Z},
title = {Rapid functional activation of horizontally transferred eukaryotic intron-containing genes in the bacterial recipient.},
journal = {Nucleic acids research},
volume = {52},
number = {14},
pages = {8344-8355},
pmid = {39011898},
issn = {1362-4962},
support = {2020YFA0908000//National Key Research and Development Program of China/ ; TSBICIP-CXRC-001//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project/ ; 2060302//The ability establishment of sustainable use for valuable Chinese medicine resources/ ; },
mesh = {*Gene Transfer, Horizontal ; *Introns/genetics ; *Escherichia coli/genetics ; Genes, Bacterial ; Escherichia coli Proteins/genetics/metabolism ; },
abstract = {Horizontal gene transfer has occurred across all domains of life and contributed substantially to the evolution of both prokaryotes and eukaryotes. Previous studies suggest that many horizontally transferred eukaryotic genes conferred selective advantages to bacterial recipients, but how these eukaryotic genes evolved into functional bacterial genes remained unclear, particularly how bacteria overcome the expressional barrier posed by eukaryotic introns. Here, we first confirmed that the presence of intron would inactivate the horizontally transferred gene in Escherichia coli even if this gene could be efficiently transcribed. Subsequent large-scale genetic screens for activation of gene function revealed that activation events could rapidly occur within several days of selective cultivation. Molecular analysis of activation events uncovered two distinct mechanisms how bacteria overcome the intron barrier: (i) intron was partially deleted and the resulting stop codon-removed mutation led to one intact foreign protein or (ii) intron was intactly retained but it mediated the translation initiation and the interaction of two split small proteins (derived from coding sequences up- and downstream of intron, respectively) to restore gene function. Our findings underscore the likelihood that horizontally transferred eukaryotic intron-containing genes could rapidly acquire functionality if they confer a selective advantage to the prokaryotic recipient.},
}
@article {pmid39010965,
year = {2024},
author = {Jinnai, M and Yamaguchi, T and Minh, DTN and Hoang, ON and Le Thi, H and Thanh, PN and Hoai, PH and Do, PN and Van, CD and Kumeda, Y and Hase, A and Nakayama, T},
title = {Edible river fish-derived extended-spectrum β-lactamase (ESBL)-producing Enterobacterales harboring transferable plasmids encoding bla CTX-M-15, bla CTX-M-27, and bla CTX-M-55.},
journal = {One health (Amsterdam, Netherlands)},
volume = {18},
number = {},
pages = {100685},
pmid = {39010965},
issn = {2352-7714},
abstract = {Transmission of extended-spectrum β-lactamase (ESBL) genes has increased the global prevalence of ESBL-producing bacteria, especially in developing countries. Human infection with these bacteria may be food-mediated but has not been fully elucidated. Therefore, we aimed to examine ESBL-producing bacteria in edible river fish and elucidate their potential for horizontal gene transfer. A total of 173 ESBL-producing Enterobacterales were isolated (Escherichia coli [n = 87], Klebsiella pneumoniae [n = 52], Enterobacter cloacae complex [n = 18], Citrobacter freundii complex [n = 14], Atlantibacter hermannii [n = 1] and Serratia fonticola [n = 1]) from 56 of 80 fish intestinal contents sampled. Among the bacterial bla CTX-M genotypes, bla CTX-M-55 was the most predominant, followed by bla CTX-M-15, bla CTX-M-27, and bla CTX-M-65. Furthermore, we found that ESBL-producing Enterobacterales were able to transfer their bla CTX-M genes to E. coli. In summary, our results suggest that ESBL-producing Enterobacterales transfer bla CTX-M to indigenous gut E. coli in humans, following the consumption of contaminated fish.},
}
@article {pmid39007976,
year = {2024},
author = {Zalewska, M and Błażejewska, A and Gawor, J and Adamska, D and Goryca, K and Szeląg, M and Kalinowski, P and Popowska, M},
title = {The IncC and IncX1 resistance plasmids present in multi-drug resistant Escherichia coli strains isolated from poultry manure in Poland.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {35},
pages = {47727-47741},
pmid = {39007976},
issn = {1614-7499},
support = {2017/25/Z/NZ7/03026//Narodowym Centrum Nauki/ ; },
mesh = {Animals ; *Escherichia coli/genetics/drug effects ; Poland ; *Plasmids ; *Drug Resistance, Multiple, Bacterial/genetics ; *Manure/microbiology ; *Anti-Bacterial Agents/pharmacology ; Poultry ; Chickens ; },
abstract = {The study describes the whole-genome sequencing of two antibiotic-resistant representative Escherichia coli strains, isolated from poultry manure in 2020. The samples were obtained from a commercial chicken meat production facility in Poland. The antibiotic resistance profile was characterized by co-resistance to β-lactam antibiotics, aminoglycosides, and fluoroquinolones. The three identified resistance plasmids (R-plasmids), pECmdr13.2, pECmdr13.3, and pECmdr14.1, harbored various genes conferring resistance to tetracyclines (tetR[A]) for, aminoglycoside (aph, aac, and aad families), β-lactam (blaCMY-2, blaTEM-176), sulfonamide (sul1, sul2), fluoroquinolone (qnrS1), and phenicol (floR). These plasmids, which have not been previously reported in Poland, were found to carry IS26 insertion elements, the intI1-integrase gene, and conjugal transfer genes, facilitating horizontal gene transfer. Plasmids pECmdr13.2 and pECmdr14.1 also possessed a mercury resistance gene operon related to transposon Tn6196; this promotes plasmid persistence even without antibiotic selection pressure due to co-selection mechanisms such as co-resistance. The chicken manure-derived plasmids belonged to the IncX1 (narrow host range) and IncC (broad host range) incompatibility groups. Similar plasmids have been identified in various environments, clinical isolates, and farm animals, including cattle, swine, and poultry. This study holds significant importance for the One Health approach, as it highlights the potential for antibiotic-resistant bacteria from livestock and food sources, particularly E. coli, to transfer through the food chain to humans and vice versa.},
}
@article {pmid39001714,
year = {2024},
author = {Williams, TA and Davin, AA and Szánthó, LL and Stamatakis, A and Wahl, NA and Woodcroft, BJ and Soo, RM and Eme, L and Sheridan, PO and Gubry-Rangin, C and Spang, A and Hugenholtz, P and Szöllősi, GJ},
title = {Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39001714},
issn = {1751-7370},
support = {GBMF9741//Gordon and Betty Moore Foundation/ ; 714774//European Union's Horizon 2020 Research and Innovation Programme/ ; /ERC_/European Research Council/International ; 947317//European Union's Horizon 2020 Research and Innovation Programme/ ; 735929LPI//Simons Foundation/ ; FL150100038//Australian Research Council Laureate Fellowship/ ; 812811//Simons Foundation/ ; 101087081//European Union's Horizon Europe ERA Chair Program/ ; URF150571//Royal Society University Research Fellowship/ ; },
mesh = {*Phylogeny ; *Archaea/genetics/classification ; Bacteria/genetics/classification ; Evolution, Molecular ; Genome, Bacterial ; Symbiosis ; Ecology ; },
abstract = {In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host-microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature, and oxygen use offer enormous potential for understanding the rich tapestry of microbial life.},
}
@article {pmid38992783,
year = {2024},
author = {Klimov, PB and Hubert, J and Erban, T and Alejandra Perotti, M and Braig, HR and Flynt, A and He, Q and Cui, Y},
title = {Genomic and metagenomic analyses of the domestic mite Tyrophagus putrescentiae identify it as a widespread environmental contaminant and a host of a basal, mite-specific Wolbachia lineage (supergroup Q).},
journal = {International journal for parasitology},
volume = {54},
number = {13},
pages = {661-674},
doi = {10.1016/j.ijpara.2024.07.001},
pmid = {38992783},
issn = {1879-0135},
mesh = {Animals ; *Wolbachia/genetics/isolation &amp; purification ; *Phylogeny ; Metagenomics ; Genomics ; Symbiosis ; Acaridae/genetics ; Environmental Pollutants ; Mites/microbiology/genetics ; },
abstract = {Tyrophagus putrescentiae (mould mite) is a global, microscopic trophic generalist that commonly occurs in various human-created habitats, causing allergies and damaging stored food. Its ubiquity and extraordinary ability to penetrate research samples or cultures through air currents or by active walking through tights spaces (such as treads of screw caps) may lead to sample contamination and introduction of its DNA to research materials in the laboratory. This prompts a thorough investigation into potential sequence contamination in public genomic databases. The trophic success of T. putrescentiae is primarily attributed to the symbiotic bacteria housed in specialized internal mite structures, facilitating adaptation to varied nutritional niches. However, recent work suggests that horizontal transfer of bacterial/fungal genes related to nutritional functionality may also contribute to the mite's trophic versatility. This aspect requires independent confirmation. Additionally, T. putrescentiae harbors an uncharacterized and genetically divergent bacterium, Wolbachia, displaying blocking and microbiome-modifying effects. The phylogenomic position and supergroup assignment of this bacterium are unknown. Here, we sequenced and assembled the T. putrescentiae genome, analyzed its microbiome, and performed detailed phylogenomic analyses of the mite-specific Wolbachia. We show that T. putrescentiae DNA is a substantial source of contamination of research samples. Its DNA may inadvertently be co-extracted with the DNA of the target organism, eventually leading to sequence contamination in public databases. We identified a diversity of bacterial species associated with T. putrescentiae, including those capable of rapidly developing antibiotic resistance, such as Escherichia coli. Despite the presence of diverse bacterial communities in T. putrescentiae, we did not detect any recent horizontal gene transfers in this mite species and/or in astigmatid (domestic) mites in general. Our phylogenomic analysis of Wolbachia recovered a basal, mite-specific lineage (supergroup Q) represented by two Wolbachia spp. from the mould mite and a gall-inducing plant mite. Fluorescence in situ hybridization confirmed the presence of Wolbachia inside the mould mite. The discovery of an early derivative Wolbachia lineage (supergroup Q) in two phylogenetically unrelated and ecologically dissimilar mites suggests that this endosymbiotic bacterial lineage formed a long-term association with mites. This finding provides a unique insight into the early evolution and host associations of Wolbachia. Further discoveries of Wolbachia diversity in acariform mites are anticipated.},
}
@article {pmid38992444,
year = {2024},
author = {Soni, K and Jyoti, K and Kumar, A and Chandra, R},
title = {Coexistence of multidrug resistance and ESBL encoding genes - blaTEM, blaSHV, and blaCTX-M; its amplification and dispersion in the environment via municipal wastewater treatment plant.},
journal = {Chemosphere},
volume = {362},
number = {},
pages = {142829},
doi = {10.1016/j.chemosphere.2024.142829},
pmid = {38992444},
issn = {1879-1298},
mesh = {*Wastewater/microbiology ; *beta-Lactamases/genetics ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Waste Disposal, Fluid ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Gene Transfer, Horizontal ; },
abstract = {Municipal wastewater treatment plants (MWWTPs) are a global source of antibiotic resistance genes (ARGs), collecting wastewater from a variety of sources, including hospital wastewater, domestic wastewater, runoff from agricultural and livestock farms, etc. These sources are contaminated with organic and inorganic pollutants, ARGs and antibiotic-resistant bacteria (ARB). Such pollutants aided eutrophication and encouraged bacterial growth. During bacterial growth horizontal gene transfer (HGT) and vertical gene transfer (VGT) of ARGs and extended-spectrum β-lactamase (ESBL) encoding genes may facilitate, resulting in the spread of antibiotic resistance exponentially. The current study investigated the prevalence of multidrug resistance (MDR) and ESBL encoding genes in various treatment units of MWWTP and their spread in the environment. A total of three sampling sites (BUT, BRO, and BFB) were chosen, and 33 morphologically distinct bacterial colonies were isolated. 14 of the 33 isolates tested positive for antibiotic resistance and were further tested for the coexistence of MDR and ESBL production. The selected 14 isolates showed the highest resistance to trimethoprim (85.71%), followed by ciprofloxacin, azithromycin, and ampicillin (71.42%), tetracycline (57.14%), and vancomycin, gentamicin, and colistin sulphate (50%). A total of 9 isolates (64.28%) were phenotypically positive for ESBL production (BUT2, BUT3, BUT5, BRO1, BRO2, BRO3, BRO4, BRO5 and BFB1). The molecular detection of ESBL encoding genes, i.e. blaTEM, blaSHV, and blaCTX-M was carried out. The most prevalent gene was blaTEM (69.23%), followed by blaSHV (46.15%), and blaCTX-M (23.07%). In this study, 9 isolates (64.28%) out of 14 showed the coexistence of MDR and ESBL encoding genes, namely BUT3, BUT4, BUT5, BUT6, BUT7, BRO1, BRO2, BRO4, and BFB1. The coexistence of ESBL encoding genes and resistance to other antibiotic classes exacerbates human health and the environment.},
}
@article {pmid38992349,
year = {2024},
author = {Nazir, R and Du, S and Shen, JP and Hu, HW and Wang, JT and He, JZ},
title = {Effect of meddling ARBs on ARGs dynamics in fungal infested soil and their selective dispersal along spatially distant mycelial networks.},
journal = {The Science of the total environment},
volume = {947},
number = {},
pages = {174594},
doi = {10.1016/j.scitotenv.2024.174594},
pmid = {38992349},
issn = {1879-1026},
mesh = {*Soil Microbiology ; *Fungi/physiology ; Bacteria/drug effects ; Soil/chemistry ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; },
abstract = {During the recent times, environmental antibiotic resistance genes (ARGs) and their potential transfer to other bacterial hosts of pathogenic importance are of serious concern. However, the dissemination strategies of such ARGs are largely unknown. We tested that saprotrophic soil fungi differentially enriched antibiotic resistant bacteria (ARBs) and subsequently contributed in spatial distribution of selective ARGs. Wafergen qPCR analysis of 295 different ARGs was conducted for manure treated pre-sterilized soil incubated or not with selected bacterial-fungal consortia. The qPCR assay detected unique ARGs specifically found in the mycosphere of ascomycetous and basidiomycetous fungi. Both fungi exerted potentially different selection pressures on ARBs, resulting in different patterns of ARGs dissemination (to distant places) along their respective growing fungal highways. The relative abundance of mobile genetic elements (MGEs) was significantly decreased along fungal highways compared to the respective inoculation points. Moreover, the decrease in MGEs and ARGs (along fungal highways) was more prominent over time which depicts the continuous selection pressure of growing fungi on ARBs for enrichment of particular ARGs in mycosphere. Such data also indicate the potential role of saprotrophic soil fungi to facilitate horizontal gene transfer within mycospheric environmental settings. Our study, therefore, advocates to emphasize the future investigations for such (bacteria-fungal) interactive microbial consortia for potential (spatial) dissemination of resistance determinants which may ultimately increase the exposure risks of ARGs.},
}
@article {pmid38990885,
year = {2024},
author = {Windels, A and Franceus, J and Pleiss, J and Desmet, T},
title = {CANDy: Automated analysis of domain architectures in carbohydrate-active enzymes.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0306410},
pmid = {38990885},
issn = {1932-6203},
mesh = {*Protein Domains ; Glycoside Hydrolases/chemistry/metabolism/genetics ; Catalytic Domain ; Software ; Carbohydrate Metabolism ; Carbohydrates/chemistry ; Animals ; },
abstract = {Carbohydrate-active enzymes (CAZymes) can be found in all domains of life and play a crucial role in metabolic and physiological processes. CAZymes often possess a modular structure, comprising not only catalytic domains but also associated domains such as carbohydrate-binding modules (CBMs) and linker domains. By exploring the modular diversity of CAZy families, catalysts with novel properties can be discovered and further insight in their biological functions and evolutionary relationships can be obtained. Here we present the carbohydrate-active enzyme domain analysis tool (CANDy), an assembly of several novel scripts, tools and databases that allows users to analyze the domain architecture of all protein sequences in a given CAZy family. CANDy's usability is shown on glycoside hydrolase family 48, a small yet underexplored family containing multi-domain enzymes. Our analysis reveals the existence of 35 distinct domain assemblies, including eight known architectures, with the remaining assemblies awaiting characterization. Moreover, we substantiate the occurrence of horizontal gene transfer from prokaryotes to insect orthologs and provide evidence for the subsequent removal of auxiliary domains, likely through a gene fission event. CANDy is available at https://github.com/PyEED/CANDy.},
}
@article {pmid38987681,
year = {2024},
author = {Elgayar, FA and Gouda, MK and Badran, AA and El Halfawy, NM},
title = {Pathogenomics analysis of high-risk clone ST147 multidrug-resistant Klebsiella pneumoniae isolated from a patient in Egypt.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {256},
pmid = {38987681},
issn = {1471-2180},
mesh = {*Klebsiella pneumoniae/genetics/drug effects/isolation &amp; purification/classification ; Humans ; Egypt ; *Drug Resistance, Multiple, Bacterial/genetics ; *Klebsiella Infections/microbiology/epidemiology ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; *Virulence Factors/genetics ; *Whole Genome Sequencing ; *Genome, Bacterial/genetics ; beta-Lactamases/genetics ; Bacterial Proteins/genetics ; Plasmids/genetics ; },
abstract = {BACKGROUND: The emergence of multi-drug-resistant Klebsiella pneumoniae (MDR-KP) represents a serious clinical health concern. Antibiotic resistance and virulence interactions play a significant role in the pathogenesis of K. pneumoniae infections. Therefore, tracking the clinical resistome and virulome through monitoring antibiotic resistance genes (ARG) and virulence factors in the bacterial genome using computational analysis tools is critical for predicting the next epidemic.<br><br>METHODS: In the current study, one hundred extended spectrum &#x3b2;-lactamase (ESBL)-producing clinical isolates were collected from Mansoura University Hospital, Egypt, in a six-month period from January to June 2022. One isolate was selected due to the high resistance phenotype, and the genetic features of MDR-KP recovered from hospitalized patient were investigated. Otherwise, the susceptibility to 25 antimicrobials was determined using the DL Antimicrobial Susceptibility Testing (AST) system. Whole genome sequencing (WGS) using Illumina NovaSeq 6000 was employed to provide genomic insights into K. pneumoniae WSF99 clinical isolate.<br><br>RESULTS: The isolate K. pneumoniae WSF99 was phenotypically resistant to the antibiotics under investigation via antibiotic susceptibility testing. WGS analysis revealed that WSF99 total genome length was 5.7&#xa0;Mb with an estimated 5,718 protein-coding genes and a G&#x2009;+&#x2009;C content of 56.98&#xa0;mol%. Additionally, the allelic profile of the WSF99 isolate was allocated to the high-risk clone ST147. Furthermore, diverse antibiotic resistance genes were determined in the genome that explain the high-level resistance phenotypes. Several &#x3b2;-lactamase genes, including blaCTX-M-15, blaTEM-1, blaTEM-12, blaSHV-11, blaSHV-67, and blaOXA-9, were detected in the WSF99 isolate. Moreover, a single carbapenemase gene, blaNDM-5, was predicted in the genome, positioned within a mobile cassette. In addition, other resistance genes were predicted in the genome including, aac(6')-Ib, aph(3')-VI, sul1, sul2, fosA, aadA, arr-2, qnrS1, tetA and tetC. Four plasmid replicons CoIRNAI, IncFIB(K), IncFIB(pQil), and IncR were predicted in the genome. The draft genome analysis revealed the occurrence of genetic mobile elements positioned around the ARGs, suggesting the ease of dissemination via horizontal gene transfer.<br><br>CONCLUSIONS: This study reports a comprehensive pathogenomic analysis of MDR-KP isolated from a hospitalized patient. These findings could be relevant for future studies investigating the diversity of antimicrobial resistance and virulence in Egypt.},
}
@article {pmid38986507,
year = {2024},
author = {Irusan, D and Akshay, SD and Shetty, VP and Karunasagar, I and Deekshit, VK and Rohit, A},
title = {Analysis of mcr family of colistin resistance genes in Gram-negative isolates from a tertiary care hospital in India.},
journal = {Journal of applied microbiology},
volume = {135},
number = {7},
pages = {},
doi = {10.1093/jambio/lxae172},
pmid = {38986507},
issn = {1365-2672},
support = {AMR/DHR/GIA/3/ECD-II/2020//ICMR/ ; },
mesh = {*Colistin/pharmacology ; India ; *Tertiary Care Centers ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Microbial Sensitivity Tests ; *Gram-Negative Bacteria/genetics/drug effects/isolation &amp; purification ; Drug Resistance, Multiple, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Gram-Negative Bacterial Infections/microbiology ; Plasmids/genetics ; Bacterial Proteins/genetics ; Escherichia coli/genetics/drug effects/isolation &amp; purification ; Acinetobacter baumannii/genetics/drug effects/isolation &amp; purification ; Pseudomonas aeruginosa/genetics/drug effects/isolation &amp; purification ; },
abstract = {AIM: Colistin serves as the drug of last resort for combating numerous multidrug-resistant (MDR) Gram-negative infections. Its efficacy is hampered by the prevalent issue of colistin resistance, which severely limits treatment options for critically ill patients. Identifying resistance genes is crucial for controlling resistance spread, with horizontal gene transfer being the primary mechanism among bacteria. This study aimed to assess the prevalence of plasmid-mediated mcr genes associated with colistin resistance in Gram-negative bacteria, utilizing both genotypic and phenotypic tests.<br><br>METHODS AND RESULTS: The clinical isolates (n&#xa0;=&#xa0;913) were obtained from a tertiary care center in Chennai, India. Colistin resistance was seen among Gram-negative isolates. These strains underwent screening for mcr-1, mcr-3, mcr-4, and mcr-5 genes via conventional PCR. Additionally, mcr-positive isolates were confirmed through Sanger sequencing and phenotypic testing. The bacterial isolates predominantly comprised Klebsiella pneumoniae (62.43%), Escherichia coli (19.71%), Pseudomonas aeruginosa (10.73%), and Acinetobacter baumannii (4.81%), along with other species. All isolates exhibited multidrug resistance to three or more antibiotic classes. Colistin resistance, determined via broth microdilution (BMD) using CLSI guidelines, was observed in 13.08% of the isolates studied. Notably, mcr-5 was detected in K. pneumoniae in PCR, despite its absence in Sanger sequencing and phenotypic tests (including the combined-disk test, colistin MIC in the presence of EDTA, and Zeta potential assays). This finding underscores the importance of employing multiple diagnostic approaches to accurately identify colistin resistance mechanisms.},
}
@article {pmid38986416,
year = {2024},
author = {Chi, W and Zou, Y and Qiu, T and Shi, W and Tang, L and Xu, M and Wu, H and Luan, X},
title = {Horizontal gene transfer plays a crucial role in the development of antibiotic resistance in an antibiotic-free shrimp farming system.},
journal = {Journal of hazardous materials},
volume = {476},
number = {},
pages = {135150},
doi = {10.1016/j.jhazmat.2024.135150},
pmid = {38986416},
issn = {1873-3336},
mesh = {*Gene Transfer, Horizontal ; Animals ; *Aquaculture ; *Penaeidae/microbiology/genetics ; Drug Resistance, Microbial/genetics ; Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Wastewater/microbiology ; Drug Resistance, Bacterial/genetics ; },
abstract = {Antibiotic selective pressure in aquaculture systems often results in the antibiotic resistance genes (ARGs) proliferation. Nonetheless, a paucity of data exists concerning the mechanisms of ARGs development in aquaculture systems without the influences of antibiotics. This study utilized metagenomic approaches to elucidate the dynamics and transfer mechanisms of ARGs throughout the aquaculture of Pacific white shrimp. A marked change in the resistome was observed throughout the aquaculture without antibiotics. The total ARGs relative abundance increased from 0.05 to 0.33 by day 90 of cultivation, with even higher in mixed wastewater (0.44). Both bacterial communities and mobile genetic elements play pivotal roles in the development of ARGs. Metagenome-assembled genomes showed enrichment of environmentally intrinsic ARGs on chromosomes including macB and mdtK. The plasmid-mediated horizontal transfer was recognized as a principal factor contributing to the rise of ARGs, particularly for tetG and floR, and this led to an escalation of resistance risk, peaking at a risks core of 35.43 on day 90. This study demonstrates that horizontal gene transfer plays a crucial role in ARGs development without antibiotic pressure, which can provide a theoretical foundation for controlling ARGs proliferation in aquaculture systems.},
}
@article {pmid38983623,
year = {2024},
author = {Chin, HS and Ravi Varadharajulu, N and Lin, ZH and Chen, WY and Zhang, ZH and Arumugam, S and Lai, CY and Yu, SS},
title = {Isolation, molecular identification, and genomic analysis of Mangrovibacter phragmitis strain ASIOC01 from activated sludge harboring the bioremediation prowess of glycerol and organic pollutants in high-salinity.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1415723},
pmid = {38983623},
issn = {1664-302X},
abstract = {The physiological and genotypic characteristics of Mangrovibacter (MGB) remain largely unexplored, including their distribution and abundance within ecosystems. M. phragmitis (MPH) ASIOC01 was successfully isolated from activated sludge (AS), which was pre-enriched by adding 1,3-dichloro-2-propanol and 3-chloro-1,2-propanediol as carbon sources. The new isolate, MPH ASIOC01, exhibited resilience in a medium containing sodium chloride concentration up to 11% (with optimal growth observed at 3%) and effectively utilizing glycerol as their sole carbon source. However, species delimitation of MGBs remains challenging due to high 16S rRNA sequence similarity (greater than 99% ANI) among different MGBs. In contrast, among the housekeeping gene discrepancies, the tryptophan synthase beta chain gene can serve as a robust marker for fast species delimitation among MGBs. Furthermore, the complete genome of MPH ASIOC01 was fully sequenced and circlized as a single contig using the PacBio HiFi sequencing method. Comparative genomics revealed genes potentially associated with various phenotypic features of MGBs, such as nitrogen-fixing, phosphate-solubilizing, cellulose-digesting, Cr-reducing, and salt tolerance. Computational analysis suggested that MPH ASIOC01 may have undergone horizontal gene transfer events, possibly contributing unique traits such as antibiotic resistance. Finally, our findings also disclosed that the introduction of MPH ASIOC01 into AS can assist in the remediation of wastewater chemical oxygen demand, which was evaluated using gas chromatograph-mass spectrometry. To the best of our knowledge, this study offers the most comprehensive understanding of the phenotypic and genotypic features of MGBs to date.},
}
@article {pmid38980659,
year = {2024},
author = {Poddar, BJ and Khardenavis, AA},
title = {Genomic Insights into the Landfill Microbial Community: Denitrifying Activity Supporting One-Carbon Utilization.},
journal = {Applied biochemistry and biotechnology},
volume = {196},
number = {12},
pages = {8866-8891},
pmid = {38980659},
issn = {1559-0291},
support = {EMR/2016/006589//SERB, New Delhi/ ; },
mesh = {*Denitrification ; Carbon/metabolism ; Waste Disposal Facilities ; Nitrates/metabolism ; Genome, Bacterial ; Methane/metabolism ; Enterobacter cloacae/genetics/metabolism/enzymology ; Genomics ; Bacillus subtilis/genetics/metabolism/enzymology ; Phylogeny ; Bacillus/genetics/metabolism/enzymology ; },
abstract = {In spite of the developments in understanding of denitrifying methylotrophy in the recent years, challenges still exist in unravelling the overall biochemistry of nitrate-dependent methane oxidation in novel or poorly characterized/not-yet-cultured bacteria. In the present study, landfill site was mined for novel C1-carbon-metabolizing bacteria which can use nitrate/nitrite as an electron acceptor. A high-throughput rapid plate assay identified three bacterial isolates with eminent ability for nitrate-dependent methane metabolism under anaerobic conditions. Taxonomic identification by whole-genome sequence-based overall genome relatedness indices accurately assigned the isolates AAK_M13, AAK_M29, and AAK_M39 at the species level to Enterobacter cloacae, Bacillus subtilis, and Bacillus halotolerans, respectively. Several genes encoding sub-components involved in alcohol utilization and denitrification pathways, such as adh, fdh, fdo, nar, nir, and nor, were identified in all the genomes. Though no gene clusters encoding MMO/AMO were annotated, sequencing of PCR amplicons revealed similarity with pMMO/AMO gene using translated nucleotide sequence of strains AAK_M29 and AAK_M39, while strain AAK_M13 showed similarity with XRE family transcriptional regulator. This suggests the horizontal gene transfer and/or presence of a truncated version of a housekeeping enzyme encoded by genes exhibiting partial sequence similarity with pMMO genes that mimicked its function at greenhouse gas emission sites. Owing to lack of conclusive evidence for presence of methane metabolism genes in the selected isolates, further experiment was performed to validate their nitrate-dependent methane oxidation capacities. Bacillus subtilis AAK_M29, Bacillus halotolerans AAK_M39, and Enterobacter cloacae AAK_M13 could oxidize 60%, 75%, and 85% of the added methane respectively accompanied by high nitrate reduction (56-62%) thus supporting the correlation between these two activities. The remarkable ability of these isolates for nitrate-dependent methane metabolism has highlighted their role in ecological contribution and biotechnological potential to serve as methane and nitrate sinks in the landfill sites.},
}
@article {pmid38977308,
year = {2024},
author = {Vakirlis, N and Kupczok, A},
title = {Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins.},
journal = {Genome research},
volume = {34},
number = {6},
pages = {888-903},
pmid = {38977308},
issn = {1549-5469},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Evolution, Molecular ; *Species Specificity ; Base Composition ; Phylogeny ; },
abstract = {Species-specific genes, also known as orphans, are ubiquitous across life's domains. In prokaryotes, species-specific orphan genes (SSOGs) are mostly thought to originate in external elements such as viruses followed by horizontal gene transfer, whereas the scenario of native origination, through rapid divergence or de novo, is mostly dismissed. However, quantitative evidence supporting either scenario is lacking. Here, we systematically analyzed genomes from 4644 human gut microbiome species and identified more than 600,000 unique SSOGs, representing an average of 2.6% of a given species' pangenome. These sequences are mostly rare within each species yet show signs of purifying selection. Overall, SSOGs use optimal codons less frequently, and their proteins are more disordered than those of conserved genes (i.e., non-SSOGs). Importantly, across species, the GC content of SSOGs closely matches that of conserved ones. In contrast, the ∼5% of SSOGs that share similarity to known viral sequences have distinct characteristics, including lower GC content. Thus, SSOGs with similarity to viruses differ from the remaining SSOGs, contrasting an external origination scenario for most of them. By examining the orthologous genomic region in closely related species, we show that a small subset of SSOGs likely evolved natively de novo and find that these genes also differ in their properties from the remaining SSOGs. Our results challenge the notion that external elements are the dominant source of prokaryotic genetic novelty and will enable future studies into the biological role and relevance of species-specific genes in the human gut.},
}
@article {pmid38975782,
year = {2024},
author = {Price, CTD and Hanford, HE and Al-Quadan, T and Santic, M and Shin, CJ and Da'as, MSJ and Abu Kwaik, Y},
title = {Amoebae as training grounds for microbial pathogens.},
journal = {mBio},
volume = {15},
number = {8},
pages = {e0082724},
pmid = {38975782},
issn = {2150-7511},
support = {R01 AI140195/AI/NIAID NIH HHS/United States ; R01AI140195//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {*Amoeba/virology/microbiology ; Animals ; Humans ; Symbiosis ; Gene Transfer, Horizontal ; Biological Evolution ; Host-Pathogen Interactions ; },
abstract = {Grazing of amoebae on microorganisms represents one of the oldest predator-prey dynamic relationships in nature. It represents a genetic "melting pot" for an ancient and continuous multi-directional inter- and intra-kingdom horizontal gene transfer between amoebae and its preys, intracellular microbial residents, endosymbionts, and giant viruses, which has shaped the evolution, selection, and adaptation of microbes that evade degradation by predatory amoeba. Unicellular phagocytic amoebae are thought to be the ancient ancestors of macrophages with highly conserved eukaryotic processes. Selection and evolution of microbes within amoeba through their evolution to target highly conserved eukaryotic processes have facilitated the expansion of their host range to mammals, causing various infectious diseases. Legionella and environmental Chlamydia harbor an immense number of eukaryotic-like proteins that are involved in ubiquitin-related processes or are tandem repeats-containing proteins involved in protein-protein and protein-chromatin interactions. Some of these eukaryotic-like proteins exhibit novel domain architecture and novel enzymatic functions absent in mammalian cells, such as ubiquitin ligases, likely acquired from amoebae. Mammalian cells and amoebae may respond similarly to microbial factors that target highly conserved eukaryotic processes, but mammalian cells may undergo an accidental response to amoeba-adapted microbial factors. We discuss specific examples of microbes that have evolved to evade amoeba predation, including the bacterial pathogens- Legionella, Chlamydia, Coxiella, Rickettssia, Francisella, Mycobacteria, Salmonella, Bartonella, Rhodococcus, Pseudomonas, Vibrio, Helicobacter, Campylobacter, and Aliarcobacter. We also discuss the fungi Cryptococcus, and Asperigillus, as well as amoebae mimiviruses/giant viruses. We propose that amoeba-microbe interactions will continue to be a major "training ground" for the evolution, selection, adaptation, and emergence of microbial pathogens equipped with unique pathogenic tools to infect mammalian hosts. However, our progress will continue to be highly dependent on additional genomic, biochemical, and cellular data of unicellular eukaryotes.},
}
@article {pmid38971740,
year = {2024},
author = {Bhat, A and Sharma, R and Desigan, K and Lucas, MM and Mishra, A and Bowers, RM and Woyke, T and Epstein, B and Tiffin, P and Pueyo, JJ and Paape, T},
title = {Horizontal gene transfer of the Mer operon is associated with large effects on the transcriptome and increased tolerance to mercury in nitrogen-fixing bacteria.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {247},
pmid = {38971740},
issn = {1471-2180},
support = {Quantitative Plant Science Initiative (QPSI)//U.S. Department of Energy/ ; Quantitative Plant Science Initiative (QPSI)//U.S. Department of Energy/ ; Quantitative Plant Science Initiative (QPSI)//U.S. Department of Energy/ ; Quantitative Plant Science Initiative (QPSI)//U.S. Department of Energy/ ; 3092-53000-001-00D//U.S. Department of Agriculture/ ; 3092-53000-001-00D//U.S. Department of Agriculture/ ; },
mesh = {*Gene Transfer, Horizontal ; *Mercury/metabolism/toxicity ; *Operon ; *Transcriptome ; *Symbiosis ; Nitrogen-Fixing Bacteria/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Nitrogen Fixation ; Rhizobium leguminosarum/genetics/metabolism ; Soil Microbiology ; },
abstract = {BACKGROUND: Mercury (Hg) is highly toxic and has the potential to cause severe health problems for humans and foraging animals when transported into edible plant parts. Soil rhizobia that form symbiosis with legumes may possess mechanisms to prevent heavy metal translocation from roots to shoots in plants by exporting metals from nodules or compartmentalizing metal ions inside nodules. Horizontal gene transfer has potential to confer immediate de novo adaptations to stress. We used comparative genomics of high quality de novo assemblies to identify structural differences in the genomes of nitrogen-fixing rhizobia that were isolated from a mercury (Hg) mine site that show high variation in their tolerance to Hg.<br><br>RESULTS: Our analyses identified multiple structurally conserved merA homologs in the genomes of Sinorhizobium medicae and Rhizobium leguminosarum but only the strains that possessed a Mer operon exhibited 10-fold increased tolerance to Hg. RNAseq analysis revealed nearly all genes in the Mer operon were significantly up-regulated in response to Hg stress in free-living conditions and in nodules. In both free-living and nodule environments, we found the Hg-tolerant strains with a Mer operon exhibited the fewest number of differentially expressed genes (DEGs) in the genome, indicating a rapid and efficient detoxification of Hg from the cells that reduced general stress responses to the Hg-treatment. Expression changes in S. medicae while in bacteroids showed that both rhizobia strain and host-plant tolerance affected the number of DEGs. Aside from Mer operon genes, nif genes which are involved in nitrogenase activity in S. medicae showed significant up-regulation in the most Hg-tolerant strain while inside the most Hg-accumulating host-plant. Transfer of a plasmid containing the Mer operon from the most tolerant strain to low-tolerant strains resulted in an immediate increase in Hg tolerance, indicating that the Mer operon is able to confer hyper tolerance to Hg.<br><br>CONCLUSIONS: Mer operons have not been previously reported in nitrogen-fixing rhizobia. This study demonstrates a pivotal role of the Mer operon in effective mercury detoxification and hypertolerance in nitrogen-fixing rhizobia. This finding has major implications not only for soil bioremediation, but also host plants growing in mercury contaminated soils.},
}
@article {pmid38971360,
year = {2024},
author = {Zhang, W and Geng, J and Sun, M and Jiang, C and Lin, H and Chen, H and Yang, Y},
title = {Distinct species turnover patterns shaped the richness of antibiotic resistance genes on eight different microplastic polymers.},
journal = {Environmental research},
volume = {259},
number = {},
pages = {119562},
doi = {10.1016/j.envres.2024.119562},
pmid = {38971360},
issn = {1096-0953},
mesh = {*Microplastics/toxicity ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects ; Genes, Bacterial ; },
abstract = {Elucidating the formation mechanism of plastisphere antibiotic resistance genes (ARGs) on different polymers is necessary to understand the ecological risks of plastisphere ARGs. Here, we explored the turnover and assembly mechanism of plastisphere ARGs on 8 different microplastic polymers (4 biodegradable (bMPs) and 4 non-biodegradable microplastics (nMPs)) by metagenomic sequencing. Our study revealed the presence of 479 ARGs with abundance ranging from 41.37 to 58.17 copies/16S rRNA gene in all plastispheres. These ARGs were predominantly multidrug resistance genes. The richness of plastisphere ARGs on different polymers had a significant correlation with the contribution of species turnover to plastisphere ARGs β diversity. Furthermore, polymer type was the most critical factor affecting the composition of plastisphere ARGs. More opportunistic pathogens carrying diverse ARGs on BMPs (PBAT, PBS, and PHA) with higher horizontal gene transfer potential may further magnify the ecological risks and human health threats. For example, the opportunistic pathogens Riemerella anatipestifer, Vibrio campbellii, and Vibrio cholerae are closely related to human production and life, which were the important potential hosts of many plastisphere ARGs and mobile genetic elements on BMPs. Thus, we emphasize the urgency of developing the formation mechanism of plastisphere ARGs and the necessity of controlling BMPs and ARG pollution, especially BMPs, with ever-increasing usage in daily life.},
}
@article {pmid38969684,
year = {2024},
author = {Salem, S and Abdelsalam, NA and Shata, AH and Mouftah, SF and Cobo-Díaz, JF and Osama, D and Atteya, R and Elhadidy, M},
title = {Unveiling the microevolution of antimicrobial resistance in selected Pseudomonas aeruginosa isolates from Egyptian healthcare settings: A genomic approach.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {15500},
pmid = {38969684},
issn = {2045-2322},
support = {CRP/EGY22-03//CRP-ICGEB grant/ ; },
mesh = {*Pseudomonas aeruginosa/genetics/drug effects/isolation &amp; purification ; Egypt/epidemiology ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; Pseudomonas Infections/microbiology/epidemiology ; Biofilms/drug effects/growth &amp; development ; Whole Genome Sequencing/methods ; Genomics/methods ; Genome, Bacterial ; Evolution, Molecular ; Drug Resistance, Bacterial/genetics ; Multilocus Sequence Typing ; Polymorphism, Single Nucleotide ; Drug Resistance, Multiple, Bacterial/genetics ; Phylogeny ; },
abstract = {The incidence of Pseudomonas aeruginosa infections in healthcare environments, particularly in low-and middle-income countries, is on the rise. The purpose of this study was to provide comprehensive genomic insights into thirteen P. aeruginosa isolates obtained from Egyptian healthcare settings. Phenotypic analysis of the antimicrobial resistance profile and biofilm formation were performed using minimum inhibitory concentration and microtiter plate assay, respectively. Whole genome sequencing was employed to identify sequence typing, resistome, virulome, and mobile genetic elements. Our findings indicate that 92.3% of the isolates were classified as extensively drug-resistant, with 53.85% of these demonstrating strong biofilm production capabilities. The predominant clone observed in the study was ST773, followed by ST235, both of which were associated with the O11 serotype. Core genome multi-locus sequence typing comparison of these clones with global isolates suggested their potential global expansion and adaptation. A significant portion of the isolates harbored Col plasmids and various MGEs, all of which were linked to antimicrobial resistance genes. Single nucleotide polymorphisms in different genes were associated with the development of antimicrobial resistance in these isolates. In conclusion, this pilot study underscores the prevalence of extensively drug-resistant P. aeruginosa isolates and emphasizes the role of horizontal gene transfer facilitated by a diverse array of mobile genetic elements within various clones. Furthermore, specific insertion sequences and mutations were found to be associated with antibiotic resistance.},
}
@article {pmid38968733,
year = {2024},
author = {Li, Y and Zhang, S and Chen, Z and Huang, W and Liu, Q and Fang, H and Chi, B and Yang, N and Zhang, Q},
title = {Deciphering the impact of organic loading rate and digestate recirculation on the occurrence patterns of antibiotics and antibiotic resistance genes in dry anaerobic digestion of kitchen waste.},
journal = {Water research},
volume = {261},
number = {},
pages = {122005},
doi = {10.1016/j.watres.2024.122005},
pmid = {38968733},
issn = {1879-2448},
mesh = {*Anti-Bacterial Agents/pharmacology ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; *Bioreactors ; Waste Disposal, Fluid ; },
abstract = {Organic loading rate (OLR) is crucial for determining the stability of dry anaerobic digestion (AD). Digestate recirculation contributes to reactor stability and enhances methane production. Nevertheless, the understanding of how OLR and digestate recirculation affect the abundance and diversity of antibiotics and antibiotic resistance genes (ARGs), as well as the mechanisms involved in the dissemination of ARGs, remains limited. This study thoroughly investigated this critical issue through a long-term pilot-scale experiment. The metabolome analyses revealed the enrichment of various antibiotics, such as aminoglycoside, tetracycline, and macrolide, under low OLR conditions (OLR ≤ 4.0 g·VS/L·d) and the reactor instability. Antibiotics abundance decreased by approximately 19.66-31.69 % during high OLR operation (OLR ≥ 6.0 g·VS/L·d) with digestate recirculation. The metagenome analyses demonstrated that although low OLR promoted reactor stability, it facilitated the proliferation of antibiotic-resistant bacteria, such as Pseudomonas, and triggered functional profiles related to ATP generation, oxidative stress response, EPS secretion, and cell membrane permeability, thereby facilitating horizontal gene transfer (HGT) of ARGs. However, under stable operation at an OLR of 6.0 g·VS/L·d, there was a decrease in ARGs abundance but a notable increase in human pathogenic bacteria (HPB) and mobile genetic elements (MGEs). Subsequently, during reactor instability, the abundance of ARGs and HPB increased. Notably, during digestate recirculation at OLR levels of 6.0 and 7.0 g·VS/L·d, the process attenuated the risk of ARGs spread by reducing the diversity of ARGs hosts, minimizing interactions among ARGs hosts, ARGs, and MGEs, and weakening functional profiles associated with HGT of ARGs. Overall, digestate recirculation aids in reducing the abundance of antibiotics and ARGs under high OLR conditions. These findings provide advanced insights into how OLR and digestate recirculation affect the occurrence patterns of antibiotics and ARGs in dry AD.},
}
@article {pmid38965531,
year = {2024},
author = {Babajanyan, SG and Garushyants, SK and Wolf, YI and Koonin, EV},
title = {Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {148},
pmid = {38965531},
issn = {1741-7007},
support = {Intramural Research Program//U.S. National Library of Medicine/ ; },
mesh = {*Gene Transfer, Horizontal ; *Microbiota/genetics ; Biodiversity ; Symbiosis/genetics ; Models, Theoretical ; Models, Biological ; },
abstract = {BACKGROUND: Microbiomes are generally characterized by high diversity of coexisting microbial species and strains, and microbiome composition typically remains stable across a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. Therefore, the long-term persistence of microbiome diversity calls for an explanation.<br><br>RESULTS: To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis were obtained, namely, pure competition, host-parasite relationship, and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environment.<br><br>CONCLUSIONS: The results of this modeling study show that basic phenomena that are universal in microbial communities, namely, environmental variation and HGT, provide for stabilization and persistence of microbial diversity, and emergence of ecological complexity.},
}
@article {pmid38964677,
year = {2024},
author = {Xu, G and Yang, S},
title = {Evolution of orphan and atypical histidine kinases and response regulators for microbial signaling diversity.},
journal = {International journal of biological macromolecules},
volume = {275},
number = {Pt 1},
pages = {133635},
doi = {10.1016/j.ijbiomac.2024.133635},
pmid = {38964677},
issn = {1879-0003},
mesh = {*Histidine Kinase/genetics/metabolism ; *Evolution, Molecular ; *Phylogeny ; *Signal Transduction/genetics ; Bacterial Proteins/genetics/metabolism/chemistry ; Bacteria/genetics/enzymology ; Gene Transfer, Horizontal ; },
abstract = {Two-component signaling systems (TCS) are the predominant means of microbes for sensing and responding to environmental stimuli. Typically, TCS is comprised of a sensor histidine kinase (HK) and a cognate response regulator (RR), which might have coevolved together. They usually involve the phosphoryl transfer signaling mechanism. However, there are also some orphan and atypical HK and RR homologs, and their evolutionary origins are still not very clear. They are not associated with cognate pairs or lack the conserved residues for phosphoryl transfer, but they could receive or respond to signals from other regulators. The objective of this study is to reveal the evolutionary history of these orphan and atypical HK and RR homologs. Structural, domain, sequence, and phylogenetic analyses indicated that their evolution process might undergo gene duplication, divergence, and domain shuffling. Meanwhile, lateral gene transfer might also be involved for their gene distribution. Evolution of orphan and atypical HK and RR homologs have increased their signaling diversity, which could be helpful for microbial adaption in complex environments.},
}
@article {pmid38964571,
year = {2024},
author = {Xu, C and Hu, C and Li, F and Liu, W and Xu, Y and Shi, D},
title = {Antibiotic resistance genes risks in relation to host pathogenicity and mobility in a typical hospital wastewater treatment process.},
journal = {Environmental research},
volume = {259},
number = {},
pages = {119554},
doi = {10.1016/j.envres.2024.119554},
pmid = {38964571},
issn = {1096-0953},
mesh = {*Wastewater/microbiology ; *Hospitals ; Waste Disposal, Fluid ; Bacteria/genetics/drug effects/pathogenicity ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; },
abstract = {Hospital wastewaters (HWWs) serve as critical reservoirs for disseminating antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB). However, the dynamics and noteworthy shifts of ARGs and their associated pathogenicity, mobility, and resistome risks during HWWs treatment processes remain poorly understood. Utilizing metagenomic sequencing and assembly, we identified 817 ARG subtypes conferring resistance to 20 classes of antibiotics across 18 HWW samples from influent to effluent. Genes encoding resistance to multidrug, aminoglycoside and beta_lactam were the most prevalent ARG types, reflecting patterns observed in clinical settings. On-site treatment efforts decreased the relative abundance of ARGs by 77.4% from influent to secondary sedimentation, whereas chlorine disinfection significantly increased their abundance in the final effluent. Deterministic processes primarily drove the taxonomic assembly, with Proteobacteria being the most abundant phylum and serving as the primary host for 15 ARG types. Contig-based analysis further revealed 114 pathogenic ARB, with Escherichia coli, Pseudomonas alcaligenes, and Pseudomonas aeruginosa exhibiting multidrug-resistant. The contributions of host bacteria and pathogenic ARB varied throughout wastewater treatment. In addition, 7.10%-31.0 % ARGs were flanked by mobile genetic elements (MGEs), predominantly mediated by transposase (74.1%). Notably, tnpA exhibited the highest potential for ARG dissemination, frequently co-occurring with beta-lactam resistance genes (35.2%). Considering ARG profiles, pathogenic hosts, and transferability, raw influent exhibited the highest antibiotic resistome risk index (ARRI), followed by the final effluent. Chlorine disinfection exacerbated resistome risks by inducing potential pathogenic ARB and mobile ARGs, posing threats to the receiving environment. This study delineates ARG occurrence patterns, highlights mechanisms of ARG carriage and horizontal gene transfer, and provides insights for assessing resistance risks and prioritizing interventions in clinical settings.},
}
@article {pmid38964386,
year = {2024},
author = {Shi, J and Sun, C and An, T and Jiang, C and Mei, S and Lv, B},
title = {Unraveling the effect of micro/nanoplastics on the occurrence and horizontal transfer of environmental antibiotic resistance genes: Advances, mechanisms and future prospects.},
journal = {The Science of the total environment},
volume = {947},
number = {},
pages = {174466},
doi = {10.1016/j.scitotenv.2024.174466},
pmid = {38964386},
issn = {1879-1026},
mesh = {*Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Microplastics ; Anti-Bacterial Agents ; Bacteria/drug effects ; Genes, Bacterial ; },
abstract = {Microplastics can not only serve as vectors of antibiotic resistance genes (ARGs), but also they and even nanoplastics potentially affect the occurrence of ARGs in indigenous environmental microorganisms, which have aroused great concern for the development of antibiotic resistance. This article specifically reviews the effects of micro/nanoplastics (concentration, size, exposure time, chemical additives) and their interactions with other pollutants on environmental ARGs dissemination. The changes of horizontal genes transfer (HGT, i.e., conjugation, transformation and transduction) of ARGs caused by micro/nanoplastics were also summarized. Further, this review systematically sums up the mechanisms of micro/nanoplastics regulating HGT process of ARGs, including reactive oxygen species production, cell membrane permeability, transfer-related genes expression, extracellular polymeric substances production, and ARG donor-recipient adsorption/contaminants adsorption/biofilm formation. The underlying mechanisms in changes of bacterial communities induced by micro/nanoplastics were also discussed as it was an important factor for structuring the profile of ARGs in the actual environment, including causing environmental stress, providing carbon sources, forming biofilms, affecting pollutants distribution and environmental factors. This review contributes to a systematical understanding of the potential risks of antibiotic resistance dissemination caused by micro/nanoplastics and provokes thinking about perspectives for future research and the management of micro/nanoplastics and plastics.},
}
@article {pmid38964320,
year = {2024},
author = {Kadibalban, AS and Landan, G and Dagan, T},
title = {The extent and characteristics of DNA transfer between plasmids and chromosomes.},
journal = {Current biology : CB},
volume = {34},
number = {14},
pages = {3189-3200.e5},
doi = {10.1016/j.cub.2024.06.030},
pmid = {38964320},
issn = {1879-0445},
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Chromosomes, Bacterial/genetics ; Bacteria/genetics ; DNA, Bacterial/genetics ; },
abstract = {Plasmids are extrachromosomal genetic elements that reside in prokaryotes. The acquisition of plasmids encoding beneficial traits can facilitate short-term survival in harsh environmental conditions or long-term adaptation of new ecological niches. Due to their ability to transfer between cells, plasmids are considered agents of gene transfer. Nonetheless, the frequency of DNA transfer between plasmids and chromosomes remains understudied. Using a novel approach for detection of homologous loci between genome pairs, we uncover gene sharing with the chromosome in 1,974 (66%) plasmids residing in 1,016 (78%) taxonomically diverse isolates. The majority of homologous loci correspond to mobile elements, which may be duplicated in the host chromosomes in tens of copies. Neighboring shared genes often encode similar functional categories, indicating the transfer of multigene functional units. Rare transfer events of antibiotics resistance genes are observed mainly with mobile elements. The frequent erosion of sequence similarity in homologous regions indicates that the transferred DNA is often devoid of function. DNA transfer between plasmids and chromosomes thus generates genetic variation that is akin to workings of endosymbiotic gene transfer in eukaryotic evolution. Our findings imply that plasmid contribution to gene transfer most often corresponds to transfer of the plasmid entity rather than transfer of protein-coding genes between plasmids and chromosomes.},
}
@article {pmid38963857,
year = {2024},
author = {Weimann, A and Dinan, AM and Ruis, C and Bernut, A and Pont, S and Brown, K and Ryan, J and Santos, L and Ellison, L and Ukor, E and Pandurangan, AP and Krokowski, S and Blundell, TL and Welch, M and Blane, B and Judge, K and Bousfield, R and Brown, N and Bryant, JM and Kukavica-Ibrulj, I and Rampioni, G and Leoni, L and Harrison, PT and Peacock, SJ and Thomson, NR and Gauthier, J and Fothergill, JL and Levesque, RC and Parkhill, J and Floto, RA},
title = {Evolution and host-specific adaptation of Pseudomonas aeruginosa.},
journal = {Science (New York, N.Y.)},
volume = {385},
number = {6704},
pages = {eadi0908},
doi = {10.1126/science.adi0908},
pmid = {38963857},
issn = {1095-9203},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Cystic Fibrosis/microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Host Adaptation ; Host Specificity ; Macrophages/microbiology/immunology ; *Pseudomonas aeruginosa/genetics/pathogenicity ; *Pseudomonas Infections/microbiology ; Host-Pathogen Interactions ; },
abstract = {The major human bacterial pathogen Pseudomonas aeruginosa causes multidrug-resistant infections in people with underlying immunodeficiencies or structural lung diseases such as cystic fibrosis (CF). We show that a few environmental isolates, driven by horizontal gene acquisition, have become dominant epidemic clones that have sequentially emerged and spread through global transmission networks over the past 200 years. These clones demonstrate varying intrinsic propensities for infecting CF or non-CF individuals (linked to specific transcriptional changes enabling survival within macrophages); have undergone multiple rounds of convergent, host-specific adaptation; and have eventually lost their ability to transmit between different patient groups. Our findings thus explain the pathogenic evolution of P. aeruginosa and highlight the importance of global surveillance and cross-infection prevention in averting the emergence of future epidemic clones.},
}
@article {pmid38962965,
year = {2024},
author = {Diamant, I and Adani, B and Sylman, M and Rahav, G and Gal-Mor, O},
title = {The transcriptional regulation of the horizontally acquired iron uptake system, yersiniabactin and its contribution to oxidative stress tolerance and pathogenicity of globally emerging salmonella strains.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2369339},
pmid = {38962965},
issn = {1949-0984},
mesh = {Animals ; *Oxidative Stress ; *Iron/metabolism ; Mice ; *Bacterial Proteins/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; *Salmonella enterica/genetics/metabolism/pathogenicity ; Virulence/genetics ; Phenols/metabolism ; Thiazoles/metabolism ; Humans ; Salmonella Infections/microbiology ; Gene Transfer, Horizontal ; Female ; Virulence Factors/genetics/metabolism ; Plasmids/genetics ; },
abstract = {The bacterial species Salmonella enterica (S. enterica) is a highly diverse pathogen containing more than 2600 distinct serovars, which can infect a wide range of animal and human hosts. Recent global emergence of multidrug resistant strains, from serovars Infantis and Muenchen is associated with acquisition of the epidemic megaplasmid, pESI that augments antimicrobial resistance and pathogenicity. One of the main pESI's virulence factors is the potent iron uptake system, yersiniabactin encoded by fyuA, irp2-irp1-ybtUTE, ybtA, and ybtPQXS gene cluster. Here we show that yersiniabactin, has an underappreciated distribution among different S. enterica serovars and subspecies, integrated in their chromosome or carried by different conjugative plasmids, including pESI. While the genetic organization and the coding sequence of the yersiniabactin genes are generally conserved, a 201-bp insertion sequence upstream to ybtA, was identified in pESI. Despite this insertion, pESI-encoded yersiniabactin is regulated by YbtA and the ancestral Ferric Uptake Regulator (Fur), which binds directly to the ybtA and irp2 promoters. Furthermore, we show that yersiniabactin genes are specifically induced during the mid-late logarithmic growth phase and in response to iron-starvation or hydrogen peroxide. Concurring, yersiniabactin was found to play a previously unknown role in oxidative stress tolerance and to enhance intestinal colonization of S. Infantis in mice. These results indicate that yersiniabactin contributes to Salmonella fitness and pathogenicity in vivo and is likely to play a role in the rapid dissemination of pESI among globally emerging Salmonella lineages.},
}
@article {pmid38962322,
year = {2024},
author = {Sobh, G and Araj, GF and Finianos, M and Sourenian, T and Hrabak, J and Pappagianitsis, CC and Chaar, ME and Bitar, I},
title = {Molecular characterization of carbapenem and ceftazidime-avibactam-resistant Enterobacterales and horizontal spread of bla NDM-5 gene at a Lebanese medical center.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1407246},
pmid = {38962322},
issn = {2235-2988},
mesh = {*Ceftazidime/pharmacology ; *Azabicyclo Compounds/pharmacology ; Humans ; Lebanon ; *beta-Lactamases/genetics/metabolism ; *Klebsiella pneumoniae/genetics/drug effects ; *Whole Genome Sequencing ; *Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics/drug effects ; *Carbapenems/pharmacology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Drug Combinations ; Plasmids/genetics ; Microbial Sensitivity Tests ; Gene Transfer, Horizontal ; Genome, Bacterial ; Carbapenem-Resistant Enterobacteriaceae/genetics/drug effects/isolation &amp; purification ; Bacterial Proteins/genetics/metabolism ; Tertiary Care Centers ; },
abstract = {INTRODUCTION: In the battle against multidrug-resistant bacterial infections, ceftazidime- avibactam (CZA) stands as a pivotal defense, particularly against carbapenemresistant (CR) Gram-negative pathogens. However, the rise in resistance against this drug poses a significant threat to its effectiveness, highlighting the critical need for in-depth studies about its resistance mechanisms.<br><br>METHODS: This research focuses on the genomic characterization of CR- and CZA-resistant Escherichia coli (n=26) and Klebsiella pneumoniae (n=34) strains, harboring the blaNDM and/or blaOXA-48-like genes, at a major Lebanese tertiary care medical center, using whole genome sequencing (WGS).<br><br>RESULTS: Our findings revealed a notable prevalence of blaNDM in all K. pneumoniae strains isolates, with 27 of these also harboring blaOXA-48. On the other hand, E. coli strains predominantly carried the blaNDM-5 gene. Whole genome sequencing (WGS) identified a predominance of ST383 among K. pneumoniae strains, which possessed a multi-replicon IncFIB-IncHI1B plasmid harboring the blaNDM-5. Additionally, various Inc group plasmids in K. pneumoniae across multiple sequence types were found to carry the blaNDM. Similarly, diverse STs of E. coli were observed to carry blaNDM-5 on different plasmids.<br><br>DISCUSSION: The study underscores NDM carbapenemases as a paramount resistance mechanism in Lebanon,jeopardizing critical last-resort treatments. It also illuminates the role of varied sequence types and mobile genetic elements in the spread of NDM resistance,stressing the urgent need for strategies to mitigate this threat, especially in nosocomial infections.},
}
@article {pmid38961341,
year = {2024},
author = {Yang, Y and Zhou, P and Tian, D and Wang, W and Zhou, Y and Jiang, X},
title = {CRISPR-Cas3 and type I restriction-modification team up against blaKPC-IncF plasmid transfer in Klebsiella pneumoniae.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {240},
pmid = {38961341},
issn = {1471-2180},
support = {82102439//National Natural Science Foundation of China/ ; 82202564//National Natural Science Foundation of China/ ; 82172315//National Natural Science Foundation of China/ ; 22YF1437500//Shanghai Sailing Program/ ; },
mesh = {*Klebsiella pneumoniae/genetics ; *Plasmids/genetics ; *CRISPR-Cas Systems ; *Conjugation, Genetic ; beta-Lactamases/genetics ; DNA Restriction-Modification Enzymes/genetics ; China ; Klebsiella Infections/microbiology ; Gene Transfer, Horizontal ; Humans ; Genome, Bacterial/genetics ; },
abstract = {OBJECTIVE: We explored whether the Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas and restriction-modification (R-M) systems are compatible and act together to resist plasmid attacks.<br><br>METHODS: 932 global whole-genome sequences from GenBank, and 459 K. pneumoniae isolates from six provinces of China, were collected to investigate the co-distribution of CRISPR-Cas, R-M systems, and blaKPC plasmid. Conjugation and transformation assays were applied to explore the anti-plasmid function of CRISPR and R-M systems.<br><br>RESULTS: We found a significant inverse correlation between the presence of CRISPR and R-M systems and blaKPC plasmids in K. pneumoniae, especially when both systems cohabited in one host. The multiple matched recognition sequences of both systems in blaKPC-IncF plasmids (97%) revealed that they were good targets for both systems. Furthermore, the results of conjugation assay demonstrated that CRISPR-Cas and R-M systems in K. pneumoniae could effectively hinder blaKPC plasmid invasion. Notably, CRISPR-Cas and R-M worked together to confer a 4-log reduction in the acquisition of blaKPC plasmid in conjugative events, exhibiting robust synergistic anti-plasmid immunity.<br><br>CONCLUSIONS: Our results indicate the synergistic role of CRISPR and R-M in regulating horizontal gene transfer in K. pneumoniae and rationalize the development of antimicrobial strategies that capitalize on the immunocompromised status of KPC-KP.},
}
@article {pmid38960277,
year = {2025},
author = {Li, W and Wang, Y and Zhao, K and Xu, L and Shi, T and Ma, B and Lv, X},
title = {Host-virus coevolution drives soil microbial function succession along a millennium land reclamation chronosequence.},
journal = {Journal of advanced research},
volume = {71},
number = {},
pages = {297-306},
doi = {10.1016/j.jare.2024.06.022},
pmid = {38960277},
issn = {2090-1224},
mesh = {*Soil Microbiology ; Metagenome ; *Host Microbial Interactions/genetics ; Virome/genetics ; Gene Transfer, Horizontal ; *DNA Viruses/genetics ; Soil/chemistry ; },
abstract = {INTRODUCTION: Gene exchange between viruses and hosts plays an important role in driving virus-host coevolution, enabling adaptation of both viruses and hosts to environmental changes. However, the mechanisms and functional significance of virus-host gene exchanges over long-term scales remain largely unexplored.<br><br>OBJECTIVE: The present study aimed to gain insights into the role of viruses in virus-host interactions and coevolution by monitoring virome dynamics along a millennium-long land reclamation chronosequence.<br><br>METHODS: We collected 24 soil samples from 8 stages of a millennium-long land reclamation chronosequence, including non-reclamation, and reclamation periods of 10, 50, 100, 300, 500, 700, and 1000&#xa0;years. We characterized their metagenomes, and identified DNA viruses within these metagenomes.<br><br>RESULTS: Our findings reveal a significant shift in viral community composition after 50&#xa0;years of land reclamation, but soil viral diversity reached a stable phase approximately 300&#xa0;years after the initial reclamation. Analysis of the virus-host network showed a scale-free degree distribution and a reduction in complexity over time, with generalist viruses emerging as key facilitators of horizontal gene transfer.<br><br>CONCLUSION: These findings highlight the integral role of viruses, especially generalist types, in mediating gene exchanges between viruses and hosts, thereby influencing the coevolutionary dynamics in soil ecosystems over significant timescales. This study offers novel insights into long-term virus-host interactions, showing how the virome responds to environmental changes, driving shifts in various microbial functions in reclaimed land.},
}
@article {pmid38949703,
year = {2024},
author = {Saula, AY and Knight, G and Bowness, R},
title = {Within-Host Mathematical Models of Antibiotic Resistance.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2833},
number = {},
pages = {79-91},
pmid = {38949703},
issn = {1940-6029},
mesh = {*Bacteria/genetics/drug effects ; Humans ; *Gene Transfer, Horizontal ; Drug Resistance, Microbial/genetics ; Models, Theoretical ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Host-Pathogen Interactions/genetics ; },
abstract = {Mathematical models have been used to study the spread of infectious diseases from person to person. More recently studies are developing within-host modeling which provides an understanding of how pathogens-bacteria, fungi, parasites, or viruses-develop, spread, and evolve inside a single individual and their interaction with the host's immune system.Such models have the potential to provide a more detailed and complete description of the pathogenesis of diseases within-host and identify other influencing factors that may not be detected otherwise. Mathematical models can be used to aid understanding of the global antibiotic resistance (ABR) crisis and identify new ways of combating this threat.ABR occurs when bacteria respond to random or selective pressures and adapt to new environments through the acquisition of new genetic traits. This is usually through the acquisition of a piece of DNA from other bacteria, a process called horizontal gene transfer (HGT), the modification of a piece of DNA within a bacterium, or through. Bacteria have evolved mechanisms that enable them to respond to environmental threats by mutation, and horizontal gene transfer (HGT): conjugation; transduction; and transformation. A frequent mechanism of HGT responsible for spreading antibiotic resistance on the global scale is conjugation, as it allows the direct transfer of mobile genetic elements (MGEs). Although there are several MGEs, the most important MGEs which promote the development and rapid spread of antimicrobial resistance genes in bacterial populations are plasmids and transposons. Each of the resistance-spread-mechanisms mentioned above can be modeled allowing us to understand the process better and to define strategies to reduce resistance.},
}
@article {pmid38948848,
year = {2024},
author = {Lv, C and Abdullah, M and Chen, W and Zhou, N and Cheng, Z and Chen, Y and Li, M and Simpson, KW and Elsaadi, A and Zhu, Y and Lipkin, SM and Chang, YF},
title = {Genomic characterization of Escherichia coli harbor a polyketide synthase (pks) island associated with colorectal cancer (CRC) development.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.06.16.599199},
pmid = {38948848},
issn = {2692-8205},
abstract = {The E. coli strain harboring the polyketide synthase (Pks) island encodes the genotoxin colibactin, a secondary metabolite reported to have severe implications for human health and for the progression of colorectal cancer. The present study involved whole-genome-wide comparison and phylogenetic analysis of pks harboring E. coli isolates to gain insight into the distribution and evolution of these organism. Fifteen E. coli strains isolated from patients with ulcerative colitis were sequenced, 13 of which harbored pks islands. In addition, 2,654 genomes from the public database were also screened for pks harboring E. coli genomes, 158 of which were pks -positive isolates. Whole-genome-wide comparison and phylogenetic analysis revealed that 171 (158+13) pks -positive isolates belonged to phylogroup B2, and most of the isolates associated to sequence types ST73 and ST95. One isolate from an ulcerative colitis (UC) patient was of the sequence type ST8303. The maximum likelihood tree based on the core genome of pks -positive isolates revealed horizontal gene transfer across sequence types and serotypes. Virulome and resistome analyses revealed the preponderance of virulence genes and a reduced number of antimicrobial genes in Pks -positive isolates. This study strongly contributes to understanding the evolution of pks islands in E. coli .},
}
@article {pmid38947372,
year = {2024},
author = {Gómez-Gaviria, M and Contreras-López, LM and Aguilera-Domínguez, JI and Mora-Montes, HM},
title = {Strategies of Pharmacological Repositioning for the Treatment of Medically Relevant Mycoses.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {2641-2658},
pmid = {38947372},
issn = {1178-6973},
abstract = {Fungal infections represent a worldwide concern for public health, due to their prevalence and significant increase in cases each year. Among the most frequent mycoses are those caused by members of the genera Candida, Cryptococcus, Aspergillus, Histoplasma, Pneumocystis, Mucor, and Sporothrix, which have been treated for years with conventional antifungal drugs, such as flucytosine, azoles, polyenes, and echinocandins. However, these microorganisms have acquired the ability to evade the mechanisms of action of these drugs, thus hindering their treatment. Among the most common evasion mechanisms are alterations in sterol biosynthesis, modifications of drug transport through the cell wall and membrane, alterations of drug targets, phenotypic plasticity, horizontal gene transfer, and chromosomal aneuploidies. Taking into account these problems, some research groups have sought new therapeutic alternatives based on drug repositioning. Through repositioning, it is possible to use existing pharmacological compounds for which their mechanism of action is already established for other diseases, and thus exploit their potential antifungal activity. The advantage offered by these drugs is that they may be less prone to resistance. In this article, a comprehensive review was carried out to highlight the most relevant repositioning drugs to treat fungal infections. These include antibiotics, antivirals, anthelmintics, statins, and anti-inflammatory drugs.},
}
@article {pmid38946899,
year = {2024},
author = {Ji, J and Zhu, Y and Zhao, F and Zhang, J and Yao, B and Zhu, M and Yu, Y and Zhang, J and Fu, Y},
title = {Co-colonization of different species harboring KPC or NDM carbapenemase in the same host gut: insight of resistance evolution by horizontal gene transfer.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1416454},
pmid = {38946899},
issn = {1664-302X},
abstract = {INTRODUCTION: The dissemination of carbapenem-resistant Enterobacteriales (CRE) in nosocomial settings is primarily associated with the horizontal transfer of plasmids. However, limited research has focused on the in-host transferability of carbapenem resistance. In this study, ten isolates were collected from gut specimens of five individuals, each hosting two different species, including Escherichia coli, Klebsiella pneumoniae, Klebsiella aerogenes, Enterobacter cloacae, or Citrobacter koseri.<br><br>METHODS: Species identification and antimicrobial susceptibility were determined by MALDI-TOF MS and broth microdilution method. Carbapenemase genes were detected and localized using PCR, S1-PFGE and southern blot. The transferability of carbapenemase genes between species was investigated through filter mating experiments, and the genetic contexts of the plasmids were analyzed using whole genome sequencing.<br><br>RESULTS AND DISCUSSION: Our results revealed that each of the ten isolates harbored a carbapenemase gene, including bla NDM-5, bla NDM-1, or bla KPC-2, on a plasmid. Five different plasmids were successfully transferred to recipient cells of E. coli, K. pneumoniae or A. baumannii by transconjugation. The genetic contexts of the carbapenemase gene were remarkably similar between the two CRE isolates from each individual. This study highlights the potential for interspecies plasmid transmission in human gut, emphasizing the colonization of CRE as a significant risk factor for the dissemination of carbapenemase genes within the host. These findings underscore the need for appropriate intestinal CRE screening and colonization prevention.},
}
@article {pmid38944065,
year = {2024},
author = {Marchetti, A and Orlando, M and Bombardi, L and Fusco, S and Mangiagalli, M and Lotti, M},
title = {Evolutionary history and activity towards oligosaccharides and polysaccharides of GH3 glycosidases from an Antarctic marine bacterium.},
journal = {International journal of biological macromolecules},
volume = {275},
number = {Pt 1},
pages = {133449},
doi = {10.1016/j.ijbiomac.2024.133449},
pmid = {38944065},
issn = {1879-0003},
mesh = {*Glycoside Hydrolases/metabolism/genetics/chemistry ; Substrate Specificity ; *Oligosaccharides/metabolism ; Antarctic Regions ; *Evolution, Molecular ; Polysaccharides/metabolism/chemistry ; Phylogeny ; Marinomonas/enzymology/genetics ; Aquatic Organisms/enzymology ; Enzyme Stability ; Catalytic Domain ; Hydrolysis ; },
abstract = {Glycoside hydrolases (GHs) are pivotal in the hydrolysis of the glycosidic bonds of sugars, which are the main carbon and energy sources. The genome of Marinomonas sp. ef1, an Antarctic bacterium, contains three GHs belonging to family 3. These enzymes have distinct architectures and low sequence identity, suggesting that they originated from separate horizontal gene transfer events. M-GH3_A and M-GH3_B, were found to differ in cold adaptation and substrate specificity. M-GH3_A is a bona fide cold-active enzyme since it retains 20 % activity at 10 °C and exhibits poor long-term thermal stability. On the other hand, M-GH3_B shows mesophilic traits with very low activity at 10 °C (< 5 %) and higher long-term thermal stability. Substrate specificity assays highlight that M-GH3_A is a promiscuous β-glucosidase mainly active on cellobiose and cellotetraose, whereas M-GH3_B is a β-xylosidase active on xylan and arabinoxylan. Structural analysis suggests that such functional differences are due to their differently shaped active sites. The active site of M-GH3_A is wider but has a narrower entrance compared to that of M-GH3_B. Genome-based prediction of metabolic pathways suggests that Marinomonas sp. ef1 can use monosaccharides derived from the GH3-catalyzed hydrolysis of oligosaccharides either as a carbon source or for producing osmolytes.},
}
@article {pmid38942826,
year = {2024},
author = {Boukouvala, S and Kontomina, E and Olbasalis, I and Patriarcheas, D and Tzimotoudis, D and Arvaniti, K and Manolias, A and Tsatiri, MA and Basdani, D and Zekkas, S},
title = {Insights into the genomic and functional divergence of NAT gene family to serve microbial secondary metabolism.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {14905},
pmid = {38942826},
issn = {2045-2322},
support = {3712//Hellenic Foundation for Research and Innovation (H.F.R.I.)/ ; MIS-5000432//State Scholarships Foundation (&#x399;&#x39a;&#x3a5;)/ ; },
mesh = {*Multigene Family ; *Secondary Metabolism/genetics ; *Bacteria/genetics/metabolism ; Archaea/genetics/metabolism ; Phylogeny ; Arylamine N-Acetyltransferase/genetics/metabolism ; Fungi/genetics ; Genomics/methods ; Gene Transfer, Horizontal ; },
abstract = {Microbial NAT enzymes, which employ acyl-CoA to acylate aromatic amines and hydrazines, have been well-studied for their role in xenobiotic metabolism. Some homologues have also been linked to secondary metabolism, but this function of NAT enzymes is not as well-known. For this comparative study, we surveyed sequenced microbial genomes to update the list of formally annotated NAT genes, adding over 4000 new sequences (mainly bacterial, but also archaeal, fungal and protist) and portraying a broad but not universal distribution of NATs in the microbiocosmos. Localization of NAT sequences within microbial gene clusters was not a rare finding, and this association was evident across all main types of biosynthetic gene clusters (BGCs) implicated in secondary metabolism. Interrogation of the MIBiG database for experimentally characterized clusters with NAT genes further supports that secondary metabolism must be a major function for microbial NAT enzymes and should not be overlooked by researchers in the field. We also show that NAT sequences can be associated with bacterial plasmids potentially involved in horizontal gene transfer. Combined, our computational predictions and MIBiG literature findings reveal the extraordinary functional diversification of microbial NAT genes, prompting further research into their role in predicted BGCs with as yet uncharacterized function.},
}
@article {pmid38942024,
year = {2024},
author = {Harder, CB and Miyauchi, S and Virágh, M and Kuo, A and Thoen, E and Andreopoulos, B and Lu, D and Skrede, I and Drula, E and Henrissat, B and Morin, E and Kohler, A and Barry, K and LaButti, K and Salamov, A and Lipzen, A and Merényi, Z and Hegedüs, B and Baldrian, P and Stursova, M and Weitz, H and Taylor, A and Koriabine, M and Savage, E and Grigoriev, IV and Nagy, LG and Martin, F and Kauserud, H},
title = {Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations.},
journal = {Cell genomics},
volume = {4},
number = {7},
pages = {100586},
pmid = {38942024},
issn = {2666-979X},
mesh = {*Genome, Fungal/genetics ; *Agaricales/genetics ; Phylogeny ; DNA Transposable Elements/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Plants/microbiology/genetics ; },
abstract = {Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.},
}
@article {pmid38942019,
year = {2024},
author = {Mason, B and Hayward, DC and Moya, A and Cooke, I and Sorenson, A and Brunner, R and Andrade, N and Huerlimann, R and Bourne, DG and Schaeffer, P and Grinblat, M and Ravasi, T and Ueda, N and Tang, SL and Ball, EE and Miller, DJ},
title = {Microbiome manipulation by corals and other Cnidaria via quorum quenching.},
journal = {Current biology : CB},
volume = {34},
number = {14},
pages = {3226-3232.e5},
doi = {10.1016/j.cub.2024.05.073},
pmid = {38942019},
issn = {1879-0445},
mesh = {Animals ; *Anthozoa/microbiology/immunology/physiology ; *Quorum Sensing ; *Microbiota ; Cnidaria/physiology/genetics ; Coral Reefs ; Acyl-Butyrolactones/metabolism ; },
abstract = {A dynamic mucous layer containing numerous micro-organisms covers the surface of corals and has multiple functions including both removal of sediment and "food gathering."[1] It is likely to also act as the primary barrier to infection; various proteins and compounds with antimicrobial activity have been identified in coral mucus, though these are thought to be largely or exclusively of microbial origin. As in Hydra,[2] anti-microbial peptides (AMPs) are likely to play major roles in regulating the microbiomes of corals.[3][,][4] Some eukaryotes employ a complementary but less obvious approach to manipulate their associated microbiome by interfering with quorum signaling, effectively preventing bacteria from coordinating gene expression across a population. Our investigation of immunity in the reef-building coral Acropora millepora,[5] however, led to the discovery of a coral gene referred to here as AmNtNH1 that can inactivate a range of acyl homoserine lactones (AHLs), common bacterial quorum signaling molecules, and is induced on immune challenge of adult corals and expressed during the larval settlement process. Closely related proteins are widely distributed within the Scleractinia (hard corals) and some other cnidarians, with multiple paralogs in Acropora, but their closest relatives are bacterial, implying that these are products of one or more lateral gene transfer events post-dating the cnidarian-bilaterian divergence. The deployment by corals of genes used by bacteria to compete with other bacteria reflects a mechanism of microbiome manipulation previously unknown in Metazoa but that may apply more generally.},
}
@article {pmid38941922,
year = {2024},
author = {Li, B and Ni, S and Liu, Y and Lin, J and Wang, X},
title = {The histone-like nucleoid-structuring protein encoded by the plasmid pMBL6842 regulates both plasmid stability and host physiology of Pseudoalteromonas rubra SCSIO 6842.},
journal = {Microbiological research},
volume = {286},
number = {},
pages = {127817},
doi = {10.1016/j.micres.2024.127817},
pmid = {38941922},
issn = {1618-0623},
mesh = {*Plasmids/genetics ; *Bacterial Proteins/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; *Pseudoalteromonas/genetics/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Conjugation, Genetic ; Histones/metabolism/genetics ; },
abstract = {Plasmids orchestrate bacterial adaptation across diverse environments and facilitate lateral gene transfer within bacterial communities. Their presence can perturb host metabolism, creating a competitive advantage for plasmid-free cells. Plasmid stability hinges on efficient replication and partition mechanisms. While plasmids commonly encode histone-like nucleoid-structuring (H-NS) family proteins, the precise influence of plasmid-encoded H-NS proteins on stability remains elusive. In this study, we examined the conjugative plasmid pMBL6842, harboring the hns gene, and observed its positive regulation of parAB transcription, critical for plasmid segregation. Deletion of hns led to rapid plasmid loss, which was remedied by hns complementation. Further investigations unveiled adverse effects of hns overexpression on the bacterial host. Transcriptome analysis revealed hns's role in regulating numerous bacterial genes, impacting both host growth and swimming motility in the presence of the hns gene. Therefore, our study unveils the multifaceted roles of H-NS in both plasmid stability and host physiology, underscoring its biological significance and paving the way for future inquiries into the involvement of H-NS in horizontal gene transfer events.},
}
@article {pmid38940556,
year = {2024},
author = {Sun, W-S and Torrens, G and Ter Beek, J and Cava, F and Berntsson, RP-A},
title = {Breaking barriers: pCF10 type 4 secretion system relies on a self-regulating muramidase to modulate the cell wall.},
journal = {mBio},
volume = {15},
number = {8},
pages = {e0048824},
pmid = {38940556},
issn = {2150-7511},
support = {2016-03599//Vetenskapsr&#xe5;det (VR)/ ; 2018-02823//Vetenskapsr&#xe5;det (VR)/ ; 2018-05882//Vetenskapsr&#xe5;det (VR)/ ; SMK-1869//Kempestiftelserna (Kempe Foundations)/ ; SMK2062//Kempestiftelserna (Kempe Foundations)/ ; },
mesh = {*Cell Wall/metabolism ; *Type IV Secretion Systems/metabolism/genetics ; *Enterococcus faecalis/genetics/enzymology/metabolism ; *Muramidase/metabolism/genetics ; Plasmids/genetics ; Bacterial Proteins/metabolism/genetics ; Conjugation, Genetic ; Catalytic Domain ; },
abstract = {Conjugative type 4 secretion systems (T4SSs) are the main driver for the spread of antibiotic resistance genes and virulence factors in bacteria. To deliver the DNA substrate to recipient cells, it must cross the cell envelopes of both donor and recipient bacteria. In the T4SS from the enterococcal conjugative plasmid pCF10, PrgK is known to be the active cell wall degrading enzyme. It has three predicted extracellular hydrolase domains: metallo-peptidase (LytM), soluble lytic transglycosylase (SLT), and cysteine, histidine-dependent amidohydrolases/peptidases (CHAP). Here, we report the structure of the LytM domain and show that its active site is degenerate and lacks the active site metal. Furthermore, we show that only the predicted SLT domain is functional in vitro and that it unexpectedly has a muramidase instead of a lytic transglycosylase activity. While we did not observe any peptidoglycan hydrolytic activity for the LytM or CHAP domain, we found that these domains downregulated the SLT muramidase activity. The CHAP domain was also found to be involved in PrgK dimer formation. Furthermore, we show that PrgK interacts with PrgL, which likely targets PrgK to the rest of the T4SS. The presented data provides important information for understanding the function of Gram-positive T4SSs.IMPORTANCEAntibiotic resistance is a large threat to human health and is getting more prevalent. One of the major contributors to the spread of antibiotic resistance among different bacteria is type 4 secretion systems (T4SS). However, mainly T4SSs from Gram-negative bacteria have been studied in detail. T4SSs from Gram-positive bacteria, which stand for more than half of all hospital-acquired infections, are much less understood. The significance of our research is in identifying the function and regulation of a cell wall hydrolase, a key component of the pCF10 T4SS from Enterococcus faecalis. This system is one of the best-studied Gram-positive T4SSs, and this added knowledge aids in our understanding of horizontal gene transfer in E. faecalis as well as other medically relevant Gram-positive bacteria.},
}
@article {pmid38940543,
year = {2024},
author = {Jian, J and Wang, Z and Chen, C and Workman, CT and Fang, X and Larsen, TO and Guo, J and Sonnenschein, EC},
title = {Two high-quality Prototheca zopfii genomes provide new insights into their evolution as obligate algal heterotrophs and their pathogenicity.},
journal = {Microbiology spectrum},
volume = {12},
number = {8},
pages = {e0414823},
pmid = {38940543},
issn = {2165-0497},
mesh = {*Prototheca/genetics/pathogenicity ; *Heterotrophic Processes ; Phylogeny ; Genome, Plastid ; Evolution, Molecular ; Photosynthesis/genetics ; Genome, Plant ; },
abstract = {UNLABELLED: The majority of the nearly 10,000 described species of green algae are photoautotrophs; however, some species have lost their ability to photosynthesize and become obligate heterotrophs that rely on parasitism for survival. Two high-quality genomes of the heterotrophic algae Prototheca zopfii Pz20 and Pz23 were obtained using short- and long-read genomic as well as transcriptomic data. The genome sizes were 31.2 Mb and 31.3 Mb, respectively, and contig N50 values of 1.99 Mb and 1.26 Mb. Although P. zopfii maintained its plastid genome, the transition to heterotrophy led to a reduction in both plastid and nuclear genome size, including the loss of photosynthesis-related genes from both the nuclear and plastid genomes and the elimination of genes encoding for carotenoid oxygenase and pheophorbide an oxygenase. The loss of genes, including basic leucine-zipper (bZIP) transcription factors, flavin adenine dinucleotide-linked oxidase, and helicase, could have played a role in the transmission of autotrophy to heterotrophs and in the processes of abiotic stress resistance and pathogenicity. A total of 66 (1.37%) and 73 (1.49%) genes were identified as potential horizontal gene transfer events in the two P. zopfii genomes, respectively. Genes for malate synthase and isocitrate lyase, which are horizontally transferred from bacteria, may play a pivotal role in carbon and nitrogen metabolism as well as the pathogenicity of Prototheca and non-photosynthetic organisms. The two high-quality P. zopfii genomes provide new insights into their evolution as obligate heterotrophs and pathogenicity.<br><br>IMPORTANCE: The genus Prototheca, characterized by its heterotrophic nature and pathogenicity, serves as an exemplary model for investigating pathobiology. The limited understanding of the protothecosis infectious disease is attributed to the lack of genomic resources. Using HiFi long-read sequencing, both nuclear and plastid genomes were generated for two strains of P. zopfii. The findings revealed a concurrent reduction in both plastid and nuclear genome size, accompanied by the loss of genes associated with photosynthesis, carotenoid oxygenase, basic leucine-zipper (bZIP) transcription factors, and others. The analysis of horizontal gene transfer revealed the presence of 1.37% and 1.49% bacterial genes, including malate synthase and isocitrate lyase, which play crucial roles in carbon and nitrogen metabolism, as well as pathogenicity and obligate heterotrophy. The two high-quality P. zopfii genomes represent valuable resources for investigating their adaptation and evolution as obligate heterotrophs, as well as for developing future prevention and treatment strategies against protothecosis.},
}
@article {pmid38940156,
year = {2024},
author = {Curry, KD and Yu, FB and Vance, SE and Segarra, S and Bhaya, D and Chikhi, R and Rocha, EPC and Treangen, TJ},
title = {Reference-free structural variant detection in microbiomes via long-read co-assembly graphs.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {Suppl 1},
pages = {i58-i67},
pmid = {38940156},
issn = {1367-4811},
support = {//Department of Energy Joint Genome Institute/ ; P01 AI152999/AI/NIAID NIH HHS/United States ; //National Institute of Allergy and Infectious Diseases/ ; //Department of Energy/ ; P01-AI152999/GF/NIH HHS/United States ; //European Union's Horizon 2020/ ; 2023333162//NSF/ ; //Office of Science/ ; //Carnegie Institution for Science/ ; //Ken Kennedy Institute Recruiting/ ; EF-2126387//MIM Universal Rules of Live/ ; //Rice University Wagoner Foreign Study Scholarship/ ; IIS-2239114//NSF/ ; 872539//Marie Sk&#x142;odowska-Curie/ ; //NSF/ ; },
mesh = {*Microbiota/genetics ; *Metagenome ; *Genome, Bacterial ; Metagenomics/methods ; Gene Transfer, Horizontal ; Bacteria/genetics ; Algorithms ; },
abstract = {MOTIVATION: The study of bacterial genome dynamics is vital for understanding the mechanisms underlying microbial adaptation, growth, and their impact on host phenotype. Structural variants (SVs), genomic alterations of 50 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to the absence of clear reference genomes and the presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing all metagenomic samples in a series (time or other metric) into a single co-assembly graph. The log fold change in graph coverage between successive samples is then calculated to call SVs that are thriving or declining.<br><br>RESULTS: We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, particularly as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between successive time and temperature samples, suggesting host advantage. Our approach leverages previous work in assembly graph structural and coverage patterns to provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial gene flux.<br><br>rhea is open source and available at: https://github.com/treangenlab/rhea.},
}
@article {pmid38936370,
year = {2024},
author = {Yu, T and Xu, X and Liu, Y and Wang, X and Wu, S and Qiu, Z and Liu, X and Pan, X and Gu, C and Wang, S and Dong, L and Li, W and Yao, X},
title = {Multi-omics signatures reveal genomic and functional heterogeneity of Cutibacterium acnes in normal and diseased skin.},
journal = {Cell host &amp; microbe},
volume = {32},
number = {7},
pages = {1129-1146.e8},
doi = {10.1016/j.chom.2024.06.002},
pmid = {38936370},
issn = {1934-6069},
mesh = {Humans ; *Skin/microbiology ; *Dermatitis, Atopic/microbiology/genetics ; *Keratinocytes/microbiology ; *Acne Vulgaris/microbiology ; *Propionibacterium acnes/genetics ; Genomics ; Genome, Bacterial ; Staphylococcus epidermidis/genetics ; Transcriptome ; Virulence Factors/genetics ; Propionibacteriaceae/genetics ; Metabolome ; Metabolomics ; Microbiota/genetics ; Multiomics ; },
abstract = {Cutibacterium acnes is the most abundant bacterium of the human skin microbiome since adolescence, participating in both skin homeostasis and diseases. Here, we demonstrate individual and niche heterogeneity of C. acnes from 1,234 isolate genomes. Skin disease (atopic dermatitis and acne) and body site shape genomic differences of C. acnes, stemming from horizontal gene transfer and selection pressure. C. acnes harbors characteristic metabolic functions, fewer antibiotic resistance genes and virulence factors, and a more stable genome compared with Staphylococcus epidermidis. Integrated genome, transcriptome, and metabolome analysis at the strain level unveils the functional characteristics of C. acnes. Consistent with the transcriptome signature, C. acnes in a sebum-rich environment induces toxic and pro-inflammatory effects on keratinocytes. L-carnosine, an anti-oxidative stress metabolite, is up-regulated in the C. acnes metabolome from atopic dermatitis and attenuates skin inflammation. Collectively, our study reveals the joint impact of genes and the microenvironment on C. acnes function.},
}
@article {pmid38936366,
year = {2024},
author = {Garric, S and Ratin, M and Marie, D and Foulon, V and Probert, I and Rodriguez, F and Six, C},
title = {Impaired photoacclimation in a kleptoplastidic dinoflagellate reveals physiological limits of early stages of endosymbiosis.},
journal = {Current biology : CB},
volume = {34},
number = {14},
pages = {3064-3076.e5},
doi = {10.1016/j.cub.2024.05.066},
pmid = {38936366},
issn = {1879-0445},
mesh = {*Dinoflagellida/physiology/genetics ; *Symbiosis ; *Photosynthesis ; *Plastids/genetics/metabolism ; Phycoerythrin/metabolism/genetics ; Cryptophyta/genetics/physiology ; Light ; },
abstract = {Dinophysis dinoflagellates are predators of Mesodinium ciliates, from which they retain only the plastids of cryptophyte origin. The absence of nuclear photosynthetic cryptophyte genes in Dinophysis raises intriguing physiological and evolutionary questions regarding the functional dynamics of these temporary kleptoplastids within a foreign cellular environment. In an experimental setup including two light conditions, the comparative analysis with Mesodinium rubrum and the cryptophyte Teleaulax amphioxeia revealed that Dinophysis acuminata possessed a smaller and less dynamic functional photosynthetic antenna for green light, a function performed by phycoerythrin. We showed that the lack of the cryptophyte nucleus prevented the synthesis of the phycoerythrin α subunit, thereby hindering the formation of a complete phycoerythrin in Dinophysis. In particular, biochemical analyses showed that Dinophysis acuminata synthesized a poorly stable, incomplete phycoerythrin composed of chromophorylated β subunits, with impaired performance. We show that, consequently, a continuous supply of new plastids is crucial for growth and effective photoacclimation in this organism. Transcriptome analyses revealed that all examined strains of Dinophysis spp. have acquired the cryptophyte pebA and pebB genes through horizontal gene transfer, suggesting a potential ability to synthesize the phycobilin pigments bound to the cryptophyte phycoerythrin. By emphasizing that a potential long-term acquisition of the cryptophyte plastid relies on establishing genetic independence for essential functions such as light harvesting, this study highlights the intricate molecular challenges inherent in the enslavement of organelles and the processes involved in the diversification of photosynthetic organisms through endosymbiosis.},
}
@article {pmid38936185,
year = {2024},
author = {Hu, CJ and Lv, YQ and Xian, WD and Jiao, JY and Lian, ZH and Tan, S and Li, MM and Luo, ZH and Liu, ZT and Lv, AP and Liu, L and Ali, M and Liu, WQ and Li, WJ},
title = {Multi-omics insights into the function and evolution of sodium benzoate biodegradation pathway in Benzoatithermus flavus gen. nov., sp. nov. from hot spring.},
journal = {Journal of hazardous materials},
volume = {476},
number = {},
pages = {135017},
doi = {10.1016/j.jhazmat.2024.135017},
pmid = {38936185},
issn = {1873-3336},
mesh = {*Sodium Benzoate/metabolism ; *Biodegradation, Environmental ; *Hot Springs/microbiology ; *Phylogeny ; Water Pollutants, Chemical/metabolism ; Multiomics ; },
abstract = {Biodegradation stands as an eco-friendly and effective approach for organic contaminant remediation. However, research on microorganisms degrading sodium benzoate contaminants in extreme environments remains limited. In this study, we report to display the isolation of a novel hot spring enriched cultures with sodium benzoate (400 mg/L) as the sole carbon source. The results revealed that the phylum Pseudomonadota was the potential sodium benzoate degrader and a novel genus within the family Geminicoccaceae of this phylum. The isolated strain was named Benzoatithermus flavus SYSU G07066[T] and was isolated from HNT-2 hot spring samples. Genomic analysis revealed that SYSU G07066[T] carried benABC genes and physiological experiments indicated the ability to utilize sodium benzoate as a sole carbon source for growth, which was further confirmed by transcriptomic data with expression of benABC. Phylogenetic analysis suggested that Horizontal Gene Transfer (HGT) plays a significant role in acquiring sodium benzoate degradation capability among prokaryotes, and SYSU G07066[T] might have acquired benABC genes through HGT from the family Acetobacteraceae. The discovery of the first microorganism with sodium benzoate degradation function from a hot spring enhances our understanding of the diverse functions within the family Geminicoccaceae. This study unearths the first novel genus capable of efficiently degrading sodium benzoate and its evolution history at high temperatures, holding promising industrial applications, and provides a new perspective for further exploring the application potential of hot spring "microbial dark matter".},
}
@article {pmid38936038,
year = {2024},
author = {Wang, F and Huang, W and Zhang, M and Zhang, Q and Luo, Y and Chen, J and Su, Y and Huang, H and Fang, F and Luo, J},
title = {Disinfectant polyhexamethylene guanidine triggered simultaneous efflux pump antibiotic- and metal-resistance genes propagation during sludge anaerobic digestion.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {357},
number = {},
pages = {124453},
doi = {10.1016/j.envpol.2024.124453},
pmid = {38936038},
issn = {1873-6424},
mesh = {*Sewage/microbiology ; *Disinfectants/toxicity/pharmacology ; *Guanidines/toxicity ; Gene Transfer, Horizontal ; Metals/toxicity ; Anaerobiosis ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology/toxicity ; Waste Disposal, Fluid ; Drug Resistance, Bacterial/genetics ; },
abstract = {The environmental transmission of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) exerted devastating threats to global public health, and their interactions with other emerging contaminants (ECs) have raised increasing concern. This study investigated that the abundances of ARGs and MRGs with the predominant type of efflux pump were simultaneously increased (8.4-59.1%) by disinfectant polyhexamethylene guanidine (PHMG) during waste activated sludge (WAS) anaerobic digestion. The aggregation of the same microorganisms (i.e., Hymenobacter and Comamonas) and different host bacteria (i.e., Azoarcus and Thauera) were occurred upon exposure to PHMG, thereby increasing the co-selection and propagation of MRGs and ARGs by vertical gene transfer. Moreover, PHMG enhanced the process of horizontal gene transfer (HGT), facilitating their co-transmission by the same mobile genetic elements (20.2-223.7%). Additionally, PHMG up-regulated the expression of critical genes (i.e., glnB, trpG and gspM) associated with the HGT of ARGs and MRGs (i.e., two-component regulatory system and quorum sensing) and exocytosis system (i.e., bacterial secretion system). Structural equation model analysis further verified that the key driver for the simultaneous enrichment of ARGs and MRGs under PHMG stress was microbial community structure. The study gives new insights into the aggravated environmental risks and mechanisms of ECs in sludge digestion system, providing guidance for subsequent regulation and control of ECs.},
}
@article {pmid38936019,
year = {2024},
author = {Liu, Y and Song, X and Hou, X and Wang, Y and Cao, X},
title = {Effect of Mn-HA on ARGs and MRGs in nitrogen-culturing sludge.},
journal = {Journal of environmental management},
volume = {365},
number = {},
pages = {121615},
doi = {10.1016/j.jenvman.2024.121615},
pmid = {38936019},
issn = {1095-8630},
mesh = {*Sewage/microbiology ; *Nitrogen/metabolism ; *Manganese ; Drug Resistance, Microbial/genetics ; Denitrification ; Bacteria/metabolism/genetics ; Metagenomics ; },
abstract = {The simultaneous escalation in ARGs (antibiotic resistance genes) and MRGs (metal resistance genes) further complicates the intricate network of factors contributing to the proliferation of microbial resistance. Manganese, which has been reported to affect the resistance of bacteria to antibiotics and metals, plays a vital role in microbial nitrogen metabolism. Moreover, nitrifying and denitrifying populations are potential hosts for ARGs. In this study, manganese was introduced in its prevalent organic chelated form in the environment (Manganese humus chelates, Mn-HA) to a N metabolism sludge to explore the effect of manganese on MRGs and ARGs dissemination. Metagenomics results revealed that manganese availability enhances nitrogen metabolism, while a decrease in ARGs was noted which may be attributed to the inhibition of horizontal gene transfer (HGT), reflected in the reduced integrase -encoded gene int. Population analysis revealed that nitrifier and denitrifier genus harbor MRGs and ARGs, indicating that nitrifier and denitrifier are hosts of MRGs and ARGs. This raises the question of whether the prevalence of ARGs is always increased in metal-contained environments.},
}
@article {pmid38935608,
year = {2024},
author = {Randriantseheno, LN and Andrianaivoarimanana, V and Pizarro-Cerdá, J and Wagner, DM and Rajerison, M},
title = {Review of genotyping methods for Yersinia pestis in Madagascar.},
journal = {PLoS neglected tropical diseases},
volume = {18},
number = {6},
pages = {e0012252},
pmid = {38935608},
issn = {1935-2735},
mesh = {*Yersinia pestis/genetics/classification/isolation &amp; purification ; Madagascar/epidemiology ; *Plague/microbiology/epidemiology ; Humans ; Animals ; Genotype ; Genotyping Techniques/methods ; },
abstract = {BACKGROUND: Plague, a zoonotic disease caused by Yersinia pestis, was responsible for 3 historical human pandemics that killed millions of people. It remains endemic in rodent populations in Africa, Asia, North America, and South America but human plague is rare in most of these locations. However, human plague is still highly prevalent in Madagascar, which typically records a significant part of all annual global cases. This has afforded an opportunity to study contemporary human plague in detail using various typing methods for Y. pestis.<br><br>AIM: This review aims to summarize the methods that have been used to type Y. pestis in Madagascar along with the major discoveries that have been made using these approaches.<br><br>METHODS: Pubmed and Google Scholar were used to search for the keywords: "typing Yersinia pestis Madagascar," "evolution Yersinia pestis Madagascar," and "diversity Yersinia pestis Madagascar." Eleven publications were relevant to our topic and further information was retrieved from references cited in those publications.<br><br>RESULTS: The history of Y. pestis typing in Madagascar can be divided in 2 periods: the pre-genomics and genomics eras. During the pre-genomics era, ribotyping, direct observation of plasmid content and plasmid restriction fragment length polymorphisms (RFLP) were employed but only revealed a limited amount of diversity among Malagasy Y. pestis strains. Extensive diversity only started to be revealed in the genomics era with the use of clustered regularly interspaced palindromic repeats (CRISPR), multiple-locus variable number tandem repeats (VNTR) analysis (MLVA), and single-nucleotide polymorphisms (SNPs) discovered from whole genome sequences. These higher-resolution genotyping methods have made it possible to highlight the distribution and persistence of genotypes in the different plague foci of Madagascar (Mahajanga and the Central and Northern Highlands) by genotyping strains from the same locations across years, to detect transfers between foci, to date the emergence of genotypes, and even to document the transmission of antimicrobial resistant (AMR) strains during a pneumonic plague outbreak. Despite these discoveries, there still remain topics that deserve to be explored, such as the contribution of horizontal gene transfer to the evolution of Malagasy Y. pestis strains and the evolutionary history of Y. pestis in Madagascar.<br><br>CONCLUSIONS: Genotyping of Y. pestis has yielded important insights on plague in Madagascar, particularly since the advent of whole-genome sequencing (WGS). These include a better understanding of plague persistence in the environment, antimicrobial AMR and multi-drug resistance in Y. pestis, and the person-to-person spread of pneumonic plague. Considering that human plague is still a significant public health threat in Madagascar, these insights can be useful for controlling and preventing human plague in Madagascar and elsewhere, and also are relevant for understanding the historical pandemics and the possible use of Y. pestis as a biological weapon.},
}
@article {pmid38935220,
year = {2024},
author = {Parra, B and Lutz, VT and Brøndsted, L and Carmona, JL and Palomo, A and Nesme, J and Van Hung Le, V and Smets, BF and Dechesne, A},
title = {Characterization and Abundance of Plasmid-Dependent Alphatectivirus Bacteriophages.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {85},
pmid = {38935220},
issn = {1432-184X},
support = {101026675//European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant/ ; 002200000279//VRID Postdoctorado from Vicerrector&#xed;a de Investigaci&#xf3;n y Desarrollo, Universidad de Concepci&#xf3;n/ ; P-PhanFARE (23046)//Villum Fonden/ ; },
mesh = {*Plasmids/genetics ; *Wastewater/virology/microbiology ; *Bacteriophages/genetics/isolation &amp; purification/physiology/classification ; Genome, Viral ; Escherichia coli/virology/genetics ; Host Specificity ; Pseudomonas putida/virology/genetics ; Salmonella enterica/virology/genetics ; Phylogeny ; },
abstract = {Antimicrobial resistance (AMR) is a major public health threat, exacerbated by the ability of bacteria to rapidly disseminate antimicrobial resistance genes (ARG). Since conjugative plasmids of the incompatibility group P (IncP) are ubiquitous mobile genetic elements that often carry ARG and are broad-host-range, they are important targets to prevent the dissemination of AMR. Plasmid-dependent phages infect plasmid-carrying bacteria by recognizing components of the conjugative secretion system as receptors. We sought to isolate plasmid-dependent phages from wastewater using an avirulent strain of Salmonella enterica carrying the conjugative IncP plasmid pKJK5. Irrespective of the site, we only obtained bacteriophages belonging to the genus Alphatectivirus. Eleven isolates were sequenced, their genomes analyzed, and their host range established using S. enterica, Escherichia coli, and Pseudomonas putida carrying diverse conjugative plasmids. We confirmed that Alphatectivirus are abundant in domestic and hospital wastewater using culture-dependent and culture-independent approaches. However, these results are not consistent with their low or undetectable occurrence in metagenomes. Therefore, overall, our results emphasize the importance of performing phage isolation to uncover diversity, especially considering the potential of plasmid-dependent phages to reduce the spread of ARG carried by conjugative plasmids, and to help combat the AMR crisis.},
}
@article {pmid38934605,
year = {2024},
author = {Burcham, ZM},
title = {Comparative genomic analysis of an emerging Pseudomonadaceae member, Thiopseudomonas alkaliphila.},
journal = {Microbiology spectrum},
volume = {12},
number = {8},
pages = {e0415723},
pmid = {38934605},
issn = {2165-0497},
support = {//University of Tennessee, Knoxville (UT)/ ; },
mesh = {*Genome, Bacterial/genetics ; *Genomics ; *Phylogeny ; Humans ; Animals ; Gene Transfer, Horizontal ; Prophages/genetics ; },
abstract = {Thiopseudomonas alkaliphila, an organism recently classified within the Pseudomonadaceae family, has been detected in diverse sources such as human tissues, animal guts, industrial fermenters, and decomposition environments, suggesting a diverse ecological role. However, a large knowledge gap exists in how T. alkaliphila functions. In this comparative genomic analysis, adaptations indicative of habitat specificity among strains and genomic similarity to known opportunistic pathogens are revealed. Genomic investigation reveals a core metabolic utilization of multiple oxidative and non-oxidative catabolic pathways, suggesting adaptability to varied environments and carbon sources. The genomic repertoire of T. alkaliphila includes secondary metabolites, such as antimicrobials and siderophores, indicative of its involvement in microbial competition and resource acquisition. Additionally, the presence of transposases, prophages, plasmids, and Clustered Regularly Interspaced Short Palindromic Repeats-Cas systems in T. alkaliphila genomes suggests mechanisms for horizontal gene transfer and defense against viral predation. This comprehensive genomic analysis expands our understanding on the ecological functions, community interactions, and potential virulence of T. alkaliphila, while emphasizing its adaptability and diverse capabilities across environmental and host-associated ecosystems.IMPORTANCEAs the microbial world continues to be explored, new organisms will emerge with beneficial and/or pathogenetic impact. Thiopseudomonas alkaliphila is a species originally isolated from clinical human tissue and fluid samples but has not been attributed to disease. Since its classification, T. alkaliphila has been found in animal guts, animal waste, decomposing remains, and biogas fermentation reactors. This is the first study to provide an in-depth view of the metabolic potential of publicly available genomes belonging to this species through a comparative genomics and draft pangenome calculation approach. It was found that T. alkaliphila is metabolically versatile and likely adapts to diverse energy sources and environments, which may make it useful for bioremediation and in industrial settings. A range of virulence factors and antibiotic resistances were also detected, suggesting T. alkaliphila may operate as an undescribed opportunistic pathogen.},
}
@article {pmid38930473,
year = {2024},
author = {Otero-Olarra, JE and Díaz-Cárdenas, G and Aguilera-Arreola, MG and Curiel-Quesada, E and Pérez-Valdespino, A},
title = {Aeromonas trota Is Highly Refractory to Acquire Exogenous Genetic Material.},
journal = {Microorganisms},
volume = {12},
number = {6},
pages = {},
pmid = {38930473},
issn = {2076-2607},
abstract = {Aeromonas trota is sensitive to most antibiotics and the sole species of this genus susceptible to ampicillin. This susceptibility profile could be related to its inability to acquire exogenous DNA. In this study, A. trota isolates were analyzed to establish their capacity to incorporate foreign DNA. Fourteen strains were identified as A. trota by multilocus phylogenetic analysis (MLPA). Minimal inhibitory concentrations of antibiotics (MIC) were assessed, confirming the susceptibility to most antibiotics tested. To explore their capacity to be transformed, A. trota strains were used as recipients in different horizontal transfer assays. Results showed that around fifty percent of A. trota strains were able to incorporate pBAMD1-2 and pBBR1MCS-3 plasmids after conjugal transfer. In all instances, conjugation frequencies were very low. Interestingly, several isoforms of plasmid pBBR1MCS-3 were observed in transconjugants. Strains could not receive pAr-32, a native plasmid from A. salmonicida. A. trota strains were unable to receive DNA by means of electroporation, natural transformation or vesiduction. These results confirm that A. trota species are extremely refractory to horizontal gene transfer, which could be associated to plasmid instability resulting from oligomerization or to the presence of defense systems against exogenous genetic material in their genomes. To explain the poor results of horizontal gene transfer (HGT), selected genomes were sequenced and analyzed, revealing the presence of defense systems, which could prevent the stable incorporation of exogenous DNA in A. trota.},
}
@article {pmid38927231,
year = {2024},
author = {Amábile-Cuevas, CF and Lund-Zaina, S},
title = {Non-Canonical Aspects of Antibiotics and Antibiotic Resistance.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {6},
pages = {},
pmid = {38927231},
issn = {2079-6382},
abstract = {The understanding of antibiotic resistance, one of the major health threats of our time, is mostly based on dated and incomplete notions, especially in clinical contexts. The "canonical" mechanisms of action and pharmacodynamics of antibiotics, as well as the methods used to assess their activity upon bacteria, have not changed in decades; the same applies to the definition, acquisition, selective pressures, and drivers of resistance. As a consequence, the strategies to improve antibiotic usage and overcome resistance have ultimately failed. This review gathers most of the "non-canonical" notions on antibiotics and resistance: from the alternative mechanisms of action of antibiotics and the limitations of susceptibility testing to the wide variety of selective pressures, lateral gene transfer mechanisms, ubiquity, and societal factors maintaining resistance. Only by having a "big picture" view of the problem can adequate strategies to harness resistance be devised. These strategies must be global, addressing the many aspects that drive the increasing prevalence of resistant bacteria aside from the clinical use of antibiotics.},
}
@article {pmid38927226,
year = {2024},
author = {Gestels, Z and Abdellati, S and Kenyon, C and Manoharan-Basil, SS},
title = {Ciprofloxacin Concentrations 100-Fold Lower than the MIC Can Select for Ciprofloxacin Resistance in Neisseria subflava: An In Vitro Study.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {6},
pages = {},
pmid = {38927226},
issn = {2079-6382},
support = {Unknown//PRESTIP/ ; },
abstract = {Neisseria gonorrhoeae can acquire antimicrobial resistance (AMR) through horizontal gene transfer (HGT) from other Neisseria spp. such as commensals like Neisseria subflava. Low doses of antimicrobials in food could select for AMR in N. subflava, which could then be transferred to N. gonorrhoeae. In this study, we aimed to determine the lowest concentration of ciprofloxacin that can induce ciprofloxacin resistance (minimum selection concentration-MSC) in a N. subflava isolate (ID-Co000790/2, a clinical isolate collected from a previous community study conducted at ITM). In this study, Neisseria subflava was serially passaged on gonococcal (GC) medium agar plates containing ciprofloxacin concentrations ranging from 1:100 to 1:10,000 below its ciprofloxacin MIC (0.006 µg/mL) for 6 days. After 6 days of serial passaging at ciprofloxacin concentrations of 1/100th of the MIC, 24 colonies emerged on the plate containing 0.06 µg/mL ciprofloxacin, which corresponds to the EUCAST breakpoint for N. gonorrhoeae. Their ciprofloxacin MICs were between 0.19 to 0.25 µg/mL, and whole genome sequencing revealed a missense mutation T91I in the gyrA gene, which has previously been found to cause reduced susceptibility to fluoroquinolones. The N. subflava MSCde novo was determined to be 0.06 ng/mL (0.00006 µg/mL), which is 100×-fold lower than the ciprofloxacin MIC. The implications of this finding are that the low concentrations of fluoroquinolones found in certain environmental samples, such as soil, river water, and even the food we eat, may be able to select for ciprofloxacin resistance in N. subflava.},
}
@article {pmid38927197,
year = {2024},
author = {Yaikhan, T and Suwannasin, S and Singkhamanan, K and Chusri, S and Pomwised, R and Wonglapsuwan, M and Surachat, K},
title = {Genomic Characterization of Multidrug-Resistant Enterobacteriaceae Clinical Isolates from Southern Thailand Hospitals: Unraveling Antimicrobial Resistance and Virulence Mechanisms.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {6},
pages = {},
pmid = {38927197},
issn = {2079-6382},
support = {B13F670075//the NSRF via the Program Management Unit for Human Resources &amp; Institutional Development, Research Innovation/ ; //the Postdoctoral Fellowship from Prince of Songkla University/ ; B13F660074//the NSRF via the Program Management Unit for Human Resources &amp; Institutional Development, Research and Innovation/ ; },
abstract = {The emergence and spread of antimicrobial resistance (AMR) among Enterobacteriaceae pose significant threats to global public health. In this study, we conducted a short-term surveillance effort in Southern Thailand hospitals to characterize the genomic diversity, AMR profiles, and virulence factors of Enterobacteriaceae strains. We identified 241 carbapenem-resistant Enterobacteriaceae, of which 12 were selected for whole-genome sequencing (WGS) and genome analysis. The strains included Proteus mirabilis, Serratia nevei, Klebsiella variicola, Klebsiella aerogenes, Klebsiella indica, Klebsiella grimontii, Phytobacter ursingii, Phytobacter palmae, Kosakonia spp., and Citrobacter freundii. The strains exhibited high levels of multidrug resistance, including resistance to carbapenem antibiotics. Whole-genome sequencing revealed a diverse array of antimicrobial resistance genes (ARGs), with strains carrying genes for ß-lactamase, efflux pumps, and resistance to other antibiotic classes. Additionally, stress response, metal tolerance, and virulence-associated genes were identified, highlighting the adaptability and pathogenic potential of these strains. A plasmid analysis identified several plasmid replicons, including IncA/C2, IncFIB(K), and Col440I, as well as several plasmids identical to those found globally, indicating the potential for the horizontal gene transfer of ARGs. Importantly, this study also identified a novel species of Kosakonia spp. PSU27, adding to the understanding of the genetic diversity and resistance mechanisms of Enterobacteriaceae in Southern Thailand. The results reported in this study highlight the critical importance of implementing effective antimicrobial management programs and developing innovative treatment approaches to urgently tackle AMR.},
}
@article {pmid38927185,
year = {2024},
author = {Peng, J and Feng, J and Ji, H and Kong, X and Hong, J and Zhu, L and Qian, H},
title = {Emergence of Rarely Reported Extensively Drug-Resistant Salmonella Enterica Serovar Paratyphi B among Patients in East China.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {6},
pages = {},
pmid = {38927185},
issn = {2079-6382},
support = {National Major S&amp;T Projects(2018ZX10714-002)//Ministry of Science and Technology of the People's Republic of China/ ; Ym2023040//Jiangsu Preventive Medicine Association/ ; },
abstract = {BACKGROUND: In recent years, global concern over increasing multidrug resistance (MDR) among various Salmonella serotypes has grown significantly. However, reports on MDR Salmonella Paratyphi B remain scarce, let alone the extensively drug-resistant (XDR) strains.<br><br>METHODS: In this retrospective study, we investigated the isolates of Salmonella Paratyphi B in Jiangsu Province over the past decade and carried out antimicrobial susceptibility tests, then the strains were sequenced and bioinformatics analyses were performed.<br><br>RESULTS: 27 Salmonella Paratyphi B strains were identified, of which the predominant STs were ST42 (11), ST86 (10), and ST2814 (5). Among these strains, we uncovered four concerning XDR Salmonella Paratyphi B ST2814 strains (4/5) which were previously unreported. These alarmingly resistant isolates showed resistance to all three major antibiotic classes for Salmonella treatment and even the last resort treatment tigecycline. Bioinformatics analysis revealed high similarity between the plasmids harbored by these XDR strains and diverse Salmonella serotypes and Escherichia coli from China and neighboring regions. Notably, these four plasmids carried the ramAp gene responsible for multiple antibiotic resistance by regulating the AcrAB-TolC pump, predominantly originating from China. Additionally, a distinct MDR ST42(1/11) strain with an ICE on chromosome was also identified. Furthermore, phylogenetic analysis of global ST42/ST2814 isolates highlighted the regional specificity of these strains, with Jiangsu isolates clustering together with domestic isolates and XDR ST2814 forming a distinct branch, suggesting adaptation to local antibiotic pressures.<br><br>CONCLUSIONS: This research underscores the pressing need for closely monitoring the MDR/XDR Salmonella Paratyphi B, particularly the emerging ST2814 strains in Jiangsu Province, to effectively curb its spread and protect public health. Moreover, surveillance should be strengthened across different ecological niches and genera to track resistance genes and horizontal gene transfer elements under the concept of "ONE HEALTH".},
}
@article {pmid38926391,
year = {2024},
author = {Brown, CL and Maile-Moskowitz, A and Lopatkin, AJ and Xia, K and Logan, LK and Davis, BC and Zhang, L and Vikesland, PJ and Pruden, A},
title = {Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {5412},
pmid = {38926391},
issn = {2041-1723},
support = {1545756//National Science Foundation (NSF)/ ; 2004751//National Science Foundation (NSF)/ ; 2125798//National Science Foundation (NSF)/ ; 4813//Water Research Foundation (WRF)/ ; },
mesh = {*Gene Transfer, Horizontal ; *Sewage/microbiology ; *Wastewater/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/classification/metabolism ; Water Purification/methods ; Metagenomics/methods ; Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid/methods ; Drug Resistance, Bacterial/genetics ; Selection, Genetic ; },
abstract = {Activated sludge is the centerpiece of biological wastewater treatment, as it facilitates removal of sewage-associated pollutants, fecal bacteria, and pathogens from wastewater through semi-controlled microbial ecology. It has been hypothesized that horizontal gene transfer facilitates the spread of antibiotic resistance genes within the wastewater treatment plant, in part because of the presence of residual antibiotics in sewage. However, there has been surprisingly little evidence to suggest that sewage-associated antibiotics select for resistance at wastewater treatment plants via horizontal gene transfer or otherwise. We addressed the role of sewage-associated antibiotics in promoting antibiotic resistance using lab-scale sequencing batch reactors fed field-collected wastewater, metagenomic sequencing, and our recently developed bioinformatic tool Kairos. Here, we found confirmatory evidence that fluctuating levels of antibiotics in sewage are associated with horizontal gene transfer of antibiotic resistance genes, microbial ecology, and microdiversity-level differences in resistance gene fate in activated sludge.},
}
@article {pmid38922012,
year = {2024},
author = {Kerek, &#xc1; and Németh, V and Szabó, &#xc1; and Papp, M and Bányai, K and Kardos, G and Kaszab, E and Bali, K and Nagy, Z and Süth, M and Jerzsele, &#xc1;},
title = {Monitoring Changes in the Antimicrobial-Resistance Gene Set (ARG) of Raw Milk and Dairy Products in a Cattle Farm, from Production to Consumption.},
journal = {Veterinary sciences},
volume = {11},
number = {6},
pages = {},
pmid = {38922012},
issn = {2306-7381},
support = {RRF-2.3.1-21-2022-00001//National Recovery Fund/ ; },
abstract = {Raw milk and dairy products can serve as potential vectors for transmissible bacterial, viral and protozoal diseases, alongside harboring antimicrobial-resistance genes. This study monitors the changes in the antimicrobial-resistance gene pool in raw milk and cheese, from farm to consumer, utilizing next-generation sequencing. Five parallel sampling runs were conducted to assess the resistance gene pool, as well as phage or plasmid carriage and potential mobility. In terms of taxonomic composition, in raw milk the Firmicutes phylum made up 41%, while the Proteobacteria phylum accounted for 58%. In fresh cheese, this ratio shifted to 93% Firmicutes and 7% Proteobacteria. In matured cheese, the composition was 79% Firmicutes and 21% Proteobacteria. In total, 112 antimicrobial-resistance genes were identified. While a notable reduction in the resistance gene pool was observed in the freshly made raw cheese compared to the raw milk samples, a significant growth in the resistance gene pool occurred after one month of maturation, surpassing the initial gene frequency. Notably, the presence of extended-spectrum beta-lactamase (ESBL) genes, such as OXA-662 (100% coverage, 99.3% identity) and OXA-309 (97.1% coverage, 96.2% identity), raised concerns; these genes have a major public health relevance. In total, nineteen such genes belonging to nine gene families (ACT, CMY, EC, ORN, OXA, OXY, PLA, RAHN, TER) have been identified. The largest number of resistance genes were identified against fluoroquinolone drugs, which determined efflux pumps predominantly. Our findings underscore the importance of monitoring gene pool variations throughout the product pathway and the potential for horizontal gene transfer in raw products. We advocate the adoption of a new approach to food safety investigations, incorporating next-generation sequencing techniques.},
}
@article {pmid38920383,
year = {2024},
author = {Rakibova, Y and Dunham, DT and Seed, KD and Freddolino, L},
title = {Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae.},
journal = {mSphere},
volume = {9},
number = {7},
pages = {e0001124},
pmid = {38920383},
issn = {2379-5042},
support = {2018257700//National Science Foundation (NSF)/ ; R01AI127652//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01 AI127652/AI/NIAID NIH HHS/United States ; AI134678//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R35 GM128637/GM/NIGMS NIH HHS/United States ; R01 AI134678/AI/NIAID NIH HHS/United States ; },
mesh = {*Bacterial Proteins/genetics/metabolism ; *Vibrio cholerae/genetics/pathogenicity/metabolism ; *Gene Expression Regulation, Bacterial ; *Cholera/microbiology ; DNA-Binding Proteins/genetics/metabolism ; Humans ; Transcription, Genetic ; Virulence ; Virulence Factors/genetics ; Gene Transfer, Horizontal ; },
abstract = {UNLABELLED: Vibrio cholerae, the causative agent of the diarrheal disease cholera, poses an ongoing health threat due to its wide repertoire of horizontally acquired elements (HAEs) and virulence factors. New clinical isolates of the bacterium with improved fitness abilities, often associated with HAEs, frequently emerge. The appropriate control and expression of such genetic elements is critical for the bacteria to thrive in the different environmental niches they occupy. H-NS, the histone-like nucleoid structuring protein, is the best-studied xenogeneic silencer of HAEs in gamma-proteobacteria. Although H-NS and other highly abundant nucleoid-associated proteins (NAPs) have been shown to play important roles in regulating HAEs and virulence in model bacteria, we still lack a comprehensive understanding of how different NAPs modulate transcription in V. cholerae. By obtaining genome-wide measurements of protein occupancy and active transcription in a clinical isolate of V. cholerae, harboring recently discovered HAEs encoding for phage defense systems, we show that a lack of H-NS causes a robust increase in the expression of genes found in many HAEs. We further found that TsrA, a protein with partial homology to H-NS, regulates virulence genes primarily through modulation of H-NS activity. We also identified few sites that are affected by TsrA independently of H-NS, suggesting TsrA may act with diverse regulatory mechanisms. Our results demonstrate how the combinatorial activity of NAPs is employed by a clinical isolate of an important pathogen to regulate recently discovered HAEs.<br><br>IMPORTANCE: New strains of the bacterial pathogen Vibrio cholerae, bearing novel horizontally acquired elements (HAEs), frequently emerge. HAEs provide beneficial traits to the bacterium, such as antibiotic resistance and defense against invading bacteriophages. Xenogeneic silencers are proteins that help bacteria harness new HAEs and silence those HAEs until they are needed. H-NS is the best-studied xenogeneic silencer; it is one of the nucleoid-associated proteins (NAPs) in gamma-proteobacteria and is responsible for the proper regulation of HAEs within the bacterial transcriptional network. We studied the effects of H-NS and other NAPs on the HAEs of a clinical isolate of V. cholerae. Importantly, we found that H-NS partners with a small and poorly characterized protein, TsrA, to help domesticate new HAEs involved in bacterial survival and in causing disease. A proper understanding of the regulatory state in emerging isolates of V. cholerae will provide improved therapies against new isolates of the pathogen.},
}
@article {pmid38918632,
year = {2024},
author = {Mei, Z and Wang, F and Bhosle, A and Dong, D and Mehta, R and Ghazi, A and Zhang, Y and Liu, Y and Rinott, E and Ma, S and Rimm, EB and Daviglus, M and Willett, WC and Knight, R and Hu, FB and Qi, Q and Chan, AT and Burk, RD and Stampfer, MJ and Shai, I and Kaplan, RC and Huttenhower, C and Wang, DD},
title = {Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes.},
journal = {Nature medicine},
volume = {30},
number = {8},
pages = {2265-2276},
pmid = {38918632},
issn = {1546-170X},
support = {K99 DK119412/DK/NIDDK NIH HHS/United States ; R01NR01999//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01 MD011389/MD/NIMHD NIH HHS/United States ; U01 CA152904/CA/NCI NIH HHS/United States ; N01HC65235/HL/NHLBI NIH HHS/United States ; R01AG077489//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; N01HC65234/HL/NHLBI NIH HHS/United States ; R01 NR019992/NR/NINR NIH HHS/United States ; P30 DK046200/DK/NIDDK NIH HHS/United States ; N01HC65237/HL/NHLBI NIH HHS/United States ; R01 AG077489/AG/NIA NIH HHS/United States ; RF1 AG083764/AG/NIA NIH HHS/United States ; R01 HL035464/HL/NHLBI NIH HHS/United States ; P30DK046200//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R00DK119412//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R24 DK110499/DK/NIDDK NIH HHS/United States ; R00 DK119412/DK/NIDDK NIH HHS/United States ; R24DK110499//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; R01 CA202704/CA/NCI NIH HHS/United States ; P01 CA055075/CA/NCI NIH HHS/United States ; 209933838//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 897161//American Heart Association (American Heart Association, Inc.)/ ; U01 CA176726/CA/NCI NIH HHS/United States ; U01 CA167552/CA/NCI NIH HHS/United States ; N01HC65236/HL/NHLBI NIH HHS/United States ; P30 DK111022/DK/NIDDK NIH HHS/United States ; N01HC65233/HL/NHLBI NIH HHS/United States ; R35 CA253185/CA/NCI NIH HHS/United States ; R01 HL060712/HL/NHLBI NIH HHS/United States ; },
mesh = {*Diabetes Mellitus, Type 2/microbiology/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenome/genetics ; *Phylogeny ; Cohort Studies ; Male ; Middle Aged ; Female ; China/epidemiology ; Dysbiosis/microbiology ; United States/epidemiology ; Israel/epidemiology ; Europe/epidemiology ; },
abstract = {The association of gut microbial features with type 2 diabetes (T2D) has been inconsistent due in part to the complexity of this disease and variation in study design. Even in cases in which individual microbial species have been associated with T2D, mechanisms have been unable to be attributed to these associations based on specific microbial strains. We conducted a comprehensive study of the T2D microbiome, analyzing 8,117 shotgun metagenomes from 10 cohorts of individuals with T2D, prediabetes, and normoglycemic status in the United States, Europe, Israel and China. Dysbiosis in 19 phylogenetically diverse species was associated with T2D (false discovery rate < 0.10), for example, enriched Clostridium bolteae and depleted Butyrivibrio crossotus. These microorganisms also contributed to community-level functional changes potentially underlying T2D pathogenesis, for example, perturbations in glucose metabolism. Our study identifies within-species phylogenetic diversity for strains of 27 species that explain inter-individual differences in T2D risk, such as Eubacterium rectale. In some cases, these were explained by strain-specific gene carriage, including loci involved in various mechanisms of horizontal gene transfer and novel biological processes underlying metabolic risk, for example, quorum sensing. In summary, our study provides robust cross-cohort microbial signatures in a strain-resolved manner and offers new mechanistic insights into T2D.},
}
@article {pmid38918467,
year = {2024},
author = {Grodner, B and Shi, H and Farchione, O and Vill, AC and Ntekas, I and Diebold, PJ and Wu, DT and Chen, CY and Kim, DM and Zipfel, WR and Brito, IL and De Vlaminck, I},
title = {Spatial mapping of mobile genetic elements and their bacterial hosts in complex microbiomes.},
journal = {Nature microbiology},
volume = {9},
number = {9},
pages = {2262-2277},
pmid = {38918467},
issn = {2058-5276},
support = {DP2 AI138242/AI/NIAID NIH HHS/United States ; 1DP2AI138242//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R33 CA235302/CA/NCI NIH HHS/United States ; S10 OD018516/OD/NIH HHS/United States ; 1R33CA235302//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; S10OD018516//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
mesh = {*Biofilms/growth &amp; development ; *Microbiota/genetics ; *In Situ Hybridization, Fluorescence/methods ; *Bacteriophages/genetics ; *Bacteria/genetics/virology/classification ; *Interspersed Repetitive Sequences/genetics ; Humans ; *Plasmids/genetics ; *Prophages/genetics ; *Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Mouth/microbiology ; },
abstract = {The exchange of mobile genetic elements (MGEs) facilitates the spread of functional traits including antimicrobial resistance within bacterial communities. Tools to spatially map MGEs and identify their bacterial hosts in complex microbial communities are currently lacking, limiting our understanding of this process. Here we combined single-molecule DNA fluorescence in situ hybridization (FISH) with multiplexed ribosomal RNA-FISH to enable simultaneous visualization of both MGEs and bacterial taxa. We spatially mapped bacteriophage and antimicrobial resistance (AMR) plasmids and identified their host taxa in human oral biofilms. This revealed distinct clusters of AMR plasmids and prophage, coinciding with densely packed regions of host bacteria. Our data suggest spatial heterogeneity in bacterial taxa results in heterogeneous MGE distribution within the community, with MGE clusters resulting from horizontal gene transfer hotspots or expansion of MGE-carrying strains. Our approach can help advance the study of AMR and phage ecology in biofilms.},
}
@article {pmid38917629,
year = {2024},
author = {Liu, F and Shen, Y and Hou, Y and Wu, J and Ting, Y and Nie, C and Tong, M},
title = {Elimination of representative antibiotic-resistant bacteria, antibiotic resistance genes and ciprofloxacin from water via photoactivation of periodate using FeS2.},
journal = {Journal of hazardous materials},
volume = {476},
number = {},
pages = {134982},
doi = {10.1016/j.jhazmat.2024.134982},
pmid = {38917629},
issn = {1873-3336},
mesh = {*Ciprofloxacin/pharmacology ; *Anti-Bacterial Agents/pharmacology/chemistry ; *Ferrous Compounds/chemistry/pharmacology ; *Drug Resistance, Bacterial/genetics ; Sunlight ; Disinfection/methods ; Water Purification/methods ; Escherichia coli/drug effects/genetics ; Water Pollutants, Chemical ; Water Microbiology ; Bacteria/drug effects/genetics/metabolism/radiation effects ; Gene Transfer, Horizontal ; },
abstract = {The propagation of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) induced by the release of antibiotics poses great threats to ecological safety and human health. In this study, periodate (PI)/FeS2/simulated sunlight (SSL) system was employed to remove representative ARB, ARGs and antibiotics in water. 1 × 10[7] CFU mL[-1] of gentamycin-resistant Escherichia coli was effectively disinfected below limit of detection in PI/FeS2/SSL system under different water matrix and in real water samples. Sulfadiazine-resistant Pseudomonas and Gram-positive Bacillus subtilis could also be efficiently sterilized. Theoretical calculation showed that (110) facet was the most reactive facet on FeS2 to activate PI for the generation of reactive species (·OH, ·O2[-], h[+] and Fe(IV)=O) to damage cell membrane and intracellular enzyme defense system. Both intracellular and extracellular ARGs could be degraded and the expression levels of multidrug resistance-related genes were downregulated during the disinfection process. Thus, horizontal gene transfer (HGT) of ARB was inhibited. Moreover, PI/FeS2/SSL system could disinfect ARB in a continuous flow reactor and in an enlarged reactor under natural sunlight irradiation. PI/FeS2/SSL system could also effectively degrade the HGT-promoting antibiotic (ciprofloxacin) via hydroxylation and ring cleavage process. Overall, PI/FeS2/SSL exhibited great promise for the elimination of antibiotic resistance from water.},
}
@article {pmid38915079,
year = {2024},
author = {Wu, CS and Wang, RJ and Chaw, SM},
title = {Integration of large and diverse angiosperm DNA fragments into Asian Gnetum mitogenomes.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {140},
pmid = {38915079},
issn = {1741-7007},
support = {No. 2022B1111040003//Guangdong Provincial Key R&amp;D Programme/ ; },
mesh = {*Phylogeny ; *Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Gnetum/genetics ; DNA, Plant/genetics ; Evolution, Molecular ; Magnoliopsida/genetics ; },
abstract = {BACKGROUND: Horizontal gene transfer (HGT) events have rarely been reported in gymnosperms. Gnetum is a gymnosperm genus comprising 25‒35 species sympatric with angiosperms in West African, South American, and Southeast Asian rainforests. Only a single acquisition of an angiosperm mitochondrial intron has been documented to date in Asian Gnetum mitogenomes. We wanted to develop a more comprehensive understanding of frequency and fragment length distribution of such events as well as their evolutionary history in this genus.<br><br>RESULTS: We sequenced and assembled mitogenomes from five Asian Gnetum species. These genomes vary remarkably in size and foreign DNA content. We identified 15 mitochondrion-derived and five plastid-derived (MTPT) foreign genes. Our phylogenetic analyses strongly indicate that these foreign genes were transferred from diverse eudicots-mostly from the Rubiaceae genus Coptosapelta and ten genera of Malpighiales. This indicates that Asian Gnetum has experienced multiple independent HGT events. Patterns of sequence evolution strongly suggest DNA-mediated transfer between mitochondria as the primary mechanism giving rise to these HGT events. Most Asian Gnetum species are lianas and often entwined with sympatric angiosperms. We therefore propose that close apposition of Gnetum and angiosperm stems presents opportunities for interspecific cell-to-cell contact through friction and wounding, leading to HGT.<br><br>CONCLUSIONS: Our study reveals that multiple HGT events have resulted in massive amounts of angiosperm mitochondrial DNA integrated into Asian Gnetum mitogenomes. Gnetum and its neighboring angiosperms are often entwined with each other, possibly accounting for frequent HGT between these two phylogenetically remote lineages.},
}
@article {pmid38914331,
year = {2024},
author = {Haffiez, N and Kalantar, E and Zakaria, BS and Azizi, SMM and Farner, JM and Dhar, BR},
title = {Impact of aging of primary and secondary polystyrene nanoplastics on the transmission of antibiotic resistance genes in anaerobic digestion.},
journal = {The Science of the total environment},
volume = {947},
number = {},
pages = {174213},
doi = {10.1016/j.scitotenv.2024.174213},
pmid = {38914331},
issn = {1879-1026},
mesh = {Anaerobiosis ; *Polystyrenes ; *Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; Microplastics/toxicity ; Waste Disposal, Fluid/methods ; Water Pollutants, Chemical/analysis/toxicity ; Bioreactors/microbiology ; },
abstract = {Sewage sludge is a significant reservoir of nano/microplastics (NPs/MPs) and antibiotic resistance genes (ARGs). Research has revealed that NPs/MPs may exert an inhibitory effect on anaerobic digestion (AD) of sludge. Moreover, NPs/MPs can influence microbial community diversity and composition, potentially increasing ARGs dissemination. The morphological changes to NPs/MPs surface due to aging contribute to modifying hydrophobic properties. To date, there is limited comprehension regarding how various surface properties of NPs influence ARGs dissemination during AD. This study investigated the impact of primary aged/non-aged and secondary aged/non-aged polystyrene nanoplastics (PSNPs) on ARGs and mobile genetic elements (MGEs) propagation during AD. The findings indicated that the UV-aging process resulted in surface oxidation and distinct morphological characteristics in both primary and secondary PSNPs, while the surface oxidation effect was more pronounced in the secondary aged PSNPs. High concentrations (150 μg/L) of primary and secondary PSNPs inhibited methane production, with secondary PSNPs causing greater inhibition by 16 to 20 % compared to control. In contrast, low concentration (25 μg/L) had negligible or slightly positive effects on methane production. PSNPs at 150 μg/L reduced total VFA concentration, indicating an inhibitory effect on the fermentation step in the AD process. Primary and secondary PSNPs exhibited changes in EPS characteristics. ARGs abundance was enriched in reactors amended with PSNPs, with the highest abundance of 8.54 × 10[5] copies/g sludge observed in the secondary aged PSNPs (150 μg/L) reactor. Reactors exposed to aged PSNPs exhibited a relatively higher abundance of ARGs compared to reactors exposed to non-aged PSNPs. Exposure to PSNPs increased the microbial community diversity within the digesters and triggered the enrichment of Comamonadaceae and Syntrophaceae, belonging to Proteobacteria phylum. On the other hand, archaeal communities tended to shift towards hydrogenotrophic methanogens in PSNPs reactors. The correlation analysis showed that Comamonadaceae were positively correlated with the majority of ARGs and intl1. A positive correlation was observed between MGEs and most ARGs, suggesting that the increased proliferation of ARGs under PSNPs exposure may be linked to the abundance of MGEs, which in turn promotes the growth of hosts carrying ARGs. These findings suggest that aged and non-aged NPs could substantially impact the spread of ARGs and MGEs, which also led to notable alterations in the composition of the microbial community. Overall, this study provides valuable insights into the multifaceted impacts of PSNPs with various characteristics on AD processes, microbial communities, and ARGs proliferation, highlighting the urgent need for comprehensive assessments of NPs pollutants in the environment.},
}
@article {pmid38913753,
year = {2024},
author = {Maier, JL and Gin, C and Callahan, B and Sheriff, EK and Duerkop, BA and Kleiner, M},
title = {Pseudo-pac site sequences used by phage P22 in generalized transduction of Salmonella.},
journal = {PLoS pathogens},
volume = {20},
number = {6},
pages = {e1012301},
pmid = {38913753},
issn = {1553-7374},
support = {R01 AI141479/AI/NIAID NIH HHS/United States ; R35 GM138362/GM/NIGMS NIH HHS/United States ; },
mesh = {*Bacteriophage P22/genetics ; *Salmonella typhimurium/virology/genetics ; Transduction, Genetic ; Gene Transfer, Horizontal ; Genome, Bacterial ; DNA Packaging ; },
abstract = {Salmonella enterica Serovar Typhimurium (Salmonella) and its bacteriophage P22 are a model system for the study of horizontal gene transfer by generalized transduction. Typically, the P22 DNA packaging machinery initiates packaging when a short sequence of DNA, known as the pac site, is recognized on the P22 genome. However, sequences similar to the pac site in the host genome, called pseudo-pac sites, lead to erroneous packaging and subsequent generalized transduction of Salmonella DNA. While the general genomic locations of the Salmonella pseudo-pac sites are known, the sequences themselves have not been determined. We used visualization of P22 sequencing reads mapped to host Salmonella genomes to define regions of generalized transduction initiation and the likely locations of pseudo-pac sites. We searched each genome region for the sequence with the highest similarity to the P22 pac site and aligned the resulting sequences. We built a regular expression (sequence match pattern) from the alignment and used it to search the genomes of two P22-susceptible Salmonella strains-LT2 and 14028S-for sequence matches. The final regular expression successfully identified pseudo-pac sites in both LT2 and 14028S that correspond with generalized transduction initiation sites in mapped read coverages. The pseudo-pac site sequences identified in this study can be used to predict locations of generalized transduction in other P22-susceptible hosts or to initiate generalized transduction at specific locations in P22-susceptible hosts with genetic engineering. Furthermore, the bioinformatics approach used to identify the Salmonella pseudo-pac sites in this study could be applied to other phage-host systems.},
}
@article {pmid38911822,
year = {2024},
author = {Banerjee, P and Eulenstein, O and Friedberg, I},
title = {Discovering genomic islands in unannotated bacterial genomes using sequence embedding.},
journal = {Bioinformatics advances},
volume = {4},
number = {1},
pages = {vbae089},
pmid = {38911822},
issn = {2635-0041},
abstract = {MOTIVATION: Genomic islands (GEIs) are clusters of genes in bacterial genomes that are typically acquired by horizontal gene transfer. GEIs play a crucial role in the evolution of bacteria by rapidly introducing genetic diversity and thus helping them adapt to changing environments. Specifically of interest to human health, many GEIs contain pathogenicity and antimicrobial resistance genes. Detecting GEIs is, therefore, an important problem in biomedical and environmental research. There have been many previous studies for computationally identifying GEIs. Still, most of these studies rely on detecting anomalies in the unannotated nucleotide sequences or on a fixed set of known features on annotated nucleotide sequences.<br><br>RESULTS: Here, we present TreasureIsland, which uses a new unsupervised representation of DNA sequences to predict GEIs. We developed a high-precision boundary detection method featuring an incremental fine-tuning of GEI borders, and we evaluated the accuracy of this framework using a new comprehensive reference dataset, Benbow. We show that TreasureIsland's accuracy rivals other GEI predictors, enabling efficient and faster identification of GEIs in unannotated bacterial genomes.<br><br>TreasureIsland is available under an MIT license at: https://github.com/FriedbergLab/GenomicIslandPrediction.},
}
@article {pmid38910035,
year = {2025},
author = {Zarlenga, DS and Hoberg, EP and Thompson, P and Rosenthal, B},
title = {Trichinella: Becoming a parasite.},
journal = {Veterinary parasitology},
volume = {333},
number = {},
pages = {110220},
doi = {10.1016/j.vetpar.2024.110220},
pmid = {38910035},
issn = {1873-2550},
mesh = {Animals ; *Biological Evolution ; Climate Change ; Gene Transfer, Horizontal ; Host-Parasite Interactions ; *Phylogeny ; *Trichinella/genetics/classification/physiology ; Trichinellosis/parasitology ; },
abstract = {Phylogenetic evidence indicates that free-living nematodes gave rise to parasitic nematodes where parasitism evolved independently at least 15 times. The high level of genetic and biological diversity among parasites dictates an equally high level of diversity in the transition to parasitism. We previously hypothesized that horizontal gene transfer (HGT) played an important role in the evolution of parasitism among early ancestors of Trichinella, mediated by an interplay of ecological and evolutionary pathways that contributed to persistence and diversification. We propose that host selection may have been associated with the metabolism of ammonia and engender a new paradigm whereby the reprogrammed nurse cell is capable of generating cyanate thereby enabling the importance of the Trichinella cyanase in the longevity of the cell. Parasites and parasitism have revealed considerable resilience against a backdrop of climate change and environmental perturbation. Here we provide a putative link between key periods in the evolution of Trichinella and major geological and climatological events dating back 500 million years. A useful lens for exploring such ideas, the Stockholm Paradigm, integrates Ecological Fitting (a foundation for host colonization and diversification), the Oscillation Hypothesis (recurring shifts between trends in generalization and specialization relative to host range), the Geographic Mosaic Theory of Coevolution (microevolutionary co-adaptive processes), and the Taxon Pulse Hypothesis (alternating events of biotic expansion i.e., exploitation in evolutionary and ecological time). Here we examine how one or more of these interactive theories, in a phylogenetic-historical context and in conjunction with HGT, may help explain the scope and depth of diversity among Trichinella genotypes.},
}
@article {pmid38908181,
year = {2024},
author = {Wu, Y and Niu, Q and Liu, Y and Zheng, X and Long, M and Chen, Y},
title = {Chlorinated organophosphorus flame retardants induce the propagation of antibiotic resistance genes in sludge fermentation systems: Insight of chromosomal mutation and microbial traits.},
journal = {Journal of hazardous materials},
volume = {476},
number = {},
pages = {134971},
doi = {10.1016/j.jhazmat.2024.134971},
pmid = {38908181},
issn = {1873-3336},
mesh = {*Flame Retardants/toxicity ; *Sewage/microbiology ; *Fermentation ; *Mutation ; Organophosphorus Compounds/toxicity/chemistry ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; Molecular Docking Simulation ; Genes, Bacterial ; Gene Transfer, Horizontal ; Bacteria/genetics/drug effects/metabolism ; Organophosphates/toxicity ; Chromosomes, Bacterial/genetics ; },
abstract = {Waste activated sludge (WAS) is a critical reservoir for antibiotic resistance genes (ARGs) due to the prevalent misuse of antibiotics. Horizontal gene transfer (HGT) is the primary mechanism for ARGs spread through mobile genetic elements (MGEs). However, the role of non-antibiotic organophosphorus flame retardants (Cl-OFRs) in ARG transmission in the WAS fermentation system remains unclear. This study examines the effects of tris(2-chloroethyl) phosphate (TCEP), a representative Cl-OFR, on ARG dynamics in WAS fermentation using molecular docking and metagenomic analysis. The results showed a 33.4 % increase in ARG abundance in the presence of TCEP. Interestingly, HGT did not appear to be the primary mechanism of ARG dissemination under TCEP stress, as evidenced by a 2.51 % decrease in MGE abundance. TCEP binds to sludge through hydrogen bonds with a binding energy of - 3.6 kJ/mol, leading to microbial damage and an increase in the proportion of non-viable cells. This interaction prompts a microbial shift toward Firmicutes with thick cell walls, which are significant ARG carriers. Additionally, TCEP induces chromosomal mutations through oxidative stress and the SOS response, contributing to ARG formation. Microorganisms also develop multidrug resistance mechanisms to expel TCEP and mitigate its toxicity. This study provides a comprehensive understanding of Cl-OFRs effects on the ARGs fates in WAS fermentation system and offers guidance for the safe and efficient treatment of Cl-OFRs and WAS.},
}
@article {pmid38906294,
year = {2024},
author = {Yao, S and Yu, J and Zhang, T and Xie, J and Yan, C and Ni, X and Guo, B and Cui, C},
title = {Comprehensive analysis of distribution characteristics and horizontal gene transfer elements of blaNDM-1-carrying bacteria.},
journal = {The Science of the total environment},
volume = {946},
number = {},
pages = {173907},
doi = {10.1016/j.scitotenv.2024.173907},
pmid = {38906294},
issn = {1879-1026},
mesh = {*beta-Lactamases/genetics ; *Gene Transfer, Horizontal ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; },
abstract = {The worldwide dissemination of New Delhi metallo-β-lactamase-1 (NDM-1), which mediates resistance to almost all clinical β-lactam antibiotics, is a major public health problem. The global distribution, species, sources, and potential transfer risk of blaNDM-1-carrying bacteria are unclear. Results of a comprehensive analysis of literature in 2010-2022 showed that a total of 6002 blaNDM-1 carrying bacteria were widely distributed around 62 countries with a high trend in the coastal areas. Opportunistic pathogens or pathogens like Klebsiella sp., Escherichia sp., Acinetobacter sp. and Pseudomonas sp. were the four main species indicating the potential microbial risk. Source analysis showed that 86.45 % of target bacteria were isolated from the source of hospital (e.g., Hospital patients and wastewater) and little from surface water (5.07 %) and farms (3.98 %). A plasmid-encoded blaNDM-1Acinetobacter sp. with the resistance mechanisms of antibiotic efflux pump, antibiotic target change and antibiotic degradation was isolated from the wastewater of a typical tertiary hospital. Insertion sequences (IS3 and IS30) located in the adjacent 5 kbp of blaNDM-1-bleMBL gene cluster indicating the transposon-mediated horizontal gene transfer risk. These results showed that the worldwide spread of blaNDM-1-carrying bacteria and its potential horizontal gene transfer risk deserve good control.},
}
@article {pmid38905247,
year = {2024},
author = {Mohamed, DS and Abd El-Baky, RM and El-Mokhtar, MA and Ghanem, SK and Yahia, R and Alqahtani, AM and Abourehab, MAS and Ahmed, EF},
title = {Influence of selected non-antibiotic pharmaceuticals on antibiotic resistance gene transfer in Escherichia coli.},
journal = {PloS one},
volume = {19},
number = {6},
pages = {e0304980},
pmid = {38905247},
issn = {1932-6203},
mesh = {*Escherichia coli/drug effects/genetics ; *Gene Transfer, Horizontal ; *Plasmids/genetics ; Metoclopramide/pharmacology ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics/drug effects ; Conjugation, Genetic ; Drug Resistance, Microbial/genetics/drug effects ; },
abstract = {BACKGROUND: Antibiotic resistance genes (ARGs) transfer rapidly among bacterial species all over the world contributing to the aggravation of antibiotic resistance crisis. Antibiotics at sub-inhibitory concentration induce horizontal gene transfer (HRT) between bacteria, especially through conjugation. The role of common non-antibiotic pharmaceuticals in the market in disseminating antibiotic resistance is not well studied.<br><br>OBJECTIVES: In this work, we indicated the effect of some commonly used non-antibiotic pharmaceuticals including antiemetic (metoclopramide HCl) and antispasmodics (hyoscine butyl bromide and tiemonium methyl sulfate) on the plasmid-mediated conjugal transfer of antibiotic resistance genes between pathogenic E. coli in the gastric intestinal tract (GIT).<br><br>METHODS: Broth microdilution assay was used to test the antibacterial activity of the tested non-antibiotic pharmaceuticals. A conjugation mating system was applied in presence of the studied non-antibiotic pharmaceuticals to test their effect on conjugal transfer frequency. Plasmid extraction and PCR were performed to confirm the conjugation process. Transmission electron microscopy (TEM) was used for imaging the effect of non-antibiotic pharmaceuticals on bacterial cells.<br><br>RESULTS: No antibacterial activity was reported for the used non-antibiotic pharmaceuticals. Plasmid-mediated conjugal transfer between isolates was induced by metoclopramide HCl but suppressed by hyoscine butyl bromide. Tiemonium methylsulfate slightly promoted conjugal transfer. Aggregation between cells and periplasmic bridges was clear in the case of metoclopramide HCl while in presence of hyoscine butyl bromide little affinity was observed.<br><br>CONCLUSION: This study indicates the contribution of non-antibiotic pharmaceuticals to the dissemination and evolution of antibiotic resistance at the community level. Metoclopramide HCl showed an important role in the spread of antibiotic resistance.},
}
@article {pmid38904756,
year = {2024},
author = {Kaur, J and Verma, H and Kaur, J and Lata, P and Dhingra, GG and Lal, R},
title = {In Silico Analysis of the Phylogenetic and Physiological Characteristics of Sphingobium indicum B90A: A Hexachlorocyclohexane-Degrading Bacterium.},
journal = {Current microbiology},
volume = {81},
number = {8},
pages = {233},
pmid = {38904756},
issn = {1432-0991},
mesh = {*Phylogeny ; *Sphingomonadaceae/genetics/metabolism/classification ; *Genome, Bacterial ; *Hexachlorocyclohexane/metabolism ; *Computer Simulation ; *Biodegradation, Environmental ; Genomic Islands ; Gene Transfer, Horizontal ; },
abstract = {The study focuses on the in silico genomic characterization of Sphingobium indicum B90A, revealing a wealth of genes involved in stress response, carbon monoxide oxidation, β-carotene biosynthesis, heavy metal resistance, and aromatic compound degradation, suggesting its potential as a bioremediation agent. Furthermore, genomic adaptations among nine Sphingomonad strains were explored, highlighting shared core genes via pangenome analysis, including those related to the shikimate pathway and heavy metal resistance. The majority of genes associated with aromatic compound degradation, heavy metal resistance, and stress response were found within genomic islands across all strains. Sphingobium indicum UT26S exhibited the highest number of genomic islands, while Sphingopyxis alaskensis RB2256 had the maximum fraction of its genome covered by genomic islands. The distribution of lin genes varied among the strains, indicating diverse genetic responses to environmental pressures. Additionally, in silico evidence of horizontal gene transfer (HGT) between plasmids pSRL3 and pISP3 of the Sphingobium and Sphingomonas genera, respectively, has been provided. The manuscript offers novel insights into strain B90A, highlighting its role in horizontal gene transfer and refining evolutionary relationships among Sphingomonad strains. The discovery of stress response genes and the czcABCD operon emphasizes the potential of Sphingomonads in consortia development, supported by genomic island analysis.},
}
@article {pmid38904697,
year = {2024},
author = {Bhattacharjee, A and Singh, AK},
title = {Delineating the Acquired Genetic Diversity and Multidrug Resistance in Alcaligenes from Poultry Farms and Nearby Soil.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {62},
number = {7},
pages = {511-523},
pmid = {38904697},
issn = {1976-3794},
support = {OLP-2035//Council for Scientific and Industrial Research/ ; OLP-2081//Council for Scientific and Industrial Research/ ; GPP-0423//DST-SERB/ ; },
mesh = {Animals ; *Drug Resistance, Multiple, Bacterial/genetics ; *Poultry/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Soil Microbiology ; *Farms ; Microbial Sensitivity Tests ; Genetic Variation ; Whole Genome Sequencing ; Genomic Islands ; Alcaligenes faecalis/genetics/isolation &amp; purification/drug effects ; Genome, Bacterial ; Feces/microbiology ; Gram-Negative Bacterial Infections/microbiology/veterinary ; },
abstract = {Alcaligenes faecalis is one of the most important and clinically significant environmental pathogens, increasing in importance due to its isolation from soil and nosocomial environments. The Gram-negative soil bacterium is associated with skin endocarditis, bacteremia, dysentery, meningitis, endophthalmitis, urinary tract infections, and pneumonia in patients. With emerging antibiotic resistance in A. faecalis, it has become crucial to understand the origin of such resistance genes within this clinically significant environmental and gut bacterium. In this research, we studied the impact of antibiotic overuse in poultry and its effect on developing resistance in A. faecalis. We sampled soil and faecal materials from five poultry farms, performed whole genome sequencing &amp; analysis and identified four strains of A. faecalis. Furthermore, we characterized the genes in the genomic islands of A. faecalis isolates. We found four multidrug-resistant A. faecalis strains that showed resistance against vancomycin (MIC >1000 μg/ml), ceftazidime (50 μg/ml), colistin (50 μg/ml) and ciprofloxacin (50 μg/ml). From whole genome comparative analysis, we found more than 180 resistance genes compared to the reference sequence. Parts of our assembled contigs were found to be similar to different bacteria which included pbp1A and pbp2 imparting resistance to amoxicillin originally a part of Helicobacter and Bordetella pertussis. We also found the Mycobacterial insertion element IS6110 in the genomic islands of all four genomes. This prominent insertion element can be transferred and induce resistance to other bacterial genomes. The results thus are crucial in understanding the transfer of resistance genes in the environment and can help in developing regimes for antibiotic use in the food and poultry industry.},
}
@article {pmid38903782,
year = {2024},
author = {Ott, LC and Mellata, M},
title = {Short-chain fatty acids inhibit bacterial plasmid transfer through conjugation in vitro and in ex vivo chicken tissue explants.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1414401},
pmid = {38903782},
issn = {1664-302X},
abstract = {The animal gut acts as a potent reservoir for spreading and maintaining conjugative plasmids that confer antimicrobial resistance (AMR), fitness, and virulence attributes. Interventions that inhibit the continued emergence and expansion of AMR and virulent strains in agricultural and clinical environments are greatly desired. This study aims to determine the presence and efficacy of short-chain fatty acids (SCFA) inhibitory effects on the conjugal transfer of AMR plasmids. In vitro broth conjugations were conducted between donor Escherichia coli strains carrying AMP plasmids and the plasmid-less Escherichia coli HS-4 recipient strain. Conjugations were supplemented with ddH2O or SCFAs at 1, 0.1, 0.01, or 0.001 molar final concentration. The addition of SCFAs completely inhibited plasmid transfer at 1 and 0.1 molar and significantly (p < 0.05) reduced transfer at 0.01 molar, regardless of SCFA tested. In explant models for the chicken ceca, either ddH2O or a final concentration of 0.025 M SCFAs were supplemented to the explants infected with donor and recipient E. coli. In every SCFA tested, significant decreases in transconjugant populations compared to ddH2O-treated control samples were observed with minimal effects on donor and recipient populations. Finally, significant reductions in transconjugants for plasmids of each incompatibility type (IncP1ε, IncFIβ, and IncI1) tested were detected. This study demonstrates for the first time the broad inhibition ability of SCFAs on bacterial plasmid transfer and eliminates AMR with minimal effect on bacteria. Implementing interventions that increase the concentrations of SCFAs in the gut may be a viable method to reduce the risk, incidence, and rate of AMR emergence in agricultural and human environments.},
}
@article {pmid38903098,
year = {2024},
author = {Sastre-Dominguez, J and DelaFuente, J and Toribio-Celestino, L and Herencias, C and Herrador-Gomez, P and Costas, C and Hernandez-Garcia, M and Canton, R and Rodriguez-Beltran, J and Santos-Lopez, A and San Millan, A},
title = {Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.03.01.582297},
pmid = {38903098},
issn = {2692-8205},
abstract = {Plasmids are extrachromosomal genetic elements commonly found in bacteria. Plasmids are known to fuel bacterial evolution through horizontal gene transfer (HGT), but recent analyses indicate that they can also promote intragenomic adaptations. However, the role of plasmids as catalysts of bacterial evolution beyond HGT remains poorly explored. In this study, we investigate the impact of a widespread conjugative plasmid, pOXA-48, on the evolution of various multidrug-resistant clinical enterobacteria. Combining experimental and within-patient evolution analyses, we unveil that plasmid pOXA-48 promotes bacterial evolution through the transposition of plasmid-encoded insertion sequence 1 (IS1) elements. Specifically, IS1-mediated gene inactivations expedite the adaptation rate of clinical strains in vitro and foster within-patient adaptation in the gut microbiota. We decipher the mechanism underlying the plasmid-mediated surge in IS1 transposition, revealing a negative feedback loop regulated by the genomic copy number of IS1. Given the overrepresentation of IS elements in bacterial plasmids, our findings propose that plasmid-mediated IS transposition represents a crucial mechanism for swift bacterial adaptation.},
}
@article {pmid38902796,
year = {2024},
author = {Chaudhari, NM and Pérez-Carrascal, OM and Overholt, WA and Totsche, KU and Küsel, K},
title = {Genome streamlining in Parcubacteria transitioning from soil to groundwater.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {41},
pmid = {38902796},
issn = {2524-6372},
abstract = {BACKGROUND: To better understand the influence of habitat on the genetic content of bacteria, with a focus on members of Candidate Phyla Radiation (CPR) bacteria, we studied the effects of transitioning from soil via seepage waters to groundwater on genomic composition of ultra-small Parcubacteria, the dominating CPR class in seepage waters, using genome resolved metagenomics.<br><br>RESULTS: Bacterial metagenome-assembled genomes (MAGs), (318 total, 32 of Parcubacteria) were generated from seepage waters and compared directly to groundwater counterparts. The estimated average genome sizes of members of major phyla Proteobacteria, Bacteroidota and Cand. Patescibacteria (Candidate Phyla Radiation - CPR bacteria) were significantly higher in soil-seepage water as compared to their groundwater counterparts. Seepage water Parcubacteria (Paceibacteria) exhibited 1.18-fold greater mean genome size and 2-fold lower mean proportion of pseudogenes than those in groundwater. Bacteroidota and Proteobacteria also showed a similar trend of reduced genomes in groundwater compared to seepage. While exploring gene loss and adaptive gains in closely related CPR lineages in groundwater, we identified a membrane protein, and a lipoglycopeptide resistance gene unique to a seepage Parcubacterium genome. A nitrite reductase gene was also identified and was unique to the groundwater Parcubacteria genomes, likely acquired from other planktonic microbes via horizontal gene transfer.<br><br>CONCLUSIONS: Overall, our data suggest that bacteria in seepage waters, including ultra-small Parcubacteria, have significantly larger genomes and higher metabolic enrichment than their groundwater counterparts, highlighting possible genome streamlining of the latter in response to habitat selection in an oligotrophic environment.},
}
@article {pmid38901473,
year = {2024},
author = {Walt, HK and Ahn, SJ and Hoffmann, FG},
title = {Horizontally transferred glycoside hydrolase 26 may aid hemipteran insects in plant tissue digestion.},
journal = {Molecular phylogenetics and evolution},
volume = {198},
number = {},
pages = {108134},
doi = {10.1016/j.ympev.2024.108134},
pmid = {38901473},
issn = {1095-9513},
mesh = {Animals ; *Gene Transfer, Horizontal ; *Hemiptera/genetics/enzymology/classification ; *Phylogeny ; *Glycoside Hydrolases/genetics ; Plants/genetics/classification ; },
abstract = {Glycoside hydrolases are enzymes that break down complex carbohydrates into simple sugars by catalyzing the hydrolysis of glycosidic bonds. There have been multiple instances of adaptive horizontal gene transfer of genes belonging to various glycoside hydrolase families from microbes to insects, as glycoside hydrolases can metabolize constituents of the carbohydrate-rich plant cell wall. In this study, we characterize the horizontal transfer of a gene from the glycoside hydrolase family 26 (GH26) from bacteria to insects of the order Hemiptera. Our phylogenies trace the horizontal gene transfer to the common ancestor of the superfamilies Pentatomoidea and Lygaeoidea, which include stink bugs and seed bugs. After horizontal transfer, the gene was assimilated into the insect genome as indicated by the gain of an intron, and a eukaryotic signal peptide. Subsequently, the gene has undergone independent losses and expansions in copy number in multiple lineages, suggesting an adaptive role of GH26s in some insects. Finally, we measured tissue-level gene expression of multiple stink bugs and the large milkweed bug using publicly available RNA-seq datasets. We found that the GH26 genes are highly expressed in tissues associated with plant digestion, especially in the principal salivary glands of the stink bugs. Our results are consistent with the hypothesis that this horizontally transferred GH26 was co-opted by the insect to aid in plant tissue digestion and that this HGT event was likely adaptive.},
}
@article {pmid38896653,
year = {2024},
author = {Elliott, JFK and McLeod, DV and Taylor, TB and Westra, ER and Gandon, S and Watson, BNJ},
title = {Conditions for the spread of CRISPR-Cas immune systems into bacterial populations.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38896653},
issn = {1751-7370},
support = {BB/T008741/1//Biotechnology and Biological Sciences Research Council SWBio DTP/ ; DH150169//Royal Society Dorothy Hodgkin Fellowship/ ; NE/S001921/1//Natural Environment Research Council/ ; BB/X010600/1//Biotechnology and Biological Sciences Research Council Discovery Fellowship/ ; },
mesh = {*CRISPR-Cas Systems ; *Bacteriophages/genetics ; *Bacteria/genetics/virology/classification ; Pseudomonas aeruginosa/virology/genetics/immunology ; Gene Transfer, Horizontal ; Clustered Regularly Interspaced Short Palindromic Repeats ; },
abstract = {Bacteria contain a wide variety of innate and adaptive immune systems which provide protection to the host against invading genetic material, including bacteriophages (phages). It is becoming increasingly clear that bacterial immune systems are frequently lost and gained through horizontal gene transfer. However, how and when new immune systems can become established in a bacterial population have remained largely unstudied. We developed a joint epidemiological and evolutionary model that predicts the conditions necessary for the spread of a CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) immune system into a bacterial population lacking this system. We found that whether bacteria carrying CRISPR-Cas will spread (increase in frequency) into a bacterial population depends on the abundance of phages and the difference in the frequency of phage resistance mechanisms between bacteria carrying a CRISPR-Cas immune system and those not (denoted as ${f}
_{\Delta }
$). Specifically, the abundance of cells carrying CRISPR-Cas will increase if there is a higher proportion of phage resistance (either via CRISPR-Cas immunity or surface modification) in the CRISPR-Cas-possessing population than in the cells lacking CRISPR-Cas. We experimentally validated these predictions in a model using Pseudomonas aeruginosa PA14 and phage DMS3vir. Specifically, by varying the initial ratios of different strains of bacteria that carry alternative forms of phage resistance, we confirmed that the spread of cells carrying CRISPR-Cas through a population can be predicted based on phage density and the relative frequency of resistance phenotypes. Understanding which conditions promote the spread of CRISPR-Cas systems helps to predict when and where these defences can become established in bacterial populations after a horizontal gene transfer event, both in ecological and clinical contexts.},
}
@article {pmid38896471,
year = {2024},
author = {Lerminiaux, N and Mitchell, R and Katz, K and Fakharuddin, K and McGill, E and Mataseje, L},
title = {Plasmid genomic epidemiology of carbapenem-hydrolysing class D β-lactamase (CDHL)-producing Enterobacterales in Canada, 2010-2021.},
journal = {Microbial genomics},
volume = {10},
number = {6},
pages = {},
pmid = {38896471},
issn = {2057-5858},
mesh = {*beta-Lactamases/genetics ; *Plasmids/genetics ; Canada/epidemiology ; Humans ; *Carbapenems/pharmacology ; *Whole Genome Sequencing ; *Bacterial Proteins/genetics ; *Enterobacteriaceae Infections/microbiology/epidemiology ; Enterobacteriaceae/genetics/drug effects/classification ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Cross Infection/microbiology/epidemiology ; },
abstract = {Carbapenems are last-resort antibiotics for treatment of infections caused by multidrug-resistant Enterobacterales, but carbapenem resistance is a rising global threat due to the acquisition of carbapenemase genes. Oxacillinase-48 (bla OXA-48)-type carbapenemases are increasing in abundance in Canada and elsewhere; these genes are frequently found on mobile genetic elements and are associated with specific transposons. This means that alongside clonal dissemination, bla OXA-48-type genes can spread through plasmid-mediated horizontal gene transfer. We applied whole genome sequencing to characterize 249 bla OXA-48-type-producing Enterobacterales isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short- and long-read sequencing, we obtained 70 complete and circular bla OXA-48-type-encoding plasmids. Using MOB-suite, four major plasmids clustered were identified, and we further estimated a plasmid cluster for 91.9 % (147/160) of incomplete bla OXA-48-type-encoding contigs. We identified different patterns of carbapenemase mobilization across Canada, including horizontal transmission of bla OXA-181/IncX3 plasmids (75/249, 30.1 %) and bla OXA-48/IncL/M plasmids (47/249, 18.9 %), and both horizontal transmission and clonal transmission of bla OXA-232 for Klebsiella pneumoniae ST231 on ColE2-type/ColKP3 plasmids (25/249, 10.0 %). Our findings highlight the diversity of OXA-48-type plasmids and indicate that multiple plasmid clusters and clonal transmission have contributed to bla OXA-48-type spread and persistence in Canada.},
}
@article {pmid38896033,
year = {2024},
author = {Huang, B and Xiao, Y and Zhang, Y},
title = {Asgard archaeal selenoproteome reveals a roadmap for the archaea-to-eukaryote transition of selenocysteine incorporation machinery.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38896033},
issn = {1751-7370},
support = {32270680//National Natural Science Foundation of China/ ; 2023SHIBS0003//Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions/ ; },
mesh = {*Selenocysteine/metabolism/genetics ; *Archaea/genetics/metabolism/classification ; *Selenoproteins/genetics/metabolism ; *Eukaryota/genetics/classification/metabolism ; Genome, Archaeal ; Proteome ; Codon, Terminator/genetics ; Archaeal Proteins/genetics/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; },
abstract = {Selenocysteine (Sec) is encoded by the UGA codon that normally functions as a stop signal and is specifically incorporated into selenoproteins via a unique recoding mechanism. The translational recoding of UGA as Sec is directed by an unusual RNA structure, the SECIS element. Although archaea and eukaryotes adopt similar Sec encoding machinery, the SECIS elements have no similarities to each other with regard to sequence and structure. We analyzed >400 Asgard archaeal genomes to examine the occurrence of both Sec encoding system and selenoproteins in this archaeal superphylum, the closest prokaryotic relatives of eukaryotes. A comprehensive map of Sec utilization trait has been generated, providing the most detailed understanding of the use of this nonstandard amino acid in Asgard archaea so far. By characterizing the selenoproteomes of all organisms, several selenoprotein-rich phyla and species were identified. Most Asgard archaeal selenoprotein genes possess eukaryotic SECIS-like structures with varying degrees of diversity. Moreover, euryarchaeal SECIS elements might originate from Asgard archaeal SECIS elements via lateral gene transfer, indicating a complex and dynamic scenario of the evolution of SECIS element within archaea. Finally, a roadmap for the transition of eukaryotic SECIS elements from archaea was proposed, and selenophosphate synthetase may serve as a potential intermediate for the generation of ancestral eukaryotic SECIS element. Our results offer new insights into a deeper understanding of the evolution of Sec insertion machinery.},
}
@article {pmid38895488,
year = {2024},
author = {Ellison, TJ and Ellison, CK},
title = {DNA binding is rate-limiting for natural transformation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38895488},
issn = {2692-8205},
support = {R35 GM150916/GM/NIGMS NIH HHS/United States ; },
abstract = {Bacteria take up environmental DNA using dynamic appendages called type IV pili (T4P) to elicit horizontal gene transfer in a process called natural transformation. Natural transformation is widespread amongst bacteria yet determining how different factors universally contribute to or limit this process across species has remained challenging. Here we show that Acinetobacter baylyi, the most naturally transformable species, is highly transformable due to its ability to robustly bind nonspecific DNA via a dedicated orphan minor pilin, FimT. We show that, compared to its homologues, A. baylyi FimT contains multiple positively charged residues that additively promote DNA binding efficiency. Expression of A. baylyi FimT in a closely related Acinetobacter pathogen is sufficient to substantially improve its capacity for natural transformation, demonstrating that T4P-DNA binding is a rate-limiting step in this process. These results demonstrate the importance of T4P-DNA binding efficiency in driving natural transformation, establishing a key factor limiting horizontal gene transfer.},
}
@article {pmid38895396,
year = {2025},
author = {Chang, TH and Pourtois, JD and Haddock, NL and Furkuawa, D and Kelly, KE and Amanatullah, DF and Burgener, E and Milla, C and Banaei, N and Bollyky, PL},
title = {Prophages are Infrequently Associated With Antibiotic Resistance in Pseudomonas aeruginosa Clinical Isolates.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.06.02.595912},
pmid = {38895396},
issn = {2692-8205},
support = {R01 HL148184/HL/NHLBI NIH HHS/United States ; },
abstract = {UNLABELLED: Lysogenic bacteriophages can integrate their genome into the bacterial chromosome in the form of a prophage and can promote genetic transfer between bacterial strains in vitro . However, the contribution of lysogenic phages to the incidence of antimicrobial resistance (AMR) in clinical settings is poorly understood. Here, in a set of 186 clinical isolates of Pseudomonas aeruginosa collected from respiratory cultures from 82 patients with cystic fibrosis (CF), we evaluate the links between prophage counts and both genomic and phenotypic resistance to six anti-pseudomonal antibiotics: tobramycin, colistin, ciprofloxacin, meropenem, aztreonam, and piperacillin-tazobactam. We identified 239 different prophages in total. We find that P. aeruginosa isolates contain on average 3.06 +/- 1.84 (SD) predicted prophages. We find no significant association between the number of prophages per isolate and the minimum inhibitory concentration (MIC) for any of these antibiotics. We then investigate the relationship between particular prophages and AMR. We identify a single lysogenic phage associated with phenotypic resistance to the antibiotic tobramycin and, consistent with this association, we observe that AMR genes associated with resistance to tobramycin are more likely to be found when this prophage is present. However we find that they are not encoded directly on prophage sequences. Additionally, we identify a single prophage statistically associated with ciprofloxacin resistance but do not identify any genes associated with ciprofloxacin phenotypic resistance. These findings suggest that prophages are only infrequently associated with the AMR genes in clinical isolates of P. aeruginosa .<br><br>IMPORTANCE: Antibiotic-resistant infections of Pseudomonas aeruginosa , a leading pathogen in patients with Cystic Fibrosis (CF) are a global health threat. While lysogenic bacteriophages are known to facilitate horizontal gene transfer, their role in promoting antibiotic resistance in clinical settings remains poorly understood. In our analysis of 186 clinical isolates of P. aeruginosa from CF patients, we find that prophage abundance does not predict phenotypic resistance to key antibiotics but that specific prophages are infrequently associated with tobramycin resistance genes. In addition, we do not find antimicrobial resistance (AMR) genes encoded directly on prophages. These results highlight that while phages can be associated with AMR, phage-mediated AMR transfer may be rare in clinical isolates and difficult to identify. This work is important for future efforts on mitigating AMR in Cystic Fibrosis and other vulnerable populations affected by Pseudomonas aeruginosa infections and advances our understanding of bacterial-phage dynamics in clinical infections.},
}
@article {pmid38895369,
year = {2024},
author = {Klein, JA and Predeus, AV and Greissl, AR and Clark-Herrera, MM and Cruz, E and Cundiff, JA and Haeberle, AL and Howell, M and Lele, A and Robinson, DJ and Westerman, TL and Wrande, M and Wright, SJ and Green, NM and Vallance, BA and McClelland, M and Mejia, A and Goodman, AG and Elfenbein, JR and Knodler, LA},
title = {Pathogenic diversification of the gut commensal Providencia alcalifaciens via acquisition of a second type III secretion system.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.06.07.595826},
pmid = {38895369},
issn = {2692-8205},
abstract = {Providencia alcalifaciens is a Gram-negative bacterium found in a wide variety of water and land environments and organisms. It has been isolated as part of the gut microbiome of animals and insects, as well as from stool samples of patients with diarrhea. Specific P. alcalifaciens strains encode gene homologs of virulence factors found in other pathogenic members of the same Enterobacterales order, such as Salmonella enterica serovar Typhimurium and Shigella flexneri. Whether these genes are also pathogenic determinants in P. alcalifaciens is not known. Here we have used P. alcalifaciens 205/92, a clinical isolate, with in vitro and in vivo infection models to investigate P. alcalifaciens -host interactions at the cellular level. Our particular focus was the role of two type III secretion systems (T3SS) belonging to the Inv-Mxi/Spa family. T3SS 1b is widespread in Providencia spp. and encoded on the chromosome. T3SS 1a is encoded on a large plasmid that is present in a subset of P. alcalifaciens strains, which are primarily isolates from diarrheal patients. Using a combination of electron and fluorescence microscopy and gentamicin protection assays we show that P. alcalifaciens 205/92 is internalized into eukaryotic cells, rapidly lyses its internalization vacuole and proliferates in the cytosol. This triggers caspase-4 dependent inflammasome responses in gut epithelial cells. The requirement for the T3SS 1a in entry, vacuole lysis and cytosolic proliferation is host-cell type specific, playing a more prominent role in human intestinal epithelial cells as compared to macrophages. In a bovine ligated intestinal loop model, P. alcalifaciens colonizes the intestinal mucosa, inducing mild epithelial damage with negligible fluid accumulation. No overt role for T3SS 1a or T3SS 1b was seen in the calf infection model. However, T3SS 1b was required for the rapid killing of Drosophila melanogaster . We propose that the acquisition of two T3SS by horizontal gene transfer has allowed P. alcalifaciens to diversify its host range, from a highly virulent pathogen of insects to an opportunistic gastrointestinal pathogen of animals.},
}
@article {pmid38891015,
year = {2024},
author = {Zhou, H and Lu, Z and Liu, X and Bie, X and Xue, F and Tang, S and Feng, Q and Cheng, Y and Yang, J},
title = {Environmentally Relevant Concentrations of Tetracycline Promote Horizontal Transfer of Antimicrobial Resistance Genes via Plasmid-Mediated Conjugation.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
pmid = {38891015},
issn = {2304-8158},
support = {32272295//National Natural Science Foundation of China/ ; BE2022684//Jiangsu Provincial Key Research and Development Program/ ; KJ2024017//the Science and Technology Project of Jiangsu Provincial Administration for Market Regulation/ ; },
abstract = {The ubiquitous presence of antimicrobial-resistant organisms and antimicrobial resistance genes (ARGs) constitutes a major threat to global public safety. Tetracycline (TET) is a common antimicrobial agent that inhibits bacterial growth and is frequently detected in aquatic environments. Although TET may display coselection for resistance, limited knowledge is available on whether and how it might influence plasmid-mediated conjugation. Subinhibitory concentrations (3.9-250 ng/mL) of TET promoted horizontal gene transfer (HGT) via the mobilizable plasmid pVP52-1 from the donor Vibrio parahaemolyticus NJIFDCVp52 to the recipient Escherichia coli EC600 by 1.47- to 3.19-fold. The transcription levels of tetracycline resistance genes [tetA, tetR(A)], conjugation-related genes (traA, traD), outer membrane protein genes (ompA, ompK, ompV), reactive oxygen species (ROS)-related genes (oxyR, rpoS), autoinducer-2 (AI-2) synthesis gene (luxS), and SOS-related genes (lexA, recA) in the donor and recipient were significantly increased. Furthermore, the overproduced intracellular ROS generation and increased cell membrane permeability under TET exposure stimulated the conjugative transfer of ARGs. Overall, this study provides important insights into the contributions of TET to the spread of antimicrobial resistance.},
}
@article {pmid38888367,
year = {2024},
author = {Li, X and Gallardo, O and August, E and Dassa, B and Court, DL and Stavans, J and Arbel-Goren, R},
title = {Stability and gene strand bias of lambda prophages and chromosome organization in Escherichia coli.},
journal = {mBio},
volume = {15},
number = {7},
pages = {e0207823},
pmid = {38888367},
issn = {2150-7511},
support = {//NIH Intramural Research Program/ ; //Kushner Fellowship/ ; //Siegfried and Irma Ullman Professorial Chair/ ; },
mesh = {*Escherichia coli/genetics/virology ; *Bacteriophage lambda/genetics/physiology ; *Chromosomes, Bacterial/genetics ; *Lysogeny/genetics ; Virus Integration ; Gene Transfer, Horizontal ; Genomic Instability ; Repressor Proteins/genetics/metabolism ; Prophages/genetics/physiology ; In Situ Hybridization, Fluorescence ; Viral Regulatory and Accessory Proteins ; },
abstract = {Temperate phage-mediated horizontal gene transfer is a potent driver of genetic diversity in the evolution of bacteria. Most lambdoid prophages in Escherichia coli are integrated into the chromosome with the same orientation with respect to the direction of chromosomal replication, and their location on the chromosome is far from homogeneous. To better understand these features, we studied the interplay between lysogenic and lytic states of phage lambda in both native and inverted integration orientations at the wild-type integration site as well as at other sites on the bacterial chromosome. Measurements of free phage released by spontaneous induction showed that the stability of lysogenic states is affected by location and orientation along the chromosome, with stronger effects near the origin of replication. Competition experiments and range expansions between lysogenic strains with opposite orientations and insertion loci indicated that there are no major differences in growth. Moreover, measurements of the level of transcriptional bursts of the cI gene coding for the lambda phage repressor using single-molecule fluorescence in situ hybridization resulted in similar levels of transcription for both orientations and prophage location. We postulate that the preference for a given orientation and location is a result of a balance between the maintenance of lysogeny and the ability to lyse.IMPORTANCEThe integration of genetic material of temperate bacterial viruses (phages) into the chromosomes of bacteria is a potent evolutionary force, allowing bacteria to acquire in one stroke new traits and restructure the information in their chromosomes. Puzzlingly, this genetic material is preferentially integrated in a particular orientation and at non-random sites on the bacterial chromosome. The work described here reveals that the interplay between the maintenance of the stability of the integrated phage, its ability to excise, and its localization along the chromosome plays a key role in setting chromosomal organization in Escherichia coli.},
}
@article {pmid38884912,
year = {2024},
author = {Libante, V and Dechêne-Tempier, M and Leblond-Bourget, N and Payot, S},
title = {Detection and Quantification of Conjugative Transfer of Mobile Genetic Elements Carrying Antibiotic Resistance Genes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2815},
number = {},
pages = {79-91},
pmid = {38884912},
issn = {1940-6029},
mesh = {*Conjugation, Genetic ; *Interspersed Repetitive Sequences/genetics ; Gene Transfer, Horizontal ; Streptococcus suis/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Polymerase Chain Reaction/methods ; Genes, Bacterial ; },
abstract = {Multidrug resistance, due to acquired antimicrobial resistance genes, is increasingly reported in the zoonotic pathogen Streptococcus suis. Most of these resistance genes are carried by chromosomal Mobile Genetic Elements (MGEs), in particular, Integrative and Conjugative Elements (ICEs) and Integrative and Mobilizable Elements (IMEs). ICEs and IMEs frequently form tandems or nested composite elements, which make their identification difficult. To evaluate their mobility, it is necessary to (i) select the suitable donor-recipient pairs for mating assays, (ii) do PCR excision tests to confirm that the genetic element is able to excise from the chromosome as a circular intermediate, and (iii) evaluate the transfer of the genetic element by conjugation by doing mating assays. In addition to a dissemination of resistance genes between S. suis strains, MGEs can lead to a spreading of resistance genes in the environment and toward pathogenic bacteria. This propagation had to be considered in a One Health perspective.},
}
@article {pmid38884260,
year = {2024},
author = {Wang, S and Jiang, Y and Che, L and Wang, RH and Li, SC},
title = {Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome.},
journal = {Nucleic acids research},
volume = {52},
number = {14},
pages = {e61},
pmid = {38884260},
issn = {1362-4962},
support = {20220814183301001//Shenzhen Science and Technology Program/ ; 9667242//Applied Research/ ; 9440262//Hong Kong Innovation and Technology Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Gene Transfer, Horizontal ; *Metagenomics/methods ; Colorectal Neoplasms/genetics/microbiology ; Diarrhea/microbiology/genetics ; Bacteria/genetics/classification ; },
abstract = {Horizontal gene transfer (HGT) phenomena pervade the gut microbiome and significantly impact human health. Yet, no current method can accurately identify complete HGT events, including the transferred sequence and the associated deletion and insertion breakpoints from shotgun metagenomic data. Here, we develop LocalHGT, which facilitates the reliable and swift detection of complete HGT events from shotgun metagenomic data, delivering an accuracy of 99.4%-verified by Nanopore data-across 200 gut microbiome samples, and achieving an average F1 score of 0.99 on 100 simulated data. LocalHGT enables a systematic characterization of HGT events within the human gut microbiome across 2098 samples, revealing that multiple recipient genome sites can become targets of a transferred sequence, microhomology is enriched in HGT breakpoint junctions (P-value = 3.3e-58), and HGTs can function as host-specific fingerprints indicated by the significantly higher HGT similarity of intra-personal temporal samples than inter-personal samples (P-value = 4.3e-303). Crucially, HGTs showed potential contributions to colorectal cancer (CRC) and acute diarrhoea, as evidenced by the enrichment of the butyrate metabolism pathway (P-value = 3.8e-17) and the shigellosis pathway (P-value = 5.9e-13) in the respective associated HGTs. Furthermore, differential HGTs demonstrated promise as biomarkers for predicting various diseases. Integrating HGTs into a CRC prediction model achieved an AUC of 0.87.},
}
@article {pmid38882494,
year = {2024},
author = {Xu, X and Feng, Q and Zhang, T and Gao, Y and Cheng, Q and Zhang, W and Wu, Q and Xu, K and Li, Y and Nguyen, N and Taft, DH and Mills, DA and Lemay, DG and Zhu, W and Mao, S and Zhang, A and Xu, K and Liu, J},
title = {Infant age inversely correlates with gut carriage of resistance genes, reflecting modifications in microbial carbohydrate metabolism during early life.},
journal = {iMeta},
volume = {3},
number = {2},
pages = {e169},
pmid = {38882494},
issn = {2770-596X},
abstract = {The infant gut microbiome is increasingly recognized as a reservoir of antibiotic resistance genes, yet the assembly of gut resistome in infants and its influencing factors remain largely unknown. We characterized resistome in 4132 metagenomes from 963 infants in six countries and 4285 resistance genes were observed. The inherent resistome pattern of healthy infants (N = 272) could be distinguished by two stages: a multicompound resistance phase (Months 0-7) and a tetracycline-mupirocin-β-lactam-dominant phase (Months 8-14). Microbial taxonomy explained 40.7% of the gut resistome of healthy infants, with Escherichia (25.5%) harboring the most resistance genes. In a further analysis with all available infants (N = 963), we found age was the strongest influencer on the resistome and was negatively correlated with the overall resistance during the first 3 years (p < 0.001). Using a random-forest approach, a set of 34 resistance genes could be used to predict age (R [2] = 68.0%). Leveraging microbial host inference analyses, we inferred the age-dependent assembly of infant resistome was a result of shifts in the gut microbiome, primarily driven by changes in taxa that disproportionately harbor resistance genes across taxa (e.g., Escherichia coli more frequently harbored resistance genes than other taxa). We performed metagenomic functional profiling and metagenomic assembled genome analyses whose results indicate that the development of gut resistome was driven by changes in microbial carbohydrate metabolism, with an increasing need for carbohydrate-active enzymes from Bacteroidota and a decreasing need for Pseudomonadota during infancy. Importantly, we observed increased acquired resistance genes over time, which was related to increased horizontal gene transfer in the developing infant gut microbiome. In summary, infant age was negatively correlated with antimicrobial resistance gene levels, reflecting a composition shift in the gut microbiome, likely driven by the changing need for microbial carbohydrate metabolism during early life.},
}
@article {pmid38880617,
year = {2024},
author = {Miyoshi, SI and Amako, K and Muraoka, M and Morinaga, H and Ueba, S},
title = {Mobile genetic elements associated with utilization of dichloromethane and methanol as energy sources in Cupriavidus metallidurans.},
journal = {Journal of microorganism control},
volume = {29},
number = {2},
pages = {55-65},
doi = {10.4265/jmc.29.2_55},
pmid = {38880617},
issn = {2758-6391},
mesh = {*Methanol/metabolism ; *Cupriavidus/genetics/metabolism/drug effects ; *Methylene Chloride/metabolism ; *Interspersed Repetitive Sequences/genetics ; Energy Metabolism/drug effects/genetics ; Genome, Bacterial/genetics ; Gene Transfer, Horizontal ; },
abstract = {Cupriavidus metallidurans strain PD11 isolated from laboratory waste drainage can use C1 compounds, such as dichloromethane (DCM) and methanol, as a sole carbon and energy source. However, strain CH34 (a type-strain) cannot grow in the medium supplemented with DCM. In the present study, we aimed to unravel the genetic elements underlying the utilization of C1 compounds by strain PD11. The genome subtraction approach indicated that only strain PD11 had several genes highly homologous to those of Herminiimonas arsenicoxydans strain ULPAs1. Moreover, a series of polymerase chain reaction (PCR) to detect the orthologs of H. arsenicoxydans genes and the comparative study of the genomes of three strains revealed that the 87.9 kb DNA fragment corresponding to HEAR1959 to HEAR2054 might be horizontally transferred to strain PD11. The 87.9 kb DNA fragment identified was found to contain three genes whose products were putatively involved in the metabolism of formaldehyde, a common intermediate of DCM and methanol. In addition, reverse transcription PCR analysis showed that all three genes were significantly expressed when strain PD11 was cultivated in the presence of DCM or methanol. These findings suggest that strain PD11 can effectively utilize the C1 compounds because of transfer of the mobile genetic elements from other bacterial species, for instance, from H. arsenicoxydans.},
}
@article {pmid38880337,
year = {2024},
author = {Sugimoto, TN and Jouraku, A and Mitsuhashi, W},
title = {Search for genes gained by horizontal gene transfer in an entomopoxvirus, with special reference to the analysis of the transfer of an ABC transporter gene.},
journal = {Virus research},
volume = {347},
number = {},
pages = {199418},
pmid = {38880337},
issn = {1872-7492},
mesh = {*Gene Transfer, Horizontal ; Animals ; *ATP-Binding Cassette Transporters/genetics/metabolism ; *Open Reading Frames ; *Entomopoxvirinae/genetics ; Coleoptera/virology/genetics ; Phylogeny ; Genes, Viral ; Genome, Viral ; Evolution, Molecular ; Viral Proteins/genetics/metabolism ; },
abstract = {Although it is generally believed that large DNA viruses capture genes by horizontal gene transfer (HGT), the detailed manner of such transfer has not been fully elucidated. Here, we searched for genes in the coleopteran entomopoxvirus (EV) Anomala cuprea entomopoxvirus (ACEV) that might have been gained by ACEV by HGT. We classified the potential source organisms for HGT into three categories: the host A. cuprea; other organisms, including viruses unrelated to EVs; and organisms with uncertain host attribution. Of the open reading frames (ORFs) of the ACEV genome, 2.1 % were suggested to have been gained from the host by ACEV or its recent ancestor via HGT; 8.7 % were possibly from organisms other than the host, and 3.7 % were possibly from the third category of organisms via HGT. The analysis showed that ACEV contains some interesting ORFs obtained by HGT, including a large ATP-binding cassette protein (ABC transporter) ORF and a tenascin ORF (IDs ACV025 and ACV123, respectively). We then performed a detailed analysis of the HGT of the ACEV large ABC transporter ORF-the largest of the ACEV ORFs. mRNA sequences obtained by RNA-seq from fat bodies-sites of ACEV replication-and midgut tissues-sites of initial infection-of the virus's host A. cuprea larvae were subjected to BLAST analysis. One type of ABC transporter ORF from the fat bodies and two types from the midgut tissues, one of which was identical to that in the fat bodies, had the greatest identity to the ABC transporter ORF of ACEV. The two types from the host had high levels of identity to each other (approximately 95 % nucleotide sequence identity), strongly suggesting that the host ABC transporter group consisting of the two types was the origin of ACV025. We then determined the sequence (12,381 bp) containing a full-length gene of the A. cuprea ABC transporter. It turned out to be a transcription template for the abovementioned mRNA found in both tissues. In addition, we determined a large part (ca. 6.9 kb) of the template sequence for the mRNA found only in the midgut tissues. The results showed that the ACEV ABC transporter ORF is missing parts corresponding to introns of the host ABC transporter genes, indicating that the ORF was likely acquired by HGT in the form of mRNA. The presence of definite duplicated sequences adjacent to the ACEV ABC transporter genes-a sign of LINE-1 retrotransposon-mediated HGT-was not observed. An approximately 2-month ACV025 transcription experiment suggested that the transporter sequence is presumed to be continuously functional. The amino acid sequence of ACV025 suggests that its product might function in the regulation of phosphatide in the host-cell membranes.},
}
@article {pmid38878503,
year = {2024},
author = {Hu, Q and Zhang, L and Yang, R and Tang, J and Dong, G},
title = {Quaternary ammonium biocides promote conjugative transfer of antibiotic resistance gene in structure- and species-dependent manner.},
journal = {Environment international},
volume = {189},
number = {},
pages = {108812},
doi = {10.1016/j.envint.2024.108812},
pmid = {38878503},
issn = {1873-6750},
mesh = {*Disinfectants/pharmacology ; *Quaternary Ammonium Compounds/pharmacology ; *Escherichia coli/drug effects/genetics ; *Conjugation, Genetic ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; },
abstract = {The linkage between biocides and antibiotic resistance has been widely suggested in laboratories and various environments. However, the action mechanism of biocides on antibiotic resistance genes (ARGs) spread is still unclear. Thus, 6 quaternary ammonium biocides (QACs) with different bonded substituents or alkyl chain lengths were selected to assess their effects on the conjugation transfer of ARGs in this study. Two conjugation models with the same donor (E. coli DH5α (RP4)) into two receptors, E. coli MG1655 and pathogenic S. sonnei SE6-1, were constructed. All QACs were found to significantly promote intra- and inter-genus conjugative transfer of ARGs, and the frequency was highly impacted by their structure and receptors. At the same environmental exposure level (4 × 10[-1] mg/L), didecyl dimethyl ammonium chloride (DDAC (C10)) promoted the most frequency of conjugative transfer, while benzathine chloride (BEC) promoted the least. With the same donor, the enhanced frequency of QACs of intra-transfer is higher than inter-transfer. Then, the acquisition mechanisms of two receptors were further determined using biochemical combined with transcriptome analysis. For the recipient E. coli, the promotion of the intragenus conjugative transfer may be associated with increased cell membrane permeability, reactive oxygen species (ROS) production and proton motive force (PMF)-induced enhancement of flagellar motility. Whereas, the increase of cell membrane permeability and decreased flagellar motility due to PMF disruption but encouraged biofilm formation, maybe the main reasons for promoting intergenus conjugative transfer in the recipient S. sonnei. As one pathogenic bacterium, S. sonnei was first found to acquire ARGs by biocide exposure.},
}
@article {pmid38878444,
year = {2024},
author = {Li, W and Zeng, J and Zheng, N and Ge, C and Li, Y and Yao, H},
title = {Polyvinyl chloride microplastics in the aquatic environment enrich potential pathogenic bacteria and spread antibiotic resistance genes in the fish gut.},
journal = {Journal of hazardous materials},
volume = {475},
number = {},
pages = {134817},
doi = {10.1016/j.jhazmat.2024.134817},
pmid = {38878444},
issn = {1873-3336},
mesh = {Animals ; *Microplastics/toxicity ; *Polyvinyl Chloride ; *Water Pollutants, Chemical/toxicity ; *Oxytetracycline/toxicity ; *Carps/microbiology ; *Anti-Bacterial Agents/pharmacology/toxicity ; Gastrointestinal Microbiome/drug effects ; Bacteria/drug effects/genetics ; Sulfamethazine/toxicity ; Genes, Bacterial/drug effects ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics/drug effects ; },
abstract = {Microplastics and antibiotics coexist in aquatic environments, especially in freshwater aquaculture areas. However, as the second largest production of polyvinyl chloride (PVC) in the world, the effects of co-exposure to microplastics particles and antibiotics on changes in antibiotic resistance gene (ARG) profiles and the microbial community structure of aquatic organism gut microorganisms are poorly understood. Therefore, in this study, carp (Cyprinus carpio) were exposed to single or combined PVC microplastic contamination and oxytetracycline (OTC) or sulfamethazine (SMZ) for 8 weeks. PVC microplastics can enrich potential pathogenic bacteria, such as Enterobacter and Acinetobacter, among intestinal microorganisms. The presence of PVC microplastics enhanced the selective enrichment and dissemination risk of ARGs. PVC microplastics combined with OTC (OPVC) treatment significantly increased the abundance of tetracycline resistance genes (1.40-fold) compared with that in the OTC exposure treatment, revealing an obvious co-selection effect. However, compared with those in the control group, the total abundance of ARGs and MGEs in the OPVC treatment groups were significantly lower, which was correlated with the reduced abundances of the potential host Enterobacter. Overall, our results emphasized the diffusion and spread of ARGs are more influenced by PVC microplastics than by antibiotics, which may lead to antibiotic resistance in aquaculture.},
}
@article {pmid38878442,
year = {2024},
author = {Ma, Y and Xu, S and Huang, Y and Du, J and Wang, J and Gao, B and Song, J and Ma, S and Jia, H and Zhan, S},
title = {The mechanism differences between sulfadiazine degradation and antibiotic resistant bacteria inactivation by iron-based graphitic biochar and peroxydisulfate system.},
journal = {Journal of hazardous materials},
volume = {475},
number = {},
pages = {134907},
doi = {10.1016/j.jhazmat.2024.134907},
pmid = {38878442},
issn = {1873-3336},
mesh = {*Charcoal/chemistry ; *Sulfadiazine/chemistry ; *Anti-Bacterial Agents/chemistry/pharmacology ; *Iron/chemistry/metabolism ; *Graphite/chemistry ; *Sulfates/chemistry/metabolism ; Water Pollutants, Chemical/chemistry ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Bacteria/metabolism/drug effects/genetics ; Water Purification/methods ; Peroxides/chemistry ; },
abstract = {In this study, the activation of peroxydisulfate (PS) by K2FeO4-activation biochar (KFeB) and acid-picking K2FeO4-activation biochar (AKFeB) was investigated to reveal the mechanism differences between iron site and graphitic structure in sulfadiazine (SDZ) degradation and ARB inactivation, respectively. KFeB/PS and AKFeB/PS systems had similar degradation property towards SDZ, but only KFeB/PS system showed excellent bactericidal property. The mechanism study demonstrated that dissolved SDZ was degraded through electron transfer pathway mediated by graphitic structure, while suspended ARB was inactivated through free radicals generated by iron-activated PS, accompanied by excellent removal on antibiotic resistance genes (ARGs). The significant decrease in conjugative transfer frequency indicated the reduced horizontal gene transfer risk of ARGs after treatment with KFeB/PS system. Transcriptome data suggested that membrane protein channel disruption and adenosine triphosphate synthesis inhibition were key reasons for conjugative transfer frequency reduction. Continuous flow reactor of KFeB/PS system can efficiently remove antibiotics and ARB, implying the potential application in practical wastewater purification. In conclusion, this study provides novel insights for classified and collaborative control of antibiotics and ARB by carbon-based catalysts driven persulfate advanced oxidation technology.},
}
@article {pmid38878435,
year = {2024},
author = {Zhang, X and Ma, L and Zhang, XX},
title = {Neglected risks of enhanced antimicrobial resistance and pathogenicity in anaerobic digestion during transition from thermophilic to mesophilic.},
journal = {Journal of hazardous materials},
volume = {475},
number = {},
pages = {134886},
doi = {10.1016/j.jhazmat.2024.134886},
pmid = {38878435},
issn = {1873-3336},
mesh = {Anaerobiosis ; *Drug Resistance, Bacterial/genetics ; Temperature ; Methane/metabolism ; Bacteria/genetics/pathogenicity/metabolism/drug effects ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Virulence Factors/genetics ; Gene Transfer, Horizontal ; Enterobacteriaceae/genetics/pathogenicity/drug effects/metabolism ; Genes, Bacterial ; },
abstract = {Minimization of antibiotic resistance genes (ARGs) and potential pathogenic antibiotic-resistant bacteria (PARB) during anaerobic digestion (AD) is significantly impacted by temperature. However, knowledge on how ARGs and PARB respond to temperature transition from thermophilic to mesophilic is limited. Here, we combined metagenomic-based with culture-based approaches and revealed the risks of antimicrobial resistance and pathogenicity during transition from 55 °C to 35 °C for AD, with strategies of sharp (ST, one-step by 20 °C/d) and mild (MT, step-wise by 1 °C/d). Results indicated a lower decrease in methane production with MT (by 38.9%) than ST (by 88.8%). Phenotypic assays characterized a significant propagation of multi-resistant lactose-fermenting Enterobacteriaceae and indicator pathogens after both transitions, especially via ST. Further genomic evidence indicated a significant increase of ARGs (29.4-fold), virulence factor genes (1.8-fold) and PARB (65.3-fold) after ST, while slight enrichment via MT. Bacterial succession and enhanced horizontal transfer mediated by mobile genetic elements promoted ARG propagation in AD during transition, which was synchronously exacerbated through horizontal transfer mechanisms mediated by cellular physiological responses (oxidative stress, membrane permeability, bacterial conjugation and transformation) and co-selection mechanisms of biomethanation metabolic functions (acidogenesis and acetogenesis). This study reveals temperature-dependent resistome and pathogenicity development in AD, facilitating microbial risk control.},
}
@article {pmid38878434,
year = {2024},
author = {Chen, MM and Zhang, YQ and Cheng, LC and Zhao, FJ and Wang, P},
title = {Photoaged nanoplastics with multienzyme-like activities significantly shape the horizontal transfer of antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {475},
number = {},
pages = {134884},
doi = {10.1016/j.jhazmat.2024.134884},
pmid = {38878434},
issn = {1873-3336},
mesh = {*Gene Transfer, Horizontal ; *Escherichia coli/genetics/drug effects ; *Plasmids/genetics ; *Reactive Oxygen Species/metabolism ; Nanoparticles/chemistry/toxicity ; Drug Resistance, Microbial/genetics ; Polystyrenes/chemistry ; Sunlight ; Drug Resistance, Bacterial/genetics ; Oxidoreductases/genetics/metabolism ; },
abstract = {Nanoplastics (NPs), identified as emerging pollutants, pose a great risk to environment and global public health, exerting profound influences on the prevalence and dissemination of antibiotic resistance genes (ARGs). Despite evidence suggesting that nano-sized plastic particles can facilitate the horizontal gene transfer (HGT) of ARGs, it is imperative to explore strategies for inhibiting the transfer of ARGs. Currently, limited information exists regarding the characteristics of environmentally aged NPs and their impact on ARGs propagation. Herein, we investigated the impact of photo-aged NPs on the transfer of ARG-carrying plasmids into Escherichia coli (E. coli) cells. Following simulated sunlight irradiation, photo-aged nano-sized polystyrene plastics (PS NPs) exhibited multiple enzyme-like activities, including peroxidase (POD) and oxidase (OXD), leading to a burst of reactive oxygen species (ROS). At relatively low concentrations (0.1, 1 μg/mL), both pristine and aged PS NPs facilitated the transfer of pUC19 and pHSG396 plasmids within E. coli due to moderate ROS production and enhanced cell membrane permeability. Intriguingly, at relatively high concentrations (5, 10 μg/mL), aged PS NPs significantly suppressed plasmids transformation. The non-unidirectional impact of aged PS NPs involved the overproduction of ROS (•OH and •O2[-]) via nanozyme activity, directly degrading ARGs and damaging plasmid structure. Additionally, oxidative damage to bacteria resulted from the presence of much toxic free radicals, causing physical damage to cell membranes, reduction of the SOS response and restriction of adenosine-triphosphate (ATP) supply, ultimately leading to inactivation of recipient cells. This study unveils the intrinsic multienzyme-like activity of environmentally aged NPs, highlighting their potential to impede the transfer and dissemination of ARGs.},
}
@article {pmid38878274,
year = {2024},
author = {Vidal-Quist, JC and Ortego, F and Rombauts, S and Hernández-Crespo, P},
title = {The genome-wide response of Dermatophagoides pteronyssinus to cystatin A, a peptidase inhibitor from human skin, sheds light on its digestive physiology and allergenicity.},
journal = {Insect molecular biology},
volume = {33},
number = {6},
pages = {662-677},
doi = {10.1111/imb.12931},
pmid = {38878274},
issn = {1365-2583},
mesh = {Animals ; *Dermatophagoides pteronyssinus/immunology ; *Cystatin A/metabolism/genetics ; Antigens, Dermatophagoides/immunology ; Arthropod Proteins/genetics/metabolism/immunology ; Digestion ; Humans ; Allergens/immunology ; Skin/metabolism/immunology ; },
abstract = {The digestive physiology of house dust mites (HDMs) is particularly relevant for their allergenicity since many of their allergens participate in digestion and are excreted into faecal pellets, a main source of exposure for allergic subjects. To gain insight into the mite dietary digestion, the genome of the HDM Dermatophagoides pteronyssinus was screened for genes encoding peptidases (n = 320), glycosylases (n = 77), lipases and esterases (n = 320), peptidase inhibitors (n = 65) and allergen-related proteins (n = 52). Basal gene expression and transcriptional responses of mites to dietary cystatin A, a cysteine endopeptidase inhibitor with previously shown antinutritional effect on mites, were analysed by RNAseq. The ingestion of cystatin A resulted in significant regulation of different cysteine endopeptidase and glycosylase genes. One Der p 1-like and two cathepsin B-like cysteine endopeptidase genes of high basal expression were induced, which suggests their prominent role in proteolytic digestion together with major allergen Der p 1. A number of genes putatively participating in the interaction of mites with their microbiota and acquired by horizontal gene transfer were repressed, including genes encoding the peptidase Der p 38, two 1,3-beta-glucanases, a lysozyme and a GH19 chitinase. Finally, the disruption of mite digestion resulted in the regulation of up to 17 allergen and isoallergen genes. Altogether, our results shed light on the putative role of specific genes in digestion and illustrate the connection between the digestive physiology of HDM and allergy.},
}
@article {pmid38876022,
year = {2024},
author = {Sivalingam, P and Sabatino, R and Sbaffi, T and Corno, G and Fontaneto, D and Borgomaneiro, G and Rogora, M and Crotti, E and Mapelli, F and Borin, S and Pilar, AL and Eckert, EM and Di Cesare, A},
title = {Anthropogenic pollution may enhance natural transformation in water, favouring the spread of antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {475},
number = {},
pages = {134885},
doi = {10.1016/j.jhazmat.2024.134885},
pmid = {38876022},
issn = {1873-3336},
mesh = {*Wastewater/microbiology ; Drug Resistance, Microbial/genetics ; Lakes/microbiology ; Genes, Bacterial/drug effects ; Water Pollution ; Water Microbiology ; Microbiota/drug effects ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; Drug Resistance, Bacterial/genetics ; Bacteria/drug effects/genetics/classification ; },
abstract = {Aquatic ecosystems are crucial in the antimicrobial resistance cycle. While intracellular DNA has been extensively studied to understand human activity's impact on antimicrobial resistance gene (ARG) dissemination, extracellular DNA is frequently overlooked. This study examines the effect of anthropogenic water pollution on microbial community diversity, the resistome, and ARG dissemination. We analyzed intracellular and extracellular DNA from wastewater treatment plant effluents and lake surface water by shotgun sequencing. We also conducted experiments to evaluate anthropogenic pollution's effect on transforming extracellular DNA (using Gfp-plasmids carrying ARGs) within a natural microbial community. Chemical analysis showed treated wastewater had higher anthropogenic pollution-related parameters than lake water. The richness of microbial community, antimicrobial resistome, and high-risk ARGs was greater in treated wastewaters than in lake waters both for intracellular and extracellular DNA. Except for the high-risk ARGs, richness was significantly higher in intracellular than in extracellular DNA. Several ARGs were associated with mobile genetic elements and located on plasmids. Furthermore, Gfp-plasmid transformation within a natural microbial community was enhanced by anthropogenic pollution levels. Our findings underscore anthropogenic pollution's pivotal role in shaping microbial communities and their antimicrobial resistome. Additionally, it may facilitate ARG dissemination through extracellular DNA plasmid uptake.},
}
@article {pmid38871331,
year = {2024},
author = {Wang, X and Li, J and Pan, X},
title = {How micro-/nano-plastics influence the horizontal transfer of antibiotic resistance genes - A review.},
journal = {The Science of the total environment},
volume = {944},
number = {},
pages = {173881},
doi = {10.1016/j.scitotenv.2024.173881},
pmid = {38871331},
issn = {1879-1026},
mesh = {*Gene Transfer, Horizontal ; *Plastics ; *Drug Resistance, Microbial/genetics ; *Microplastics ; },
abstract = {Plastic debris such as microplastics (MPs) and nanoplastics (NPTs), along with antibiotic resistance genes (ARGs), are pervasive in the environment and are recognized as significant global health and ecological concerns. Micro-/nano-plastics (MNPs) have been demonstrated to favor the spread of ARGs by enhancing the frequency of horizontal gene transfer (HGT) through various pathways. This paper comprehensively and systematically reviews the current study with focus on the influence of plastics on the HGT of ARGs. The critical role of MNPs in the HGT of ARGs has been well illustrated in sewage sludge, livestock farms, constructed wetlands and landfill leachate. A summary of the performed HGT assay and the underlying mechanism of plastic-mediated transfer of ARGs is presented in the paper. MNPs could facilitate or inhibit HGT of ARGs, and their effects depend on the type, size, and concentration. This review provides a comprehensive insight into the effects of MNPs on the HGT of ARGs, and offers suggestions for further study. Further research should attempt to develop a standard HGT assay and focus on investigating the impact of different plastics, including the oligomers they released, under real environmental conditions on the HGT of ARGs.},
}
@article {pmid38871190,
year = {2024},
author = {Skalny, M and Rokowska, A and Szuwarzynski, M and Gajewska, M and Dziewit, L and Bajda, T},
title = {Nanoscale surface defects of goethite governing DNA adsorption process and formation of the Goethite-DNA conjugates.},
journal = {Chemosphere},
volume = {362},
number = {},
pages = {142602},
doi = {10.1016/j.chemosphere.2024.142602},
pmid = {38871190},
issn = {1879-1298},
mesh = {*Iron Compounds/chemistry ; Adsorption ; *Minerals/chemistry ; *DNA/chemistry ; Porosity ; Particle Size ; },
abstract = {In urbanized areas, extracellular DNA (exDNA) is suspected of carrying genes with undesirable traits like virulence genes (VGs) or antibiotic resistance genes (ARGs), which can spread through horizontal gene transfer (HGT). Hence, it is crucial to develop novel approaches for the mitigation of exDNA in the environment. Our research explores the role of goethite, a common iron mineral with high adsorption capabilities, in exDNA adsorption processes. We compare well-crystalline, semi-crystalline, and nano goethites with varying particle sizes to achieve various specific surface areas (SSAs) (18.7-161.6 m[2]/g) and porosities. We conducted batch adsorption experiments using DNA molecules of varying chain lengths (DNA sizes: <11 Kb, <6 Kb, and <3 Kb) and assessed the impact of Ca[2+] and biomacromolecules on the adsorption efficacy and mechanisms. Results show that porosity and pore structure significantly influence DNA adsorption capacity. Goethite with well-developed meso- and macroporosity demonstrated enhanced DNA adsorption. The accumulation of DNA on the goethite interface led to substantial aggregation in the system, thus the formation of DNA-goethite conjugates, indicating the bridging between mineral particles. DNA chain length, the presence of Ca[2+], and the biomacromolecule matrix also affected the adsorption capacity and mechanism. Interactions between DNA and positively charged biomacromolecules or Ca[2+] led to DNA compaction, allowing greater DNA accumulation in pores. However, a high concentration of biomacromolecules led to the saturation of the goethite surface, inhibiting DNA adsorption. AFM imaging of goethite particles after adsorption suggested the formation of the DNA multilayer. The study advances understanding of the environmental behavior of exDNA and its interaction with iron oxyhydroxides, offering insights into developing more effective methods for ARGs removal in wastewater treatment plants. By manipulating the textural properties of goethite, it's possible to enhance exDNA removal, potentially reducing the spread of biocontamination in urban and industrial environments.},
}
@article {pmid38870897,
year = {2024},
author = {Kennedy, NW and Comstock, LE},
title = {Mechanisms of bacterial immunity, protection, and survival during interbacterial warfare.},
journal = {Cell host &amp; microbe},
volume = {32},
number = {6},
pages = {794-803},
pmid = {38870897},
issn = {1934-6069},
support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; R01 AI093771/AI/NIAID NIH HHS/United States ; T32 DK007074/DK/NIDDK NIH HHS/United States ; },
mesh = {*Bacteria/immunology/genetics ; *Bacterial Toxins/metabolism/immunology ; Gene Transfer, Horizontal ; Humans ; Microbial Viability ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/metabolism/genetics ; },
abstract = {Most bacteria live in communities, often with closely related strains and species with whom they must compete for space and resources. Consequently, bacteria have acquired or evolved mechanisms to antagonize competitors through the production of antibacterial toxins. Similar to bacterial systems that combat phage infection and mechanisms to thwart antibiotics, bacteria have also acquired and evolved features to protect themselves from antibacterial toxins. Just as there is a large body of research identifying and characterizing antibacterial proteins and toxin delivery systems, studies of bacterial mechanisms to resist and survive assault from competitors' weapons have also expanded tremendously. Emerging data are beginning to reveal protective processes and mechanisms that are as diverse as the toxins themselves. Protection against antibacterial toxins can be acquired by horizontal gene transfer, receptor or target alteration, induction of protective functions, physical barriers, and other diverse processes. Here, we review recent studies in this rapidly expanding field.},
}
@article {pmid38870889,
year = {2024},
author = {Zhang, P and Wang, Y and Lin, H and Liang, J and Wang, J and Bai, Y and Qu, J and Wang, A},
title = {Bacterial evolution in Biofiltration of drinking water treatment plant: Different response of phage and plasmid to varied water sources.},
journal = {Water research},
volume = {259},
number = {},
pages = {121887},
doi = {10.1016/j.watres.2024.121887},
pmid = {38870889},
issn = {1879-2448},
mesh = {*Plasmids ; *Drinking Water/microbiology ; *Water Purification ; *Bacteriophages/genetics ; *Bacteria ; Filtration ; Gene Transfer, Horizontal ; Groundwater ; },
abstract = {Biofiltration in drinking water treatment (BDWT) are popular as it holds promise as an alternative to chemical treatments, yet our understanding of the key drivers and trends underlying bacterial evolution within this process remains limited. While plasmids and phages are recognized as the main vectors of horizontal gene transfer (HGT), their roles in shaping bacterial evolution in BDWT remain largely unknown. Here we leverage global metagenomic data to unravel the primary forces driving bacterial evolution in BDWT. Our results revealed that the primary vector of HGT varies depending on the type of source water (groundwater and surface water). Both plasmids and phages accelerated bacterial evolution in BDWT by enhancing genetic diversity within species, but they drove contrasting evolutionary trends in functional redundancy in different source water types. Specifically, trends towards and away from functional redundancy (indicated as gene-protein ratio) were observed in surface-water and groundwater biofilters, respectively. Virulent phages drove bacterial evolution through synergistic interactions with bacterial species capable of natural transformation and with certain natural compounds that disrupt bacterial cytoplasmic membranes. Genes relating to water purification (such as Mn(II)-oxidizing genes), microbial risks (antibiotic resistance genes), and chemical risk (polycyclic aromatic hydrocarbons) were enriched via HGT in BDWT, highlighting the necessity for heighted focus on these useful and risky objects. Overall, these discoveries enhance our understanding of bacterial evolution in BDWT and have implications for the optimization of water treatment strategies.},
}
@article {pmid38867468,
year = {2024},
author = {Qi, L and Wang, W and Fang, L and Li, J and Qi, L and Wang, D and Liu, J and Xiao, Y and Zhou, W and Fang, X},
title = {DNA Molecular Glue Assisted Bacterial Conjugative Transfer.},
journal = {Chemistry (Weinheim an der Bergstrasse, Germany)},
volume = {30},
number = {52},
pages = {e202401399},
doi = {10.1002/chem.202401399},
pmid = {38867468},
issn = {1521-3765},
support = {2022YFA1304500,2022YFC3401003//the National Key Scientific Program of China/ ; Nos. 21735006//National Natural Science Foundation of China/ ; Nos.21890742//National Natural Science Foundation of China/ ; },
mesh = {*Escherichia coli/genetics ; *Conjugation, Genetic ; *DNA, Single-Stranded/chemistry ; Click Chemistry ; Gene Transfer, Horizontal ; Oligonucleotides/chemistry ; },
abstract = {Bacterial conjugation, a commonly used method to horizontally transfer functional genes from donor to recipient strains, plays an important role in the genetic manipulation of bacteria for basic research and industrial production. Successful conjugation depends on the donor-recipient cell recognition and a tight mating junction formation. However, the efficiency of conjugative transfer is usually very low. In this work, we developed a new technique that employed DNA molecule "glue" to increase the match frequency and the interaction stability between the donor and recipient cells. We used two E. coli strains, ETZ and BL21, as a model system, and modified them with the complementary ssDNA oligonucleotides by click chemistry. The conjugation efficiency of the modified bacteria was improved more than 4 times from 10 %-46 %. This technique is simple and generalizable as it only relies on the active amino groups on the bacterial surface. It is expected to have broad applications in constructing engineered bacteria.},
}
@article {pmid38861577,
year = {2024},
author = {Elsen, S and Simon, V and Attrée, I},
title = {Cross-regulation and cross-talk of conserved and accessory two-component regulatory systems orchestrate Pseudomonas copper resistance.},
journal = {PLoS genetics},
volume = {20},
number = {6},
pages = {e1011325},
pmid = {38861577},
issn = {1553-7404},
mesh = {*Copper/metabolism ; *Pseudomonas/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; *Operon/genetics ; *Bacterial Proteins/genetics/metabolism ; Drug Resistance, Bacterial/genetics ; Signal Transduction/genetics ; },
abstract = {Bacteria use diverse strategies and molecular machinery to maintain copper homeostasis and to cope with its toxic effects. Some genetic elements providing copper resistance are acquired by horizontal gene transfer; however, little is known about how they are controlled and integrated into the central regulatory network. Here, we studied two copper-responsive systems in a clinical isolate of Pseudomonas paraeruginosa and deciphered the regulatory and cross-regulation mechanisms. To do so, we combined mutagenesis, transcriptional fusion analyses and copper sensitivity phenotypes. Our results showed that the accessory CusRS two-component system (TCS) responds to copper and activates both its own expression and that of the adjacent nine-gene operon (the pcoA2 operon) to provide resistance to elevated levels of extracellular copper. The same locus was also found to be regulated by two core-genome-encoded TCSs-the copper-responsive CopRS and the zinc-responsive CzcRS. Although the target palindromic sequence-ATTCATnnATGTAAT-is the same for the three response regulators, transcriptional outcomes differ. Thus, depending on the operon/regulator pair, binding can result in different activation levels (from none to high), with the systems demonstrating considerable plasticity. Unexpectedly, although the classical CusRS and the noncanonical CopRS TCSs rely on distinct signaling mechanisms (kinase-based vs. phosphatase-based), we discovered cross-talk in the absence of the cognate sensory kinases. This cross-talk occurred between the proteins of these two otherwise independent systems. The cusRS-pcoA2 locus is part of an Integrative and Conjugative Element and was found in other Pseudomonas strains where its expression could provide copper resistance under appropriate conditions. The results presented here illustrate how acquired genetic elements can become part of endogenous regulatory networks, providing a physiological advantage. They also highlight the potential for broader effects of accessory regulatory proteins through interference with core regulatory proteins.},
}
@article {pmid38853947,
year = {2024},
author = {Wendt, G and Collins, JJ},
title = {Horizontal gene transfer of a functional cki homolog in the human pathogen Schistosoma mansoni.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38853947},
issn = {2692-8205},
support = {HHSN272201700014C/AI/NIAID NIH HHS/United States ; R01 AI121037/AI/NIAID NIH HHS/United States ; R01 AI150776/AI/NIAID NIH HHS/United States ; },
abstract = {Schistosomes are parasitic flatworms responsible for the neglected tropical disease schistosomiasis, causing devastating morbidity and mortality in the developing world. The parasites are protected by a skin-like tegument, and maintenance of this tegument is controlled by a schistosome ortholog of the tumor suppressor TP53. To understand mechanistically how p53-1 controls tegument production, we identified a cyclin dependent kinase inhibitor homolog (cki) that was co-expressed with p53-1. RNA interference of cki resulted in a hyperproliferation phenotype, that, in combination with p53-1 RNA interference yielded abundant tumor-like growths, indicating that cki and p53-1 are bona fide tumor suppressors in Schistosoma mansoni. Interestingly, cki homologs are widely present throughout parasitic flatworms but evidently absent from their free-living ancestors, suggesting this cki homolog came from an ancient horizontal gene transfer event. This in turn implies that the evolution of parasitism in flatworms may have been aided by a highly unusual means of metazoan genetic inheritance.},
}
@article {pmid38843310,
year = {2024},
author = {Coelho, MA and David-Palma, M and Shea, T and Bowers, K and McGinley-Smith, S and Mohammad, AW and Gnirke, A and Yurkov, AM and Nowrousian, M and Sun, S and Cuomo, CA and Heitman, J},
title = {Comparative genomics of the closely related fungal genera Cryptococcus and Kwoniella reveals karyotype dynamics and suggests evolutionary mechanisms of pathogenesis.},
journal = {PLoS biology},
volume = {22},
number = {6},
pages = {e3002682},
pmid = {38843310},
issn = {1545-7885},
support = {R01 AI039115/AI/NIAID NIH HHS/United States ; R01 AI050113/AI/NIAID NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; U54 HG003067/HG/NHGRI NIH HHS/United States ; },
mesh = {*Cryptococcus/genetics/pathogenicity/classification ; *Chromosomes, Fungal/genetics ; *Genome, Fungal ; *Karyotype ; *Genomics/methods ; *Evolution, Molecular ; Phylogeny ; Synteny ; Centromere/genetics ; Cryptococcosis/microbiology ; Humans ; },
abstract = {In exploring the evolutionary trajectories of both pathogenesis and karyotype dynamics in fungi, we conducted a large-scale comparative genomic analysis spanning the Cryptococcus genus, encompassing both global human fungal pathogens and nonpathogenic species, and related species from the sister genus Kwoniella. Chromosome-level genome assemblies were generated for multiple species, covering virtually all known diversity within these genera. Although Cryptococcus and Kwoniella have comparable genome sizes (about 19.2 and 22.9 Mb) and similar gene content, hinting at preadaptive pathogenic potential, our analysis found evidence of gene gain (via horizontal gene transfer) and gene loss in pathogenic Cryptococcus species, which might represent evolutionary signatures of pathogenic development. Genome analysis also revealed a significant variation in chromosome number and structure between the 2 genera. By combining synteny analysis and experimental centromere validation, we found that most Cryptococcus species have 14 chromosomes, whereas most Kwoniella species have fewer (11, 8, 5, or even as few as 3). Reduced chromosome number in Kwoniella is associated with formation of giant chromosomes (up to 18 Mb) through repeated chromosome fusion events, each marked by a pericentric inversion and centromere loss. While similar chromosome inversion-fusion patterns were observed in all Kwoniella species with fewer than 14 chromosomes, no such pattern was detected in Cryptococcus. Instead, Cryptococcus species with less than 14 chromosomes showed reductions primarily through rearrangements associated with the loss of repeat-rich centromeres. Additionally, Cryptococcus genomes exhibited frequent interchromosomal translocations, including intercentromeric recombination facilitated by transposons shared between centromeres. Overall, our findings advance our understanding of genetic changes possibly associated with pathogenicity in Cryptococcus and provide a foundation to elucidate mechanisms of centromere loss and chromosome fusion driving distinct karyotypes in closely related fungal species, including prominent global human pathogens.},
}
@article {pmid38842312,
year = {2024},
author = {Klepa, MS and diCenzo, GC and Hungria, M},
title = {Comparative genomic analysis of Bradyrhizobium strains with natural variability in the efficiency of nitrogen fixation, competitiveness, and adaptation to stressful edaphoclimatic conditions.},
journal = {Microbiology spectrum},
volume = {12},
number = {7},
pages = {e0026024},
pmid = {38842312},
issn = {2165-0497},
support = {465133/2014-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 043/2019//Funda&#xe7;&#xe3;o Arauc&#xe1;ria-STI/ ; RGPIN-2020-07000//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; FR71100//Mitacs (Mitacs Canada)/ ; },
mesh = {*Bradyrhizobium/genetics/classification/isolation &amp; purification ; *Nitrogen Fixation/genetics ; Brazil ; *Phylogeny ; *Glycine max/microbiology ; *Symbiosis/genetics ; *Genome, Bacterial ; Genetic Variation ; Adaptation, Physiological/genetics ; Root Nodules, Plant/microbiology ; Soil Microbiology ; Genomics ; },
abstract = {Bradyrhizobium is known for fixing atmospheric nitrogen in symbiosis with agronomically important crops. This study focused on two groups of strains, each containing eight natural variants of the parental strains, Bradyrhizobium japonicum SEMIA 586 (=CNPSo 17) or Bradyrhizobium diazoefficiens SEMIA 566 (=CNPSo 10). CNPSo 17 and CNPSo 10 were used as commercial inoculants for soybean crops in Brazil at the beginning of the crop expansion in the southern region in the 1960s-1970s. Variants derived from these parental strains were obtained in the late 1980s through a strain selection program aimed at identifying elite strains adapted to a new cropping frontier in the central-western Cerrado region, with a higher capacity of biological nitrogen fixation (BNF) and competitiveness. Here, we aimed to detect genetic variations possibly related to BNF, competitiveness for nodule occupancy, and adaptation to the stressful conditions of the Brazilian Cerrado soils. High-quality genome assemblies were produced for all strains. The core genome phylogeny revealed that strains of each group are closely related, as confirmed by high average nucleotide identity values. However, variants accumulated divergences resulting from horizontal gene transfer, genomic rearrangements, and nucleotide polymorphisms. The B. japonicum group presented a larger pangenome and a higher number of nucleotide polymorphisms than the B. diazoefficiens group, possibly due to its longer adaptation time to the Cerrado soil. Interestingly, five strains of the B. japonicum group carry two plasmids. The genetic variability found in both groups is discussed considering the observed differences in their BNF capacity, competitiveness for nodule occupancy, and environmental adaptation.IMPORTANCEToday, Brazil is a global leader in the study and use of biological nitrogen fixation with soybean crops. As Brazilian soils are naturally void of soybean-compatible bradyrhizobia, strain selection programs were established, starting with foreign isolates. Selection searched for adaptation to the local edaphoclimatic conditions, higher efficiency of nitrogen fixation, and strong competitiveness for nodule occupancy. We analyzed the genomes of two parental strains of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens and eight variant strains derived from each parental strain. We detected two plasmids in five strains and several genetic differences that might be related to adaptation to the stressful conditions of the soils of the Brazilian Cerrado biome. We also detected genetic variations in specific regions that may impact symbiotic nitrogen fixation. Our analysis contributes to new insights into the evolution of Bradyrhizobium, and some of the identified differences may be applied as genetic markers to assist strain selection programs.},
}
@article {pmid38839049,
year = {2024},
author = {Middlebrook, EA and Katani, R and Fair, JM},
title = {OrthoPhyl-streamlining large-scale, orthology-based phylogenomic studies of bacteria at broad evolutionary scales.},
journal = {G3 (Bethesda, Md.)},
volume = {14},
number = {8},
pages = {},
pmid = {38839049},
issn = {2160-1836},
support = {//Defense Threat Reduction Agency/ ; 89233218CNA000001//Los Alamos National Laboratory/ ; },
mesh = {*Phylogeny ; *Genome, Bacterial ; *Genomics/methods ; *Software ; Bacteria/genetics/classification ; Computational Biology/methods ; Evolution, Molecular ; },
abstract = {There are a staggering number of publicly available bacterial genome sequences (at writing, 2.0 million assemblies in NCBI's GenBank alone), and the deposition rate continues to increase. This wealth of data begs for phylogenetic analyses to place these sequences within an evolutionary context. A phylogenetic placement not only aids in taxonomic classification but informs the evolution of novel phenotypes, targets of selection, and horizontal gene transfer. Building trees from multi-gene codon alignments is a laborious task that requires bioinformatic expertise, rigorous curation of orthologs, and heavy computation. Compounding the problem is the lack of tools that can streamline these processes for building trees from large-scale genomic data. Here we present OrthoPhyl, which takes bacterial genome assemblies and reconstructs trees from whole genome codon alignments. The analysis pipeline can analyze an arbitrarily large number of input genomes (>1200 tested here) by identifying a diversity-spanning subset of assemblies and using these genomes to build gene models to infer orthologs in the full dataset. To illustrate the versatility of OrthoPhyl, we show three use cases: E. coli/Shigella, Brucella/Ochrobactrum and the order Rickettsiales. We compare trees generated with OrthoPhyl to trees generated with kSNP3 and GToTree along with published trees using alternative methods. We show that OrthoPhyl trees are consistent with other methods while incorporating more data, allowing for greater numbers of input genomes, and more flexibility of analysis.},
}
@article {pmid38830804,
year = {2024},
author = {Dadeh Amirfard, K and Moriyama, M and Suzuki, S and Sano, D},
title = {Effect of environmental factors on conjugative transfer of antibiotic resistance genes in aquatic settings.},
journal = {Journal of applied microbiology},
volume = {135},
number = {6},
pages = {},
doi = {10.1093/jambio/lxae129},
pmid = {38830804},
issn = {1365-2672},
support = {16H01782//KAKENHI/ ; },
mesh = {*Gene Transfer, Horizontal ; *Anti-Bacterial Agents/pharmacology ; *Conjugation, Genetic ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Water Microbiology ; Escherichia coli/genetics/drug effects ; Genes, Bacterial ; Acinetobacter/genetics/drug effects ; Biofilms/drug effects ; },
abstract = {Antimicrobial-resistance genes (ARGs) are spread among bacteria by horizontal gene transfer, however, the effect of environmental factors on the dynamics of the ARG in water environments has not been very well understood. In this systematic review, we employed the regression tree algorithm to identify the environmental factors that facilitate/inhibit the transfer of ARGs via conjugation in planktonic/biofilm-formed bacterial cells based on the results of past relevant research. Escherichia coli strains were the most studied genus for conjugation experiments as donor/recipient in the intra-genera category. Conversely, Pseudomonas spp., Acinetobacter spp., and Salmonella spp. were studied primarily as recipients across inter-genera bacteria. The conjugation efficiency (ce) was found to be highly dependent on the incubation period. Some antibiotics, such as nitrofurantoin (at ≥0.2 µg ml-1) and kanamycin (at ≥9.5 mg l-1) as well as metallic compounds like mercury (II) chloride (HgCl2, ≥3 µmol l-1), and vanadium (III) chloride (VCl3, ≥50 µmol l-1) had enhancing effect on conjugation. The highest ce value (-0.90 log10) was achieved at 15°C-19°C, with linoleic acid concentrations <8 mg l-1, a recognized conjugation inhibitor. Identifying critical environmental factors affecting ARG dissemination in aquatic environments will accelerate strategies to control their proliferation and combat antibiotic resistance.},
}
@article {pmid38830497,
year = {2024},
author = {Zhang, X and Li, P and Wang, J and Fu, D and Zhao, B and Dong, W and Liu, Y},
title = {Comparative genomic and phylogenetic analyses of mitochondrial genomes of hawthorn (Crataegus spp.) in Northeast China.},
journal = {International journal of biological macromolecules},
volume = {272},
number = {Pt 1},
pages = {132795},
doi = {10.1016/j.ijbiomac.2024.132795},
pmid = {38830497},
issn = {1879-0003},
mesh = {*Crataegus/genetics/classification ; *Genome, Mitochondrial/genetics ; *Phylogeny ; China ; Genomics/methods ; Genome, Plant ; },
abstract = {Hawthorn (Crataegus spp.) plants are major sources of health food and medicines. Twenty species and seven variations of Crataegus are present in China. A variety of unique Crataegus species was found in their natural distribution in northeast China. In the present study, we assembled and annotated the mitochondrial genomes of five Crataegus species from northeastern China. The sizes of the newly sequenced mitochondrial genomes ranged from 245,907 bp to 410,837 bp. A total of 45-55 genes, including 12-19 transfer RNA genes, three ribosomal RNA genes, and 29-33 protein-coding genes (PCGs) were encoded by these mitochondrial genomes. Seven divergent hotspot regions were identified by comparative analyses: atp6, nad3, ccmFN, matR, nad1, nad5, and rps1. The most conserved genes among the Crataegus species, according to the whole-genome correlation analysis, were nad1, matR, nad5, ccmFN, cox1, nad4, trnQ-TTG, trnK-TTT, trnE-TTC, and trnM-CAT. Horizontal gene transfer between organellar genomes was common in Crataegus plants. Based on the phylogenetic trees of mitochondrial PCGs, C. maximowiczii, C. maximowiczii var. ninganensis, and C. bretschneideri shared similar maternal relationships. This study improves Crataegus mitochondrial genome resources and offers important insights into the taxonomy and species identification of this genus.},
}
@article {pmid38830094,
year = {2024},
author = {Attah, V and Milner, DS and Fang, Y and Yan, X and Leonard, G and Heitman, J and Talbot, NJ and Richards, TA},
title = {Duplication and neofunctionalization of a horizontally transferred xyloglucanase as a facet of the Red Queen coevolutionary dynamic.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {24},
pages = {e2218927121},
pmid = {38830094},
issn = {1091-6490},
support = {R01 AI039115/AI/NIAID NIH HHS/United States ; PLP-2014-147//Leverhulme Trust/ ; URF/R/191005//Royal Society (The Royal Society)/ ; },
mesh = {*Gene Transfer, Horizontal ; *Glycoside Hydrolases/metabolism/genetics ; *Phylogeny ; Phytophthora/pathogenicity/genetics ; Plant Diseases/microbiology/parasitology ; Evolution, Molecular ; Gene Duplication ; },
abstract = {Oomycete protists share phenotypic similarities with fungi, including the ability to cause plant diseases, but branch in a distant region of the tree of life. It has been suggested that multiple horizontal gene transfers (HGTs) from fungi-to-oomycetes contributed to the evolution of plant-pathogenic traits. These HGTs are predicted to include secreted proteins that degrade plant cell walls, a barrier to pathogen invasion and a rich source of carbohydrates. Using a combination of phylogenomics and functional assays, we investigate the diversification of a horizontally transferred xyloglucanase gene family in the model oomycete species Phytophthora sojae. Our analyses detect 11 xyloglucanase paralogs retained in P. sojae. Using heterologous expression in yeast, we show consistent evidence that eight of these paralogs have xyloglucanase function, including variants with distinct protein characteristics, such as a long-disordered C-terminal extension that can increase xyloglucanase activity. The functional variants analyzed subtend a phylogenetic node close to the fungi-to-oomycete transfer, suggesting the horizontally transferred gene was a bona fide xyloglucanase. Expression of three xyloglucanase paralogs in Nicotiana benthamiana triggers high-reactive oxygen species (ROS) generation, while others inhibit ROS responses to bacterial immunogens, demonstrating that the paralogs differentially stimulate pattern-triggered immunity. Mass spectrometry of detectable enzymatic products demonstrates that some paralogs catalyze the production of variant breakdown profiles, suggesting that secretion of variant xyloglucanases increases efficiency of xyloglucan breakdown as well as diversifying the damage-associated molecular patterns released. We suggest that this pattern of neofunctionalization and the variant host responses represent an aspect of the Red Queen host-pathogen coevolutionary dynamic.},
}
@article {pmid38827508,
year = {2024},
author = {Tang, N and Wei, D and Zeng, Y and Zhang, G and Wang, C and Feng, J and Song, Y},
title = {Understanding the rapid spread of antimicrobial resistance genes mediated by IS26.},
journal = {mLife},
volume = {3},
number = {1},
pages = {101-109},
pmid = {38827508},
issn = {2770-100X},
abstract = {Insertion sequences (ISs) promote the transmission of antimicrobial resistance genes (ARGs) across bacterial populations. However, their contributions and dynamics during the transmission of resistance remain unclear. In this study, we selected IS26 as a representative transposable element to decipher the relationship between ISs and ARGs and to investigate their transfer features and transmission trends. We retrieved 2656 translocatable IS 26 -bounded units with ARGs (tIS26-bUs-ARGs) in complete bacterial genomes from the NCBI RefSeq database. In total, 124 ARGs spanning 12 classes of antibiotics were detected, and the average contribution rate of IS26 to these genes was 41.2%. We found that IS 26 -bounded units (IS26-bUs) mediated extensive ARG dissemination within the bacteria of the Gammaproteobacteria class, showing strong transfer potential between strains, species, and even phyla. The IS26-bUs expanded in bacterial populations over time, and their temporal expansion trend was significantly correlated with antibiotic usage. This wide dissemination could be due to the nonspecific target site preference of IS26. Finally, we experimentally confirmed that the introduction of a single copy of IS26 could lead to the formation of a composite transposon mediating the transmission of "passenger" genes. These observations extend our knowledge of the IS26 and provide new insights into the mediating role of ISs in the dissemination of antibiotic resistance.},
}
@article {pmid38823616,
year = {2024},
author = {Peng, J and Wang, D and He, P and Wei, P and Zhang, L and Lan, W and Zhang, X and Guan, J and Chen, Y and Li, W and Zheng, Y and Li, Y and Chen, W and Zhao, Z and Jiang, L and Zhou, L},
title = {Seasonal dynamics of antibiotic resistance genes and mobile genetic elements in a subtropical coastal ecosystem: Implications for environmental health risks.},
journal = {Environmental research},
volume = {257},
number = {},
pages = {119298},
doi = {10.1016/j.envres.2024.119298},
pmid = {38823616},
issn = {1096-0953},
mesh = {*Seasons ; China ; *Ecosystem ; *Drug Resistance, Microbial/genetics ; Interspersed Repetitive Sequences ; Environmental Health ; Microbiota/drug effects ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Antibiotic resistance poses a considerable global public health concern, leading to heightened rates of illness and mortality. However, the impact of seasonal variations and environmental factors on the health risks associated with antibiotic resistance genes (ARGs) and their assembly mechanisms is not fully understood. Based on metagenomic sequencing, this study investigated the antibiotic resistome, mobile genetic elements (MGEs), and microbiomes in a subtropical coastal ecosystem of the Beibu Gulf, China, over autumn and winter, and explored the factors influencing seasonal changes in ARG and MGE abundance and diversity. Results indicated that ARG abundance and diversity were higher in winter than in autumn, with beta-lactam and multidrug resistance genes being the most diverse and abundant, respectively. Similarly, MGE abundance and diversity increased in winter and were strongly correlated with ARGs. In contrast, more pronounced associations between microbial communities, especially archaea, and the antibiotic resistome were observed in autumn than in winter. The co-occurrence network identified multiple interactions between MGEs and various multidrug efflux pumps in winter, suggesting a potential for ARG dissemination. Multivariate correlation analyses and path modeling indicated that environmental factors driving microbial community changes predominantly influenced antibiotic resistome assembly in autumn, while the relative importance of MGEs increased significantly in winter. These findings suggest an elevated health risk associated with antimicrobial resistance in the Beibu Gulf during winter, attributed to the dissemination of ARGs by horizontal gene transfer. The observed seasonal variations highlight the dynamic nature of antibiotic resistance dissemination in coastal ecosystems, emphasizing the need for comprehensive surveillance and management measures to address the growing threat of antimicrobial resistance in vulnerable environments.},
}
@article {pmid38823494,
year = {2024},
author = {Tang, C and Shen, S and Yang, W and Shi, Q and Ding, L and Han, R and Hu, F},
title = {Dynamic evolution of ceftazidime-avibactam resistance from a single patient through the IncX3_NDM-5 plasmid transfer and blaKPC mutation.},
journal = {International journal of antimicrobial agents},
volume = {64},
number = {2},
pages = {107228},
doi = {10.1016/j.ijantimicag.2024.107228},
pmid = {38823494},
issn = {1872-7913},
mesh = {*Ceftazidime/pharmacology ; *Azabicyclo Compounds/pharmacology ; *Drug Combinations ; *Plasmids/genetics ; Humans ; *Klebsiella pneumoniae/genetics/drug effects ; *beta-Lactamases/genetics ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; *Enterobacter cloacae/genetics/drug effects ; *Mutation ; *Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/genetics/drug effects ; Klebsiella Infections/microbiology/drug therapy ; Bacterial Proteins/genetics ; Gene Transfer, Horizontal ; Carbapenem-Resistant Enterobacteriaceae/genetics/drug effects ; },
abstract = {The rapid dissemination of carbapenem-resistant Enterobacterales (CRE) especially carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a great threat to global public health. Ceftazidime-avibactam, a novel β-lactam/β-lactamase inhibitor combination, has been widely used due to its excellent antibacterial activity against KPC-producing K. pneumoniae. However, several resistance mechanisms have been reported since its use. Here, we conducted a series of in vitro experiments to reveal and demonstrate the dynamic evolution of ceftazidime-avibactam resistance including interspecies IncX3_NDM-5 plasmid transfer between Enterobacter cloacae and K. pneumoniae and blaKPC mutation from blaKPC-2 to blaKPC-33. Through the analysis of conjugation frequency and fitness cost, the IncX3_NDM-5 plasmid in this study showed strong transmissibility and stability in E. coli EC600 and clinical strain K. pneumoniae 5298 as recipient strain. With increasing ceftazidime-avibactam concentration, the conjugation frequency remained at 10[-3]-10[-5], while the mutation frequency of K. pneumoniae 5298 was 10[-6]-10[-8] at the same concentration. Further plasmid analysis (the IncX3_NDM plasmid from this study and other 658 plasmids from the NCBI database) revealed the diverse origin and genetic structure of blaNDM-5 carrying plasmids. E. coli (42.9%), China (43.9%), IncX3 (66.6%) are the most common strains, regions, and Inc types respectively. By analysing of genetic environment detected in IncX3 plasmids, the dominant structures (168/258, 65.1%) were identified: ISKox3-IS26-blaNDM-5-IS5-ISAba125-Tn3000-Tn3. In additon, several structural variations were found in the core gene structure. In conclusion, the high fitness and transmissibility of the IncX3_NDM-5 plasmids were noteworthy. More importantly, the diverse ceftazidime-avibactam resistance mechanisms including blaNDM-5 tranfer and blaKPC-2 mutation highlighted the importance of the continuous monitoring of antimicrobial susceptibility and carbapenemases subtype during ceftazidime-avibactam treatment.},
}
@article {pmid38820540,
year = {2024},
author = {Morel-Letelier, I and Yuen, B and Kück, AC and Camacho-García, YE and Petersen, JM and Lara, M and Leray, M and Eisen, JA and Osvatic, JT and Gros, O and Wilkins, LGE},
title = {Adaptations to nitrogen availability drive ecological divergence of chemosynthetic symbionts.},
journal = {PLoS genetics},
volume = {20},
number = {5},
pages = {e1011295},
pmid = {38820540},
issn = {1553-7404},
support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; S10 OD010786/OD/NIH HHS/United States ; },
mesh = {*Symbiosis/genetics ; Animals ; *Phylogeny ; *Nitrogen Fixation/genetics ; *Nitrogen/metabolism ; *Bivalvia/microbiology/genetics ; *Gene Transfer, Horizontal ; Bacteria/genetics/classification/metabolism ; Adaptation, Physiological/genetics ; Genome, Bacterial ; Caribbean Region ; Panama ; },
abstract = {Bacterial symbionts, with their shorter generation times and capacity for horizontal gene transfer (HGT), play a critical role in allowing marine organisms to cope with environmental change. The closure of the Isthmus of Panama created distinct environmental conditions in the Tropical Eastern Pacific (TEP) and Caribbean, offering a "natural experiment" for studying how closely related animals evolve and adapt under environmental change. However, the role of bacterial symbionts in this process is often overlooked. We sequenced the genomes of endosymbiotic bacteria in two sets of sister species of chemosymbiotic bivalves from the genera Codakia and Ctena (family Lucinidae) collected on either side of the Isthmus, to investigate how differing environmental conditions have influenced the selection of symbionts and their metabolic capabilities. The lucinid sister species hosted different Candidatus Thiodiazotropha symbionts and only those from the Caribbean had the genetic potential for nitrogen fixation, while those from the TEP did not. Interestingly, this nitrogen-fixing ability did not correspond to symbiont phylogeny, suggesting convergent evolution of nitrogen fixation potential under nutrient-poor conditions. Reconstructing the evolutionary history of the nifHDKT operon by including other lucinid symbiont genomes from around the world further revealed that the last common ancestor (LCA) of Ca. Thiodiazotropha lacked nif genes, and populations in oligotrophic habitats later re-acquired the nif operon through HGT from the Sedimenticola symbiont lineage. Our study suggests that HGT of the nif operon has facilitated niche diversification of the globally distributed Ca. Thiodiazotropha endolucinida species clade. It highlights the importance of nitrogen availability in driving the ecological diversification of chemosynthetic symbiont species and the role that bacterial symbionts may play in the adaptation of marine organisms to changing environmental conditions.},
}
@article {pmid38819554,
year = {2024},
author = {Hellmuth, M and Stadler, PF},
title = {The Theory of Gene Family Histories.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2802},
number = {},
pages = {1-32},
pmid = {38819554},
issn = {1940-6029},
mesh = {*Phylogeny ; *Multigene Family ; *Gene Transfer, Horizontal ; *Evolution, Molecular ; Models, Genetic ; Computational Biology/methods ; },
abstract = {Most genes are part of larger families of evolutionary-related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene family histories, i.e., the precise dating of evolutionary events relative to phylogenetic tree of the underlying species has remained a challenging topic despite their importance as a basis for detailed investigations into adaptation and functional evolution of individual members of the gene family. The identification of orthologs, moreover, is a particularly important subproblem of the more general setting considered here. In the last few years, an extensive body of mathematical results has appeared that tightly links orthology, a formal notion of best matches among genes, and horizontal gene transfer. The purpose of this chapter is to broadly outline some of the key mathematical insights and to discuss their implication for practical applications. In particular, we focus on tree-free methods, i.e., methods to infer orthology or horizontal gene transfer as well as gene trees, species trees, and reconciliations between them without using a priori knowledge of the underlying trees or statistical models for the inference of phylogenetic trees. Instead, the initial step aims to extract binary relations among genes.},
}
@article {pmid38818268,
year = {2023},
author = {Konstantinidis, KT},
title = {Sequence-discrete species for prokaryotes and other microbes: A historical perspective and pending issues.},
journal = {mLife},
volume = {2},
number = {4},
pages = {341-349},
pmid = {38818268},
issn = {2770-100X},
abstract = {Whether prokaryotes, and other microorganisms, form distinct clusters that can be recognized as species remains an issue of paramount theoretical as well as practical consequence in identifying, regulating, and communicating about these organisms. In the past decade, comparisons of thousands of genomes of isolates and hundreds of metagenomes have shown that prokaryotic diversity may be predominantly organized in such sequence-discrete clusters, albeit organisms of intermediate relatedness between the identified clusters are also frequently found. Accumulating evidence suggests, however, that the latter "intermediate" organisms show enough ecological and/or functional distinctiveness to be considered different species. Notably, the area of discontinuity between clusters often-but not always-appears to be around 85%-95% genome-average nucleotide identity, consistently among different taxa. More recent studies have revealed remarkably similar diversity patterns for viruses and microbial eukaryotes as well. This high consistency across taxa implies a specific mechanistic process that underlies the maintenance of the clusters. The underlying mechanism may be a substantial reduction in the efficiency of homologous recombination, which mediates (successful) horizontal gene transfer, around 95% nucleotide identity. Deviations from the 95% threshold (e.g., species showing lower intraspecies diversity) may be caused by ecological differentiation that imposes barriers to otherwise frequent gene transfer. While this hypothesis that clusters are driven by ecological differentiation coupled to recombination frequency (i.e., higher recombination within vs. between groups) is appealing, the supporting evidence remains anecdotal. The data needed to rigorously test the hypothesis toward advancing the species concept are also outlined.},
}
@article {pmid38817968,
year = {2024},
author = {Zhao, Y and Ding, WJ and Xu, L and Sun, JQ},
title = {A comprehensive comparative genomic analysis revealed that plant growth promoting traits are ubiquitous in strains of Stenotrophomonas.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1395477},
pmid = {38817968},
issn = {1664-302X},
abstract = {Stenotrophomonas strains, which are often described as plant growth promoting (PGP) bacteria, are ubiquitous in many environments. A total of 213 genomes of strains of Stenotrophomonas were analyzed using comparative genomics to better understand the ecological roles of these bacteria in the environment. The pan-genome of the 213 strains of Stenotrophomonas consists of 27,186 gene families, including 710 core gene families, 11,039 unique genes and 15,437 accessory genes. Nearly all strains of Stenotrophomonas harbor the genes for GH3-family cellulose degradation and GH2- and GH31-family hemicellulose hydrolase, as well as intact glycolysis and tricarboxylic acid cycle pathways. These abilities suggest that the strains of this genus can easily obtain carbon and energy from the environment. The Stenotrophomonas strains can respond to oxidative stress by synthesizing catalase, superoxide dismutase, methionine sulfoxide reductase, and disulfide isomerase, as well as managing their osmotic balance by accumulating potassium and synthesizing compatible solutes, such as betaine, trehalose, glutamate, and proline. Each Stenotrophomonas strain also contains many genes for resistance to antibiotics and heavy metals. These genes that mediate stress tolerance increase the ability of Stenotrophomonas strains to survive in extreme environments. In addition, many functional genes related to attachment and plant colonization, growth promotion and biocontrol were identified. In detail, the genes associated with flagellar assembly, motility, chemotaxis and biofilm formation enable the strains of Stenotrophomonas to effectively colonize host plants. The presence of genes for phosphate-solubilization and siderophore production and the polyamine, indole-3-acetic acid, and cytokinin biosynthetic pathways confer the ability to promote plant growth. These strains can produce antimicrobial compounds, chitinases, lipases and proteases. Each Stenotrophomonas genome contained 1-9 prophages and 17-60 genomic islands, and the genes related to antibiotic and heavy metal resistance and the biosynthesis of polyamines, indole-3-acetic acid, and cytokinin may be acquired by horizontal gene transfer. This study demonstrates that strains of Stenotrophomonas are highly adaptable for different environments and have strong potential for use as plant growth-promoting bacteria.},
}
@article {pmid38817813,
year = {2023},
author = {Li, L and Zhang, T},
title = {Roadmap to tackle antibiotic resistance in the environment under the One Health framework.},
journal = {mLife},
volume = {2},
number = {3},
pages = {224-228},
pmid = {38817813},
issn = {2770-100X},
abstract = {Antibiotic resistance has been recognized as a major challenge worldwide for humans. "One Health" has been recognized as a key concept for containment of antibiotic resistance. Under the framework, the role of the environment in the development of antibiotic resistance genes (ARGs) has become increasingly obvious. Despite numerous efforts, response to antibiotic resistance is considered to be inadequate, which is probably due to the lack of a clear roadmap. Here, we propose a "One Health" roadmap to combat antibiotic resistance in the environment through (1) understanding environmental resistome. The environmental gene pool has long been recognized as the single largest reservoir of both known and novel ARGs. (2) Standardizing ARG quantification. Systematic joint efforts based on standardized quantification are urgently needed to understand the true tempospatial profiles of the environmental resistome. (3) Identifying mechanisms of resistome development. Horizontal gene transfer and co-selection have been recognized as the two main mechanisms contributing to the environmental resistome. (4) Establishing a risk-assessment framework. The first critical step for large-scale cost-effective targeted ARG management in the environment is the risk assessment to identify the priority ARGs for control. (5) Formulating regulatory standards. By correlating the environmental ARG profile with public health, we may identify the indicator ARGs that can be integrated into current environmental quality standards. (6) Developing control strategies. Systematic analysis of available control technologies is required to identify the most feasible ones to curtail the spread of ARGs in the environment. The proposed roadmap under the "One Health" framework provides a guide to tackle antibiotic resistance in the environment.},
}
@article {pmid38816863,
year = {2024},
author = {Pontes, A and Paraíso, F and Silva, M and Lagoas, C and Aires, A and Brito, PH and Rosa, CA and Lachance, MA and Sampaio, JP and Gonçalves, C and Gonçalves, P},
title = {Extensive remodeling of sugar metabolism through gene loss and horizontal gene transfer in a eukaryotic lineage.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {128},
pmid = {38816863},
issn = {1741-7007},
support = {UIDB/04378/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0140/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIA-EVL/1100/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIA-EVL/0604/2021//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2023.09581.CPCA.A1//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2022.15871.CPCA.A2//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04378/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0140/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIA-EVL/1100/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIA-EVL/0604/2021//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2023.09581.CPCA.A1//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2022.15871.CPCA.A2//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; #406564/2022-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 0457499/2014-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 313088/2020-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 408733/2021//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; #406564/2022-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CNPq process numbers 0457499/2014-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 313088/2020-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 408733/2021//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; APQ-01525-14//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; APQ-02552-15//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; APQ-01525-14//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; APQ-02552-15//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; },
mesh = {*Gene Transfer, Horizontal ; Phylogeny ; Carbohydrate Metabolism/genetics ; Sugars/metabolism ; Evolution, Molecular ; Genome, Fungal ; },
abstract = {BACKGROUND: In yeasts belonging to the subphylum Saccharomycotina, genes encoding components of the main metabolic pathways, like alcoholic fermentation, are usually conserved. However, in fructophilic species belonging to the floral Wickerhamiella and Starmerella genera (W/S clade), alcoholic fermentation was uniquely shaped by events of gene loss and horizontal gene transfer (HGT).<br><br>RESULTS: Because HGT and gene losses were first identified when only eight W/S-clade genomes were available, we collected publicly available genome data and sequenced the genomes of 36 additional species. A total of 63 genomes, representing most of the species described in the clade, were included in the analyses. Firstly, we inferred the phylogenomic tree of the clade and inspected the genomes for the presence of HGT-derived genes involved in fructophily and alcoholic fermentation. We predicted nine independent HGT events and several instances of secondary loss pertaining to both pathways. To investigate the possible links between gene loss and acquisition events and evolution of sugar metabolism, we conducted phenotypic characterization of 42 W/S-clade species including estimates of sugar consumption rates and fermentation byproduct formation. In some instances, the reconciliation of genotypes and phenotypes yielded unexpected results, such as the discovery of fructophily in the absence of the cornerstone gene (FFZ1) and robust alcoholic fermentation in the absence of the respective canonical pathway.<br><br>CONCLUSIONS: These observations suggest that reinstatement of alcoholic fermentation in the W/S clade triggered a surge of innovation that goes beyond the utilization of xenologous enzymes, with fructose metabolism playing a key role.},
}
@article {pmid38813783,
year = {2024},
author = {Wolyniak, MJ and Frazier, RH and Gemborys, PK and Loehr, HE},
title = {Malate dehydrogenase: a story of diverse evolutionary radiation.},
journal = {Essays in biochemistry},
volume = {68},
number = {2},
pages = {213-220},
pmid = {38813783},
issn = {1744-1358},
support = {//Hampden-Sydney College Office of Undergraduate Research/ ; },
mesh = {*Malate Dehydrogenase/metabolism/genetics ; *Evolution, Molecular ; Bacteria/enzymology/genetics ; Phylogeny ; Archaea/genetics/enzymology ; Symbiosis ; Humans ; Eukaryota/enzymology/genetics ; Gene Transfer, Horizontal ; },
abstract = {Malate dehydrogenase (MDH) is a ubiquitous enzyme involved in cellular respiration across all domains of life. MDH's ubiquity allows it to act as an excellent model for considering the history of life and how the rise of aerobic respiration and eukaryogenesis influenced this evolutionary process. Here, we present the diversity of the MDH family of enzymes across bacteria, archaea, and eukarya, the relationship between MDH and lactate dehydrogenase (LDH) in the formation of a protein superfamily, and the connections between MDH and endosymbiosis in the formation of mitochondria and chloroplasts. The development of novel and powerful DNA sequencing techniques has challenged some of the conventional wisdom underlying MDH evolution and suggests a history dominated by gene duplication, horizontal gene transfer, and cryptic endosymbiosis events and adaptation to a diverse range of environments across all domains of life over evolutionary time. The data also suggest a superfamily of proteins that do not share high levels of sequential similarity but yet retain strong conservation of core function via key amino acid residues and secondary structural components. As DNA sequencing and 'big data' analysis techniques continue to improve in the life sciences, it is likely that the story of MDH will continue to refine as more examples of superfamily diversity are recovered from nature and analyzed.},
}
@article {pmid38811160,
year = {2024},
author = {Breidenstein, A and Lamy, A and Bader, CP and Sun, WS and Wanrooij, PH and Berntsson, RP},
title = {PrgE: an OB-fold protein from plasmid pCF10 with striking differences to prototypical bacterial SSBs.},
journal = {Life science alliance},
volume = {7},
number = {8},
pages = {},
pmid = {38811160},
issn = {2575-1077},
mesh = {*Plasmids/genetics ; *DNA-Binding Proteins/metabolism/genetics/chemistry ; *Bacterial Proteins/genetics/metabolism/chemistry ; *Enterococcus faecalis/genetics/metabolism ; *DNA, Single-Stranded/metabolism/genetics ; Protein Binding ; Conjugation, Genetic/genetics ; Type IV Secretion Systems/genetics/metabolism ; Models, Molecular ; Gene Transfer, Horizontal ; DNA, Bacterial/genetics/metabolism ; },
abstract = {A major pathway for horizontal gene transfer is the transmission of DNA from donor to recipient cells via plasmid-encoded type IV secretion systems (T4SSs). Many conjugative plasmids encode for a single-stranded DNA-binding protein (SSB) together with their T4SS. Some of these SSBs have been suggested to aid in establishing the plasmid in the recipient cell, but for many, their function remains unclear. Here, we characterize PrgE, a proposed SSB from the Enterococcus faecalis plasmid pCF10. We show that PrgE is not essential for conjugation. Structurally, it has the characteristic OB-fold of SSBs, but it has very unusual DNA-binding properties. Our DNA-bound structure shows that PrgE binds ssDNA like beads on a string supported by its N-terminal tail. In vitro studies highlight the plasticity of PrgE oligomerization and confirm the importance of the N-terminus. Unlike other SSBs, PrgE binds both double- and single-stranded DNA equally well. This shows that PrgE has a quaternary assembly and DNA-binding properties that are very different from the prototypical bacterial SSB, but also different from eukaryotic SSBs.},
}
@article {pmid38810941,
year = {2024},
author = {Zhang, Y and Liu, M and Zhang, J and Wu, J and Hong, L and Zhu, L and Long, J},
title = {Large-scale comparative analysis reveals phylogenomic preference of blaNDM-1 and blaKPC-2 transmission among Klebsiella pneumoniae.},
journal = {International journal of antimicrobial agents},
volume = {64},
number = {2},
pages = {107225},
doi = {10.1016/j.ijantimicag.2024.107225},
pmid = {38810941},
issn = {1872-7913},
mesh = {*beta-Lactamases/genetics ; *Klebsiella pneumoniae/genetics/drug effects/classification ; *Klebsiella Infections/transmission/microbiology/epidemiology ; Humans ; *Phylogeny ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Microbial Sensitivity Tests ; Carbapenems/pharmacology ; },
abstract = {blaNDM-1 and blaKPC-2 are responsible for the global increase in carbapenem-resistant Klebsiella pneumoniae, posing a great challenge to public health. However, the impact of phylogenetic factors on the dissemination of blaNDM-1 and blaKPC-2 is not yet fully understood. This study established a global dataset of 4051 blaNDM-1+ and 10,223 blaKPC-2+ K. pneumoniae genomes, and compared their transmission modes on a global scale. The results showed that blaNDM-1+ K. pneumoniae genomes exhibited a broader geographical distribution and higher sequence type (ST) richness than blaKPC-2+ genomes, indicating higher transmissibility of the blaNDM-1 gene. Furthermore, blaNDM-1+ genomes displayed significant differences in ST lineage, antibiotic resistance gene composition, virulence gene composition and genetic environments compared with blaKPC-2+ genomes, suggesting distinct dissemination mechanisms. blaNDM-1+ genomes were predominantly associated with ST147 and ST16, whereas blaKPC-2+ genomes were mainly found in ST11 and ST258. Significantly different accessory genes were identified between blaNDM-1+ and blaKPC-2+ genomes. The preference for blaKPC-2 distribution across certain countries, ST lineages and genetic environments underscores vertical spread as the primary mechanism driving the expansion of blaKPC-2. In contrast, blaNDM-1+ genomes did not display such a strong preference, confirming that the dissemination of blaNDM-1 mainly depends on horizontal gene transfer. Overall, this study demonstrates different phylogenetic drivers for the dissemination of blaNDM-1 and blaKPC-2, providing new insights into their global transmission dynamics.},
}
@article {pmid38808732,
year = {2024},
author = {He, J and Yang, Z and Wang, M and Jia, R and Chen, S and Liu, M and Zhao, X and Yang, Q and Wu, Y and Zhang, S and Huang, J and Ou, X and Sun, D and Tian, B and He, Y and Wu, Z and Cheng, A and Zhu, D},
title = {Integrative and conjugative elements of Pasteurella multocida: Prevalence and signatures in population evolution.},
journal = {Virulence},
volume = {15},
number = {1},
pages = {2359467},
pmid = {38808732},
issn = {2150-5608},
mesh = {*Pasteurella multocida/genetics/classification ; *Gene Transfer, Horizontal ; Animals ; *Phylogeny ; *Pasteurella Infections/microbiology/epidemiology/transmission ; *Genome, Bacterial ; DNA Transposable Elements ; Conjugation, Genetic ; Evolution, Molecular ; Poultry/microbiology ; Prevalence ; High-Throughput Nucleotide Sequencing ; },
abstract = {Pasteurella multocida (P. multocida) is a bacterial pathogen responsible for a range of infections in humans and various animal hosts, causing significant economic losses in farming. Integrative and conjugative elements (ICEs) are important horizontal gene transfer elements, potentially enabling host bacteria to enhance adaptability by acquiring multiple functional genes. However, the understanding of ICEs in P. multocida and their impact on the transmission of this pathogen remains limited. In this study, 42 poultry-sourced P. multocida genomes obtained by high-throughput sequencing together with 393 publicly available P. multocida genomes were used to analyse the horizontal transfer of ICEs. Eighty-two ICEs were identified in P. multocida, including SXT/R391 and Tn916 subtypes, as well as three subtypes of ICEHin1056 family, with the latter being widely prevalent in P. multocida and carrying multiple resistance genes. The correlations between insertion sequences and resistant genes in ICEs were also identified, and some ICEs introduced the carbapenem gene blaOXA-2 and the bleomycin gene bleO to P. multocida. Phylogenetic and collinearity analyses of these bioinformatics found that ICEs in P. multocida were transmitted vertically and horizontally and have evolved with host specialization. These findings provide insight into the transmission and evolution mode of ICEs in P. multocida and highlight the importance of understanding these elements for controlling the spread of antibiotic resistance.},
}
@article {pmid38808121,
year = {2024},
author = {Haimlich, S and Fridman, Y and Khandal, H and Savaldi-Goldstein, S and Levy, A},
title = {Widespread horizontal gene transfer between plants and bacteria.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae073},
pmid = {38808121},
issn = {2730-6151},
abstract = {Plants host a large array of commensal bacteria that interact with the host. The growth of both bacteria and plants is often dependent on nutrients derived from the cognate partners, and the bacteria fine-tune host immunity against pathogens. This ancient interaction is common in all studied land plants and is critical for proper plant health and development. We hypothesized that the spatial vicinity and the long-term relationships between plants and their microbiota may promote cross-kingdom horizontal gene transfer (HGT), a phenomenon that is relatively rare in nature. To test this hypothesis, we analyzed the Arabidopsis thaliana genome and its extensively sequenced microbiome to detect events of horizontal transfer of full-length genes that transferred between plants and bacteria. Interestingly, we detected 75 unique genes that were horizontally transferred between plants and bacteria. Plants and bacteria exchange in both directions genes that are enriched in carbohydrate metabolism functions, and bacteria transferred to plants genes that are enriched in auxin biosynthesis genes. Next, we provided a proof of concept for the functional similarity between a horizontally transferred bacterial gene and its Arabidopsis homologue in planta. The Arabidopsis DET2 gene is essential for biosynthesis of the brassinosteroid phytohormones, and loss of function of the gene leads to dwarfism. We found that expression of the DET2 homologue from Leifsonia bacteria of the Actinobacteria phylum in the Arabidopsis det2 background complements the mutant and leads to normal plant growth. Together, these data suggest that cross-kingdom HGT events shape the metabolic capabilities and interactions between plants and bacteria.},
}
@article {pmid38806321,
year = {2024},
author = {Craske, MW and Wilson, JS and Fogg, PCM},
title = {Gene transfer agents: structural and functional properties of domesticated viruses.},
journal = {Trends in microbiology},
volume = {32},
number = {12},
pages = {1200-1211},
doi = {10.1016/j.tim.2024.05.002},
pmid = {38806321},
issn = {1878-4380},
mesh = {*Gene Transfer, Horizontal ; *Bacteriophages/genetics/physiology ; Rhodobacter capsulatus/virology/genetics/metabolism ; Archaea/virology/genetics ; Bacteria/virology/genetics/metabolism ; Evolution, Molecular ; DNA, Viral/genetics ; },
abstract = {Horizontal exchange of DNA between bacteria and archaea is prevalent and has major potential implications for genome evolution, plasticity, and population fitness. Several transfer mechanisms have been identified, including gene transfer agents (GTAs). GTAs are intricately regulated domesticated viruses that package host DNA into virus-like capsids and transfer this DNA throughout the bacterial community. Several important advances have recently been made in our understanding of these unusual particles. In this review, we highlight some of these findings, primarily for the model GTA produced by Rhodobacter capsulatus but also for newly identified GTA producers. We provide key insights into these important genetic elements, including the differences between GTAs from their ancestral bacteriophages, their regulation and control, and their elusive evolutionary function.},
}
@article {pmid38802023,
year = {2024},
author = {Ji, W and Ma, J and Zheng, Z and Al-Herrawy, AZ and Xie, B and Wu, D},
title = {Algae blooms with resistance in fresh water: Potential interplay between Microcystis and antibiotic resistance genes.},
journal = {The Science of the total environment},
volume = {940},
number = {},
pages = {173528},
doi = {10.1016/j.scitotenv.2024.173528},
pmid = {38802023},
issn = {1879-1026},
mesh = {*Microcystis/genetics/physiology ; *Drug Resistance, Microbial/genetics ; *Microcystins ; *Fresh Water/microbiology ; Eutrophication ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; },
abstract = {Microcystis, a type of cyanobacteria known for producing microcystins (MCs), is experiencing a global increase in blooms. They have been recently recognized as potential contributors to the widespread of antibiotic resistance genes (ARGs). By reviewing approximately 150 pieces of recent studies, a hypothesis has been formulated suggesting that significant fluctuations in MCs concentrations and microbial community structure during Microcystis blooms could influence the dynamics of waterborne ARGs. Among all MCs, microcystin-LR (MC-LR) is the most widely distributed worldwide, notably abundant in reservoirs during summer. MCs inhibit protein phosphatases or increase reactive oxygen species (ROS), inducing oxidative stresses, enhancing membrane permeability, and causing DNA damage. This further enhances selective pressures and horizontal gene transfer (HGT) chances of ARGs. The mechanisms by which Microcystis regulates ARG dissemination have been systematically organized for the first time, focusing on the secretion of MCs and the alterations of bacterial community structure. However, several knowledge gaps remain, particularly concerning how MCs interfere with the electron transport chain and how Microcystis facilitates HGT of ARGs. Concurrently, the predominance of Microcystis forming the algal microbial aggregates is considered a hotspot for preserving and transferring ARGs. Yet, Microcystis can deplete the nutrients from other taxa within these aggregates, thereby reducing the density of ARG-carrying bacteria. Therefore, further studies are needed to explore the 'symbiotic - competitive' relationships between Microcystis and ARG-hosting bacteria under varied nutrient conditions. Addressing these knowledge gaps is crucial to understand the impacts of the algal aggregates on dynamics of waterborne antibiotic resistome, and underscores the need for effective control of Microcystis to curb the spread of antibiotic resistance. Constructed wetlands and photocatalysis represent advantageous strategies for halting the spread of ARGs from the perspective of Microcystis blooms, as they can effectively control Microcystis and MCs while maintaining the stability of aquatic ecosystem.},
}
@article {pmid38789482,
year = {2024},
author = {Puginier, C and Libourel, C and Otte, J and Skaloud, P and Haon, M and Grisel, S and Petersen, M and Berrin, JG and Delaux, PM and Dal Grande, F and Keller, J},
title = {Phylogenomics reveals the evolutionary origins of lichenization in chlorophyte algae.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4452},
pmid = {38789482},
issn = {2041-1723},
mesh = {*Lichens/genetics/microbiology ; *Phylogeny ; *Symbiosis/genetics ; *Chlorophyta/genetics ; Gene Transfer, Horizontal ; Evolution, Molecular ; Biological Evolution ; Transcriptome ; Glycoside Hydrolases/genetics/metabolism ; Genomics ; },
abstract = {Mutualistic symbioses have contributed to major transitions in the evolution of life. Here, we investigate the evolutionary history and the molecular innovations at the origin of lichens, which are a symbiosis established between fungi and green algae or cyanobacteria. We de novo sequence the genomes or transcriptomes of 12 lichen algal symbiont (LAS) and closely related non-symbiotic algae (NSA) to improve the genomic coverage of Chlorophyte algae. We then perform ancestral state reconstruction and comparative phylogenomics. We identify at least three independent gains of the ability to engage in the lichen symbiosis, one in Trebouxiophyceae and two in Ulvophyceae, confirming the convergent evolution of the lichen symbioses. A carbohydrate-active enzyme from the glycoside hydrolase 8 (GH8) family was identified as a top candidate for the molecular-mechanism underlying lichen symbiosis in Trebouxiophyceae. This GH8 was acquired in lichenizing Trebouxiophyceae by horizontal gene transfer, concomitantly with the ability to associate with lichens fungal symbionts (LFS) and is able to degrade polysaccharides found in the cell wall of LFS. These findings indicate that a combination of gene family expansion and horizontal gene transfer provided the basis for lichenization to evolve in chlorophyte algae.},
}
@article {pmid38789462,
year = {2024},
author = {Wranne, MS and Karami, N and Kk, S and Jaén-Luchoro, D and Yazdanshenas, S and Lin, YL and Kabbinale, A and Flach, CF and Westerlund, F and Åhrén, C},
title = {Comparison of CTX-M encoding plasmids present during the early phase of the ESBL pandemic in western Sweden.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {11880},
pmid = {38789462},
issn = {2045-2322},
support = {C4A 2020-02518//V&#xe4;stra G&#xf6;talandsregionen/ ; ALF-965000//V&#xe4;stra G&#xf6;talandsregionen/ ; 2021-00922//Svenska Forskningsr&#xe5;det Formas/ ; 634890//EU Horizon 2020 program BeyondSeq/ ; },
mesh = {Sweden/epidemiology ; *Plasmids/genetics ; *beta-Lactamases/genetics ; *Escherichia coli/genetics ; Humans ; Pandemics ; Escherichia coli Infections/epidemiology/microbiology ; Gene Transfer, Horizontal ; Escherichia coli Proteins/genetics ; Whole Genome Sequencing ; },
abstract = {Plasmids encoding blaCTX-M genes have greatly shaped the evolution of E. coli producing extended-spectrum beta-lactamases (ESBL-E. coli) and adds to the global threat of multiresistant bacteria by promoting horizontal gene transfer (HGT). Here we screened the similarity of 47 blaCTX-M -encoding plasmids, from 45 epidemiologically unrelated and disperse ESBL-E. coli strains, isolated during the early phase (2009-2014) of the ESBL pandemic in western Sweden. Using optical DNA mapping (ODM), both similar and rare plasmids were identified. As many as 57% of the plasmids formed five ODM-plasmid groups of at least three similar plasmids per group. The most prevalent type (28%, IncIl, pMLST37) encoded blaCTX-M-15 (n = 10), blaCTX-M-3 (n = 2) or blaCTX-M-55 (n = 1). It was found in isolates of various sequence types (STs), including ST131. This could indicate ongoing local HGT as whole-genome sequencing only revealed similarities with a rarely reported, IncIl plasmid. The second most prevalent type (IncFII/FIA/FIB, F1:A2:B20) harboring blaCTX-M-27, was detected in ST131-C1-M27 isolates, and was similar to plasmids previously reported for this subclade. The results also highlight the need for local surveillance of plasmids and the importance of temporospatial epidemiological links so that detection of a prevalent plasmid is not overestimated as a potential plasmid transmission event in outbreak investigations.},
}
@article {pmid38788585,
year = {2024},
author = {Liu, T and Lee, S and Kim, M and Fan, P and Boughton, RK and Boucher, C and Jeong, KC},
title = {A study at the wildlife-livestock interface unveils the potential of feral swine as a reservoir for extended-spectrum β-lactamase-producing Escherichia coli.},
journal = {Journal of hazardous materials},
volume = {473},
number = {},
pages = {134694},
doi = {10.1016/j.jhazmat.2024.134694},
pmid = {38788585},
issn = {1873-3336},
support = {R01 AI141810/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; *Escherichia coli/genetics/drug effects/enzymology ; *beta-Lactamases/genetics/metabolism ; *Animals, Wild/microbiology ; Swine ; *Disease Reservoirs/microbiology ; Cattle ; Gene Transfer, Horizontal ; Livestock/microbiology ; Drug Resistance, Bacterial ; Escherichia coli Infections/microbiology/veterinary ; },
abstract = {Wildlife is known to serve as carriers and sources of antimicrobial resistance (AMR). Due to their unrestricted movements and behaviors, they can spread antimicrobial resistant bacteria among livestock, humans, and the environment, thereby accelerating the dissemination of AMR. Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is one of major concerns threatening human and animal health, yet transmission mechanisms at the wildlife-livestock interface are not well understood. Here, we investigated the mechanisms of ESBL-producing bacteria spreading across various hosts, including cattle, feral swine, and coyotes in the same habitat range, as well as from environmental samples over a two-year period. We report a notable prevalence and clonal dissemination of ESBL-producing E. coli in feral swine and coyotes, suggesting their persistence and adaptation within wildlife hosts. In addition, in silico studies showed that horizontal gene transfer, mediated by conjugative plasmids and insertion sequences elements, may play a key role in spreading the ESBL genes among these bacteria. Furthermore, the shared gut resistome of cattle and feral swine suggests the dissemination of antibiotic resistance genes at the wildlife-livestock interface. Taken together, our results suggest that feral swine may serve as a reservoir of ESBL-producing E. coli.},
}
@article {pmid38788579,
year = {2024},
author = {Zhou, CS and Cao, GL and Liu, BF and Liu, W and Ma, WL and Ren, NQ},
title = {Deciphering the reduction of antibiotic resistance genes (ARGs) during medium-chain fatty acids production from waste activated sludge: Driven by inhibition of ARGs transmission and shift of microbial community.},
journal = {Journal of hazardous materials},
volume = {473},
number = {},
pages = {134676},
doi = {10.1016/j.jhazmat.2024.134676},
pmid = {38788579},
issn = {1873-3336},
mesh = {*Sewage/microbiology ; *Fatty Acids/metabolism ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects/metabolism ; Microbiota/drug effects ; Gene Transfer, Horizontal ; Genes, Bacterial ; Waste Disposal, Fluid/methods ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Medium-chain fatty acids (MCFAs) production from waste activated sludge (WAS) by chain extension (CE) is a promising technology. However, the effects and mechanisms of CE process on the fate of antibiotic resistance genes (ARGs) remain unclear. In this study, the results showed that the removal efficiency of ARGs was 81.15 % in CE process, suggesting its efficacy in reducing environmental risks. Further, the observed decrease in mobile genetic elements (MGEs) indicated that CE process restricted the horizontal gene transfer (HGT). Complementing this, the increase in soluble organic matters and extracellular 16 S rDNA confirmed that MCFAs production caused bacterial damage. Decreased intracellular ARGs and increased extracellular ARGs further revealed that MCFAs production impaired ARGs hosts, thereby limiting the vertical gene transfer (VGT) of ARGs. Shift of microbial community combined with co-occurrence network analysis demonstrated that functional bacteria without host potential for ARGs were enriched, but potential ARGs and MGEs hosts decreased, showing the role of functional bacterial phylogeny and selection pressure of MCFAs in reducing ARGs. Finally, partial least squares path model was used to systematic verify the mechanism of ARGs removal in CE process, which was attributed to the inhibition of ARGs transmission (HGT and VGT) and shift of microbial community.},
}
@article {pmid38786183,
year = {2024},
author = {Sabtcheva, S and Stoikov, I and Ivanov, IN and Donchev, D and Lesseva, M and Georgieva, S and Teneva, D and Dobreva, E and Christova, I},
title = {Genomic Characterization of Carbapenemase-Producing Enterobacter hormaechei, Serratia marcescens, Citrobacter freundii, Providencia stuartii, and Morganella morganii Clinical Isolates from Bulgaria.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {5},
pages = {},
pmid = {38786183},
issn = {2079-6382},
abstract = {Carbapenemase-producing Enterobacter spp. Serratia marcescens, Citrobacter freundii, Providencia spp., and Morganella morganii (CP-ESCPM) are increasingly identified as causative agents of nosocomial infections but are still not under systematic genomic surveillance. In this study, using a combination of whole-genome sequencing and conjugation experiments, we sought to elucidate the genomic characteristics and transferability of resistance genes in clinical CP-ESCPM isolates from Bulgaria. Among the 36 sequenced isolates, NDM-1 (12/36), VIM-4 (11/36), VIM-86 (8/36), and OXA-48 (7/36) carbapenemases were identified; two isolates carried both NDM-1 and VIM-86. The majority of carbapenemase genes were found on self-conjugative plasmids. IncL plasmids were responsible for the spread of OXA-48 among E. hormaechei, C. freundii, and S. marcescens. IncM2 plasmids were generally associated with the spread of NDM-1 in C. freundii and S. marcescens, and also of VIM-4 in C. freundii. IncC plasmids were involved in the spread of the recently described VIM-86 in P. stuartii isolates. IncC plasmids carrying blaNDM-1 and blaVIM-86 were observed too. blaNDM-1 was also detected on IncX3 in S. marcescens and on IncT plasmid in M. morganii. The significant resistance transfer rates we observed highlight the role of the ESCPM group as a reservoir of resistance determinants and stress the need for strengthening infection control measures.},
}
@article {pmid38786161,
year = {2024},
author = {Lamichhane, J and Choi, BI and Stegman, N and Fontes Noronha, M and Wolfe, AJ},
title = {Macrolide Resistance in the Aerococcus urinae Complex: Implications for Integrative and Conjugative Elements.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {5},
pages = {},
pmid = {38786161},
issn = {2079-6382},
support = {Pathnostics//Pathnostics/ ; },
abstract = {The recognition of the Aerococcus urinae complex (AUC) as an emerging uropathogen has led to growing concerns due to a limited understanding of its disease spectrum and antibiotic resistance profiles. Here, we investigated the prevalence of macrolide resistance within urinary AUC isolates, shedding light on potential genetic mechanisms. Phenotypic testing revealed a high rate of macrolide resistance: 45%, among a total of 189 urinary AUC isolates. Genomic analysis identified integrative and conjugative elements (ICEs) as carriers of the macrolide resistance gene ermA, suggesting horizontal gene transfer as a mechanism of resistance. Furthermore, comparison with publicly available genomes of related pathogens revealed high ICE sequence homogeneity, highlighting the potential for cross-species dissemination of resistance determinants. Understanding mechanisms of resistance is crucial for developing effective surveillance strategies and improving antibiotic use. Furthermore, the findings underscore the importance of considering the broader ecological context of resistance dissemination, emphasizing the need for community-level surveillance to combat the spread of antibiotic resistance within the urinary microbiome.},
}
@article {pmid38786130,
year = {2024},
author = {Monecke, S and Burgold-Voigt, S and Braun, SD and Diezel, C and Liebler-Tenorio, EM and Müller, E and Nassar, R and Reinicke, M and Reissig, A and Senok, A and Ehricht, R},
title = {Characterisation of PVL-Positive Staphylococcus argenteus from the United Arab Emirates.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {5},
pages = {},
pmid = {38786130},
issn = {2079-6382},
support = {13GW0456//Federal Ministry of Education and Research/ ; 13N15717//Federal Ministry of Education and Research/ ; },
abstract = {Staphylococcus argenteus is a recently described staphylococcal species that is related to Staphylococcus aureus but lacks the staphyloxanthin operon. It is able to acquire both resistance markers such as the SCCmec elements and mobile genetic elements carrying virulence-associated genes from S. aureus. This includes those encoding the Panton-Valentine leukocidin (PVL), which is associated mainly with severe and/or recurrent staphylococcal skin and soft tissue infections. Here, we describe the genome sequences of two PVL-positive, mecA-negative S. argenteus sequence type (ST) 2250 isolates from the United Arab Emirates in detail. The isolates were found in a dental clinic in the United Arab Emirates (UAE). Both were sequenced using Oxford Nanopore Technology (ONT). This demonstrated the presence of temperate bacteriophages in the staphylococcal genomes, including a PVL prophage. It was essentially identical to the published sequence of phiSa2wa_st78 (GenBank NC_055048), a PVL phage from an Australian S. aureus clonal complex (CC) 88 isolate. Besides the PVL prophage, one isolate carried another prophage and the second isolate carried two additional prophages, whereby the region between these two prophages was inverted. This "flipped" region comprised about 1,083,000 bp, or more than a third of the strain's genome, and it included the PVL prophage. Prophages were induced by Mitomycin C treatment and subjected to transmission electron microscopy (TEM). This yielded, in accordance to the sequencing results, one or, respectively, two distinct populations of icosahedral phages. It also showed prolate phages which presumptively might be identified as the PVL phage. This observation highlights the significance bacteriophages have as agents of horizontal gene transfer as well as the need for monitoring emerging staphylococcal strains, especially in cosmopolitan settings such as the UAE.},
}
@article {pmid38783378,
year = {2024},
author = {Brattig, N and Bergquist, R and Vienneau, D and Zhou, XN},
title = {Geography and health: role of human translocation and access to care.},
journal = {Infectious diseases of poverty},
volume = {13},
number = {1},
pages = {37},
pmid = {38783378},
issn = {2049-9957},
mesh = {Humans ; *Health Services Accessibility ; Animals ; *Zoonoses/epidemiology ; COVID-19/transmission/epidemiology ; Communicable Diseases/epidemiology/transmission ; SARS-CoV-2 ; Geography ; },
abstract = {Natural, geographical barriers have historically limited the spread of communicable diseases. This is no longer the case in today's interconnected world, paired with its unprecedented environmental and climate change, emphasising the intersection of evolutionary biology, epidemiology and geography (i.e. biogeography). A total of 14 articles of the special issue entitled "Geography and health: role of human translocation and access to care" document enhanced disease transmission of diseases, such as malaria, leishmaniasis, schistosomiasis, COVID-19 (Severe acute respiratory syndrome corona 2) and Oropouche fever in spite of spatiotemporal surveillance. High-resolution satellite images can be used to understand spatial distributions of transmission risks and disease spread and to highlight the major avenue increasing the incidence and geographic range of zoonoses represented by spill-over transmission of coronaviruses from bats to pigs or civets. Climate change and globalization have increased the spread and establishment of invasive mosquitoes in non-tropical areas leading to emerging outbreaks of infections warranting improved physical, chemical and biological vector control strategies. The translocation of pathogens and their vectors is closely connected with human mobility, migration and the global transport of goods. Other contributing factors are deforestation with urbanization encroaching into wildlife zones. The destruction of natural ecosystems, coupled with low income and socioeconomic status, increase transmission probability of neglected tropical and zoonotic diseases. The articles in this special issue document emerging or re-emerging diseases and surveillance of fever symptoms. Health equity is intricately connected to accessibility to health care and the targeting of healthcare resources, necessitating a spatial approach. Public health comprises successful disease management integrating spatial surveillance systems, including access to sanitation facilities. Antimicrobial resistance caused, e.g. by increased use of antibiotics in health, agriculture and aquaculture, or acquisition of resistance genes, can be spread by horizontal gene transfer. This editorial reviews the key findings of this 14-article special issue, identifies important gaps relevant to our interconnected world and makes a number of specific recommendations to mitigate the transmission risks of infectious diseases in the post-COVID-19 pandemic era.},
}
@article {pmid38783210,
year = {2024},
author = {Han, D and Ma, S and He, C and Yang, Y and Li, P and Lu, L},
title = {Unveiling the genetic architecture and transmission dynamics of a novel multidrug-resistant plasmid harboring blaNDM-5 in E. Coli ST167: implications for antibiotic resistance management.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {178},
pmid = {38783210},
issn = {1471-2180},
support = {2022B1154//Health Projects of Zhongshan City/ ; 2018B1081//Health Projects of Zhongshan City/ ; },
mesh = {*Plasmids/genetics ; *Escherichia coli/genetics/drug effects ; *Drug Resistance, Multiple, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *beta-Lactamases/genetics ; Humans ; *Escherichia coli Infections/microbiology/transmission ; *Microbial Sensitivity Tests ; China ; Gene Transfer, Horizontal ; Carbapenems/pharmacology ; },
abstract = {BACKGROUND: The emergence of multidrug-resistant (MDR) Escherichia coli strains poses significant challenges in clinical settings, particularly when these strains harbor New Delhi metallo-ß-lactamase (NDM) gene, which confer resistance to carbapenems, a critical class of last-resort antibiotics. This study investigates the genetic characteristics and implications of a novel blaNDM-5-carrying plasmid pNDM-5-0083 isolated from an E. coli strain GZ04-0083 from clinical specimen in Zhongshan, China.<br><br>RESULTS: Phenotypic and genotypic evaluations confirmed that the E. coli ST167 strain GZ04-0083 is a multidrug-resistant organism, showing resistance to diverse classes of antibiotics including &#xdf;-lactams, carbapenems, fluoroquinolones, aminoglycosides, and sulfonamides, while maintaining susceptibility to monobactams. Investigations involving S1 pulsed-field gel electrophoresis, Southern blot analysis, and conjugation experiments, alongside genomic sequencing, confirmed the presence of the blaNDM-5 gene within a 146-kb IncFIB plasmid pNDM-5-0083. This evidence underscores a significant risk for the horizontal transfer of resistance genes among bacterial populations. Detailed annotations of genetic elements-such as resistance genes, transposons, and insertion sequences-and comparative BLAST analyses with other blaNDM-5-carrying plasmids, revealed a unique architectural configuration in the pNDM-5-0083. The MDR region of this plasmid shares a conserved gene arrangement (repA-IS15DIV-blaNDM-5-bleMBL-IS91-suI2-aadA2-dfrA12) with three previously reported plasmids, indicating a potential for dynamic genetic recombination and evolution within the MDR region. Additionally, the integration of virulence factors, including the iro and sit gene clusters and enolase, into its genetic architecture poses further therapeutic challenges by enhancing the strain's pathogenicity through improved host tissue colonization, immune evasion, and increased infection severity.<br><br>CONCLUSIONS: The detailed identification and characterization of pNDM-5-0083 enhance our understanding of the mechanisms facilitating the spread of carbapenem resistance. This study illuminates the intricate interplay among various genetic elements within the novel blaNDM-5-carrying plasmid, which are crucial for the stability and mobility of resistance genes across bacterial populations. These insights highlight the urgent need for ongoing surveillance and the development of effective strategies to curb the proliferation of antibiotic resistance.},
}
@article {pmid38783209,
year = {2024},
author = {Gevin, M and Latifi, A and Talla, E},
title = {The modular architecture of sigma factors in cyanobacteria: a framework to assess their diversity and understand their evolution.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {512},
pmid = {38783209},
issn = {1471-2164},
support = {ANR-21-CE20-0025-01//Agence Nationale de la Recherche/ ; ANR-21-CE20-0025-01//Agence Nationale de la Recherche/ ; ANR-21-CE20-0025-01//Agence Nationale de la Recherche/ ; },
mesh = {*Sigma Factor/genetics/metabolism ; *Evolution, Molecular ; *Cyanobacteria/genetics/metabolism ; *Phylogeny ; Bacterial Proteins/genetics/metabolism ; Genetic Variation ; },
abstract = {BACKGROUND: Bacterial RNA polymerase holoenzyme requires sigma70 factors to start transcription by identifying promoter elements. Cyanobacteria possess multiple sigma70 factors to adapt to a wide variety of ecological niches. These factors are grouped into two categories: primary sigma factor initiates transcription of housekeeping genes during normal growth conditions, while alternative sigma factors initiate transcription of specific genes under particular conditions. However, the present classification does not consider the modular organization of their structural domains, introducing therefore multiple functional and structural biases. A comprehensive analysis of this protein family in cyanobacteria is needed to address these limitations.<br><br>RESULTS: We investigated the structure and evolution of sigma70 factors in cyanobacteria, analyzing their modular architecture and variation among unicellular, filamentous, and heterocyst-forming morphotypes. 4,193 sigma70 homologs were found with 59 distinct modular patterns, including six essential and 29 accessory domains, such as DUF6596. 90% of cyanobacteria typically have 5 to 17 sigma70 homologs and this number likely depends on the strain morphotype, the taxonomic order and the genome size. We classified sigma70 factors into 12 clans and 36 families. According to taxonomic orders and phenotypic traits, the number of homologs within the 14 main families was variable, with the A.1 family including the primary sigma factor since this family was found in all cyanobacterial species. The A.1, A.5, C.1, E.1, J.1, and K.1 families were found to be key sigma families that distinguish heterocyst-forming strains. To explain the diversification and evolution of sigma70, we propose an evolutionary scenario rooted in the diversification of a common ancestor of the A1 family. This scenario is characterized by evolutionary events including domain losses, gains, insertions, and modifications. The high occurrence of the DUF6596 domain in bacterial sigma70 proteins, and its association with the highest prevalence observed in Actinobacteria, suggests that this domain might be important for sigma70 function. It also implies that the domain could have emerged in Actinobacteria and been transferred through horizontal gene transfer.<br><br>CONCLUSION: Our analysis provides detailed insights into the modular domain architecture of sigma70, introducing a novel robust classification. It also proposes an evolutionary scenario explaining their diversity across different taxonomical orders.},
}
@article {pmid38781445,
year = {2024},
author = {Vuruputoor, VS and Starovoitov, A and Cai, Y and Liu, Y and Rahmatpour, N and Hedderson, TA and Wilding, N and Wegrzyn, JL and Goffinet, B},
title = {Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana.},
journal = {G3 (Bethesda, Md.)},
volume = {14},
number = {7},
pages = {},
pmid = {38781445},
issn = {2160-1836},
support = {DEB-0919284//US National Science Foundation/ ; },
mesh = {*Gene Transfer, Horizontal ; *Bryopsida/genetics ; *Genome, Plant ; *Phylogeny ; Genomics/methods ; Molecular Sequence Annotation ; },
abstract = {The first chromosome-scale reference genome of the rare narrow-endemic African moss Physcomitrellopsis africana (P. africana) is presented here. Assembled from 73 × Oxford Nanopore Technologies (ONT) long reads and 163 × Beijing Genomics Institute (BGI)-seq short reads, the 414 Mb reference comprises 26 chromosomes and 22,925 protein-coding genes [Benchmarking Universal Single-Copy Ortholog (BUSCO) scores: C:94.8% (D:13.9%)]. This genome holds 2 genes that withstood rigorous filtration of microbial contaminants, have no homolog in other land plants, and are thus interpreted as resulting from 2 unique horizontal gene transfers (HGTs) from microbes. Further, P. africana shares 176 of the 273 published HGT candidates identified in Physcomitrium patens (P. patens), but lacks 98 of these, highlighting that perhaps as many as 91 genes were acquired in P. patens in the last 40 million years following its divergence from its common ancestor with P. africana. These observations suggest rather continuous gene gains via HGT followed by potential losses during the diversification of the Funariaceae. Our findings showcase both dynamic flux in plant HGTs over evolutionarily "short" timescales, alongside enduring impacts of successful integrations, like those still functionally maintained in extant P. africana. Furthermore, this study describes the informatic processes employed to distinguish contaminants from candidate HGT events.},
}
@article {pmid38777914,
year = {2024},
author = {Zhang, F and Shi, X and Xu, J and Yuan, W and Li, Z},
title = {Tandem gene duplication selected by activation of horizontally transferred gene in bacteria.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {340},
pmid = {38777914},
issn = {1432-0614},
support = {2020YFA0908000//The National Key R&amp;D Program of China/ ; TSBICIP-CXRC-001//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project/ ; 2060302//Key project at central government level: The ability establishment of sustainable use for valuable Chinese medicine resource/ ; },
mesh = {*Gene Duplication ; *Gene Transfer, Horizontal ; *Escherichia coli/genetics/metabolism ; *Plasmids/genetics ; Bacteria/genetics/metabolism ; Gene Dosage ; Recombination, Genetic ; },
abstract = {Horizontal gene transfer occurs frequently in bacteria, but the mechanism driving activation and optimization of the expression of horizontally transferred genes (HTGs) in new recipient strains is not clear. Our previous study found that spontaneous tandem DNA duplication resulted in rapid activation of HTGs. Here, we took advantage of this finding to develop a novel technique for tandem gene duplication, named tandem gene duplication selected by activation of horizontally transferred gene in bacteria (TDAH), in which tandem duplication was selected by the activation of horizontally transferred selectable marker gene. TDAH construction does not contain any reported functional elements based on homologous or site-specific recombination and DNA amplification. TDAH only contains an essential selectable marker for copy number selection and 9-bp-microhomology border sequences for precise illegitimate recombination. One transformation and 3 days were enough to produce a high-copy strain, so its procedure is simple and fast. Without subsequent knockout of the endogenous recombination system, TDAH could also generate the relatively stable high-copy tandem duplication for plasmid-carried and genome-integrated DNA. TDAH also showed an excellent capacity for increase gene expression and worked well in different industrial bacteria. We also applied TDAH to select the optimal high copy number of ribA for vitamin B2 production in E. coli; the yield was improved by 3.5 times and remained stable even after 12 subcultures. TDAH is a useful tool for recombinant protein production and expression optimization of biosynthetic pathways. KEY POINTS: • We develop a novel and efficient technique (TDAH) for tandem gene duplication in bacterium. TDAH is based on the mechanism of HTG rapid activation. TDAH does not contain any reported functional elements based on homologous recombination and DNA amplification. TDAH only contains an essential selectable marker for copy number selection, so its construction and procedure are very simple and fast. • TDAH is the first reported selected and stable tandem-gene-duplication technique in which the selected high-copy plasmid-carried and genome-integrated DNA could remain stable without the subsequent knockout of recombination system. • TDAH showed an excellent capacity for regulating gene expression and worked well in different industrial bacteria, indicating it is a useful tool for recombinant protein production and expression optimization of biosynthetic pathways. • TDAH was applied to select the optimal high copy number of ribA for vitamin B2 production in E. coli; the yield was improved by 3.5-fold and remained stable even after 12 subcultures.},
}
@article {pmid38772228,
year = {2024},
author = {Xu, M and Gao, P and Gao, Y and Xiong, SJ and Chen, HQ and Shen, XX},
title = {Impacts of microplastic type on the fate of antibiotic resistance genes and horizontal gene transfer mechanism during anaerobic digestion.},
journal = {Journal of environmental management},
volume = {360},
number = {},
pages = {121090},
doi = {10.1016/j.jenvman.2024.121090},
pmid = {38772228},
issn = {1095-8630},
mesh = {*Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Microplastics ; Anaerobiosis ; *Sewage/microbiology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Microplastics (MPs) and antibiotic resistance genes (ARGs) are important pollutants in waste activated sludge (WAS), but their interactions during anaerobic digestion (AD) still need to be further explored. This study investigated variations in ARGs, mobile genetic elements (MGEs), and host bacteria during AD under the pressure of polyamide (PA), polyethylene (PE), and polypropylene (PP). The results showed that the MPs increased methane production by 11.7-35.5%, and decreased ARG abundance by 5.6-24.6%. Correlation analysis showed that the decrease of MGEs (plasmid, prophage, etc.) promoted the decrease of the abundance of multidrug, aminoglycoside and tetracycline resistance genes. Metagenomic annotation revealed that the reduction of key host bacteria (Arenimonas, Lautropia, etc.) reduced the abundance of major ARGs (rsmA, rpoB2, etc.). Moreover, PP MPs contributed to a reduction in the abundance of functional genes related to the production of reactive oxygen species, ATP synthesis, and cell membrane permeability, which was conducive to reducing the potential for horizontal gene transfer of ARGs. These findings provide insights into the treatment of organic waste containing MPs.},
}
@article {pmid38772218,
year = {2024},
author = {Kang, J and Zhang, C and Wan, S and Li, W and Zhao, W and Li, L and Shang, Y and Du, XD and Liu, D and Yao, H},
title = {Prevalence and characterization of aminoglycoside resistance gene aph(2")-If-carrying Campylobacter jejuni.},
journal = {International journal of food microbiology},
volume = {419},
number = {},
pages = {110747},
doi = {10.1016/j.ijfoodmicro.2024.110747},
pmid = {38772218},
issn = {1879-3460},
mesh = {*Campylobacter jejuni/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Aminoglycosides/pharmacology ; Animals ; *Phylogeny ; *Anti-Bacterial Agents/pharmacology ; *Multilocus Sequence Typing ; *Campylobacter Infections/microbiology/veterinary/epidemiology ; Whole Genome Sequencing ; Humans ; Prevalence ; China ; Food Microbiology ; Microbial Sensitivity Tests ; },
abstract = {Campylobacter jejuni is recognized as a significant foodborne pathogen, and recent studies have indicated a rising trend of aminoglycosides resistance gene aph(2″)-If among C. jejuni isolates from food-producing animals in China. However, systematic information about aph(2″)-If-positive C. jejuni from food-producing animals and other sources worldwide based on whole-genome analysis remains a knowledge gap. In this study, we aimed to analyze the worldwide distribution, genetic environment and phylogenetic tree of aph(2″)-If by utilizing Whole Genome Sequencing (WGS) data obtained, coupled with information in the GenBank database. A total of 160C. jejuni isolates in the GenBank database and 14C. jejuni isolates in our laboratory carrying aph(2″)-If gene were performed for further analysis. WGS analysis revealed the global distribution of aph(2″)-If among C. jejuni from 6 countries. Multilocus Sequence Typing(MLST) results indicated that 70 STs were involved in the dissemination of aph(2″)-If, with ST10086 being the predominant ST. Whole-genome Multilocus Sequence Typing(wg-MLST) analysis according to times, countries, and origins of C. jejuni isolation further demonstrated a close relationship between aph(2″)-If carrying C. jejuni isolates from farm and food. The findings also revealed the existence of 32 distinct types of genetic environments surrounding aph(2″)-If among these isolates. Notably, Type 30, characterized by the arrangement ISsag10-deoD-ant(9)-hp-hp-aph(2″)-If, emerged as the predominant genetic environment. In conclusion, our analysis provides the inaugural perspective on the worldwide distribution of aph(2″)-If. This resistance gene demonstrates horizontal transferability and regional diffusion in a clonal pattern. The close association observed among aph(2″)-If-positive C. jejuni strains isolated from poultry, food, and clinical environments underscores the potential for zoonotic transmission from these isolates.},
}
@article {pmid38771049,
year = {2024},
author = {Muñoz-Gutiérrez, I and Cantu, L and Shanahan, J and Girguis, M and de la Cruz, M and Mota-Bravo, L},
title = {Cryptic environmental conjugative plasmid recruits a novel hybrid transposon resulting in a new plasmid with higher dispersion potential.},
journal = {mSphere},
volume = {9},
number = {6},
pages = {e0025224},
pmid = {38771049},
issn = {2379-5042},
support = {T34 GM136498/GM/NIGMS NIH HHS/United States ; GM136498//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*Plasmids/genetics ; *DNA Transposable Elements/genetics ; *Escherichia coli/genetics/drug effects ; *Conjugation, Genetic ; *Anti-Bacterial Agents/pharmacology ; Lakes/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; },
abstract = {UNLABELLED: Cryptic conjugative plasmids lack antibiotic-resistance genes (ARGs). These plasmids can capture ARGs from the vast pool of the environmental metagenome, but the mechanism to recruit ARGs remains to be elucidated. To investigate the recruitment of ARGs by a cryptic plasmid, we sequenced and conducted mating experiments with Escherichia coli SW4848 (collected from a lake) that has a cryptic IncX (IncX4) plasmid and an IncF (IncFII/IncFIIB) plasmid with five genes that confer resistance to aminoglycosides (strA and strB), sulfonamides (sul2), tetracycline [tet(A)], and trimethoprim (dfrA5). In a conjugation experiment, a novel hybrid Tn21/Tn1721 transposon of 22,570 bp (designated Tn7714) carrying the five ARG mobilized spontaneously from the IncF plasmid to the cryptic IncX plasmid. The IncF plasmid was found to be conjugative when it was electroporated into E. coli DH10B (without the IncX plasmid). Two parallel conjugations with the IncF and the new IncX (carrying the novel Tn7714 transposon) plasmids in two separate E. coli DH10B as donors and E. coli J53 as the recipient revealed that the conjugation rate of the new IncX plasmid (with the novel Tn7714 transposon and five ARGs) is more than two orders of magnitude larger than the IncF plasmid. For the first time, this study shows experimental evidence that cryptic environmental plasmids can capture and transfer transposons with ARGs to other bacteria, creating novel multidrug-resistant conjugative plasmids with higher dispersion potential.<br><br>IMPORTANCE: Cryptic conjugative plasmids are extrachromosomal DNA molecules without antibiotic-resistance genes (ARGs). Environmental bacteria carrying cryptic plasmids with a high conjugation rate threaten public health because they can capture clinically relevant ARGs and rapidly spread them to pathogenic bacteria. However, the mechanism to recruit ARG by cryptic conjugative plasmids in environmental bacteria has not been observed experimentally. Here, we document the first translocation of a transposon with multiple clinically relevant ARGs to a cryptic environmental conjugative plasmid. The new multidrug-resistant conjugative plasmid has a conjugation rate that is two orders of magnitude higher than the original plasmid that carries the ARG (i.e., the new plasmid from the environment can spread ARG more than two orders of magnitude faster). Our work illustrates the importance of studying the mobilization of ARGs in environmental bacteria. It sheds light on how cryptic conjugative plasmids recruit ARGs, a phenomenon at the root of the antibiotic crisis.},
}
@article {pmid38771034,
year = {2024},
author = {Chong, TN and Shapiro, L},
title = {Bacterial cell differentiation enables population level survival strategies.},
journal = {mBio},
volume = {15},
number = {6},
pages = {e0075824},
pmid = {38771034},
issn = {2150-7511},
support = {R35 GM118071/GM/NIGMS NIH HHS/United States ; //Chan Zuckerberg Initiative (CZI)/ ; R35-GM118071//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*Bacteria/genetics ; Bacterial Physiological Phenomena ; Cell Differentiation ; Adaptation, Physiological ; Microbial Viability ; Signal Transduction ; },
abstract = {Clonal reproduction of unicellular organisms ensures the stable inheritance of genetic information. However, this means of reproduction lacks an intrinsic basis for genetic variation, other than spontaneous mutation and horizontal gene transfer. To make up for this lack of genetic variation, many unicellular organisms undergo the process of cell differentiation to achieve phenotypic heterogeneity within isogenic populations. Cell differentiation is either an inducible or obligate program. Induced cell differentiation can occur as a response to a stimulus, such as starvation or host cell invasion, or it can be a stochastic process. In contrast, obligate cell differentiation is hardwired into the organism's life cycle. Whether induced or obligate, bacterial cell differentiation requires the activation of a signal transduction pathway that initiates a global change in gene expression and ultimately results in a morphological change. While cell differentiation is considered a hallmark in the development of multicellular organisms, many unicellular bacteria utilize this process to implement survival strategies. In this review, we describe well-characterized cell differentiation programs to highlight three main survival strategies used by bacteria capable of differentiation: (i) environmental adaptation, (ii) division of labor, and (iii) bet-hedging.},
}
@article {pmid38770060,
year = {2024},
author = {Tamayo-Leiva, J and Alcorta, J and Sepúlveda, F and Fuentes-Alburquenque, S and Arroyo, JI and González-Pastor, JE and Díez, B},
title = {Structure and dispersion of the conjugative mobilome in surface ocean bacterioplankton.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae059},
pmid = {38770060},
issn = {2730-6151},
abstract = {Mobile genetic elements (MGEs), collectively referred to as the "mobilome", can have a significant impact on the fitness of microbial communities and therefore on ecological processes. Marine MGEs have mainly been associated with wide geographical and phylogenetic dispersal of adaptative traits. However, whether the structure of this mobilome exhibits deterministic patterns in the natural community is still an open question. The aim of this study was to characterize the structure of the conjugative mobilome in the ocean surface bacterioplankton by searching the publicly available marine metagenomes from the TARA Oceans survey, together with molecular markers, such as relaxases and type IV coupling proteins of the type IV secretion system (T4SS). The T4SS machinery was retrieved in more abundance than relaxases in the surface marine bacterioplankton. Moreover, among the identified MGEs, mobilizable elements were the most abundant, outnumbering self-conjugative sequences. Detection of a high number of incomplete T4SSs provides insight into possible strategies related to trans-acting activity between MGEs, and accessory functions of the T4SS (e.g. protein secretion), allowing the host to maintain a lower metabolic burden in the highly dynamic marine system. Additionally, the results demonstrate a wide geographical dispersion of MGEs throughout oceanic regions, while the Southern Ocean appears segregated from other regions. The marine mobilome also showed a high similarity of functions present in known plasmid databases. Moreover, cargo genes were mostly related to DNA processing, but scarcely associated with antibiotic resistance. Finally, within the MGEs, integrative and conjugative elements showed wider marine geographic dispersion than plasmids.},
}
@article {pmid38769479,
year = {2024},
author = {Talat, A and Khan, F and Khan, AU},
title = {Genome analyses of colistin-resistant high-risk blaNDM-5 producing Klebsiella pneumoniae ST147 and Pseudomonas aeruginosa ST235 and ST357 in clinical settings.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {174},
pmid = {38769479},
issn = {1471-2180},
mesh = {*Klebsiella pneumoniae/genetics/drug effects/isolation &amp; purification ; *Pseudomonas aeruginosa/genetics/drug effects/isolation &amp; purification ; *Colistin/pharmacology ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Whole Genome Sequencing ; *Microbial Sensitivity Tests ; *Pseudomonas Infections/microbiology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Genome, Bacterial/genetics ; *Klebsiella Infections/microbiology ; Gene Transfer, Horizontal ; India ; beta-Lactamases/genetics ; Plasmids/genetics ; },
abstract = {BACKGROUND: Colistin is a last-resort antibiotic used in extreme cases of multi-drug resistant (MDR) Gram-negative bacterial infections. Colistin resistance has increased in recent years and often goes undetected due to the inefficiency of predominantly used standard antibiotic susceptibility tests (AST). To address this challenge, we aimed to detect the prevalence of colistin resistance strains through both Vitek®2 and broth micro-dilution. We investigated 1748 blood, tracheal aspirate, and pleural fluid samples from the Intensive Care Unit (ICU), Neonatal Intensive Care Unit (NICU), and Tuberculosis and Respiratory Disease centre (TBRD) in an India hospital. Whole-genome sequencing (WGS) of extremely drug-resitant (XDR) and pan-drug resistant (PDR) strains revealed the resistance mechanisms through the Resistance Gene Identifier (RGI.v6.0.0) and Snippy.v4.6.0. Abricate.v1.0.1, PlasmidFinder.v2.1, MobileElementFinder.v1.0.3 etc. detected virulence factors, and mobile genetic elements associated to uncover the pathogenecity and the role of horizontal gene transfer (HGT).<br><br>RESULTS: This study reveals compelling insights into colistin resistance among global high-risk clinical isolates: Klebsiella pneumoniae ST147 (16/20), Pseudomonas aeruginosa ST235 (3/20), and ST357 (1/20). Vitek&#xae;2 found 6 colistin-resistant strains (minimum inhibitory concentrations, MIC&#x2009;=&#x2009;4&#x2009;&#x3bc;g/mL), while broth microdilution identified 48 (MIC&#x2009;=&#x2009;32-128&#x2009;&#x3bc;g/mL), adhering to CLSI guidelines. Despite the absence of mobile colistin resistance (mcr) genes, mechanisms underlying colistin resistance included mgrB deletion, phosphoethanolamine transferases arnT, eptB, ompA, and mutations in pmrB (T246A, R256G) and eptA (V50L, A135P, I138V, C27F) in K. pneumoniae. P. aeruginosa harbored phosphoethanolamine transferases basS/pmrb, basR, arnA, cprR, cprS, alongside pmrB (G362S), and parS (H398R) mutations. Both strains carried diverse clinically relevant antimicrobial resistance genes (ARGs), including plasmid-mediated blaNDM-5 (K. pneumoniae ST147) and chromosomally mediated blaNDM-1 (P. aeruginosa ST357).<br><br>CONCLUSION: The global surge in MDR, XDR and PDR bacteria necessitates last-resort antibiotics such as colistin. However, escalating resistance, particularly to colistin, presents a critical challenge. Inefficient colistin resistance detection methods, including Vitek2, alongside limited surveillance resources, accentuate the need for improved strategies. Whole-genome sequencing revealed alarming colistin resistance among K. pneumoniae and P. aeruginosa in an Indian hospital. The identification of XDR and PDR strains underscores urgency for enhanced surveillance and infection control. SNP analysis elucidated resistance mechanisms, highlighting the complexity of combatting resistance.},
}
@article {pmid38767750,
year = {2024},
author = {S, V and T, J and E, AP and A, MHA},
title = {Antibiotic resistance of heterotrophic bacteria from the sediments of adjoining high Arctic fjords, Svalbard.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {55},
number = {3},
pages = {2371-2383},
pmid = {38767750},
issn = {1678-4405},
mesh = {*Geologic Sediments/microbiology ; Arctic Regions ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Anti-Bacterial Agents/pharmacology ; Svalbard ; *Drug Resistance, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Microbial Sensitivity Tests ; Estuaries ; Phylogeny ; Heterotrophic Processes ; },
abstract = {Antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs) are now considered major global threats. The Kongsfjorden and Krossfjorden are the interlinked fjords in the Arctic that are currently experiencing the effects of climate change and receiving input of pollutants from distant and regional sources. The present study focused on understanding the prevalence of antibiotic resistance of retrievable heterotrophic bacteria from the sediments of adjacent Arctic fjords Kongsfjorden and Krossfjorden. A total of 237 bacterial isolates were tested against 16 different antibiotics. The higher resistance observed towards Extended Spectrum β-lactam antibiotic (ESBL) includes ceftazidime (45.56%) followed by trimethoprim (27%) and sulphamethizole (24.05%). The extent of resistance was meagre against tetracycline (2.53%) and gentamycin (2.95%). The 16S rRNA sequencing analysis identified that Proteobacteria (56%) were the dominant antibiotic resistant phyla, followed by Firmicutes (35%), Actinobacteria (8%) and Bacteroidetes. The dominant resistant bacterial isolates are Bacillus cereus (10%), followed by Alcaligenes faecalis (6.47%), Cytobacillus firmus (5.75%) Salinibacterium sp. (5%) and Marinobacter antarcticus (5%). Our study reveals the prevalence of antibiotic resistance showed significant differences in both the inner and outer fjords of Kongsfjorden and Krossfjorden (p < 0.05). This may be the input of antibiotic resistance bacteria released into the fjords from the preserved permafrost due to the melting of glaciers, horizontal gene transfer, and human influence in the Arctic region act as a selection pressure for the development and dissemination of more antibiotic resistant bacteria in Arctic fjords.},
}
@article {pmid38765968,
year = {2025},
author = {Mancuso, CP and Baker, JS and Qu, E and Tripp, AD and Balogun, IO and Lieberman, TD},
title = {Intraspecies warfare restricts strain coexistence in human skin microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38765968},
issn = {2692-8205},
support = {DP2 GM140922/GM/NIGMS NIH HHS/United States ; },
abstract = {Determining why only a fraction of encountered or applied strains engraft in a given person's microbiome is crucial for understanding and engineering these communities. Previous work has established that metabolic competition can restrict colonization success in vivo, but the relevance of bacterial warfare in preventing commensal engraftment has been less explored. Here, we demonstrate that intraspecies warfare presents a significant barrier to strain coexistence in the human skin microbiome by profiling 14,884 pairwise interactions between Staphylococcus epidermidis isolates cultured from eighteen people from six families. We find that intraspecies antagonisms are abundant, mechanistically diverse, independent of strain relatedness, and consistent with rapid evolution via horizontal gene transfer. Critically, these antagonisms are significantly depleted among strains residing on the same person relative to random assemblages, indicating a significant in vivo role. Together, our results emphasize that accounting for intraspecies warfare may be essential to the design of long-lasting probiotic therapeutics.},
}
@article {pmid38765680,
year = {2024},
author = {Tan, BSY and Mohan, L and Watthanaworawit, W and Ngamprasertchai, T and Nosten, FH and Ling, C and Bifani, P},
title = {Detection of florfenicol resistance in opportunistic Acinetobacter spp. infections in rural Thailand.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1368813},
pmid = {38765680},
issn = {1664-302X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Florfenicol (Ff) is an antimicrobial agent belonging to the class amphenicol used for the treatment of bacterial infections in livestock, poultry, and aquaculture (animal farming). It inhibits protein synthesis. Ff is an analog of chloramphenicol, an amphenicol compound on the WHO essential medicine list that is used for the treatment of human infections. Due to the extensive usage of Ff in animal farming, zoonotic pathogens have developed resistance to this antimicrobial agent. There are numerous reports of resistance genes from organisms infecting or colonizing animals found in human pathogens, suggesting a possible exchange of genetic materials. One of these genes is floR, a gene that encodes for an efflux pump that removes Ff from bacterial cells, conferring resistance against amphenicol, and is often associated with mobile genetic elements and other resistant determinants. In this study, we analyzed bacterial isolates recovered in rural Thailand from patients and environmental samples collected for disease monitoring. Whole genome sequencing was carried out for all the samples collected. Speciation and genome annotation was performed revealing the presence of the floR gene in the bacterial genome. The minimum inhibitory concentration (MIC) was determined for Ff and chloramphenicol. Chromosomal and phylogenetic analyses were performed to investigate the acquisition pattern of the floR gene. The presence of a conserved floR gene in unrelated Acinetobacter spp. isolated from human bacterial infections and environmental samples was observed, suggesting multiple and independent inter-species genetic exchange of drug-resistant determinants. The floR was found to be in the variable region containing various mobile genetic elements and other antibiotic resistance determinants; however, no evidence of HGT could be found. The floR gene identified in this study is chromosomal for all isolates. The study highlights a plausible impact of antimicrobials used in veterinary settings on human health. Ff shares cross-resistance with chloramphenicol, which is still in use in several countries. Furthermore, by selecting for floR-resistance genes, we may be selecting for and facilitating the zoonotic and reverse zoonotic exchange of other flanking resistance markers between human and animal pathogens or commensals with detrimental public health consequences.},
}
@article {pmid38760381,
year = {2024},
author = {Nguyen, Q and Nguyen, YTP and Ha, TT and Tran, DTN and Voong, PV and Chau, V and Nguyen, PLN and Le, NTQ and Nguyen, LPH and Nguyen, TTN and Trinh, TV and Carrique-Mas, JJ and Baker, S and Thwaites, G and Rabaa, MA and Choisy, M and Chung, HT and Pham, DT},
title = {Genomic insights unveil the plasmid transfer mechanism and epidemiology of hypervirulent Klebsiella pneumoniae in Vietnam.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4187},
pmid = {38760381},
issn = {2041-1723},
support = {222983/Z/21/Z//Wellcome Trust (Wellcome)/ ; 0010734//Oxford University | John Fell Fund, University of Oxford (John Fell OUP Research Fund)/ ; },
mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/isolation &amp; purification ; Vietnam/epidemiology ; Humans ; *Plasmids/genetics ; *Klebsiella Infections/epidemiology/microbiology ; *Phylogeny ; *Whole Genome Sequencing ; Virulence/genetics ; Adult ; Female ; Gene Transfer, Horizontal ; Male ; Genome, Bacterial ; Middle Aged ; Anti-Bacterial Agents/pharmacology ; Child ; Genomics ; Drug Resistance, Bacterial/genetics ; },
abstract = {Hypervirulent Klebsiella pneumoniae (hvKp) is a significant cause of severe invasive infections in Vietnam, yet data on its epidemiology, population structure and dynamics are scarce. We screened hvKp isolates from patients with bloodstream infections (BSIs) at a tertiary infectious diseases hospital in Vietnam and healthy individuals, followed by whole genome sequencing and plasmid analysis. Among 700 BSI-causing Kp strains, 100 (14.3%) were hvKp. Thirteen hvKp isolates were identified from 350 rectal swabs of healthy adults; none from 500 rectal swabs of healthy children. The hvKp isolates were genetically diverse, encompassing 17 sequence types (STs), predominantly ST23, ST86 and ST65. Among the 113 hvKp isolates, 14 (12.6%) carried at least one antimicrobial resistance (AMR) gene, largely mediated by IncFII, IncR, and IncA/C plasmids. Notably, the acquisition of AMR conjugative plasmids facilitated horizontal transfer of the non-conjugative virulence plasmid between K. pneumoniae strains. Phylogenetic analysis demonstrated hvKp isolates from BSIs and human carriage clustered together, suggesting a significant role of intestinal carriage in hvKp transmission. Enhanced surveillance is crucial to understand the factors driving intestinal carriage and hvKp transmission dynamics for informing preventive measures. Furthermore, we advocate the clinical use of our molecular assay for diagnosing hvKp infections to guide effective management.},
}
@article {pmid38756985,
year = {2024},
author = {Roughgarden, J},
title = {Lytic/Lysogenic Transition as a Life-History Switch.},
journal = {Virus evolution},
volume = {10},
number = {1},
pages = {veae028},
pmid = {38756985},
issn = {2057-1577},
abstract = {The transition between lytic and lysogenic life cycles is the most important feature of the life-history of temperate viruses. To explain this transition, an optimal life-history model is offered based a discrete-time formulation of phage/bacteria population dynamics that features infection of bacteria by Poisson sampling of virions from the environment. The time step is the viral latency period. In this model, density-dependent viral absorption onto the bacterial surface produces virus/bacteria coexistence and density dependence in bacterial growth is not needed. The formula for the transition between lytic and lysogenic phases is termed the 'fitness switch'. According to the model, the virus switches from lytic to lysogenic when its population grows faster as prophage than as virions produced by lysis of the infected cells, and conversely for the switch from lysogenic to lytic. A prophage that benefits the bacterium it infects automatically incurs lower fitness upon exiting the bacterial genome, resulting in its becoming locked into the bacterial genome in what is termed here as a 'prophage lock'. The fitness switch qualitatively predicts the ecogeographic rule that environmental enrichment leads to microbialization with a concomitant increase in lysogeny, fluctuating environmental conditions promote virus-mediated horizontal gene transfer, and prophage-containing bacteria can integrate into the microbiome of a eukaryotic host forming a functionally integrated tripartite holobiont. These predictions accord more with the 'Piggyback-the-Winner' hypothesis than with the 'Kill-the-Winner' hypothesis in virus ecology.},
}
@article {pmid38756231,
year = {2024},
author = {Pobeguts, OV and Galaymina, MA and Sikamov, KV and Urazaeva, DR and Avshalumov, AS and Mikhailycheva, MV and Babenko, VV and Smirnov, IP and Gorbachev, AY},
title = {Unraveling the adaptive strategies of Mycoplasma hominis through proteogenomic profiling of clinical isolates.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1398706},
pmid = {38756231},
issn = {2235-2988},
mesh = {Humans ; *Mycoplasma hominis/genetics/metabolism ; *Proteogenomics ; *Mycoplasma Infections/microbiology ; *Adaptation, Physiological ; Biofilms/growth &amp; development ; Genome, Bacterial ; Phenotype ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Bacterial/genetics ; },
abstract = {INTRODUCTION: Mycoplasma hominis (M. hominis) belongs to the class Mollicutes, characterized by a very small genome size, reduction of metabolic pathways, including transcription factors, and the absence of a cell wall. Despite this, they adapt well not only to specific niches within the host organism but can also spread throughout the body, colonizing various organs and tissues. The adaptation mechanisms of M. hominis, as well as their regulatory pathways, are poorly understood. It is known that, when adapting to adverse conditions, Mycoplasmas can undergo phenotypic switches that may persist for several generations.<br><br>METHODS: To investigate the adaptive properties of M. hominis related to survival in the host, we conducted a comparative phenotypic and proteogenomic analysis of eight clinical isolates of M. hominis obtained from patients with urogenital infections and the laboratory strain H-34.<br><br>RESULTS: We have shown that clinical isolates differ in phenotypic features from the laboratory strain, form biofilms more effectively and show resistance to ofloxacin. The comparative proteogenomic analysis revealed that, unlike the laboratory strain, the clinical isolates possess several features related to stress survival: they switch carbon metabolism, activating the energetically least advantageous pathway of nucleoside utilization, which allows slowing down cellular processes and transitioning to a starvation state; they reconfigure the repertoire of membrane proteins; they have integrative conjugative elements in their genomes, which are key mediators of horizontal gene transfer. The upregulation of the methylating subunit of the restriction-modification (RM) system type I and the additional components of RM systems found in clinical isolates suggest that DNA methylation may play a role in regulating the adaptation mechanisms of M. hominis in the host organism. It has been shown that based on the proteogenomic profile, namely the genome sequence, protein content, composition of the RM systems and additional subunits HsdM, HsdS and HsdR, composition and number of transposable elements, as well as the sequence of the main variable antigen Vaa, we can divide clinical isolates into two phenotypes: typical colonies (TC), which have a high growth rate, and atypical (aTC) mini-colonies, which have a slow growth rate and exhibit properties similar to persisters.<br><br>DISCUSSION: We believe that the key mechanism of adaptation of M. hominis in the host is phenotypic restructuring, leading to a slowing down cellular processes and the formation of small atypical colonies. This is due to a switch in carbon metabolism and activation the pathway of nucleoside utilization. We hypothesize that DNA methylation may play a role in regulating this switch.},
}
@article {pmid38755134,
year = {2024},
author = {Fujino, T and Sonoda, R and Higashinagata, T and Mishiro-Sato, E and Kano, K and Murakami, H},
title = {Ser/Leu-swapped cell-free translation system constructed with natural/in vitro transcribed-hybrid tRNA set.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4143},
pmid = {38755134},
issn = {2041-1723},
support = {23H05456//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 21K05270//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
mesh = {*Cell-Free System ; *Protein Biosynthesis ; *Escherichia coli/genetics/metabolism ; RNA, Transfer, Leu/genetics/metabolism ; RNA, Transfer, Ser/metabolism/genetics ; Genetic Code ; RNA, Transfer/genetics/metabolism ; Green Fluorescent Proteins/metabolism/genetics ; Protein Engineering/methods ; Transcription, Genetic ; Anticodon/genetics/metabolism ; },
abstract = {The Ser/Leu-swapped genetic code can act as a genetic firewall, mitigating biohazard risks arising from horizontal gene transfer in genetically modified organisms. Our prior work demonstrated the orthogonality of this swapped code to the standard genetic code using a cell-free translation system comprised of 21 in vitro transcribed tRNAs. In this study, to advance this system for protein engineering, we introduce a natural/in vitro transcribed-hybrid tRNA set. This set combines natural tRNAs from Escherichia coli (excluding Ser, Leu, and Tyr) and in vitro transcribed tRNAs, encompassing anticodon-swapped tRNA[Ser]GAG and tRNA[Leu]GGA. This approach reduces the number of in vitro transcribed tRNAs required from 21 to only 4. In this optimized system, the production of a model protein, superfolder green fluorescent protein, increases to 3.5-fold. With this hybrid tRNA set, the Ser/Leu-swapped cell-free translation system will stand as a potent tool for protein production with reduced biohazard concerns in future biological endeavors.},
}
@article {pmid38755022,
year = {2024},
author = {Figueroa, W and Cazares, D and Cazares, A},
title = {Phage-plasmids: missed links between mobile genetic elements.},
journal = {Trends in microbiology},
volume = {32},
number = {7},
pages = {622-623},
doi = {10.1016/j.tim.2024.04.014},
pmid = {38755022},
issn = {1878-4380},
mesh = {*Bacteriophages/genetics ; *Plasmids/genetics ; *Interspersed Repetitive Sequences ; *Bacteria/genetics/virology ; Gene Transfer, Horizontal ; Gene Flow ; Evolution, Molecular ; },
abstract = {Phages and plasmids are discrete mobile genetic elements (MGEs) with critical roles in gene dissemination across bacteria but limited scope for exchanging DNA between them. By investigating recent gene-sharing events, Pfeifer and Rocha describe how the hybrid elements phage-plasmids (P-Ps) promote gene flow between MGE types and evolve into new ones.},
}
@article {pmid38754503,
year = {2024},
author = {Wei, L and Han, Y and Zheng, J and Xu, X and Zhu, L},
title = {Accelerated dissemination of antibiotic resistant genes via conjugative transfer driven by deficient denitrification in biochar-based biofiltration systems.},
journal = {The Science of the total environment},
volume = {934},
number = {},
pages = {173268},
doi = {10.1016/j.scitotenv.2024.173268},
pmid = {38754503},
issn = {1879-1026},
mesh = {*Denitrification ; *Charcoal/chemistry ; *Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents ; Filtration/methods ; Waste Disposal, Fluid/methods ; Wastewater/microbiology ; Biofilms ; },
abstract = {Biofiltration systems harbored and disseminated antibiotic resistance genes (ARGs), when confronting antibiotic-contained wastewater. Biochar, a widely used environmental remediation material, can mitigate antibiotic stress on adjoining microbes by lowering the availability of sorbed antibiotics, and enhance the attachment of denitrifiers. Herein, bench-scale biofiltration systems, packed with commercial biochars, were established to explore the pivotal drivers affecting ARG emergence. Results showed that biofiltration columns, achieving higher TN removal and denitrification capacity, showed a significant decrease in ARG accumulation (p < 0.05). The relative abundance of ARGs (0.014 ± 0.0008) in the attached biofilms decreased to 1/5-folds of that in the control group (0.065 ± 0.004). Functional analysis indicated ARGs' accumulation was less attributed to ARG activation or horizontal gene transfer (HGT) driven by sorbed antibiotics. Most denitrifiers, like Bradyrhizobium, Geothrix, etc., were found to be enriched and host ARGs. Nitrosative stress from deficient denitrification was demonstrated to be the dominant driver for affecting ARG accumulation and dissemination. Metagenomic and metaproteomic analysis revealed that nitrosative stress promoted the conjugative HGT of ARGs mainly via increasing the transmembrane permeability and enhancing the amino acid transport and metabolism, such as cysteine, methionine, and valine metabolism. Overall, this study highlighted the risks of deficient denitrification in promoting ARG transfer and transmission in biofiltration systems and natural ecosystems.},
}
@article {pmid38754416,
year = {2024},
author = {Benz, F and Camara-Wilpert, S and Russel, J and Wandera, KG and Čepaitė, R and Ares-Arroyo, M and Gomes-Filho, JV and Englert, F and Kuehn, JA and Gloor, S and Mestre, MR and Cuénod, A and Aguilà-Sans, M and Maccario, L and Egli, A and Randau, L and Pausch, P and Rocha, EPC and Beisel, CL and Madsen, JS and Bikard, D and Hall, AR and Sørensen, SJ and Pinilla-Redondo, R},
title = {Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans.},
journal = {Cell host &amp; microbe},
volume = {32},
number = {6},
pages = {875-886.e9},
doi = {10.1016/j.chom.2024.04.016},
pmid = {38754416},
issn = {1934-6069},
mesh = {*CRISPR-Cas Systems ; *Plasmids/genetics ; *Klebsiella pneumoniae/genetics ; *Conjugation, Genetic ; Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Transfer, Horizontal ; Bacteriophages/genetics ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Plasmid-encoded type IV-A CRISPR-Cas systems lack an acquisition module, feature a DinG helicase instead of a nuclease, and form ribonucleoprotein complexes of unknown biological functions. Type IV-A3 systems are carried by conjugative plasmids that often harbor antibiotic-resistance genes and their CRISPR array contents suggest a role in mediating inter-plasmid conflicts, but this function remains unexplored. Here, we demonstrate that a plasmid-encoded type IV-A3 system co-opts the type I-E adaptation machinery from its host, Klebsiella pneumoniae (K. pneumoniae), to update its CRISPR array. Furthermore, we reveal that robust interference of conjugative plasmids and phages is elicited through CRISPR RNA-dependent transcriptional repression. By silencing plasmid core functions, type IV-A3 impacts the horizontal transfer and stability of targeted plasmids, supporting its role in plasmid competition. Our findings shed light on the mechanisms and ecological function of type IV-A3 systems and demonstrate their practical efficacy for countering antibiotic resistance in clinically relevant strains.},
}
@article {pmid38753980,
year = {2024},
author = {He, Z and Dechesne, A and Schreiber, F and Zhu, YG and Larsson, DGJ and Smets, BF},
title = {Understanding Stimulation of Conjugal Gene Transfer by Nonantibiotic Compounds: How Far Are We?.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {21},
pages = {9017-9030},
doi = {10.1021/acs.est.3c06060},
pmid = {38753980},
issn = {1520-5851},
mesh = {*Conjugation, Genetic ; Reactive Oxygen Species/metabolism ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; },
abstract = {A myriad of nonantibiotic compounds is released into the environment, some of which may contribute to the dissemination of antimicrobial resistance by stimulating conjugation. Here, we analyzed a collection of studies to (i) identify patterns of transfer stimulation across groups and concentrations of chemicals, (ii) evaluate the strength of evidence for the proposed mechanisms behind conjugal stimulation, and (iii) examine the plausibility of alternative mechanisms. We show that stimulatory nonantibiotic compounds act at concentrations from 1/1000 to 1/10 of the minimal inhibitory concentration for the donor strain but that stimulation is always modest (less than 8-fold). The main proposed mechanisms for stimulation via the reactive oxygen species/SOS cascade and/or an increase in cell membrane permeability are not unequivocally supported by the literature. However, we identify the reactive oxygen species/SOS cascade as the most likely mechanism. This remains to be confirmed by firm molecular evidence. Such evidence and more standardized and high-throughput conjugation assays are needed to create technologies and solutions to limit the stimulation of conjugal gene transfer and contribute to mitigating global antibiotic resistance.},
}
@article {pmid38752994,
year = {2024},
author = {Ortiz Charneco, G and McDonnell, B and Kelleher, P and Buivydas, A and Dashko, S and de Waal, PP and van Rijswijck, I and van Peij, NNME and Mahony, J and Van Sinderen, D},
title = {Plasmid-mediated horizontal gene mobilisation: Insights from two lactococcal conjugative plasmids.},
journal = {Microbial biotechnology},
volume = {17},
number = {5},
pages = {e14421},
pmid = {38752994},
issn = {1751-7915},
support = {//dsm-firmenich, Taste, Texture &amp; Health/ ; 12/RC/2273/SFI_/Science Foundation Ireland/Ireland ; 17/SP/4678/SFI_/Science Foundation Ireland/Ireland ; },
mesh = {*Plasmids/genetics ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; Bacterial Proteins/genetics/metabolism ; Lactococcus lactis/genetics ; },
abstract = {The distinct conjugation machineries encoded by plasmids pNP40 and pUC11B represent the most prevalent plasmid transfer systems among lactococcal strains. In the current study, we identified genetic determinants that underpin pNP40- and pUC11B-mediated, high-frequency mobilisation of other, non-conjugative plasmids. The mobilisation frequencies of the smaller, non-conjugative plasmids and the minimal sequences required for their mobilisation were determined, owing to the determination of the oriT sequences of both pNP40 and pUC11B, which allowed the identification of similar sequences in some of the non-conjugative plasmids that were shown to promote their mobilisation. Furthermore, the auxiliary gene mobC, two distinct functional homologues of which are present in several plasmids harboured by the pNP40- and pUC11B-carrying host strains, was observed to confer a high-frequency mobilisation phenotype. These findings provide mechanistic insights into how lactococcal conjugative plasmids achieve conjugation and promote mobilisation of non-conjugative plasmids. Ultimately, these insights would be harnessed to optimise conjugation and mobilisation strategies for the rapid and predictable development of robust and technologically improved strains.},
}
@article {pmid38752745,
year = {2024},
author = {Tomasch, J and Kopejtka, K and Shivaramu, S and Mujakić, I and Koblížek, M},
title = {On the evolution of chromosomal regions with high gene strand bias in bacteria.},
journal = {mBio},
volume = {15},
number = {6},
pages = {e0060224},
pmid = {38752745},
issn = {2150-7511},
support = {GX19-28778X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky (GA&#x10c;R)/ ; },
mesh = {*Chromosomes, Bacterial/genetics ; *Evolution, Molecular ; *DNA Replication ; Bacteria/genetics/classification ; Genome, Bacterial ; Gene Transfer, Horizontal ; DNA, Bacterial/genetics ; },
abstract = {On circular bacterial chromosomes, the majority of genes are coded on the leading strand. This gene strand bias (GSB) ranges from up to 85% in some Bacillota to a little more than 50% in other phyla. The factors determining the extent of the strand bias remain to be found. Here, we report that species in the phylum Gemmatimonadota share a unique chromosome architecture, distinct from neighboring phyla: in a conserved 600-kb region around the terminus of replication, almost all genes were located on the leading strands, while on the remaining part of the chromosome, the strand preference was more balanced. The high strand bias (HSB) region harbors the rRNA clusters, core, and highly expressed genes. Selective pressure for reduction of collisions with DNA replication to minimize detrimental mutations can explain the conservation of essential genes in this region. Repetitive and mobile elements are underrepresented, suggesting reduced recombination frequency by structural isolation from other parts of the chromosome. We propose that the HSB region forms a distinct chromosomal domain. Gemmatimonadota chromosomes evolved mainly by expansion through horizontal gene transfer and duplications outside of the ancient high strand bias region. In support of our hypothesis, we could further identify two Spiroplasma strains on a similar evolutionary path.IMPORTANCEOn bacterial chromosomes, a preferred location of genes on the leading strand has evolved to reduce conflicts between replication and transcription. Despite a vast body of research, the question why bacteria show large differences in their gene strand bias is still not solved. The discovery of "hybrid" chromosomes in different phyla, including Gemmatimonadota, in which a conserved high strand bias is found exclusively in a region at ter, points toward a role of nucleoid structure, additional to replication, in the evolution of strand preferences. A fine-grained structural analysis of the ever-increasing number of available bacterial genomes could help to better understand the forces that shape the sequential and spatial organization of the cell's information content.},
}
@article {pmid38750628,
year = {2024},
author = {Mrnjavac, N and Nagies, FSP and Wimmer, JLE and Kapust, N and Knopp, MR and Trost, K and Modjewski, L and Bremer, N and Mentel, M and Esposti, MD and Mizrahi, I and Allen, JF and Martin, WF},
title = {The radical impact of oxygen on prokaryotic evolution-enzyme inhibition first, uninhibited essential biosyntheses second, aerobic respiration third.},
journal = {FEBS letters},
volume = {598},
number = {14},
pages = {1692-1714},
pmid = {38750628},
issn = {1873-3468},
support = {101018894//H2020 European Research Council/ ; MA 1426/21-1//Deutsche Forschungsgemeinschaft/ ; 1/0457/24//Scientific Grant Agency of the Ministry of Education of the Slovak Republic (VEGA)/ ; 2476/2-1//German-Israeli Project Cooperation (DIP)/ ; 1426/23-1//German-Israeli Project Cooperation (DIP)/ ; 101018894/ERC_/European Research Council/International ; 96742//Volkswagen Foundation/ ; },
mesh = {*Oxygen/metabolism ; Aerobiosis ; Phylogeny ; Prokaryotic Cells/metabolism ; Evolution, Molecular ; Oxidation-Reduction ; Enzymes/metabolism/genetics ; },
abstract = {Molecular oxygen is a stable diradical. All O2-dependent enzymes employ a radical mechanism. Generated by cyanobacteria, O2 started accumulating on Earth 2.4 billion years ago. Its evolutionary impact is traditionally sought in respiration and energy yield. We mapped 365 O2-dependent enzymatic reactions of prokaryotes to phylogenies for the corresponding 792 protein families. The main physiological adaptations imparted by O2-dependent enzymes were not energy conservation, but novel organic substrate oxidations and O2-dependent, hence O2-tolerant, alternative pathways for O2-inhibited reactions. Oxygen-dependent enzymes evolved in ancestrally anaerobic pathways for essential cofactor biosynthesis including NAD[+], pyridoxal, thiamine, ubiquinone, cobalamin, heme, and chlorophyll. These innovations allowed prokaryotes to synthesize essential cofactors in O2-containing environments, a prerequisite for the later emergence of aerobic respiratory chains.},
}
@article {pmid38747597,
year = {2024},
author = {Stindt, KR and McClean, MN},
title = {Tuning interdomain conjugation to enable in situ population modification in yeasts.},
journal = {mSystems},
volume = {9},
number = {6},
pages = {e0005024},
pmid = {38747597},
issn = {2379-5077},
support = {R01 AI154940/AI/NIAID NIH HHS/United States ; P30CA014520//University of Wisconsin Carbone Cancer Center (UWCCC)/ ; P30 CA014520/CA/NCI NIH HHS/United States ; R35 GM128873/GM/NIGMS NIH HHS/United States ; 135AAI9593//Wisconsin Alumni Research Foundation (WARF)/ ; R35GM128873//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32 GM130550/GM/NIGMS NIH HHS/United States ; T32GM130550//Molecular Biophysics Training Grant/ ; R01AI154940//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {*Saccharomyces cerevisiae/genetics ; *Escherichia coli/genetics/metabolism ; Conjugation, Genetic ; },
abstract = {The ability to modify and control natural and engineered microbiomes is essential for biotechnology and biomedicine. Fungi are critical members of most microbiomes, yet technology for modifying the fungal members of a microbiome has lagged far behind that for bacteria. Interdomain conjugation (IDC) is a promising approach, as DNA transfer from bacterial cells to yeast enables in situ modification. While such genetic transfers have been known to naturally occur in a wide range of eukaryotes and are thought to contribute to their evolution, IDC has been understudied as a technique to control fungal or fungal-bacterial consortia. One major obstacle to the widespread use of IDC is its limited efficiency. In this work, we manipulated metabolic and physical interactions between genetically tractable Escherichia coli and Saccharomyces cerevisiae to control the incidence of IDC. We test the landscape of population interactions between the bacterial donors and yeast recipients to find that bacterial commensalism leads to maximized IDC, both in culture and in mixed colonies. We demonstrate the capacity of cell-to-cell binding via mannoproteins to assist both IDC incidence and bacterial commensalism in culture and model how these tunable controls can predictably yield a range of IDC outcomes. Furthermore, we demonstrate that these controls can be utilized to irreversibly alter a recipient yeast population, by both "rescuing" a poor-growing recipient population and collapsing a stable population via a novel IDC-mediated CRISPR/Cas9 system.IMPORTANCEFungi are important but often unaddressed members of most natural and synthetic microbial communities. This work highlights opportunities for modifying yeast microbiome populations through bacterial conjugation. While conjugation has been recognized for its capacity to deliver engineerable DNA to a range of cells, its dependence on cell contact has limited its efficiency. Here, we find "knobs" to control DNA transfer, by engineering the metabolic dependence between bacterial donors and yeast recipients and by changing their ability to physically adhere to each other. Importantly, we functionally validate these "knobs" by irreversibly altering yeast populations. We use these controls to "rescue" a failing yeast population, demonstrate the capacity of conjugated CRISPR/Cas9 to depress or collapse populations, and show that conjugation can be easily interrupted by disrupting cell-to-cell binding. These results offer building blocks toward in situ mycobiome editing, with significant implications for clinical treatments of fungal pathogens and other fungal system engineering.},
}
@article {pmid38746121,
year = {2024},
author = {García-Bayona, L and Said, N and Coyne, MJ and Flores, K and Elmekki, NM and Sheahan, ML and Camacho, AG and Hutt, K and Yildiz, FH and Kovács, &#xc1;T and Waldor, MK and Comstock, LE},
title = {A pervasive large conjugative plasmid mediates multispecies biofilm formation in the intestinal microbiota increasing resilience to perturbations.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.29.590671},
pmid = {38746121},
issn = {2692-8205},
support = {K99 AI167064/AI/NIAID NIH HHS/United States ; P30 DK042086/DK/NIDDK NIH HHS/United States ; R00 AI167064/AI/NIAID NIH HHS/United States ; R25 GM109439/GM/NIGMS NIH HHS/United States ; },
abstract = {Although horizontal gene transfer is pervasive in the intestinal microbiota, we understand only superficially the roles of most exchanged genes and how the mobile repertoire affects community dynamics. Similarly, little is known about the mechanisms underlying the ability of a community to recover after a perturbation. Here, we identified and functionally characterized a large conjugative plasmid that is one of the most frequently transferred elements among Bacteroidales species and is ubiquitous in diverse human populations. This plasmid encodes both an extracellular polysaccharide and fimbriae, which promote the formation of multispecies biofilms in the mammalian gut. We use a hybridization-based approach to visualize biofilms in clarified whole colon tissue with unprecedented 3D spatial resolution. These biofilms increase bacterial survival to common stressors encountered in the gut, increasing strain resiliency, and providing a rationale for the plasmid's recent spread and high worldwide prevalence.},
}
@article {pmid38743630,
year = {2024},
author = {Dewar, AE and Hao, C and Belcher, LJ and Ghoul, M and West, SA},
title = {Bacterial lifestyle shapes pangenomes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {21},
pages = {e2320170121},
pmid = {38743630},
issn = {1091-6490},
support = {834164/ERC_/European Research Council/International ; 834164//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; },
mesh = {*Genome, Bacterial ; *Bacteria/genetics/classification ; *Phylogeny ; },
abstract = {Pangenomes vary across bacteria. Some species have fluid pangenomes, with a high proportion of genes varying between individual genomes. Other species have less fluid pangenomes, with different genomes tending to contain the same genes. Two main hypotheses have been suggested to explain this variation: differences in species' bacterial lifestyle and effective population size. However, previous studies have not been able to test between these hypotheses because the different features of lifestyle and effective population size are highly correlated with each other, and phylogenetically conserved, making it hard to disentangle their relative importance. We used phylogeny-based analyses, across 126 bacterial species, to tease apart the causal role of different factors. We found that pangenome fluidity was lower in i) host-associated compared with free-living species and ii) host-associated species that are obligately dependent on a host, live inside cells, and are more pathogenic and less motile. In contrast, we found no support for the competing hypothesis that larger effective population sizes lead to more fluid pangenomes. Effective population size appears to correlate with pangenome variation because it is also driven by bacterial lifestyle, rather than because of a causal relationship.},
}
@article {pmid38742878,
year = {2024},
author = {Mies, US and Hervé, V and Kropp, T and Platt, K and Sillam-Dussès, D and Šobotník, J and Brune, A},
title = {Genome reduction and horizontal gene transfer in the evolution of Endomicrobia-rise and fall of an intracellular symbiosis with termite gut flagellates.},
journal = {mBio},
volume = {15},
number = {6},
pages = {e0082624},
pmid = {38742878},
issn = {2150-7511},
support = {//Max-Planck-Institut f&#xfc;r Terrestrische Mikrobiologie (MPI for Terrestrial Microbiology)/ ; SFB 987//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {Animals ; *Isoptera/microbiology/parasitology ; *Symbiosis ; *Gene Transfer, Horizontal ; *Gastrointestinal Microbiome ; *Phylogeny ; *Genome, Bacterial ; *Bacteria/genetics/classification ; Evolution, Molecular ; Metagenome ; },
abstract = {Bacterial endosymbionts of eukaryotic hosts typically experience massive genome reduction, but the underlying evolutionary processes are often obscured by the lack of free-living relatives. Endomicrobia, a family-level lineage of host-associated bacteria in the phylum Elusimicrobiota that comprises both free-living representatives and endosymbionts of termite gut flagellates, are an excellent model to study evolution of intracellular symbionts. We reconstructed 67 metagenome-assembled genomes (MAGs) of Endomicrobiaceae among more than 1,700 MAGs from the gut microbiota of a wide range of termites. Phylogenomic analysis confirmed a sister position of representatives from termites and ruminants, and allowed to propose eight new genera in the radiation of Endomicrobiaceae. Comparative genome analysis documented progressive genome erosion in the new genus Endomicrobiellum, which comprises all flagellate endosymbionts characterized to date. Massive gene losses were accompanied by the acquisition of new functions by horizontal gene transfer, which led to a shift from a glucose-based energy metabolism to one based on sugar phosphates. The breakdown of glycolysis and many anabolic pathways for amino acids and cofactors in several subgroups was compensated by the independent acquisition of new uptake systems, including an ATP/ADP antiporter, from other gut microbiota. The putative donors are mostly flagellate endosymbionts from other bacterial phyla, including several, hitherto unknown lineages of uncultured Alphaproteobacteria, documenting the importance of horizontal gene transfer in the convergent evolution of these intracellular symbioses. The loss of almost all biosynthetic capacities in some lineages of Endomicrobiellum suggests that their originally mutualistic relationship with flagellates is on its decline.IMPORTANCEUnicellular eukaryotes are frequently colonized by bacterial and archaeal symbionts. A prominent example are the cellulolytic gut flagellates of termites, which harbor diverse but host-specific bacterial symbionts that occur exclusively in termite guts. One of these lineages, the so-called Endomicrobia, comprises both free-living and endosymbiotic representatives, which offers the unique opportunity to study the evolutionary processes underpinning the transition from a free-living to an intracellular lifestyle. Our results revealed a progressive gene loss in energy metabolism and biosynthetic pathways, compensated by the acquisition of new functions via horizontal gene transfer from other gut bacteria, and suggest the eventual breakdown of an initially mutualistic symbiosis. Evidence for convergent evolution of unrelated endosymbionts reflects adaptations to the intracellular environment of termite gut flagellates.},
}
@article {pmid38741889,
year = {2024},
author = {Carrera Páez, LC and Olivier, M and Gambino, AS and Poklepovich, T and Aguilar, AP and Quiroga, MP and Centrón, D},
title = {Sporadic clone Escherichia coli ST615 as a vector and reservoir for dissemination of crucial antimicrobial resistance genes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1368622},
pmid = {38741889},
issn = {2235-2988},
mesh = {*Escherichia coli/genetics/drug effects ; *Plasmids/genetics ; Humans ; *Escherichia coli Infections/microbiology ; *beta-Lactamases/genetics ; *Gene Transfer, Horizontal ; *Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Escherichia coli Proteins/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Latin America ; Drug Resistance, Bacterial/genetics ; },
abstract = {There is scarce information concerning the role of sporadic clones in the dissemination of antimicrobial resistance genes (ARGs) within the nosocomial niche. We confirmed that the clinical Escherichia coli M19736 ST615 strain, one of the first isolates of Latin America that harbors a plasmid with an mcr-1 gene, could receive crucial ARG by transformation and conjugation using as donors critical plasmids that harbor bla CTX-M-15, bla KPC-2, bla NDM-5, bla NDM-1, or aadB genes. Escherichia coli M19736 acquired bla CTX-M-15, bla KPC-2, bla NDM-5, bla NDM-1, and aadB genes, being only blaNDM-1 maintained at 100% on the 10th day of subculture. In addition, when the evolved MDR-E. coli M19736 acquired sequentially bla CTX-M-15 and bla NDM-1 genes, the maintenance pattern of the plasmids changed. In addition, when the evolved XDR-E. coli M19736 acquired in an ulterior step the paadB plasmid, a different pattern of the plasmid's maintenance was found. Interestingly, the evolved E. coli M19736 strains disseminated simultaneously the acquired conjugative plasmids in different combinations though selection was ceftazidime in all cases. Finally, we isolated and characterized the extracellular vesicles (EVs) from the native and evolved XDR-E. coli M19736 strains. Interestingly, EVs from the evolved XDR-E. coli M19736 harbored bla CTX-M-15 though the pDCAG1-CTX-M-15 was previously lost as shown by WGS and experiments, suggesting that EV could be a relevant reservoir of ARG for susceptible bacteria. These results evidenced the genetic plasticity of a sporadic clone of E. coli such as ST615 that could play a relevant transitional link in the clinical dynamics and evolution to multidrug/extensively/pandrug-resistant phenotypes of superbugs within the nosocomial niche by acting simultaneously as a vector and reservoir of multiple ARGs which later could be disseminated.},
}
@article {pmid38741746,
year = {2024},
author = {Ghaly, TM and Gillings, MR and Rajabal, V and Paulsen, IT and Tetu, SG},
title = {Horizontal gene transfer in plant microbiomes: integrons as hotspots for cross-species gene exchange.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1338026},
pmid = {38741746},
issn = {1664-302X},
abstract = {Plant microbiomes play important roles in plant health and fitness. Bacterial horizontal gene transfer (HGT) can influence plant health outcomes, driving the spread of both plant growth-promoting and phytopathogenic traits. However, community dynamics, including the range of genetic elements and bacteria involved in this process are still poorly understood. Integrons are genetic elements recently shown to be abundant in plant microbiomes, and are associated with HGT across broad phylogenetic boundaries. They facilitate the spread of gene cassettes, small mobile elements that collectively confer a diverse suite of adaptive functions. Here, we analysed 5,565 plant-associated bacterial genomes to investigate the prevalence and functional diversity of integrons in this niche. We found that integrons are particularly abundant in the genomes of Pseudomonadales, Burkholderiales, and Xanthomonadales. In total, we detected nearly 9,000 gene cassettes, and found that many could be involved in plant growth promotion or phytopathogenicity, suggesting that integrons might play a role in bacterial mutualistic or pathogenic lifestyles. The rhizosphere was enriched in cassettes involved in the transport and metabolism of diverse substrates, suggesting that they may aid in adaptation to this environment, which is rich in root exudates. We also found that integrons facilitate cross-species HGT, which is particularly enhanced in the phyllosphere. This finding may provide an ideal opportunity to promote plant growth by fostering the spread of genes cassettes relevant to leaf health. Together, our findings suggest that integrons are important elements in plant microbiomes that drive HGT, and have the potential to facilitate plant host adaptation.},
}
@article {pmid38741126,
year = {2024},
author = {Blanco-Melo, D and Campbell, MA and Zhu, H and Dennis, TPW and Modha, S and Lytras, S and Hughes, J and Gatseva, A and Gifford, RJ},
title = {A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {120},
pmid = {38741126},
issn = {1474-760X},
support = {MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; *Vertebrates/genetics/virology ; *Genome ; *Fossils ; *Phylogeny ; Evolution, Molecular ; Humans ; Gene Transfer, Horizontal ; Viruses/genetics ; Genomics/methods ; Endogenous Retroviruses/genetics ; DNA Transposable Elements ; },
abstract = {BACKGROUND: Genomic regions that remain poorly understood, often referred to as the dark genome, contain a variety of functionally relevant and biologically informative features. These include endogenous viral elements (EVEs)-virus-derived sequences that can dramatically impact host biology and serve as a virus fossil record. In this study, we introduce a database-integrated genome screening (DIGS) approach to investigate the dark genome in silico, focusing on EVEs found within vertebrate genomes.<br><br>RESULTS: Using DIGS on 874 vertebrate genomes, we uncover approximately 1.1 million EVE sequences, with over 99% originating from endogenous retroviruses or transposable elements that contain EVE DNA. We show that the remaining 6038 sequences represent over a thousand distinct horizontal gene transfer events across 10 virus families, including some that have not previously been reported as EVEs. We explore the genomic and phylogenetic characteristics of non-retroviral EVEs and determine their rates of acquisition during vertebrate evolution. Our study uncovers novel virus diversity, broadens knowledge of virus distribution among vertebrate hosts, and provides new insights into the ecology and evolution of vertebrate viruses.<br><br>CONCLUSIONS: We comprehensively catalog and analyze EVEs within 874 vertebrate genomes, shedding light on the distribution, diversity, and long-term evolution of viruses and reveal their extensive impact on vertebrate genome evolution. Our results demonstrate the power of linking a relational database management system to a similarity search-based screening pipeline for in silico exploration of the dark genome.},
}
@article {pmid38738821,
year = {2024},
author = {Liao, L and Qin, Q and Yi, D and Lai, Q and Cong, B and Zhang, H and Shao, Z and Zhang, J and Chen, B},
title = {Evolution and adaptation of terrestrial plant-associated Plantibacter species into remote marine environments.},
journal = {Molecular ecology},
volume = {33},
number = {12},
pages = {e17385},
doi = {10.1111/mec.17385},
pmid = {38738821},
issn = {1365-294X},
support = {2022YFC2807501//National Key Research and Development Program of China/ ; 2023YFC2812600//National Key Research and Development Program of China/ ; 41976224//National Natural Science Foundation of China/ ; },
mesh = {*Gene Transfer, Horizontal ; Plants/microbiology/genetics ; Microbiota/genetics ; Phylogeny ; Adaptation, Physiological/genetics ; Genome, Bacterial/genetics ; Ecosystem ; Atlantic Ocean ; Biological Evolution ; Seawater/microbiology ; },
abstract = {Microbes are thought to be distributed and circulated around the world, but the connection between marine and terrestrial microbiomes remains largely unknown. We use Plantibacter, a representative genus associated with plants, as our research model to investigate the global distribution and adaptation of plant-related bacteria in plant-free environments, particularly in the remote Southern Ocean and the deep Atlantic Ocean. The marine isolates and their plant-associated relatives shared over 98% whole-genome average nucleotide identity (ANI), indicating recent divergence and ongoing speciation from plant-related niches to marine environments. Comparative genomics revealed that the marine strains acquired new genes via horizontal gene transfer from non-Plantibacter species and refined existing genes through positive selection to improve adaptation to new habitats. Meanwhile, marine strains retained the ability to interact with plants, such as modifying root system architecture and promoting germination. Furthermore, Plantibacter species were found to be widely distributed in marine environments, revealing an unrecognized phenomenon that plant-associated microbiomes have colonized the ocean, which could serve as a reservoir for plant growth-promoting microbes. This study demonstrates the presence of an active reservoir of terrestrial plant growth-promoting bacteria in remote marine systems and advances our understanding of the microbial connections between plant-associated and plant-free environments at the genome level.},
}
@article {pmid38736754,
year = {2024},
author = {Singh, H and Gibb, B and Abdi, R},
title = {Abundance and diversity of methicillin-resistant bacteria from bathroom surfaces at workplaces using CHROMagar media, 16S, and dnaJ gene sequence typing.},
journal = {International journal of molecular epidemiology and genetics},
volume = {15},
number = {2},
pages = {12-21},
pmid = {38736754},
issn = {1948-1756},
abstract = {University campus communities consist of dynamic and diverse human populations originated from different regions of the country or the world. Their national/global movement to and from campus may contribute to the spread and buildup of methicillin-resistant (MR) bacteria, including MR Staphylococci (MRS) on high-touch surfaces, sinks, and toilets. However, studies on MR bacteria contamination of surfaces, sinks, and toilets are scarce in workplaces outside of healthcare settings. Hence, little is known whether university communities contaminate campus bathrooms by MR bacteria. This study evaluated the abundance, identity, and phylogenetics of MR bacteria grown on CHROMagar MRSA media from bathrooms at workplaces. We collected 21 sink and 21 toilet swab samples from 10 buildings on campus and cultured them on CHROMagar MRSA media, extracted DNA from MR bacteria colonies, sequenced PCR products of 16S and dnaJ primers, determined the sequence identities by BLAST search, and constructed a phylogenetic tree. Of 42 samples, 57.1% (24/42) harbored MR bacteria. MR bacteria were more prevalent on the sink (61.9%) than in the toilet (52.2%) and in male bathrooms (54.2%) than in female bathrooms (41.7%). The colony count on the bathroom surfaces of 42 samples varied in that 42.9% (18/42), 33.3, 14.3, and 9.5% of samples harbored 0, 100, and > 1000 MR bacteria colonies, respectively. Of MR bacteria sequenced, BLAST search and phylogenetic analysis showed that Staphylococcus accounted for 60% of the MR bacteria and the rest were non-Staphylococci. Of Staphylococcus carrying MR (n = 15), 53.3% were S. hemolyticus followed by S. lugdunensis (26.7%), S. epidermidis (8%), and a newly discovered S. borealis in 2020 (4%). Of non-Staphylococci MR bacteria, 20% accounted for Sphingomonas koreensis. Campus bathrooms serve as a reservoir for diverse bacteria carrying MR, which pose a direct risk of infection and a potential source of horizontal gene transfer. To reduce the health risk posed by MR bacteria in high traffic areas such as bathrooms additional environmental monitoring and improved decontamination practices are needed.},
}
@article {pmid38733792,
year = {2024},
author = {Musat, F and Kjeldsen, KU and Rotaru, AE and Chen, SC and Musat, N},
title = {Archaea oxidizing alkanes through alkyl-coenzyme M reductases.},
journal = {Current opinion in microbiology},
volume = {79},
number = {},
pages = {102486},
doi = {10.1016/j.mib.2024.102486},
pmid = {38733792},
issn = {1879-0364},
mesh = {*Alkanes/metabolism ; *Archaea/enzymology/genetics/metabolism ; *Oxidation-Reduction ; *Oxidoreductases/metabolism/genetics ; *Phylogeny ; Electron Transport ; Archaeal Proteins/metabolism/genetics/chemistry ; Gene Transfer, Horizontal ; Bacteria/enzymology/genetics/metabolism/classification ; },
abstract = {This review synthesizes recent discoveries of novel archaea clades capable of oxidizing higher alkanes, from volatile ones like ethane to longer-chain alkanes like hexadecane. These archaea, termed anaerobic multicarbon alkane-oxidizing archaea (ANKA), initiate alkane oxidation using alkyl-coenzyme M reductases, enzymes similar to the methyl-coenzyme M reductases of methanogenic and anaerobic methanotrophic archaea (ANME). The polyphyletic alkane-oxidizing archaea group (ALOX), encompassing ANME and ANKA, harbors increasingly complex alkane degradation pathways, correlated with the alkane chain length. We discuss the evolutionary trajectory of these pathways emphasizing metabolic innovations and the acquisition of metabolic modules via lateral gene transfer. Additionally, we explore the mechanisms by which archaea couple alkane oxidation with the reduction of electron acceptors, including electron transfer to partner sulfate-reducing bacteria (SRB). The phylogenetic and functional constraints that shape ALOX-SRB associations are also discussed. We conclude by highlighting the research needs in this emerging research field and its potential applications in biotechnology.},
}
@article {pmid40078307,
year = {2024},
author = {Salman, S and Umar, Z and Xiao, Y},
title = {Current epidemiologic features and health dynamics of ESBL-producing Escherichia coli in China.},
journal = {Biosafety and health},
volume = {6},
number = {1},
pages = {40-49},
pmid = {40078307},
issn = {2590-0536},
abstract = {Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) are widespread in China, with occurrences documented in humans, animals, and the environment. The dissemination of ESBL-producing E. coli is likely facilitated by the widespread use of antibiotics in human and animal agriculture, the presence of antibiotic-resistant bacteria (ARBs) in animal feces, and close human-animal interactions. Plasmids, particularly those belonging to incompatibility (Inc) group, such as IncF, IncI, and IncH families, play a vital role in facilitating the horizontal gene transfer of ESBL genes across various sectors, from humans to animals and the environment. IS26 and IS1 elements also significantly influences the mobilization and evolution of antibiotic-resistance genes (ARGs), contributing to the spread of ESBL-producing E. coli. bla CTX-M-14, bla CTX-15, and bla CTX-M-55 are prevalent in ESBL-producing E. coli across the three domains and are often found in conjunction with other ARGs. Considering these challenges, it is imperative to take proactive measures to prevent the further spread of ARBs. This includes the judicious and responsible use of antibiotics and efforts to minimize contact with animal feces. Sector-specific strategies should be developed to effectively educate and engage relevant personnel in tackling this multifaceted problem. These efforts are vital to combat the dissemination of ESBL-producing E. coli and preserve public health.},
}
@article {pmid39295911,
year = {2023},
author = {Panwar, S and Kumari, S and Verma, J and Bakshi, S and Narendrakumar, L and Paul, D and Das, B},
title = {Toxin-linked mobile genetic elements in major enteric bacterial pathogens.},
journal = {Gut microbiome (Cambridge, England)},
volume = {4},
number = {},
pages = {e5},
pmid = {39295911},
issn = {2632-2897},
abstract = {One of the fascinating outcomes of human microbiome studies adopting multi-omics technology is its ability to decipher millions of microbial encoded functions in the most complex and crowded microbial ecosystem, including the human gastrointestinal (GI) tract without cultivating the microbes. It is well established that several functions that modulate the human metabolism, nutrient assimilation, immunity, infections, disease severity and therapeutic efficacy of drugs are mostly of microbial origins. In addition, these microbial functions are dynamic and can disseminate between microbial taxa residing in the same ecosystem or other microbial ecosystems through horizontal gene transfer. For clinicians and researchers alike, understanding the toxins, virulence factors and drug resistance traits encoded by the microbes associated with the human body is of utmost importance. Nevertheless, when such traits are genetically linked with mobile genetic elements (MGEs) that make them transmissible, it creates an additional burden to public health. This review mainly focuses on the functions of gut commensals and the dynamics and crosstalk between commensal and pathogenic bacteria in the gut. Also, the review summarises the plethora of MGEs linked with virulence genes present in the genomes of various enteric bacterial pathogens, which are transmissible among other pathogens and commensals.},
}
@article {pmid40166126,
year = {2025},
author = {Zhang, Y and Zhang, B and Ahmed, I and Zhang, H and He, Y},
title = {Profiles and natural drivers of antibiotic resistome in multiple environmental media in penguin-colonized area in Antarctica.},
journal = {Fundamental research},
volume = {5},
number = {1},
pages = {269-281},
pmid = {40166126},
issn = {2667-3258},
abstract = {Profiles and driving mechanisms of antibiotic resistome in the polar region are important for exploring the natural evolution of antibiotic resistance genes (ARGs). Here, we evaluated the profiles of antibiotic resistome in multiple media on Inexpressible Island, Terra Nova Bay, Antarctica. Average concentrations of ARGs in intracellular DNA (iARGs) among water (3.98 × 10[6] copies/L), soil (3.41 × 10[7] copies/kg), and penguin guano (7.04 × 10[7] copies/kg) were higher than those of ARGs in extracellular DNA (eARGs) among water (1.99 × 10[4] copies/L), soil (1.75 × 10[6] copies/kg), and penguin guano (8.02 × 10[6] copies/kg). It was indicated that the transmission of ARGs across different media occurs with around 77.8% of iARGs from soil and 86.7% of iARGs from penguins observed in water, and 80.7% of iARGs and 56.7% of eARGs from penguins found in soil. Annual inputs of ARGs from Adélie penguins on Inexpressible Island have increased since 1983. Bacitracin, multidrug, and aminoglycoside resistance genes were the main ARGs among water, soil, and penguin guano. Primary medium-risk ARGs associated with human pathogenic bacteria were multidrug resistance genes, and main low-risk ARGs associated with mobile genetic elements (MGEs) were aminoglycoside resistance genes. Antibiotic-resistant bacteria (ARB) from soil and penguins were more phylogenetically related to aquatic antibiotic-resistant mesophiles than aquatic antibiotic-resistant psychrophiles. MGEs, ARB, bacterial diversities, antibiotics, and metals could explain total ARGs between water and soil. Intracellular MGEs were the most significant in-situ driver of iARGs in water, reflecting that horizontal gene transfer could facilitate the spread of ARGs in water. Penguins were important ex-situ drivers of environmental antibiotic resistome, which was linked with risky ARGs between water and soil. These findings highlight the major roles of natural drivers (e.g., MGEs and penguins) in shaping environmental antibiotic resistome in polar areas, improving our understanding of the evolution of environmental microbiome.},
}
@article {pmid38818484,
year = {2022},
author = {Zhou, Z and Liu, Y and Anantharaman, K and Li, M},
title = {The expanding Asgard archaea invoke novel insights into Tree of Life and eukaryogenesis.},
journal = {mLife},
volume = {1},
number = {4},
pages = {374-381},
pmid = {38818484},
issn = {2770-100X},
abstract = {The division of organisms on the Tree of Life into either a three-domain (3D) tree or a two-domain (2D) tree has been disputed for a long time. Ever since the discovery of Archaea by Carl Woese in 1977 using 16S ribosomal RNA sequence as the evolutionary marker, there has been a great advance in our knowledge of not only the growing diversity of Archaea but also the evolutionary relationships between different lineages of living organisms. Here, we present this perspective to summarize the progress of archaeal diversity and changing notion of the Tree of Life. Meanwhile, we provide the latest progress in genomics/physiology-based discovery of Asgard archaeal lineages as the closest relative of Eukaryotes. Furthermore, we propose three major directions for future research on exploring the "next one" closest Eukaryote relative, deciphering the function of archaeal eukaryotic signature proteins and eukaryogenesis from both genomic and physiological aspects, and understanding the roles of horizontal gene transfer, viruses, and mobile elements in eukaryogenesis.},
}
@article {pmid39816412,
year = {2022},
author = {Arredondo-Hernandez, R and Siebe, C and Castillo-Rojas, G and Ponce de León, S and López-Vidal, Y},
title = {The synergistic interaction of systemic inflammation, dysbiosis and antimicrobial resistance promotes growth restriction in children with acute severe malnutrition: An emphasis on Escherichia coli.},
journal = {Frontiers in antibiotics},
volume = {1},
number = {},
pages = {1001717},
pmid = {39816412},
issn = {2813-2467},
abstract = {A healthy development is denied to millions of children worldwide as harsh life conditions manifest themselves in an altered inflammation-prone microbiome crosstalk environment. Keynote of this tragedy is that insufficient nutritious amino acid blocks lipids-intake to sustain diverse microbiota, and promotes the generalist strategy followed by Escherichia coli -besides other proteobacteria- of shifting gut metabolism, subverting the site specificity of first immune reaction. Furthermore, it could be hypothesized that selective success lies in their ability to induce inflammation, since this phenomenon also fuels horizontal gene transfer (HGT). In this review, we dilucidate how immune mechanisms of environmental enteric dysfunction affect overgrowth restriction, infectious morbidity rate, and acquired lifelong risks among severe acute malnourished children. Also, despite acknowledging complexities of antimicrobial resistant enrichment, we explore and speculate over the links between virulence regulation and HGT as an indissociable part in the quest for new inflammatory niches by open genome bacteria, particularly when both collide in the most vulnerable.},
}
@article {pmid38818326,
year = {2022},
author = {Da Cunha, V and Gaïa, M and Forterre, P},
title = {The expanding Asgard archaea and their elusive relationships with Eukarya.},
journal = {mLife},
volume = {1},
number = {1},
pages = {3-12},
pmid = {38818326},
issn = {2770-100X},
abstract = {The discovery of Asgard archaea and the exploration of their diversity over the last 6 years have deeply impacted the scientific community working on eukaryogenesis, rejuvenating an intense debate on the topology of the universal tree of life (uTol). Here, we discuss how this debate is impacted by two recent publications that expand the number of Asgard lineages and eukaryotic signature proteins (ESPs). We discuss some of the main difficulties that can impair the phylogenetic reconstructions of the uTol and suggest that the debate about its topology is not settled. We notably hypothesize the existence of horizontal gene transfers between ancestral Asgards and proto-eukaryotes that could result in the observed abnormal behaviors of some Asgard ESPs and universal marker proteins. This hypothesis is relevant regardless of the scenario considered regarding eukaryogenesis. It implies that the Asgards were already diversified before the last eukaryotic common ancestor and shared the same biotopes with proto-eukaryotes. We suggest that some Asgards might be still living in symbiosis today with modern Eukarya.},
}
@article {pmid38733104,
year = {2024},
author = {Quiñonero-Coronel, MDM and Devos, DP and Garcillán-Barcia, MP},
title = {Specificities and commonalities of the Planctomycetes plasmidome.},
journal = {Environmental microbiology},
volume = {26},
number = {5},
pages = {e16638},
doi = {10.1111/1462-2920.16638},
pmid = {38733104},
issn = {1462-2920},
support = {9733//Moore-Simons Project on the Origin of the Eukaryotic Cell/ ; FPU20/04579//Ministerio de Universidades/ ; PID2020-117923GB-I0//Ministerio de Ciencia e Innovaci&#xf3;n/ ; },
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; Bacteria/genetics/classification ; Bacterial Proteins/genetics ; Conjugation, Genetic ; Phylogeny ; Planctomycetales/genetics ; Evolution, Molecular ; Replication Origin/genetics ; },
abstract = {Plasmids, despite their critical role in antibiotic resistance and modern biotechnology, are understood in only a few bacterial groups in terms of their natural ecological dynamics. The bacterial phylum Planctomycetes, known for its unique molecular and cellular biology, has a largely unexplored plasmidome. This study offers a thorough exploration of the diversity of natural plasmids within Planctomycetes, which could serve as a foundation for developing various genetic research tools for this phylum. Planctomycetes plasmids encode a broad range of biological functions and appear to have coevolved significantly with their host chromosomes, sharing many homologues. Recent transfer events of insertion sequences between cohabiting chromosomes and plasmids were also observed. Interestingly, 64% of plasmid genes are distantly related to either chromosomally encoded genes or have homologues in plasmids from other bacterial groups. The planctomycetal plasmidome is composed of 36% exclusive proteins. Most planctomycetal plasmids encode a replication initiation protein from the Replication Protein A family near a putative iteron-containing replication origin, as well as active type I partition systems. The identification of one conjugative and three mobilizable plasmids suggests the occurrence of horizontal gene transfer via conjugation within this phylum. This comprehensive description enhances our understanding of the plasmidome of Planctomycetes and its potential implications in antibiotic resistance and biotechnology.},
}
@article {pmid38728817,
year = {2024},
author = {Wen, X and Xu, J and Worrich, A and Li, X and Yuan, X and Ma, B and Zou, Y and Wang, Y and Liao, X and Wu, Y},
title = {Priority establishment of soil bacteria in rhizosphere limited the spread of tetracycline resistance genes from pig manure to soil-plant systems based on synthetic communities approach.},
journal = {Environment international},
volume = {187},
number = {},
pages = {108732},
doi = {10.1016/j.envint.2024.108732},
pmid = {38728817},
issn = {1873-6750},
mesh = {*Manure/microbiology ; Animals ; *Soil Microbiology ; Swine ; *Rhizosphere ; *Tetracycline Resistance/genetics ; Arabidopsis/microbiology/genetics ; Bacteria/genetics ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The spread of antibiotic resistance genes (ARGs) in agroecosystems through the application of animal manure is a global threat to human and environmental health. However, the adaptability and colonization ability of animal manure-derived bacteria determine the spread pathways of ARG in agroecosystems, which have rarely been studied. Here, we performed an invasion experiment by creating a synthetic communities (SynCom) with ten isolates from pig manure and followed its assembly during gnotobiotic cultivation of a soil-Arabidopsis thaliana (A. thaliana) system. We found that Firmicutes in the SynCom were efficiently filtered out in the rhizosphere, thereby limiting the entry of tetracycline resistance genes (TRGs) into the plant. However, Proteobacteria and Actinobacteria in the SynCom were able to establish in all compartments of the soil-plant system thereby spreading TRGs from manure to soil and plant. The presence of native soil bacteria prevented the establishment of manure-borne bacteria and effectively reduced the spread of TRGs. Achromobacter mucicolens and Pantoea septica were the main vectors for the entry of tetA into plants. Furthermore, doxycycline stress promoted the horizontal gene transfer (HGT) of the conjugative resistance plasmid RP4 within the SynCom in A. thaliana by upregulating the expression of HGT-related mRNAs. Therefore, this study provides evidence for the dissemination pathways of ARGs in agricultural systems through the invasion of manure-derived bacteria and HGT by conjugative resistance plasmids and demonstrates that the priority establishment of soil bacteria in the rhizosphere limited the spread of TRGs from pig manure to soil-plant systems.},
}
@article {pmid38727238,
year = {2024},
author = {Lee, D-H and Lee, K and Kim, Y-S and Cha, C-J},
title = {Comprehensive genomic landscape of antibiotic resistance in Staphylococcus epidermidis.},
journal = {mSystems},
volume = {9},
number = {6},
pages = {e0022624},
pmid = {38727238},
issn = {2379-5077},
support = {2016001350004//Ministry of Environment (MOE)/ ; NRF-2023R1A2C1003654//National Research Foundation of Korea (NRF)/ ; },
mesh = {*Staphylococcus epidermidis/genetics/drug effects/isolation &amp; purification ; *Genome, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Genomics ; Humans ; Genes, Bacterial/genetics ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Bacterial Proteins/genetics ; Plasmids/genetics ; },
abstract = {UNLABELLED: Staphylococcus epidermidis, a common commensal bacterium found on human skin, can cause infections in clinical settings, and the presence of antibiotic resistance genes (ARGs) impedes the treatment of S. epidermidis infections. However, studies characterizing the ARGs in S. epidermidis with regard to genomic and ecological diversities are limited. Thus, we performed a comprehensive and comparative analysis of 405 high-quality S. epidermidis genomes, including those of 35 environmental isolates from the Han River, to investigate the genomic diversity of antibiotic resistance in this pathogen. Comparative genomic analysis revealed the prevalence of ARGs in S. epidermidis genomes associated with multi-locus sequence types. The genes encoding dihydrofolate reductase (dfrC) and multidrug efflux pump (norA) were genome-wide core ARGs. β-Lactam class ARGs were also highly prevalent in the S. epidermidis genomes, which was consistent with the resistance phenotype observed in river isolates. Furthermore, we identified chloramphenicol acetyltransferase genes (cat) in the plasmid-like sequences of the six river isolates, which have not been reported previously in S. epidermidis genomes. These genes were identical to those harbored by the Enterococcus faecium plasmids and associated with the insertion sequence 6 family transposases, homologous to those found in Staphylococcus aureus plasmids, suggesting the possibility of horizontal gene transfer between these Gram-positive pathogens. Comparison of the ARG and virulence factor profiles between S. epidermidis and S. aureus genomes revealed that these two species were clearly distinguished, suggesting genomic demarcation despite ecological overlap. Our findings provide a comprehensive understanding of the genomic diversity of antibiotic resistance in S. epidermidis.<br><br>IMPORTANCE: A comprehensive understanding of the antibiotic resistance gene (ARG) profiles of the skin commensal bacterium and opportunistic pathogen Staphylococcus epidermidis needs to be documented from a genomic point of view. Our study encompasses a comparative analysis of entire S. epidermidis genomes from various habitats, including those of 35 environmental isolates from the Han River sequenced in this study. Our results shed light on the distribution and diversity of ARGs within different S. epidermidis multi-locus sequence types, providing valuable insights into the ecological and genetic factors associated with antibiotic resistance. A comparison between S. epidermidis and Staphylococcus aureus revealed marked differences in ARG and virulence factor profiles, despite their overlapping ecological niches.},
}
@article {pmid38723713,
year = {2024},
author = {Na, IY and Seo, J and Jin, Y and Ko, KS},
title = {Whole-plasmid analysis of NDM-1-producing Acinetobacter seifertii isolate and its fitness in several Acinetobacter species.},
journal = {Journal of global antimicrobial resistance},
volume = {38},
number = {},
pages = {223-226},
doi = {10.1016/j.jgar.2024.05.003},
pmid = {38723713},
issn = {2213-7173},
mesh = {*Acinetobacter/genetics/drug effects/isolation &amp; purification/enzymology ; *beta-Lactamases/genetics ; *Plasmids/genetics ; Humans ; *Microbial Sensitivity Tests ; Republic of Korea ; *Anti-Bacterial Agents/pharmacology ; *Acinetobacter Infections/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Genotype ; Carbapenems/pharmacology ; Conjugation, Genetic ; },
abstract = {OBJECTIVES: The aim of this study was to characterize an NDM-1-producing Acinetobacter seifertii isolates from a patient in South Korea.<br><br>METHODS: Antibiotic susceptibility testing and genotyping using multigene sequencing were performed and whole plasmid sequences were determined.<br><br>RESULTS: The genotype of A. seifertii was ST1899 and was resistant to ceftazidime, trimethoprim-sulfamethoxazole, and piperacillin-tazobactam, in addition to carbapenem. blaNDM-1 was surrounded by the ISAba125 insertion sequence within the structure of Tn125 in the 47 kb-sized plasmid. The plasmid exhibited a structure similar to that of other plasmids of diverse Acinetobacter sp. found worldwide. Transconjugation and the growth curve indicated that the plasmid was adapted to A. seifertii rather than other closely related Acinetobacter sp.<br><br>CONCLUSIONS: Acquisition of carbapenem resistance by horizontal transfer of the blaNDM-1-carrying plasmid from another Acinetobacter species was found with no growth defect.},
}
@article {pmid38721599,
year = {2024},
author = {Yang, Z and Chai, Z and Wang, X and Zhang, Z and Zhang, F and Kang, F and Liu, W and Ren, H and Jin, Y and Yue, J},
title = {Comparative genomic analysis provides insights into the genetic diversity and pathogenicity of the genus Brucella.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1389859},
pmid = {38721599},
issn = {1664-302X},
abstract = {Some Brucella spp. are important pathogens. According to the latest prokaryotic taxonomy, the Brucella genus consists of facultative intracellular parasitic Brucella species and extracellular opportunistic or environmental Brucella species. Intracellular Brucella species include classical and nonclassical types, with different species generally exhibiting host preferences. Some classical intracellular Brucella species can cause zoonotic brucellosis, including B. melitensis, B. abortus, B. suis, and B. canis. Extracellular Brucella species comprise opportunistic or environmental species which belonged formerly to the genus Ochrobactrum and thus nowadays renamed as for example Brucella intermedia or Brucella anthropi, which are the most frequent opportunistic human pathogens within the recently expanded genus Brucella. The cause of the diverse phenotypic characteristics of different Brucella species is still unclear. To further investigate the genetic evolutionary characteristics of the Brucella genus and elucidate the relationship between its genomic composition and prediction of phenotypic traits, we collected the genomic data of Brucella from the NCBI Genome database and conducted a comparative genomics study. We found that classical and nonclassical intracellular Brucella species and extracellular Brucella species exhibited differences in phylogenetic relationships, horizontal gene transfer and distribution patterns of mobile genetic elements, virulence factor genes, and antibiotic resistance genes, showing the close relationship between the genetic variations and prediction of phenotypic traits of different Brucella species. Furthermore, we found significant differences in horizontal gene transfer and the distribution patterns of mobile genetic elements, virulence factor genes, and antibiotic resistance genes between the two chromosomes of Brucella, indicating that the two chromosomes had distinct dynamics and plasticity and played different roles in the survival and evolution of Brucella. These findings provide new directions for exploring the genetic evolutionary characteristics of the Brucella genus and could offer new clues to elucidate the factors influencing the phenotypic diversity of the Brucella genus.},
}
@article {pmid38717818,
year = {2024},
author = {Nair, S and Barker, CR and Bird, M and Greig, DR and Collins, C and Painset, A and Chattaway, M and Pickard, D and Larkin, L and Gharbia, S and Didelot, X and Ribeca, P},
title = {Presence of phage-plasmids in multiple serovars of Salmonella enterica.},
journal = {Microbial genomics},
volume = {10},
number = {5},
pages = {},
pmid = {38717818},
issn = {2057-5858},
mesh = {*Plasmids/genetics ; *Salmonella enterica/virology/genetics ; *Serogroup ; Salmonella Infections/microbiology ; Bacteriophages/genetics/classification ; Salmonella Phages/genetics/classification ; Humans ; Phylogeny ; Gene Transfer, Horizontal ; Retrospective Studies ; },
abstract = {Evidence is accumulating in the literature that the horizontal spread of antimicrobial resistance (AMR) genes mediated by bacteriophages and bacteriophage-like plasmid (phage-plasmid) elements is much more common than previously envisioned. For instance, we recently identified and characterized a circular P1-like phage-plasmid harbouring a bla CTX-M-15 gene conferring extended-spectrum beta-lactamase (ESBL) resistance in Salmonella enterica serovar Typhi. As the prevalence and epidemiological relevance of such mechanisms has never been systematically assessed in Enterobacterales, in this study we carried out a follow-up retrospective analysis of UK Salmonella isolates previously sequenced as part of routine surveillance protocols between 2016 and 2021. Using a high-throughput bioinformatics pipeline we screened 47 784 isolates for the presence of the P1 lytic replication gene repL, identifying 226 positive isolates from 25 serovars and demonstrating that phage-plasmid elements are more frequent than previously thought. The affinity for phage-plasmids appears highly serovar-dependent, with several serovars being more likely hosts than others; most of the positive isolates (170/226) belonged to S. Typhimurium ST34 and ST19. The phage-plasmids ranged between 85.8 and 98.2 kb in size, with an average length of 92.1 kb; detailed analysis indicated a high amount of diversity in gene content and genomic architecture. In total, 132 phage-plasmids had the p0111 plasmid replication type, and 94 the IncY type; phylogenetic analysis indicated that both horizontal and vertical gene transmission mechanisms are likely to be involved in phage-plasmid propagation. Finally, phage-plasmids were present in isolates that were resistant and non-resistant to antimicrobials. In addition to providing a first comprehensive view of the presence of phage-plasmids in Salmonella, our work highlights the need for a better surveillance and understanding of phage-plasmids as AMR carriers, especially through their characterization with long-read sequencing.},
}
@article {pmid38717786,
year = {2024},
author = {Zhang, Y and Wang, J and Yu, J},
title = {PSA: an effective method for predicting horizontal gene transfers through parsimonious phylogenetic networks.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {40},
number = {4},
pages = {443-455},
doi = {10.1111/cla.12578},
pmid = {38717786},
issn = {1096-0031},
support = {NJYT24036//2024 Youth Science and Technology Talent Development Project (Youth Science and Technology Talents) of Education Department of Inner Mongolia Autonomous Region of China/ ; NMGIRT2318//University Youth Science and Technology Talent Development Project (Innovation Group Development Plan) of Inner Mongolia A. R. of China/ ; 2022MS01002//Natural Science Foundation of Inner Mongolia Province/ ; 12002175//National Natural Science Foundation of China/ ; 62002181//National Natural Science Foundation of China/ ; 62061035//National Natural Science Foundation of China/ ; },
mesh = {*Gene Transfer, Horizontal ; *Phylogeny ; *Algorithms ; Models, Genetic ; Evolution, Molecular ; Computer Simulation ; },
abstract = {Horizontal gene transfer (HGT) from one organism to another, according to some researchers, can be abundant in the evolution of species. A phylogenetic network is a network structure that describes the HGTs among species. Several studies have proposed methods to construct phylogenetic networks to predict HGTs based on parsimony values. Existing definitions of parsimony values for a phylogenetic network are based on the assumption that each gene site or segment evolves independently along different trees in the network. However, in the current study, we define a novel parsimony value, denoted the p definition, for phylogenetic networks, considering that a gene as a whole typically evolves along a tree. Using Simulated Annealing, a new method called the Phylogeny with Simulated Annealing (PSA) algorithm is proposed to search for an optimal network based on the p definition. The PSA method is tested on the simulated data. The results reveal that the parsimonious networks constructed using PSA can better represent the evolutionary relationships of species involving HGTs. Additionally, the HGTs predicted using PSA are more accurate than those predicted using other methods. The PSA algorithm is publicly accessible at http://github.com/imustu/sap.},
}
@article {pmid38716477,
year = {2024},
author = {Cheewapat, R and Redkimned, J and Lekuthai, S and Kitti, T and Tasanapak, K and Thanwisai, A and Sitthisak, S and Sornda, T and Impheng, H and Onsurathum, S and Leungtongkam, U and Lamlertthon, S and Kucharoenphaibul, S and Wongwigkarn, J and Singkum, P and Chanchaithong, P and Thummeepak, R},
title = {Genomic Landscape Reveals Chromosomally-Mediated Antimicrobial Resistome and Virulome of a High-Risk International Clone II Acinetobacter baumannii AB073 from Thailand.},
journal = {Global health, epidemiology and genomics},
volume = {2024},
number = {},
pages = {8872463},
pmid = {38716477},
issn = {2054-4200},
mesh = {*Acinetobacter baumannii/genetics/drug effects ; Thailand/epidemiology ; *Acinetobacter Infections/microbiology/epidemiology/drug therapy ; Humans ; Genome, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Drug Resistance, Multiple, Bacterial/genetics ; Carbapenems/pharmacology ; Virulence/genetics ; },
abstract = {This study utilized integrative bioinformatics' tools together with phenotypic assays to understand the whole-genome features of a carbapenem-resistant international clone II Acinetobacter baumannii AB073. Overall, we found the isolate to be resistant to seven antibiotic classes, penicillins, β-lactam/β-lactamase inhibitor combinations, cephalosporins, carbapenems, aminoglycosides, fluoroquinolones, and folate pathway antagonists. These resistance phenotypes are related to various chromosomal-located antibiotic resistance determinants involved in different mechanisms such as reduced permeability, antibiotic target protection, antibiotic target alteration, antibiotic inactivation, and antibiotic efflux. IC2 A. baumannii AB073 could not transfer antibiotic resistance by conjugation experiments. Likewise, mobilome analysis found that AB073 did not carry genetic determinants involving horizontal gene transfer. Moreover, this isolate also carried multiple genes associated with the ability of iron uptake, biofilm formation, immune invasion, virulence regulations, and serum resistance. In addition, the genomic epidemiological study showed that AB073-like strains were successful pathogens widespread in various geographic locations and clinical sources. In conclusion, the comprehensive analysis demonstrated that AB073 contained multiple genomic determinants which were important characteristics to classify this isolate as a successful international clone II obtained from Thailand.},
}
@article {pmid38714248,
year = {2024},
author = {Wang, S and Tian, R and Bi, Y and Meng, F and Zhang, R and Wang, C and Wang, D and Liu, L and Zhang, B},
title = {A review of distribution and functions of extracellular DNA in the environment and wastewater treatment systems.},
journal = {Chemosphere},
volume = {359},
number = {},
pages = {142264},
doi = {10.1016/j.chemosphere.2024.142264},
pmid = {38714248},
issn = {1879-1298},
mesh = {*Wastewater ; DNA, Environmental/analysis ; Biofilms ; Biodiversity ; Environmental Monitoring/methods ; Gene Transfer, Horizontal ; Waste Disposal, Fluid/methods ; },
abstract = {Extracellular DNA refers to DNA fragments existing outside the cell, originating from various cell release mechanisms, including active secretion, cell lysis, and phage-mediated processes. Extracellular DNA serves as a vital environmental biomarker, playing crucial ecological and environmental roles in water bodies. This review is summarized the mechanisms of extracellular DNA release, including pathways involving cell lysis, extracellular vesicles, and type IV secretion systems. Then, the extraction and detection methods of extracellular DNA from water, soil, and biofilm are described and analyzed. Finally, we emphasize the role of extracellular DNA in microbial community systems, including its significant contributions to biofilm formation, biodiversity through horizontal gene transfer, and electron transfer processes. This review offers a comprehensive insight into the sources, distribution, functions, and impacts of extracellular DNA within aquatic environments, aiming to foster further exploration and understanding of extracellular DNA dynamics in aquatic environments as well as other environments.},
}
@article {pmid38714231,
year = {2024},
author = {Wang, YL and Ikuma, K and Brown, AMV and Deonarine, A},
title = {Global survey of hgcA-carrying genomes in marine and freshwater sediments: Insights into mercury methylation processes.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {352},
number = {},
pages = {124117},
doi = {10.1016/j.envpol.2024.124117},
pmid = {38714231},
issn = {1873-6424},
mesh = {*Geologic Sediments/chemistry/microbiology ; *Mercury/metabolism ; Methylation ; *Water Pollutants, Chemical/metabolism ; *Fresh Water ; Methylmercury Compounds/metabolism ; Seawater/chemistry/microbiology ; Bacteria/genetics/metabolism ; Metagenome ; },
abstract = {Mercury (Hg) methylation is a microbially mediated process that produces methylmercury (MeHg), a bioaccumulative neurotoxin. A highly conserved gene pair, hgcAB, is required for Hg methylation, which provides a basis for identifying Hg methylators and evaluating their genomic composition. In this study, we conducted a large-scale omics analysis in which 281 metagenomic freshwater and marine sediment samples from 46 geographic locations across the globe were queried. Specific objectives were to examine the prevalence of Hg methylators, to identify horizontal gene transfer (HGT) events involving hgcAB within Hg methylator communities, and to identify associations between hgcAB and microbial biochemical functions/genes. Hg methylators from the phyla Desulfobacterota and Bacteroidota were dominant in both freshwater and marine sediments while Firmicutes and methanogens belonging to Euryarchaeota were identified only in freshwater sediments. Novel Hg methylators were found in the Phycisphaerae and Planctomycetia classes within the phylum Planctomycetota, including potential hgcA-carrying anammox metagenome-assembled genomes (MAGs) from Candidatus Brocadiia. HGT of hgcA and hgcB were identified in both freshwater and marine methylator communities. Spearman's correlation analysis of methylator genomes suggested that in addition to sulfide, thiosulfate, sulfite, and ammonia may be important parameters for Hg methylation processes in sediments. Overall, our results indicated that the biochemical drivers of Hg methylation vary between marine and freshwater sites, lending insight into the influence of environmental perturbances, such as a changing climate, on Hg methylation processes.},
}
@article {pmid38712952,
year = {2024},
author = {Fidopiastis, PM and Childs, C and Esin, JJ and Stellern, J and Darin, A and Lorenzo, A and Mariscal, VT and Lorenz, J and Gopan, V and McAnulty, S and Visick, KL},
title = {Corrected and republished from: "Vibrio fischeri Possesses Xds and Dns Nucleases That Differentially Influence Phosphate Scavenging, Aggregation, Competence, and Symbiotic Colonization of Squid".},
journal = {Applied and environmental microbiology},
volume = {90},
number = {6},
pages = {e0032824},
pmid = {38712952},
issn = {1098-5336},
support = {R35 GM130355/GM/NIGMS NIH HHS/United States ; },
mesh = {*Aliivibrio fischeri/genetics/physiology/enzymology ; *Decapodiformes/microbiology ; Animals ; *Symbiosis ; *Phosphates/metabolism ; *Bacterial Proteins/metabolism/genetics ; Deoxyribonucleases/metabolism/genetics ; },
abstract = {Cells of Vibrio fischeri colonize the light organ of Euprymna scolopes, providing the squid bioluminescence in exchange for nutrients and protection. The bacteria encounter DNA-rich mucus throughout their transition to a symbiotic lifestyle, leading us to hypothesize a role for nuclease activity in the colonization process. In support of this, we detected abundant extracellular nuclease activity in growing cells of V. fischeri. To discover the gene(s) responsible for this activity, we screened a V. fischeri transposon mutant library for nuclease-deficient strains. Interestingly, only one strain, whose transposon insertion mapped to nuclease gene VF_1451, showed a complete loss of nuclease activity in our screens. A database search revealed that VF_1451 is homologous to the nuclease-encoding gene xds in Vibrio cholerae. However, V. fischeri strains lacking xds eventually revealed slight nuclease activity on plates upon prolonged incubation. This led us to hypothesize that a second secreted nuclease, identified through a database search as VF_0437, a homolog of V. cholerae dns, might be responsible for the residual nuclease activity. Here, we show that Xds and/or Dns are involved in essential aspects of V. fischeri biology, including natural transformation, aggregation, and phosphate scavenging. Furthermore, strains lacking either nuclease were outcompeted by the wild type for squid colonization. Understanding the specific role of nuclease activity in the squid colonization process represents an intriguing area of future research.IMPORTANCEFrom soil and water to host-associated secretions such as mucus, environments that bacteria inhabit are awash in DNA. Extracellular DNA (eDNA) is a nutritious resource that microbes dedicate significant energy to exploit. Calcium binds eDNA to promote cell-cell aggregation and horizontal gene transfer. eDNA hydrolysis impacts the construction of and dispersal from biofilms. Strategies in which pathogens use nucleases to avoid phagocytosis or disseminate by degrading host secretions are well-documented; significantly less is known about nucleases in mutualistic associations. This study describes the role of nucleases in the mutualism between Vibrio fischeri and its squid host Euprymna scolopes. We find that nuclease activity is an important determinant of colonization in V. fischeri, broadening our understanding of how microbes establish and maintain beneficial associations.},
}
@article {pmid38712904,
year = {2024},
author = {Muelbaier, H and Arthen, F and Collins, G and Hickler, T and Hohberg, K and Lehmitz, R and Pauchet, Y and Pfenninger, M and Potapov, A and Romahn, J and Schaefer, I and Scheu, S and Schneider, C and Ebersberger, I and Bálint, M},
title = {Genomic evidence for the widespread presence of GH45 cellulases among soil invertebrates.},
journal = {Molecular ecology},
volume = {33},
number = {20},
pages = {e17351},
doi = {10.1111/mec.17351},
pmid = {38712904},
issn = {1365-294X},
support = {LOEWE/1/10/519/03/03.001(0014)/52//Landes-Offensive zur Entwicklung Wissenschaftlich-&#xf6;konomischer Exzellenz (LOEWE)/ ; BA 4843/4-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; *Phylogeny ; *Soil/chemistry ; *Invertebrates/genetics/enzymology ; *Cellulases/genetics/metabolism ; Lignin/metabolism ; Mites/genetics/enzymology ; Cellulose/metabolism ; Genomics ; },
abstract = {Lignocellulose is a major component of vascular plant biomass. Its decomposition is crucial for the terrestrial carbon cycle. Microorganisms are considered primary decomposers, but evidence increases that some invertebrates may also decompose lignocellulose. We investigated the taxonomic distribution and evolutionary origins of GH45 hydrolases, important enzymes for the decomposition of cellulose and hemicellulose, in a collection of soil invertebrate genomes. We found that these genes are common in springtails and oribatid mites. Phylogenetic analysis revealed that cellulase genes were acquired early in the evolutionary history of these groups. Domain architectures and predicted 3D enzyme structures indicate that these cellulases are functional. Patterns of presence and absence of these genes across different lineages prompt further investigation into their evolutionary and ecological benefits. The ubiquity of cellulase genes suggests that soil invertebrates may play a role in lignocellulose decomposition, independently or in synergy with microorganisms. Understanding the ecological and evolutionary implications might be crucial for understanding soil food webs and the carbon cycle.},
}
@article {pmid38712252,
year = {2024},
author = {Buck, CB and Welch, N and Belford, AK and Varsani, A and Pastrana, DV and Tisza, MJ and Starrett, GJ},
title = {Widespread Horizontal Gene Transfer Among Animal Viruses.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38712252},
issn = {2692-8205},
abstract = {The initial objective of this study was to shed light on the evolution of small DNA tumor viruses by analyzing de novo assemblies of publicly available deep sequencing datasets. The survey generated a searchable database of contig snapshots representing more than 100,000 Sequence Read Archive records. Using modern structure-aware search tools, we iteratively broadened the search to include an increasingly wide range of other virus families. The analysis revealed a surprisingly diverse range of chimeras involving different virus groups. In some instances, genes resembling known DNA-replication modules or known virion protein operons were paired with unrecognizable sequences that structural predictions suggest may represent previously unknown replicases and novel virion architectures. Discrete clades of an emerging group called adintoviruses were discovered in datasets representing humans and other primates. As a proof of concept, we show that the contig database is also useful for discovering RNA viruses and candidate archaeal phages. The ancillary searches revealed additional examples of chimerization between different virus groups. The observations support a gene-centric taxonomic framework that should be useful for future virus-hunting efforts.},
}
@article {pmid38710287,
year = {2024},
author = {Zuo, Y and Yang, J and Zhang, H and Li, L and Luo, J and Lv, Y and Yuan, M and Yang, K},
title = {Genome comparison of long-circulating field CnmeGV isolates from the same region.},
journal = {Virus research},
volume = {345},
number = {},
pages = {199390},
pmid = {38710287},
issn = {1872-7492},
mesh = {*Genome, Viral ; Animals ; *Genetic Variation ; Phylogeny ; China ; Granulovirus/genetics/classification/isolation &amp; purification ; Whole Genome Sequencing ; Oryza/virology ; Tandem Repeat Sequences/genetics ; Plant Diseases/virology ; Recombination, Genetic ; },
abstract = {Cnaphalocrocis medinalis granulovirus (CnmeGV), belonging to Betabaculovirus cnamedinalis, can infect the rice pest, the rice leaf roller. In 1979, a CnmeGV isolate, CnmeGV-EP, was collected from Enping County, China. In 2014, we collected another CnmeGV isolate, CnmeGV-EPDH3, at the same location and obtained the complete virus genome sequence using Illumina and ONT sequencing technologies. By combining these two virus isolates, we updated the genome annotation of CnmeGV and conducted an in-depth analysis of its genome features. CnmeGV genome contains abundant tandem repeat sequences, and the repeating units in the homologous regions (hrs) exhibit overlapping and nested patterns. The genetic variations within EPDH3 population show the high stability of CnmeGV genome, and tandem repeats are the only region of high genetic variation in CnmeGV genome replication. Some defective viral genomes formed by recombination were found within the population. Comparison analysis of the two virus isolates collected from Enping showed that the proteins encoded by the CnmeGV-specific genes were less conserved relative to the baculovirus core genes. At the genomic level, there are a large number of SNPs and InDels between the two virus isolates, especially in and around the bro genes and hrs. Additionally, we discovered that CnmeGV acquired a segment of non-ORF sequence from its host, which does not provide any new proteins but rather serves as redundant genetic material integrated into the viral genome. Furthermore, we observed that the host's transposon piggyBac has inserted into some virus genes. Together, dsDNA viruses could acquire non-coding genetic material from their hosts to expand the size of their genomes. These findings provide new insights into the evolution of dsDNA viruses.},
}
@article {pmid38710286,
year = {2024},
author = {Zhao, F and Wang, J},
title = {Another piece of puzzle for the human microbiome: the gut virome under dietary modulation.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {51},
number = {10},
pages = {983-996},
doi = {10.1016/j.jgg.2024.04.013},
pmid = {38710286},
issn = {1673-8527},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Virome/genetics ; *Diet ; Bacteriophages/genetics/physiology ; Bacteria/genetics/classification/virology ; Gene Transfer, Horizontal ; Viruses/genetics ; },
abstract = {The virome is the most abundant and highly variable microbial consortium in the gut. Because of difficulties in isolating and culturing gut viruses and the lack of reference genomes, the virome has remained a relatively elusive aspect of the human microbiome. In recent years, studies on the virome have accumulated growing evidence showing that the virome is diet-modulated and widely involved in regulating health. Here, we review the responses of the gut virome to dietary intake and the potential health implications, presenting changes in the gut viral community and preferences of viral members to particular diets. We further discuss how viral-bacterial interactions and phage lifestyle shifts shape the gut microbiota. We also discuss the specific functions conferred by diet on the gut virome and bacterial community in the context of horizontal gene transfer, as well as the import of new viral members along with the diet. Collating these studies will expand our understanding of the dietary regulation of the gut virome and inspire dietary interventions and health maintenance strategies targeting the gut microbiota.},
}
@article {pmid38707295,
year = {2024},
author = {Cochran, JP and Zhang, L and Parrott, BB and Seaman, JC},
title = {Plasmid size determines adsorption to clay and breakthrough in a saturated sand column.},
journal = {Heliyon},
volume = {10},
number = {9},
pages = {e29679},
pmid = {38707295},
issn = {2405-8440},
abstract = {Horizontal gene transfer (HGT) is a major factor in the spread of antibiotic resistant genes (ARG). Transformation, one mode of HGT, involves the acquisition and expression of extracellular DNA (eDNA). eDNA in soils is degraded rapidly by extracellular nucleases. However, if bound to a clay particle, eDNA can persist for long periods of time without losing its transformation ability. To better understand the mechanism of eDNA persistence in soil, this experiment assessed the effects of 1) clay mineralogy, 2) mixed salt solution, 3) plasmid size on DNA adsorption to clay and 4) breakthrough behavior of three differently sized plasmids in an environmentally relevant solution. Batch test methods were used to determine adsorption trends of three differently sized DNA plasmids, pUC19, pBR322, and pTYB21, to several pure clay minerals, goethite (α-FeOOH), illite, and kaolinite, and one environmental soil sample. Results show not all sorbents have equal adsorption capacity based on surface area with adsorption capacities decreasing from goethite > illite = kaolinite > bulk soil, and low ionic strength solutions will likely not significantly alter sorption trends. Additionally, plasmid DNA size (i.e., length) was shown to be a significant predictor of adsorption efficiency and that size affects DNA breakthrough, with breakthroughs occurring later with larger plasmids. Given that DNA persistence is linked to its adsorption to soil constituents and breakthrough, eDNA size is likely an important contributor to the spread of ARG within natural microbial communities.},
}
@article {pmid38705616,
year = {2024},
author = {Bui, QTN and Kim, HS and Ki, JS},
title = {Polyphyletic origin of saxitoxin biosynthesis genes in the marine dinoflagellate Alexandrium revealed by comparative transcriptomics.},
journal = {Harmful algae},
volume = {134},
number = {},
pages = {102620},
doi = {10.1016/j.hal.2024.102620},
pmid = {38705616},
issn = {1878-1470},
mesh = {*Dinoflagellida/genetics/metabolism ; *Saxitoxin/genetics/biosynthesis ; *Phylogeny ; *Transcriptome ; Gene Expression Profiling ; Evolution, Molecular ; },
abstract = {The marine dinoflagellate Alexandrium is known to form harmful algal blooms, and at least 14 species within the genus can produce saxitoxins (STXs). STX biosynthesis genes (sxt) are individually revealed in toxic dinoflagellates; however, the evolutionary history remains controversial. Herein, we determined the transcriptome sequences of toxic Alexandrium (A. catenella and A. pacificum) and non-toxic Alexandrium (A. fraterculus and A. fragae) and characterized their sxt by focusing on evolutionary events and STX production. Comparative transcriptome analysis revealed higher homology of the sxt in toxic Alexandrium than in non-toxic species. Notably, non-toxic Alexandrium spp. were found to have lost two sxt core genes, namely sxtA4 and sxtG. Expression levels of 28 transcripts related to eight sxt core genes showed that sxtA, sxtG, and sxtI were relatively high (>1.5) in the toxic group compared to the non-toxic group. In contrast, the non-toxic group showed high expression levels in sxtU (1.9) and sxtD (1.7). Phylogenetic tree comparisons revealed distinct evolutionary patterns between 28S rDNA and sxtA, sxtB, sxtI, sxtD, and sxtU. However, similar topology was observed between 28S rDNA, sxtS, and sxtH/T. In the sxtB and sxtI phylogeny trees, toxic Alexandrium and cyanobacteria were clustered together, separating from non-toxic species. These suggest that Alexandrium may acquire sxt genes independently via horizontal gene transfer from toxic cyanobacteria and other multiple sources, demonstrating monocistronic transcripts of sxt in dinoflagellates.},
}
@article {pmid38705297,
year = {2024},
author = {Xu, Q and Ali, S and Afzal, M and Nizami, AS and Han, S and Dar, MA and Zhu, D},
title = {Advancements in bacterial chemotaxis: Utilizing the navigational intelligence of bacteria and its practical applications.},
journal = {The Science of the total environment},
volume = {931},
number = {},
pages = {172967},
doi = {10.1016/j.scitotenv.2024.172967},
pmid = {38705297},
issn = {1879-1026},
mesh = {*Chemotaxis ; *Bacterial Physiological Phenomena ; *Bacteria ; Biodegradation, Environmental ; },
abstract = {The fascinating world of microscopic life unveils a captivating spectacle as bacteria effortlessly maneuver through their surroundings with astonishing accuracy, guided by the intricate mechanism of chemotaxis. This review explores the complex mechanisms behind this behavior, analyzing the flagellum as the driving force and unraveling the intricate signaling pathways that govern its movement. We delve into the hidden costs and benefits of this intricate skill, analyzing its potential to propagate antibiotic resistance gene while shedding light on its vital role in plant colonization and beneficial symbiosis. We explore the realm of human intervention, considering strategies to manipulate bacterial chemotaxis for various applications, including nutrient cycling, algal bloom and biofilm formation. This review explores the wide range of applications for bacterial capabilities, from targeted drug delivery in medicine to bioremediation and disease control in the environment. Ultimately, through unraveling the intricacies of bacterial movement, we can enhance our comprehension of the intricate web of life on our planet. This knowledge opens up avenues for progress in fields such as medicine, agriculture, and environmental conservation.},
}
@article {pmid38704526,
year = {2024},
author = {Kobakhidze, S and Koulouris, S and Kakabadze, N and Kotetishvili, M},
title = {Genetic recombination-mediated evolutionary interactions between phages of potential industrial importance and prophages of their hosts within or across the domains of Escherichia, Listeria, Salmonella, Campylobacter, and Staphylococcus.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {155},
pmid = {38704526},
issn = {1471-2180},
mesh = {*Prophages/genetics ; *Recombination, Genetic ; Campylobacter/virology/genetics ; Staphylococcus/virology/genetics ; Gene Transfer, Horizontal ; Bacteriophages/genetics/physiology/classification ; Listeria/virology/genetics ; Salmonella/virology/genetics ; Evolution, Molecular ; Bacteria/virology/genetics ; },
abstract = {BACKGROUND: The in-depth understanding of the role of lateral genetic transfer (LGT) in phage-prophage interactions is essential to rationalizing phage applications for human and animal therapy, as well as for food and environmental safety. This in silico study aimed to detect LGT between phages of potential industrial importance and their hosts.<br><br>METHODS: A large array of genetic recombination detection algorithms, implemented in SplitsTree and RDP4, was applied to detect LGT between various Escherichia, Listeria, Salmonella, Campylobacter, Staphylococcus, Pseudomonas, and Vibrio phages and their hosts. PHASTER and RAST were employed respectively to identify prophages across the host genome and to annotate LGT-affected genes with unknown functions. PhageAI was used to gain deeper insights into the life cycle history of recombined phages.<br><br>RESULTS: The split decomposition inferences (bootstrap values: 91.3-100; fit: 91.433-100), coupled with the Phi (0.0-2.836E-12) and RDP4 (P being well below 0.05) statistics, provided strong evidence for LGT between certain Escherichia, Listeria, Salmonella, and Campylobacter virulent phages and prophages of their hosts. The LGT events entailed mainly the phage genes encoding for hypothetical proteins, while some of these genetic loci appeared to have been affected even by intergeneric recombination in specific E. coli and S. enterica virulent phages when interacting with their host prophages. Moreover, it is shown that certain L. monocytogenes virulent phages could serve at least as the donors of the gene loci, involved in encoding for the basal promoter specificity factor, for L. monocytogenes. In contrast, the large genetic clusters were determined to have been simultaneously exchanged by many S. aureus prophages and some Staphylococcus temperate phages proposed earlier as potential therapeutic candidates (in their native or modified state). The above genetic clusters were found to encompass multiple genes encoding for various proteins, such as e.g., phage tail proteins, the capsid and scaffold proteins, holins, and transcriptional terminator proteins.<br><br>CONCLUSIONS: It is suggested that phage-prophage interactions, mediated by LGT (including intergeneric recombination), can have a far-reaching impact on the co-evolutionary trajectories of industrial phages and their hosts especially when excessively present across microbially rich environments.},
}
@article {pmid38704005,
year = {2024},
author = {Lv, B and Jiang, C and Han, Y and Wu, D and Jin, L and Zhu, G and An, T and Shi, J},
title = {Diverse bacterial hosts and potential risk of antibiotic resistomes in ship ballast water revealed by metagenomic binning.},
journal = {Environmental research},
volume = {253},
number = {},
pages = {119056},
doi = {10.1016/j.envres.2024.119056},
pmid = {38704005},
issn = {1096-0953},
mesh = {*Ships ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Metagenomics ; Water Microbiology ; Anti-Bacterial Agents/pharmacology ; Metagenome ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; },
abstract = {Ship ballast water promoting the long-range migration of antibiotic resistance genes (ARGs) has raised a great concern. This study attempted to reveal ARGs profile in ballast water and decipher their hosts and potential risk using metagenomic approaches. In total, 710 subtypes across 26 ARG types were identified among the ballast water samples from 13 ships of 11 countries and regions, and multidrug resistance genes were the most dominant ARGs. The composition of ARGs were obviously different across samples, and only 5% of the ARG subtypes were shared by all samples. Procrustes analysis showed the bacterial community contributed more than the mobile genetic elements (MGEs) in shaping the antibiotic resistome. Further, 79 metagenome-assembled genomes (46 genera belong to four phyla) were identified as ARG hosts, with predominantly affiliated with the Proteobacteria. Notably, potential human pathogens (Alcaligenes, Mycolicibacterium, Rhodococcus and Pseudomonas) were also recognized as the ARG hosts. Above 30% of the ARGs hosts contained the MGEs simultaneously, supporting a pronounced horizontal gene transfer capability. A total of 43 subtypes (six percent of overall ARGs) of ARGs were assessed with high-risk, of which 23 subtypes belonged to risk Rank I (including rsmA, ugd, etc.) and 20 subtypes to the risk Rank II (including aac(6)-I, sul1, etc.). In addition, antibiotic resistance risk index indicated the risk of ARGs in ballast water from choke points of maritime trade routes was significantly higher than that from other regions. Overall, this study offers insights for risk evaluation and management of antibiotic resistance in ballast water.},
}
@article {pmid38700770,
year = {2024},
author = {Zhang, Y and Ji, Y and Tang, X and Chen, M and Su, J},
title = {Spread of plasmids carrying antibiotic resistance genes in soil-lettuce-snail food chain.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {23},
pages = {34295-34308},
pmid = {38700770},
issn = {1614-7499},
support = {41701564//National Natural Science Foundation of China/ ; SNG201613//Science and Technology Program of Suzhou/ ; },
mesh = {*Plasmids/genetics ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; Animals ; *Food Chain ; Snails ; Soil/chemistry ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Fertilization can change the composition of antibiotic resistance genes(ARGs) and their host bacteria in agricultural fields, while complex microbial activities help ARGs into crops and transmit them to humans through agricultural products.Therefore, this study constructed a farmland food chain with soil-lettuce-snail as a typical structure, added genetically engineered Pseudomonas fluorescens containing multidrug-resistant plasmid RP4 to track its spread in the farmland food chain, and used different fertilization methods to explore its influence on the spread and diffusion of ARGs and intl1 in the farmland food chain. It was found that exogenous Pseudomonas can enter plants from soil and pass into snails' intestines, and there is horizontal gene transfer phenomenon of RP4 plasmid in bacteria. At different interfaces of the constructed food chain, the addition of exogenous drug-resistant bacteria had different effects on the total abundance of ARGs and intl1. Fertilization, especially manure, not only promoted the spread of Pseudomonas aeruginosa and the transfer of RP4 plasmid levels, but also significantly increased the total abundance of ARGs and intl1 at all interfaces of the constructed food chain. The main ARGs host bacteria in the constructed food chain include Proteobacteria, Bacteroides, and Firmicutes, while Flavobacterium of Bacteroides is the unique potential host bacteria of RP4 plasmid. In conclusion, this study provides a reference for the risk assessment of ARGs transmitted to the human body through the food chain, and has important practical significance to reduce the antibiotic resistance contamination of agricultural products and ensure the safety of vegetable basket.},
}
@article {pmid38698002,
year = {2024},
author = {Da Silva Morais, E and Grimaud, GM and Warda, A and Stanton, C and Ross, P},
title = {Genome plasticity shapes the ecology and evolution of Phocaeicola dorei and Phocaeicola vulgatus.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {10109},
pmid = {38698002},
issn = {2045-2322},
support = {101054719/ERC_/European Research Council/International ; BACtheWINNER, Project No. 101054719/ERC_/European Research Council/International ; },
mesh = {*Phylogeny ; *Genome, Bacterial ; Humans ; Gastrointestinal Microbiome/genetics ; Gene Transfer, Horizontal ; Evolution, Molecular ; Genomics/methods ; Bacteroidetes/genetics ; },
abstract = {Phocaeicola dorei and Phocaeicola vulgatus are very common and abundant members of the human gut microbiome and play an important role in the infant gut microbiome. These species are closely related and often confused for one another; yet, their genome comparison, interspecific diversity, and evolutionary relationships have not been studied in detail so far. Here, we perform phylogenetic analysis and comparative genomic analyses of these two Phocaeicola species. We report that P. dorei has a larger genome yet a smaller pan-genome than P. vulgatus. We found that this is likely because P. vulgatus is more plastic than P. dorei, with a larger repertoire of genetic mobile elements and fewer anti-phage defense systems. We also found that P. dorei directly descends from a clade of P. vulgatus¸ and experienced genome expansion through genetic drift and horizontal gene transfer. Overall, P. dorei and P. vulgatus have very different functional and carbohydrate utilisation profiles, hinting at different ecological strategies, yet they present similar antimicrobial resistance profiles.},
}
@article {pmid38696408,
year = {2024},
author = {Aldaihani, R and Heath, LS},
title = {Investigating the nature of prokaryotic genomic island locations within a genome.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0301172},
pmid = {38696408},
issn = {1932-6203},
mesh = {*Genomic Islands ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genome, Archaeal ; Replication Origin/genetics ; Prokaryotic Cells/metabolism ; },
abstract = {Horizontal gene transfer (HGT) is a powerful evolutionary force that considerably shapes the structure of prokaryotic genomes and is associated with genomic islands (GIs). A GI is a DNA segment composed of transferred genes that can be found within a prokaryotic genome, obtained through HGT. Much research has focused on detecting GIs in genomes, but here we pursue a new course, which is identifying possible preferred locations of GIs in the prokaryotic genome. Here, we identify the locations of the GIs within prokaryotic genomes to examine patterns in those locations. Prokaryotic GIs were analyzed according to the genome structure that they are located in, whether it be a circular or a linear genome. The analytical investigations employed are: (1) studying the GI locations in relation to the origin of replication (oriC); (2) exploring the distances between GIs; and (3) determining the distribution of GIs across the genomes. For each of the investigations, the analysis was performed on all of the GIs in the data set. Moreover, to void bias caused by the distribution of the genomes represented, the GIs in one genome from each species and the GIs of the most frequent species are also analyzed. Overall, the results showed that there are preferred sites for the GIs in the genome. In the linear genomes, these sites are usually located in the oriC region and terminus region, while in the circular genomes, they are located solely in the terminus region. These results also showed that the distance distribution between the GIs is almost exponential, which proves that GIs have preferred sites within genomes. The oriC and termniuns are preferred sites for the GIs and a possible natural explanation for this could be connected to the content of the oriC region. Moreover, the content of the GIs in terms of its protein families was studied and the results demonstrated that the majority of frequent protein families are close to identical in each section.},
}
@article {pmid38695851,
year = {2024},
author = {Fang, L and Li, M and Zhang, J and Jia, C and Qiang, Y and He, X and Liu, T and Zhou, Q and Luo, D and Han, Y and Li, Z and Liu, W and Yang, Y and Liu, J and Liu, Z},
title = {Chromosome-level genome assembly of Pedicularis kansuensis illuminates genome evolution of facultative parasitic plant.},
journal = {Molecular ecology resources},
volume = {24},
number = {5},
pages = {e13966},
doi = {10.1111/1755-0998.13966},
pmid = {38695851},
issn = {1755-0998},
support = {CCPTZX2023N04//National Grassland Technology Innovation Center (Preparatory) of China/ ; 32201463//National Natural Science Foundation of China/ ; 32071862//National Natural Science Foundation of China/ ; 2023-NK-147//Qinghai Province Talented Scientists Responsibility System Project/ ; },
mesh = {*Genome, Plant/genetics ; *Gene Transfer, Horizontal ; *Pedicularis/genetics ; *Evolution, Molecular ; Genome Size ; Phylogeny ; Chromosomes, Plant/genetics ; Retroelements/genetics ; Tibet ; },
abstract = {Parasitic plants have a heterotrophic lifestyle, in which they withdraw all or part of their nutrients from their host through the haustorium. Despite the release of many draft genomes of parasitic plants, the genome evolution related to the parasitism feature of facultative parasites remains largely unknown. In this study, we present a high-quality chromosomal-level genome assembly for the facultative parasite Pedicularis kansuensis (Orobanchaceae), which invades both legume and grass host species in degraded grasslands on the Qinghai-Tibet Plateau. This species has the largest genome size compared with other parasitic species, and expansions of long terminal repeat retrotransposons accounting for 62.37% of the assembly greatly contributed to the genome size expansion of this species. A total of 42,782 genes were annotated, and the patterns of gene loss in P. kansuensis differed from other parasitic species. We also found many mobile mRNAs between P. kansuensis and one of its host species, but these mobile mRNAs could not compensate for the functional losses of missing genes in P. kansuensis. In addition, we identified nine horizontal gene transfer (HGT) events from rosids and monocots, as well as one single-gene duplication events from HGT genes, which differ distinctly from that of other parasitic species. Furthermore, we found evidence for HGT through transferring genomic fragments from phylogenetically remote host species. Taken together, these findings provide genomic insights into the evolution of facultative parasites and broaden our understanding of the diversified genome evolution in parasitic plants and the molecular mechanisms of plant parasitism.},
}
@article {pmid38695606,
year = {2024},
author = {Wang, X-Q and Du, K and Chen, C and Hou, P and Li, W-F and Chen, Y and Li, Q and Zhou, C-Z},
title = {Profiling the interplay and coevolution of Microcystis aeruginosa and cyanosiphophage Mic1.},
journal = {Microbiology spectrum},
volume = {12},
number = {6},
pages = {e0029824},
pmid = {38695606},
issn = {2165-0497},
support = {32000112//MOST | National Natural Science Foundation of China (NSFC)/ ; U19A2020//MOST | National Natural Science Foundation of China (NSFC)/ ; 2018YFA0903100//Ministry of Science and Technology of the People's Republic of China (MOST)/ ; WK2070000195//MOE | Fundamental Research Funds for the Central Universities (Fundamental Research Fund for the Central Universities)/ ; },
mesh = {*Microcystis/virology/genetics/metabolism ; *Bacteriophages/genetics/physiology ; China ; Transcriptome ; Lakes/microbiology/virology ; Genome, Viral/genetics ; Evolution, Molecular ; },
abstract = {UNLABELLED: The cyanosiphophage Mic1 specifically infects the bloom-forming Microcystis aeruginosa FACHB 1339 from Lake Chaohu, China. Previous genomic analysis showed that its 92,627 bp double-stranded DNA genome consists of 98 putative open reading frames, 63% of which are of unknown function. Here, we investigated the transcriptome dynamics of Mic1 and its host using RNA sequencing. In the early, middle, and late phases of the 10 h lytic cycle, the Mic1 genes are sequentially expressed and could be further temporally grouped into two distinct clusters in each phase. Notably, six early genes, including gp49 that encodes a TnpB-like transposase, immediately reach the highest transcriptional level in half an hour, representing a pioneer cluster that rapidly regulates and redirects host metabolism toward the phage. An in-depth analysis of the host transcriptomic profile in response to Mic1 infection revealed significant upregulation of a polyketide synthase pathway and a type III-B CRISPR system, accompanied by moderate downregulation of the photosynthesis and key metabolism pathways. The constant increase of phage transcripts and relatively low replacement rate over the host transcripts indicated that Mic1 utilizes a unique strategy to gradually take over a small portion of host metabolism pathways after infection. In addition, genomic analysis of a less-infective Mic1 and a Mic1-resistant host strain further confirmed their dynamic interplay and coevolution via the frequent horizontal gene transfer. These findings provide insights into the mutual benefit and symbiosis of the highly polymorphic cyanobacteria M. aeruginosa and cyanophages.<br><br>IMPORTANCE: The highly polymorphic Microcystis aeruginosa is one of the predominant bloom-forming cyanobacteria in eutrophic freshwater bodies and is infected by diverse and abundant cyanophages. The presence of a large number of defense systems in M. aeruginosa genome suggests a dynamic interplay and coevolution with the cyanophages. In this study, we investigated the temporal gene expression pattern of Mic1 after infection and the corresponding transcriptional responses of its host. Moreover, the identification of a less-infective Mic1 and a Mic1-resistant host strain provided the evolved genes in the phage-host coevolution during the multiple-generation cultivation in the laboratory. Our findings enrich the knowledge on the interplay and coevolution of M. aeruginosa and its cyanophages and lay the foundation for the future application of cyanophage as a potential eco-friendly and bio-safe agent in controlling the succession of harmful cyanobacterial blooms.},
}
@article {pmid38695519,
year = {2024},
author = {Garrido, V and Arrieta-Gisasola, A and Migura-García, L and Laorden, L and Grilló, MJ},
title = {Multidrug resistance in Salmonella isolates of swine origin: mobile genetic elements and plasmids associated with cephalosporin resistance with potential transmission to humans.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {5},
pages = {e0026424},
pmid = {38695519},
issn = {1098-5336},
support = {IIQ14061.RI1//Direcci&#xf3;n General de Industria, Energia y Proyectos Estrategicos S3, Gobierno de Navarra (Department of Industry of the Government of Navarra)/ ; PA20/03//Centres de Recerca de Catalunya (CERCA)/ ; Grant PIF-19/290//Basque Country University (UPV/EHU)/ ; },
mesh = {Animals ; Swine/microbiology ; *Plasmids/genetics ; *Salmonella/genetics/drug effects/isolation &amp; purification ; *Interspersed Repetitive Sequences ; *Drug Resistance, Multiple, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Humans ; Cephalosporin Resistance/genetics ; Salmonella Infections, Animal/microbiology ; Spain ; Swine Diseases/microbiology ; Cephalosporins/pharmacology ; Gene Transfer, Horizontal ; },
abstract = {The emergence of foodborne Salmonella strains carrying antimicrobial resistance (AMR) in mobile genetic elements (MGE) is a significant public health threat in a One Health context requiring continuous surveillance. Resistance to ciprofloxacin and cephalosporins is of particular concern. Since pigs are a relevant source of foodborne Salmonella for human beings, we studied transmissible AMR genes and MGE in a collection of 83 strains showing 9 different serovars and 15 patterns of multidrug resistant (MDR) previously isolated from pigs raised in the conventional breeding system of Northern Spain. All isolates were susceptible to ciprofloxacin and three isolates carried blaCMY-2 or blaCTX-M-9 genes responsible for cefotaxime resistance. Filter mating experiments showed that the two plasmids carrying blaCTX-M-9 were conjugative while that carrying blaCMY-2 was self-transmissible by transformation. Whole-genome sequencing and comparative analyses were performed on the isolates and plasmids. The IncC plasmid pSB109, carrying blaCMY-2, was similar to one found in S. Reading from cattle, indicating potential horizontal transfer between serovars and animal sources. The IncHI2 plasmids pSH102 in S. Heidelberg and pSTM45 in S. Typhimurium ST34, carrying blaCTX-M-9, shared similar backbones and two novel "complex class 1 integrons" containing different AMR and heavy metal genes. Our findings emphasize the importance of sequencing techniques to identify emerging AMR regions in conjugative and stable plasmids from livestock production. The presence of MGE carrying clinically relevant AMR genes raises public health concerns, requiring monitoring to mitigate the emergence of bacteria carrying AMR genes and subsequent spread through animals and food.IMPORTANCEThe emergence of foodborne Salmonella strains carrying antimicrobial resistance (AMR) in mobile genetic elements (MGE) is a significant public health threat in a One Health context. Since pigs are a relevant source of foodborne Salmonella for humans, in this study, we investigate different aspects of AMR in a collection of 83 Salmonella showing nine different serovars and 15 patterns of multidrug resistant (MDR) isolated from pigs raised in the conventional breeding system. Our findings emphasize the importance of sequencing techniques to identify emerging AMR regions in conjugative and stable plasmids from livestock production. The presence of MGE carrying clinically relevant AMR genes raises public health concerns, requiring monitoring to mitigate the emergence of bacteria carrying AMR genes and subsequent spread through animals and food.},
}
@article {pmid38695111,
year = {2024},
author = {Van Etten, J and Stephens, TG and Chille, E and Lipzen, A and Peterson, D and Barry, K and Grigoriev, IV and Bhattacharya, D},
title = {Diverse fates of ancient horizontal gene transfers in extremophilic red algae.},
journal = {Environmental microbiology},
volume = {26},
number = {5},
pages = {e16629},
doi = {10.1111/1462-2920.16629},
pmid = {38695111},
issn = {1462-2920},
support = {80NSSC19K0462/NASA/NASA/United States ; 80NSSC19K1542/NASA/NASA/United States ; },
mesh = {*Gene Transfer, Horizontal ; *Rhodophyta/genetics ; *Extremophiles/genetics ; *Arsenic/metabolism ; Mercury/metabolism ; Stress, Physiological/genetics ; Inactivation, Metabolic/genetics ; Evolution, Molecular ; },
abstract = {Horizontal genetic transfer (HGT) is a common phenomenon in eukaryotic genomes. However, the mechanisms by which HGT-derived genes persist and integrate into other pathways remain unclear. This topic is of significant interest because, over time, the stressors that initially favoured the fixation of HGT may diminish or disappear. Despite this, the foreign genes may continue to exist if they become part of a broader stress response or other pathways. The conventional model suggests that the acquisition of HGT equates to adaptation. However, this model may evolve into more complex interactions between gene products, a concept we refer to as the 'Integrated HGT Model' (IHM). To explore this concept further, we studied specialized HGT-derived genes that encode heavy metal detoxification functions. The recruitment of these genes into other pathways could provide clear examples of IHM. In our study, we exposed two anciently diverged species of polyextremophilic red algae from the Galdieria genus to arsenic and mercury stress in laboratory cultures. We then analysed the transcriptome data using differential and coexpression analysis. Our findings revealed that mercury detoxification follows a 'one gene-one function' model, resulting in an indivisible response. In contrast, the arsH gene in the arsenite response pathway demonstrated a complex pattern of duplication, divergence and potential neofunctionalization, consistent with the IHM. Our research sheds light on the fate and integration of ancient HGTs, providing a novel perspective on the ecology of extremophiles.},
}
@article {pmid38694799,
year = {2024},
author = {Zhang, Y and Xue, G and Wang, F and Zhang, J and Xu, L and Yu, C},
title = {The impact of antibiotic exposure on antibiotic resistance gene dynamics in the gut microbiota of inflammatory bowel disease patients.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1382332},
pmid = {38694799},
issn = {1664-302X},
abstract = {BACKGROUND: While antibiotics are commonly used to treat inflammatory bowel disease (IBD), their widespread application can disturb the gut microbiota and foster the emergence and spread of antibiotic resistance. However, the dynamic changes to the human gut microbiota and direction of resistance gene transmission under antibiotic effects have not been clearly elucidated.<br><br>METHODS: Based on the Human Microbiome Project, a total of 90 fecal samples were collected from 30 IBD patients before, during and after antibiotic treatment. Through the analysis workflow of metagenomics, we described the dynamic process of changes in bacterial communities and resistance genes pre-treatment, during and post-treatment. We explored potential consistent relationships between gut microbiota and resistance genes, and established gene transmission networks among species before and after antibiotic use.<br><br>RESULTS: Exposure to antibiotics can induce alterations in the composition of the gut microbiota in IBD patients, particularly a reduction in probiotics, which gradually recovers to a new steady state after cessation of antibiotics. Network analyses revealed intra-phylum transfers of resistance genes, predominantly between taxonomically close organisms. Specific resistance genes showed increased prevalence and inter-species mobility after antibiotic cessation.<br><br>CONCLUSION: This study demonstrates that antibiotics shape the gut resistome through selective enrichment and promotion of horizontal gene transfer. The findings provide insights into ecological processes governing resistance gene dynamics and dissemination upon antibiotic perturbation of the microbiota. Optimizing antibiotic usage may help limit unintended consequences like increased resistance in gut bacteria during IBD management.},
}
@article {pmid38694026,
year = {2024},
author = {Reem, A and Almansoob, S and Senan, AM and Kumar Raj, A and Shah, R and Kumar Shrewastwa, M and Kumal, JPP},
title = {Pseudomonas aeruginosa and related antibiotic resistance genes as indicators for wastewater treatment.},
journal = {Heliyon},
volume = {10},
number = {9},
pages = {e29798},
pmid = {38694026},
issn = {2405-8440},
abstract = {This review aims to examine the existence of Pseudomonas aeruginosa (P. aeruginosa) and their antibiotic resistance genes (ARGs) in aquatic settings and the alternative treatment ways. P. aeruginosa in a various aquatic environment have been identified as contaminants with impacts on human health and the environment. P. aeruginosa resistance to multiple antibiotics, such as sulfamethoxazole, ciprofloxacin, quinolone, trimethoprim, tetracycline, vancomycin, as well as specific antibiotic resistance genes including sul1, qnrs, blaVIM, blaTEM, blaCTX, blaAIM-1, tetA, ampC, blaVIM. The development of resistance can occur naturally, through mutations, or via horizontal gene transfer facilitated by sterilizing agents. In addition, an overview of the current knowledge on inactivation of Pseudomonas aeruginosa and ARG and the mechanisms of action of various disinfection processes in water and wastewater (UV chlorine processes, catalytic oxidation, Fenton reaction, and ozonation) is given. An overview of the effects of nanotechnology and the resulting wetlands is also given.},
}
@article {pmid38693917,
year = {2024},
author = {Filgueiras, JPC and Zámocký, M and Turchetto-Zolet, AC},
title = {Unraveling the evolutionary origin of the P5CS gene: a story of gene fusion and horizontal transfer.},
journal = {Frontiers in molecular biosciences},
volume = {11},
number = {},
pages = {1341684},
pmid = {38693917},
issn = {2296-889X},
abstract = {The accumulation of proline in response to the most diverse types of stress is a widespread defense mechanism. In prokaryotes, fungi, and certain unicellular eukaryotes (green algae), the first two reactions of proline biosynthesis occur through two distinct enzymes, γ-glutamyl kinase (GK E.C. 2.7.2.11) and γ-glutamyl phosphate reductase (GPR E.C. 1.2.1.41), encoded by two different genes, ProB and ProA, respectively. Plants, animals, and a few unicellular eukaryotes carry out these reactions through a single bifunctional enzyme, the Δ[1]-pyrroline-5-carboxylate synthase (P5CS), which has the GK and GPR domains fused. To better understand the origin and diversification of the P5CS gene, we use a robust phylogenetic approach with a broad sampling of the P5CS, ProB and ProA genes, including species from all three domains of life. Our results suggest that the collected P5CS genes have arisen from a single fusion event between the ProA and ProB gene paralogs. A peculiar fusion event occurred in an ancestral eukaryotic lineage and was spread to other lineages through horizontal gene transfer. As for the diversification of this gene family, the phylogeny of the P5CS gene in plants shows that there have been multiple independent processes of duplication and loss of this gene, with the duplications being related to old polyploidy events.},
}
@article {pmid38693486,
year = {2024},
author = {Rork, AM and Bala, AS and Renner, T},
title = {Dynamic evolution of the mTHF gene family associated with primary metabolism across life.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {432},
pmid = {38693486},
issn = {1471-2164},
mesh = {*Evolution, Molecular ; *Phylogeny ; *Methylenetetrahydrofolate Dehydrogenase (NADP)/genetics/metabolism ; *Multigene Family ; Archaea/genetics/metabolism ; Eukaryota/genetics/metabolism ; Metabolic Networks and Pathways/genetics ; Gene Transfer, Horizontal ; },
abstract = {BACKGROUND: The folate cycle of one-carbon (C1) metabolism, which plays a central role in the biosynthesis of nucleotides and amino acids, demonstrates the significance of metabolic adaptation. We investigated the evolutionary history of the methylenetetrahydrofolate dehydrogenase (mTHF) gene family, one of the main drivers of the folate cycle, across life.<br><br>RESULTS: Through comparative genomic and phylogenetic analyses, we found that several lineages of Archaea lacked domains vital for folate cycle function such as the mTHF catalytic and NAD(P)-binding domains of FolD. Within eukaryotes, the mTHF gene family diversified rapidly. For example, several duplications have been observed in lineages including the Amoebozoa, Opisthokonta, and Viridiplantae. In a common ancestor of Opisthokonta, FolD and FTHFS underwent fusion giving rise to the gene MTHFD1, possessing the domains of both genes.<br><br>CONCLUSIONS: Our evolutionary reconstruction of the mTHF gene family associated with a primary metabolic pathway reveals dynamic evolution, including gene birth-and-death, gene fusion, and potential horizontal gene transfer events and/or amino acid convergence.},
}
@article {pmid38692276,
year = {2024},
author = {Li, C and Li, CQ and Chen, ZB and Liu, BQ and Sun, X and Wei, KH and Li, CY and Luan, JB},
title = {Wolbachia symbionts control sex in a parasitoid wasp using a horizontally acquired gene.},
journal = {Current biology : CB},
volume = {34},
number = {11},
pages = {2359-2372.e9},
doi = {10.1016/j.cub.2024.04.035},
pmid = {38692276},
issn = {1879-0445},
mesh = {Animals ; *Wolbachia/physiology/genetics ; *Wasps/physiology/microbiology/genetics ; *Symbiosis/genetics ; Female ; Male ; *Gene Transfer, Horizontal ; Parthenogenesis/genetics ; Insect Proteins/genetics/metabolism ; Sex Determination Processes/genetics ; },
abstract = {Host reproduction can be manipulated by bacterial symbionts in various ways. Parthenogenesis induction is the most effective type of reproduction manipulation by symbionts for their transmission. Insect sex is determined by regulation of doublesex (dsx) splicing through transformer2 (tra2) and transformer (tra) interaction. Although parthenogenesis induction by symbionts has been studied since the 1970s, its underlying molecular mechanism is unknown. Here we identify a Wolbachia parthenogenesis-induction feminization factor gene (piff) that targets sex-determining genes and causes female-producing parthenogenesis in the haplodiploid parasitoid Encarsia formosa. We found that Wolbachia elimination repressed expression of female-specific dsx and enhanced expression of male-specific dsx, which led to the production of wasp haploid male offspring. Furthermore, we found that E. formosa tra is truncated and non-functional, and Wolbachia has a functional tra homolog, termed piff, with an insect origin. Wolbachia PIFF can colocalize and interact with wasp TRA2. Moreover, Wolbachia piff has coordinated expression with tra2 and dsx of E. formosa. Our results demonstrate the bacterial symbiont Wolbachia has acquired an insect gene to manipulate the host sex determination cascade and induce parthenogenesis in wasps. This study reveals insect-to-bacteria horizontal gene transfer drives the evolution of animal sex determination systems, elucidating a striking mechanism of insect-microbe symbiosis.},
}
@article {pmid38692255,
year = {2024},
author = {Li, H and Wang, Q and Wang, Y and Liu, Y and Zhou, J and Wang, T and Zhu, L and Guo, J},
title = {EDTA enables to alleviate impacts of metal ions on conjugative transfer of antibiotic resistance genes.},
journal = {Water research},
volume = {257},
number = {},
pages = {121659},
doi = {10.1016/j.watres.2024.121659},
pmid = {38692255},
issn = {1879-2448},
mesh = {*Edetic Acid/pharmacology/chemistry ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Plasmids ; Metals, Heavy/chemistry ; Escherichia coli/drug effects/genetics ; Metals ; Ions ; },
abstract = {Various heavy metals are reported to be able to accelerate horizontal transfer of antibiotic resistance genes (ARGs). In real water environmental settings, ubiquitous complexing agents would affect the environmental behaviors of heavy metal ions due to the formation of metal-organic complexes. However, little is known whether the presence of complexing agents would change horizontal gene transfer due to heavy metal exposure. This study aimed to fill this gap by investigating the impacts of a typical complexing agent ethylenediaminetetraacetic acid (EDTA) on the conjugative transfer of plasmid-mediated ARGs induced by a range of heavy metal ions. At the environmentally relevant concentration (0.64 mg L[-1]) of metal ions, all the tested metal ions (Mg[2+], Ca[2+], Co[2+], Pb[2+], Ni[2+], Cu[2+], and Fe[3+]) promoted conjugative transfer of ARGs, while an inhibitory effect was observed at a relatively higher concentration (3.20 mg L[-1]). In contrast, EDTA (0.64 mg L[-1]) alleviated the effects of metal ions on ARGs conjugation transfer, evidenced by 11 %-66 % reduction in the conjugate transfer frequency. Molecular docking and dynamics simulations disclosed that this is attributed to the stronger binding of metal ions with the lipids in cell membranes. Under metal-EDTA exposure, gene expressions related to oxidative stress response, cell membrane permeability, intercellular contact, energy driving force, mobilization, and channels of plasmid transfer were suppressed compared with the metal ions exposure. This study offers insights into the alleviation mechanisms of complexing agents on ARGs transfer induced by free metal ions.},
}
@article {pmid38692150,
year = {2024},
author = {Cai, Y and Chen, C and Sun, T and Li, G and Wang, W and Zhao, H and An, T},
title = {Mariculture waters as yet another hotbed for the creation and transfer of new antibiotic-resistant pathogenome.},
journal = {Environment international},
volume = {187},
number = {},
pages = {108704},
doi = {10.1016/j.envint.2024.108704},
pmid = {38692150},
issn = {1873-6750},
mesh = {*Aquaculture ; *Bacteria/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; *RNA, Ribosomal, 16S/genetics ; China ; Water Microbiology ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Microbial/genetics ; Metagenomics ; },
abstract = {With the rapid growth of aquaculture globally, large amounts of antibiotics have been used to treat aquatic disease, which may accelerate induction and spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in aquaculture environments. Herein, metagenomic and 16S rRNA analyses were used to analyze the potentials and co-occurrence patterns of pathogenome (culturable and unculturable pathogens), antibiotic resistome (ARGs), and mobilome (mobile genetic elements (MGEs)) from mariculture waters near 5000 km coast of South China. Total 207 species of pathogens were identified, with only 10 culturable species. Furthermore, more pathogen species were detected in mariculture waters than those in coastal waters, and mariculture waters were prone to become reservoirs of unculturable pathogens. In addition, 913 subtypes of 21 ARG types were also identified, with multidrug resistance genes as the majority. MGEs including plasmids, integrons, transposons, and insertion sequences were abundantly present in mariculture waters. The co-occurrence network pattern between pathogenome, antibiotic resistome, and mobilome suggested that most of pathogens may be potential multidrug resistant hosts, possibly due to high frequency of horizontal gene transfer. These findings increase our understanding of mariculture waters as reservoirs of antibiotic resistome and mobilome, and as yet another hotbed for creation and transfer of new antibiotic-resistant pathogenome.},
}
@article {pmid38689039,
year = {2024},
author = {Shepherd, MJ and Fu, T and Harrington, NE and Kottara, A and Cagney, K and Chalmers, JD and Paterson, S and Fothergill, JL and Brockhurst, MA},
title = {Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance.},
journal = {Nature reviews. Microbiology},
volume = {22},
number = {10},
pages = {650-665},
pmid = {38689039},
issn = {1740-1534},
mesh = {Humans ; *Bacteria/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal ; *Bacterial Infections/microbiology/drug therapy ; Evolution, Molecular ; Mutation ; },
abstract = {The ecological and evolutionary mechanisms of antimicrobial resistance (AMR) emergence within patients and how these vary across bacterial infections are poorly understood. Increasingly widespread use of pathogen genome sequencing in the clinic enables a deeper understanding of these processes. In this Review, we explore the clinical evidence to support four major mechanisms of within-patient AMR emergence in bacteria: spontaneous resistance mutations; in situ horizontal gene transfer of resistance genes; selection of pre-existing resistance; and immigration of resistant lineages. Within-patient AMR emergence occurs across a wide range of host niches and bacterial species, but the importance of each mechanism varies between bacterial species and infection sites within the body. We identify potential drivers of such differences and discuss how ecological and evolutionary analysis could be embedded within clinical trials of antimicrobials, which are powerful but underused tools for understanding why these mechanisms vary between pathogens, infections and individuals. Ultimately, improving understanding of how host niche, bacterial species and antibiotic mode of action combine to govern the ecological and evolutionary mechanism of AMR emergence in patients will enable more predictive and personalized diagnosis and antimicrobial therapies.},
}
@article {pmid38688912,
year = {2024},
author = {Yang, QE and Ma, X and Li, M and Zhao, M and Zeng, L and He, M and Deng, H and Liao, H and Rensing, C and Friman, VP and Zhou, S and Walsh, TR},
title = {Evolution of triclosan resistance modulates bacterial permissiveness to multidrug resistance plasmids and phages.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3654},
pmid = {38688912},
issn = {2041-1723},
support = {32100150//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42277436//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Triclosan/pharmacology ; *Plasmids/genetics ; *Klebsiella pneumoniae/drug effects/genetics/virology ; *Bacteriophages/genetics/physiology ; Drug Resistance, Multiple, Bacterial/genetics ; Mutation ; Gene Transfer, Horizontal ; Whole Genome Sequencing ; Evolution, Molecular ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The horizontal transfer of plasmids has been recognized as one of the key drivers for the worldwide spread of antimicrobial resistance (AMR) across bacterial pathogens. However, knowledge remain limited about the contribution made by environmental stress on the evolution of bacterial AMR by modulating horizontal acquisition of AMR plasmids and other mobile genetic elements. Here we combined experimental evolution, whole genome sequencing, reverse genetic engineering, and transcriptomics to examine if the evolution of chromosomal AMR to triclosan (TCS) disinfectant has correlated effects on modulating bacterial pathogen (Klebsiella pneumoniae) permissiveness to AMR plasmids and phage susceptibility. Herein, we show that TCS exposure increases the evolvability of K. pneumoniae to evolve TCS-resistant mutants (TRMs) by acquiring mutations and altered expression of several genes previously associated with TCS and antibiotic resistance. Notably, nsrR deletion increases conjugation permissiveness of K. pneumoniae to four AMR plasmids, and enhances susceptibility to various Klebsiella-specific phages through the downregulation of several bacterial defense systems and changes in membrane potential with altered reactive oxygen species response. Our findings suggest that unrestricted use of TCS disinfectant imposes a dual impact on bacterial antibiotic resistance by augmenting both chromosomally and horizontally acquired AMR mechanisms.},
}
@article {pmid38688811,
year = {2024},
author = {Szczepankowska, AK and Łobocka, M},
title = {Exploring the role of phage plasmids in gene transfers.},
journal = {Trends in genetics : TIG},
volume = {40},
number = {7},
pages = {555-557},
doi = {10.1016/j.tig.2024.04.011},
pmid = {38688811},
issn = {0168-9525},
mesh = {Bacteria/genetics/virology ; *Bacteriophages/genetics ; *Gene Transfer, Horizontal/genetics ; *Plasmids/genetics ; },
abstract = {Bacteriophages and plasmids drive horizontal gene transfer (HGT) in bacteria. Phage-plasmids (P-Ps) are hybrids of plasmid and phages. Pfeifer and Rocha recently demonstrated that P-Ps can serve as intermediates in gene exchanges between these two types of elements, identified categories of preferentially transferred genes, and reconstructed gene flows involving phage P1-like P-Ps.},
}
@article {pmid38683832,
year = {2024},
author = {Guillén-Chable, F and Valdez Iuit, JO and Avila Castro, LA and Rosas, C and Merino, E and Rodríguez-Escamilla, Z and Martínez-Núñez, MA},
title = {Geographical distribution of mobile genetic elements in microbial communities along the Yucatan coast.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0301642},
pmid = {38683832},
issn = {1932-6203},
mesh = {*Interspersed Repetitive Sequences/genetics ; *Gene Transfer, Horizontal ; *Microbiota/genetics ; Mexico ; Bacteria/genetics/classification ; Proteobacteria/genetics ; },
abstract = {Horizontal gene transfer (HGT) is a well-documented strategy used by bacteria to enhance their adaptability to challenging environmental conditions. Through HGT, a group of conserved genetic elements known as mobile genetic elements (MGEs) is disseminated within bacterial communities. MGEs offer numerous advantages to the host, increasing its fitness by acquiring new functions that help bacteria contend with adverse conditions, including exposure to heavy metal and antibiotics. This study explores MGEs within microbial communities along the Yucatan coast using a metatranscriptomics approach. Prior to this research, nothing was known about the coastal Yucatan's microbial environmental mobilome and HGT processes between these bacterial communities. This study reveals a positive correlation between MGEs and antibiotic resistance genes (ARGs) along the Yucatan coast, with higher MGEs abundance in more contaminated sites. The Proteobacteria and Firmicutes groups exhibited the highest number of MGEs. It's important to highlight that the most abundant classes of MGEs might not be the ones most strongly linked to ARGs, as observed for the recombination/repair class. This work presents the first geographical distribution of the environmental mobilome in Yucatan Peninsula mangroves.},
}
@article {pmid38683670,
year = {2024},
author = {Ferrari, E and Di Benedetto, G and Firrincieli, A and Presentato, A and Frascari, D and Cappelletti, M},
title = {Unravelling the role of the group 6 soluble di-iron monooxygenase (SDIMO) SmoABCD in alkane metabolism and chlorinated alkane degradation.},
journal = {Microbial biotechnology},
volume = {17},
number = {5},
pages = {e14453},
pmid = {38683670},
issn = {1751-7915},
mesh = {*Alkanes/metabolism ; *Mixed Function Oxygenases/metabolism/genetics ; Genetic Complementation Test ; Mutagenesis, Insertional ; Biotransformation ; DNA Transposable Elements ; Hydrocarbons, Chlorinated/metabolism ; },
abstract = {Soluble di-iron monooxygenases (SDIMOs) are multi-component enzymes catalysing the oxidation of various substrates. These enzymes are characterized by high sequence and functional diversity that is still not well understood despite their key role in biotechnological processes including contaminant biodegradation. In this study, we analysed a mutant of Rhodoccocus aetherivorans BCP1 (BCP1-2.10) characterized by a transposon insertion in the gene smoA encoding the alpha subunit of the plasmid-located SDIMO SmoABCD. The mutant BCP1-2.10 showed a reduced capacity to grow on propane, lost the ability to grow on butane, pentane and n-hexane and was heavily impaired in the capacity to degrade chloroform and trichloroethane. The expression of the additional SDIMO prmABCD in BCP1-2.10 probably allowed the mutant to partially grow on propane and to degrade it, to some extent, together with the other short-chain n-alkanes. The complementation of the mutant, conducted by introducing smoABCD in the genome as a single copy under a constitutive promoter or within a plasmid under a thiostreptone-inducible promoter, allowed the recovery of the alkanotrophic phenotype as well as the capacity to degrade chlorinated n-alkanes. The heterologous expression of smoABCD allowed a non-alkanotrophic Rhodococcus strain to grow on pentane and n-hexane when the gene cluster was introduced together with the downstream genes encoding alcohol and aldehyde dehydrogenases and a GroEL chaperon. BCP1 smoA gene was shown to belong to the group 6 SDIMOs, which is a rare group of monooxygenases mostly present in Mycobacterium genus and in a few Rhodococcus strains. SmoABCD originally evolved in Mycobacterium and was then acquired by Rhodococcus through horizontal gene transfer events. This work extends the knowledge of the biotechnologically relevant SDIMOs by providing functional and evolutionary insights into a group 6 SDIMO in Rhodococcus and demonstrating its key role in the metabolism of short-chain alkanes and degradation of chlorinated n-alkanes.},
}
@article {pmid38683013,
year = {2024},
author = {Taylor, AJ and Yahara, K and Pascoe, B and Ko, S and Mageiros, L and Mourkas, E and Calland, JK and Puranen, S and Hitchings, MD and Jolley, KA and Kobras, CM and Bayliss, S and Williams, NJ and van Vliet, AHM and Parkhill, J and Maiden, MCJ and Corander, J and Hurst, LD and Falush, D and Keim, P and Didelot, X and Kelly, DJ and Sheppard, SK},
title = {Epistasis, core-genome disharmony, and adaptation in recombining bacteria.},
journal = {mBio},
volume = {15},
number = {6},
pages = {e0058124},
pmid = {38683013},
issn = {2150-7511},
support = {MR/L015080/1//UKRI | Medical Research Council (MRC)/ ; 088786/C/09/Z//Wellcome Trust (WT)/ ; 2022/23//Cowden Endowment for Food Microbiology/ ; FS101087//Food Standards Agency (FSA)/ ; /WT_/Wellcome Trust/United Kingdom ; BB/S014497/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; MR/M501608/1//UKRI | Medical Research Council (MRC)/ ; },
mesh = {*Epistasis, Genetic ; *Genome, Bacterial ; *Gene Transfer, Horizontal ; *Campylobacter jejuni/genetics ; *Recombination, Genetic ; *Campylobacter coli/genetics ; Evolution, Molecular ; Adaptation, Physiological/genetics ; Adaptation, Biological/genetics ; },
abstract = {Recombination of short DNA fragments via horizontal gene transfer (HGT) can introduce beneficial alleles, create genomic disharmony through negative epistasis, and create adaptive gene combinations through positive epistasis. For non-core (accessory) genes, the negative epistatic cost is likely to be minimal because the incoming genes have not co-evolved with the recipient genome and are frequently observed as tightly linked cassettes with major effects. By contrast, interspecific recombination in the core genome is expected to be rare because disruptive allelic replacement is likely to introduce negative epistasis. Why then is homologous recombination common in the core of bacterial genomes? To understand this enigma, we take advantage of an exceptional model system, the common enteric pathogens Campylobacter jejuni and C. coli that are known for very high magnitude interspecies gene flow in the core genome. As expected, HGT does indeed disrupt co-adapted allele pairings, indirect evidence of negative epistasis. However, multiple HGT events enable recovery of the genome's co-adaption between introgressing alleles, even in core metabolism genes (e.g., formate dehydrogenase). These findings demonstrate that, even for complex traits, genetic coalitions can be decoupled, transferred, and independently reinstated in a new genetic background-facilitating transition between fitness peaks. In this example, the two-step recombinational process is associated with C. coli that are adapted to the agricultural niche.IMPORTANCEGenetic exchange among bacteria shapes the microbial world. From the acquisition of antimicrobial resistance genes to fundamental questions about the nature of bacterial species, this powerful evolutionary force has preoccupied scientists for decades. However, the mixing of genes between species rests on a paradox: 0n one hand, promoting adaptation by conferring novel functionality; on the other, potentially introducing disharmonious gene combinations (negative epistasis) that will be selected against. Taking an interdisciplinary approach to analyze natural populations of the enteric bacteria Campylobacter, an ideal example of long-range admixture, we demonstrate that genes can independently transfer across species boundaries and rejoin in functional networks in a recipient genome. The positive impact of two-gene interactions appears to be adaptive by expanding metabolic capacity and facilitating niche shifts through interspecific hybridization. This challenges conventional ideas and highlights the possibility of multiple-step evolution of multi-gene traits by interspecific introgression.},
}
@article {pmid38682189,
year = {2024},
author = {Almatroudi, A},
title = {Investigating Biofilms: Advanced Methods for Comprehending Microbial Behavior and Antibiotic Resistance.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {29},
number = {4},
pages = {133},
doi = {10.31083/j.fbl2904133},
pmid = {38682189},
issn = {2768-6698},
mesh = {*Biofilms/drug effects/growth &amp; development ; Humans ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Extracellular Polymeric Substance Matrix/metabolism ; Bacteria/genetics/drug effects/metabolism ; },
abstract = {Biofilms, which consist of microorganisms enclosed in an extracellular polymeric material (EPS), hold immense importance in the fields of environmental research, industry, and medicine. They play a significant role in ecosystem dynamics and stability, but they also pose issues such as biofouling, corrosion, and pollution. Biofilms in medical environments are linked to persistent infections and elevated healthcare expenses. The EPS matrix plays a crucial role in maintaining the structural integrity and antibiotic resistance of these structures. The research primarily investigates the role of the EPS matrix in facilitating horizontal gene transfer among biofilm communities, with a particular emphasis on EPS and its impact on this process. The process is recognized as a pivotal mechanism in the emergence of antibiotic resistance, underscoring the crucial function of EPS in the dynamics of biofilms. The analysis also highlights the significant financial constraints caused by biofilms in several industries. Biofilm-associated infections in the healthcare sector result in escalated treatment expenses and extended hospitalization periods. In an industrial context, biofilms have a role in increasing maintenance expenses and product contamination, emphasizing the need for efficient management solutions. This review presents the most recent progress in biofilm research, emphasizing the utilization of sophisticated imaging tools and molecular methodologies. In addition to conventional imaging techniques, the research explores the utilization of sophisticated molecular tools, such as DNA and RNA sequencing, in conjunction with proteomics. These approaches are essential for assessing the genetic and metabolic mechanisms that regulate biofilm development and antibiotic resistance. The review underscores the significance of employing an interdisciplinary methodology in the study of biofilms. By incorporating a range of approaches, such as sophisticated imaging and molecular analysis, a comprehensive understanding of biofilm dynamics may be achieved. This approach also opens up possibilities for developing novel solutions to address the negative impacts of biofilms on health, industry, and the environment.},
}
@article {pmid38678226,
year = {2024},
author = {Alexa, EA and Cobo-Díaz, JF and Renes, E and O Callaghan, TF and Kilcawley, K and Mannion, D and Skibinska, I and Ruiz, L and Margolles, A and Fernández-Gómez, P and Alvarez-Molina, A and Puente-Gómez, P and Crispie, F and López, M and Prieto, M and Cotter, PD and Alvarez-Ordóñez, A},
title = {The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {78},
pmid = {38678226},
issn = {2049-2618},
support = {818368//European Commission under the European Union&#xb4;s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union&#xb4;s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union&#xb4;s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union&#xb4;s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union&#xb4;s Horizon 2020 research and innovation program/ ; AGL2016-78085-P//Ministry of Science and Innovation of the Spanish Government/ ; AGL2016-78085-P//Ministry of Science and Innovation of the Spanish Government/ ; AGL2016-78085-P//Ministry of Science and Innovation of the Spanish Government/ ; },
mesh = {*Cheese/microbiology/standards ; *Food Microbiology ; *Microbiota/physiology ; Gene Transfer, Horizontal/genetics ; Metagenome/genetics ; Drug Resistance, Microbial/genetics ; },
abstract = {BACKGROUND: Artisanal cheeses usually contain a highly diverse microbial community which can significantly impact their quality and safety. Here, we describe a detailed longitudinal study assessing the impact of ripening in three natural caves on the microbiome and resistome succession across three different producers of Cabrales blue-veined cheese.<br><br>RESULTS: Both the producer and cave in which cheeses were ripened significantly influenced the cheese microbiome. Lactococcus and the former Lactobacillus genus, among other taxa, showed high abundance in cheeses at initial stages of ripening, either coming from the raw material, starter culture used, and/or the environment of processing plants. Along cheese ripening in caves, these taxa were displaced by other bacteria, such as Tetragenococcus, Corynebacterium, Brevibacterium, Yaniella, and Staphylococcus, predominantly originating from cave environments (mainly food contact surfaces), as demonstrated by source-tracking analysis, strain analysis at read level, and the characterization of 613 metagenome-assembled genomes. The high abundance of Tetragenococcus koreensis and Tetragenococcus halophilus detected in cheese has not been found previously in cheese metagenomes. Furthermore, Tetragenococcus showed a high level of horizontal gene transfer with other members of the cheese microbiome, mainly with Lactococcus and Staphylococcus, involving genes related to carbohydrate metabolism functions. The resistome analysis revealed that raw milk and the associated processing environments are a rich reservoir of antimicrobial resistance determinants, mainly associated with resistance to aminoglycosides, tetracyclines, and &#x3b2;-lactam antibiotics and harbored by aerobic gram-negative bacteria of high relevance from a safety point of view, such as Escherichia coli, Salmonella enterica, Acinetobacter, and Klebsiella pneumoniae, and that the displacement of most raw milk-associated taxa by cave-associated taxa during ripening gave rise to a significant decrease in the load of ARGs and, therefore, to a safer end product.<br><br>CONCLUSION: Overall, the cave environments represented an important source of non-starter microorganisms which may play a relevant role in the quality and safety of the end products. Among them, we have identified novel taxa and taxa not previously regarded as being dominant components of the cheese microbiome (Tetragenococcus spp.), providing very valuable information for the authentication of this protected designation of origin artisanal cheese. Video Abstract.},
}
@article {pmid38678007,
year = {2024},
author = {Wang, X and Tang, Y and Yue, X and Wang, S and Yang, K and Xu, Y and Shen, Q and Friman, VP and Wei, Z},
title = {The role of rhizosphere phages in soil health.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {5},
pages = {},
pmid = {38678007},
issn = {1574-6941},
support = {2022YFC3501501//National Key Research and Development Program of China/ ; 42325704//National Natural Science Foundation of China/ ; //Nanjing Agricultural University/ ; },
mesh = {*Soil Microbiology ; *Rhizosphere ; *Bacteriophages/genetics ; *Microbiota ; *Bacteria/virology/genetics ; Gene Transfer, Horizontal ; Plants/microbiology/virology ; Ecosystem ; },
abstract = {While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation, and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness, and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.},
}
@article {pmid38669903,
year = {2024},
author = {Liu, H and Al-Dhabi, NA and Jiang, H and Liu, B and Qing, T and Feng, B and Ma, T and Tang, W and Zhang, P},
title = {Toward nitrogen recovery: Co-cultivation of microalgae and bacteria enhances the production of high-value nitrogen-rich cyanophycin.},
journal = {Water research},
volume = {256},
number = {},
pages = {121624},
doi = {10.1016/j.watres.2024.121624},
pmid = {38669903},
issn = {1879-2448},
mesh = {*Nitrogen/metabolism ; *Microalgae/metabolism ; Bacteria/metabolism ; Bioreactors ; Waste Disposal, Fluid/methods ; Wastewater ; Bacterial Proteins ; },
abstract = {The algal-bacterial wastewater treatment process has been proven to be highly efficient in removing nutrients and recovering nitrogen (N). However, the recovery of the valuable N-rich biopolymer, cyanophycin, remains limited. This research explored the synthesis mechanism and recovery potential of cyanophycin within two algal-bacterial symbiotic reactors. The findings reveal that the synergy between algae and bacteria enhances the removal of N and phosphorus. The crude contents of cyanophycin in the algal-bacterial consortia reached 115 and 124 mg/g of mixed liquor suspended solids (MLSS), respectively, showing an increase of 11.7 %-20.4 % (p < 0.001) compared with conventional activated sludge. Among the 170 metagenome-assembled genomes (MAGs) analyzed, 50 were capable of synthesizing cyanophycin, indicating that cyanophycin producers are common in algal-bacterial systems. The compositions of cyanophycin producers in the two algal-bacterial reactors were affected by different lighting initiation time. The study identified two intracellular synthesis pathways for cyanophycin. Approximately 36 MAGs can synthesize cyanophycin de novo using ammonium and glucose, while the remaining 14 MAGs require exogenous arginine for production. Notably, several MAGs with high abundance are capable of assimilating both nitrate and ammonium into cyanophycin, demonstrating a robust N utilization capability. This research also marks the first identification of potential horizontal gene transfer of the cyanophycin synthase encoding gene (cphA) within the wastewater microbial community. This suggests that the spread of cphA could expand the population of cyanophycin producers. The study offers new insights into recycling the high-value N-rich biopolymer cyanophycin, contributing to the advancement of wastewater resource utilization.},
}
@article {pmid38664322,
year = {2024},
author = {Vincent, J and Tenore, A and Mattei, MR and Frunzo, L},
title = {Modelling Plasmid-Mediated Horizontal Gene Transfer in Biofilms.},
journal = {Bulletin of mathematical biology},
volume = {86},
number = {6},
pages = {63},
pmid = {38664322},
issn = {1522-9602},
support = {861088//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; },
mesh = {*Biofilms/growth &amp; development ; *Gene Transfer, Horizontal ; *Plasmids/genetics ; *Mathematical Concepts ; *Models, Biological ; *Models, Genetic ; Conjugation, Genetic ; Anti-Bacterial Agents/pharmacology ; },
abstract = {In this study, we present a mathematical model for plasmid spread in a growing biofilm, formulated as a nonlocal system of partial differential equations in a 1-D free boundary domain. Plasmids are mobile genetic elements able to transfer to different phylotypes, posing a global health problem when they carry antibiotic resistance factors. We model gene transfer regulation influenced by nearby potential receptors to account for recipient-sensing. We also introduce a promotion function to account for trace metal effects on conjugation, based on literature data. The model qualitatively matches experimental results, showing that contaminants like toxic metals and antibiotics promote plasmid persistence by favoring plasmid carriers and stimulating conjugation. Even at higher contaminant concentrations inhibiting conjugation, plasmid spread persists by strongly inhibiting plasmid-free cells. The model also replicates higher plasmid density in biofilm's most active regions.},
}
@article {pmid38658529,
year = {2024},
author = {Xie, O and Zachreson, C and Tonkin-Hill, G and Price, DJ and Lacey, JA and Morris, JM and McDonald, MI and Bowen, AC and Giffard, PM and Currie, BJ and Carapetis, JR and Holt, DC and Bentley, SD and Davies, MR and Tong, SYC},
title = {Overlapping Streptococcus pyogenes and Streptococcus dysgalactiae subspecies equisimilis household transmission and mobile genetic element exchange.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3477},
pmid = {38658529},
issn = {2041-1723},
support = {/WT_/Wellcome Trust/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Streptococcus pyogenes/genetics/isolation &amp; purification/classification ; *Streptococcal Infections/transmission/microbiology ; Humans ; *Streptococcus/genetics/isolation &amp; purification ; *Interspersed Repetitive Sequences/genetics ; *Gene Transfer, Horizontal ; Australia ; Genome, Bacterial/genetics ; Female ; Male ; Child ; Family Characteristics ; Adult ; Child, Preschool ; Adolescent ; Longitudinal Studies ; Drug Resistance, Bacterial/genetics ; Young Adult ; },
abstract = {Streptococcus dysgalactiae subspecies equisimilis (SDSE) and Streptococcus pyogenes share skin and throat niches with extensive genomic homology and horizontal gene transfer (HGT) possibly underlying shared disease phenotypes. It is unknown if cross-species transmission interaction occurs. Here, we conduct a genomic analysis of a longitudinal household survey in remote Australian First Nations communities for patterns of cross-species transmission interaction and HGT. Collected from 4547 person-consultations, we analyse 294 SDSE and 315 S. pyogenes genomes. We find SDSE and S. pyogenes transmission intersects extensively among households and show that patterns of co-occurrence and transmission links are consistent with independent transmission without inter-species interference. We identify at least one of three near-identical cross-species mobile genetic elements (MGEs) carrying antimicrobial resistance or streptodornase virulence genes in 55 (19%) SDSE and 23 (7%) S. pyogenes isolates. These findings demonstrate co-circulation of both pathogens and HGT in communities with a high burden of streptococcal disease, supporting a need to integrate SDSE and S. pyogenes surveillance and control efforts.},
}
@article {pmid38658407,
year = {2024},
author = {Kuwata, K and Sato-Takabe, Y and Nakai, R and Sugimura, Y and Tazato, N and Kunihiro, T and Morohoshi, S and Iwataki, M and Hamasaki, K and Shiozaki, T},
title = {Novel aerobic anoxygenic phototrophic bacterium Jannaschia pagri sp. nov., isolated from seawater around a fish farm.},
journal = {Antonie van Leeuwenhoek},
volume = {117},
number = {1},
pages = {70},
pmid = {38658407},
issn = {1572-9699},
support = {80635839//MEXT Grants-in-Aid for Young Scientists/ ; JP19H04263//JSPS KAKENHI/ ; },
mesh = {*Phylogeny ; *Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; Japan ; Aquaculture ; DNA, Bacterial/genetics ; Photosynthesis ; Bacterial Typing Techniques ; Aerobiosis ; Animals ; Bacteriochlorophyll A/analysis ; },
abstract = {The genus Jannaschia is one of the representatives of aerobic anoxygenic phototrophic (AAP) bacteria, which is a strictly aerobic bacterium, producing a photosynthetic pigment bacteriochlorophyll (BChl) a. However, a part of the genus Jannaschia members have not been confirmed the photosynthetic ability. The partly presence of the ability in the genus Jannaschia could suggest the complexity of evolutionary history for anoxygenic photosynthesis in the genus, which is expected as gene loss and/or horizontal gene transfer. Here a novel AAP bacterium designated as strain AI_62[T] (= DSM 115720[ T] = NBRC 115938[ T]), was isolated from coastal seawater around a fish farm in the Uwa Sea, Japan. Its closest relatives were identified as Jannaschia seohaensis SMK-146[ T] (95.6% identity) and J. formosa 12N15[T] (94.6% identity), which have been reported to produce BChl a. The genomic characteristic of strain AI_62[T] clearly showed the possession of the anoxygenic photosynthesis related gene sets. This could be a useful model organism to approach the evolutionary mystery of anoxygenic photosynthesis in the genus Jannaschia. Based on a comprehensive consideration of both phylogenetic and phenotypic characteristics, we propose the classification of a novel species within the genus Jannaschia, designated as Jannaschia pagri sp. nov. The type strain for this newly proposed species is AI_62[T] (= DSM 115720[ T] = NBRC 115938[ T]).},
}
@article {pmid38657817,
year = {2024},
author = {Gong, W and Guo, L and Huang, C and Xie, B and Jiang, M and Zhao, Y and Zhang, H and Wu, Y and Liang, H},
title = {A systematic review of antibiotics and antibiotic resistance genes (ARGs) in mariculture wastewater: Antibiotics removal by microalgal-bacterial symbiotic system (MBSS), ARGs characterization on the metagenomic.},
journal = {The Science of the total environment},
volume = {930},
number = {},
pages = {172601},
doi = {10.1016/j.scitotenv.2024.172601},
pmid = {38657817},
issn = {1879-1026},
mesh = {*Wastewater/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Microalgae/genetics/physiology ; Waste Disposal, Fluid/methods ; Bacteria ; Metagenomics ; Aquaculture ; Water Pollutants, Chemical/analysis ; Symbiosis ; Genes, Bacterial ; },
abstract = {Antibiotic residues in mariculture wastewater seriously affect the aquatic environment. Antibiotic Resistance Genes (ARGs) produced under antibiotic stress flow through the environment and eventually enter the human body, seriously affecting human health. Microalgal-bacterial symbiotic system (MBSS) can remove antibiotics from mariculture and reduce the flow of ARGs into the environment. This review encapsulates the present scenario of mariculture wastewater, the removal mechanism of MBSS for antibiotics, and the biomolecular information under metagenomic assay. When confronted with antibiotics, there was a notable augmentation in the extracellular polymeric substances (EPS) content within MBSS, along with a concurrent elevation in the proportion of protein (PN) constituents within the EPS, which limits the entry of antibiotics into the cellular interior. Quorum sensing stimulates the microorganisms to produce biological responses (DNA synthesis - for adhesion) through signaling. Oxidative stress promotes gene expression (coupling, conjugation) to enhance horizontal gene transfer (HGT) in MBSS. The microbial community under metagenomic detection is dominated by aerobic bacteria in the bacterial-microalgal system. Compared to aerobic bacteria, anaerobic bacteria had the significant advantage of decreasing the distribution of ARGs. Overall, MBSS exhibits remarkable efficacy in mitigating the challenges posed by antibiotics and resistant genes from mariculture wastewater.},
}
@article {pmid38651513,
year = {2025},
author = {Gomathinayagam, S and Kodiveri Muthukaliannan, G},
title = {Dynamics of antibiotic resistance genes in plasmids and bacteriophages.},
journal = {Critical reviews in microbiology},
volume = {51},
number = {2},
pages = {219-228},
doi = {10.1080/1040841X.2024.2339262},
pmid = {38651513},
issn = {1549-7828},
mesh = {*Plasmids/genetics ; *Bacteriophages/genetics ; *Bacteria/genetics/virology/drug effects ; Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Prophages/genetics ; },
abstract = {This brief review explores the intricate interplay between bacteriophages and plasmids in the context of antibiotic resistance gene (ARG) dissemination. Originating from studies in the late 1950s, the review traces the evolution of knowledge regarding extrachromosomal factors facilitating horizontal gene transfer and adaptation in bacteria. Analyzing the gene repertoires of plasmids and bacteriophages, the study highlights their contributions to bacterial evolution and adaptation. While plasmids encode essential and accessory genes influencing host characteristics, bacteriophages carry auxiliary metabolic genes (AMGs) that augment host metabolism. The debate on phages carrying ARGs is explored through a critical evaluation of various studies, revealing contrasting findings from researchers. Additionally, the review addresses the interplay between prophages and plasmids, underlining their similarities and divergences. Based on the available literature evidence, we conclude that plasmids generally encode ARGs while bacteriophages typically do not contain ARGs. But extra-chromosomaly present prophages with plasmid characteristics can encode and disseminate ARGs.},
}
@article {pmid38648967,
year = {2024},
author = {Se, J and Xie, Y and Ma, Q and Zhu, L and Fu, Y and Xu, X and Shen, C and Nannipieri, P},
title = {Drying-wetting cycle enhances stress resistance of Escherichia coli O157:H7 in a model soil.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {350},
number = {},
pages = {123988},
doi = {10.1016/j.envpol.2024.123988},
pmid = {38648967},
issn = {1873-6424},
mesh = {*Escherichia coli O157/physiology ; *Soil Microbiology ; *Soil/chemistry ; Stress, Physiological ; Proteomics ; },
abstract = {Outbreaks of Escherichia coli (E. coli) O157:H7 in farms are often triggered by heavy rains and flooding. Most cells die with the decreasing of soil moisture, while few cells enter a dormant state and then resuscitate after rewetting. The resistance of dormant cells to stress has been extensively studied, whereas the molecular mechanisms of the cross-resistance development of the resuscitated cells are poorly known. We performed a comparative proteomic analysis on O157:H7 before and after undergoing soil dry-wet alternation. A differential expression of 820 proteins was identified in resuscitated cells compared to exponential-phase cells, as determined by proteomics analysis. The GO and KEGG pathway enrichment analyses revealed that up-regulated proteins were associated with oxidative phosphorylation, glycolysis/gluconeogenesis, the citrate cycle (TCA cycle), aminoacyl-tRNA biosynthesis, ribosome activity, and transmembrane transporters, indicating increased energy production and protein synthesis in resuscitated O157:H7. Moreover, proteins related to acid, osmotic, heat, oxidative, antibiotic stress and horizontal gene transfer efficiency were up-regulated, suggesting a potential improvement in stress resistance. Subsequent validation experiments demonstrated that the survival rates of the resuscitated cells were 476.54 and 7786.34 times higher than the exponential-phase cells, with pH levels of 1.5 and 2.5, respectively. Similarly, resuscitated cells showed higher survival rates under osmotic stress, with 7.5%, 15%, and 30% NaCl resulting in survival rates that were 460.58, 1974.55, and 3475.31 times higher. Resuscitated cells also exhibited increased resistance to heat stress, with survival rates 69.64 and 139.72 times higher at 55 °C and 90 °C, respectively. Furthermore, the horizontal gene transfer (HGT) efficiency of resuscitated cells was significantly higher (153.12-fold) compared to exponential phase cells. This study provides new insights into bacteria behavior under changing soil moisture and this may explain O157:H7 outbreaks following rainfall and flooding, as the dry-wet cycle promotes stress cross-resistance development.},
}
@article {pmid38647527,
year = {2024},
author = {Ruhluel, D and Fisher, L and Barton, TE and Leighton, H and Kumar, S and Amores Morillo, P and O'Brien, S and Fothergill, JL and Neill, DR},
title = {Secondary messenger signalling influences Pseudomonas aeruginosa adaptation to sinus and lung environments.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38647527},
issn = {1751-7370},
support = {//UK Cystic Fibrosis Trust/ ; SRC 022//Strategic Research Centre/ ; //CF Foundation/ ; 204457/Z/16/Z//Wellcome and Royal Society Sir Henry Dale/ ; /WT_/Wellcome Trust/United Kingdom ; NC/S001700/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; NC/S00100/1//NC3Rs/ ; },
mesh = {*Pseudomonas aeruginosa/genetics/physiology/metabolism ; *Pseudomonas Infections/microbiology ; *Adaptation, Physiological ; *Biofilms/growth &amp; development ; Animals ; Lung/microbiology ; Fimbriae, Bacterial/genetics/metabolism ; Second Messenger Systems ; Cystic Fibrosis/microbiology ; Mice ; Humans ; Anti-Bacterial Agents/pharmacology ; Cyclic GMP/metabolism/analogs &amp; derivatives ; Mutation ; Phenotype ; },
abstract = {Pseudomonas aeruginosa is a cause of chronic respiratory tract infections in people with cystic fibrosis (CF), non-CF bronchiectasis, and chronic obstructive pulmonary disease. Prolonged infection allows the accumulation of mutations and horizontal gene transfer, increasing the likelihood of adaptive phenotypic traits. Adaptation is proposed to arise first in bacterial populations colonizing upper airway environments. Here, we model this process using an experimental evolution approach. Pseudomonas aeruginosa PAO1, which is not airway adapted, was serially passaged, separately, in media chemically reflective of upper or lower airway environments. To explore whether the CF environment selects for unique traits, we separately passaged PAO1 in airway-mimicking media with or without CF-specific factors. Our findings demonstrated that all airway environments-sinus and lungs, under CF and non-CF conditions-selected for loss of twitching motility, increased resistance to multiple antibiotic classes, and a hyper-biofilm phenotype. These traits conferred increased airway colonization potential in an in vivo model. CF-like conditions exerted stronger selective pressures, leading to emergence of more pronounced phenotypes. Loss of twitching was associated with mutations in type IV pili genes. Type IV pili mediate surface attachment, twitching, and induction of cAMP signalling. We additionally identified multiple evolutionary routes to increased biofilm formation involving regulation of cyclic-di-GMP signalling. These included the loss of function mutations in bifA and dipA phosphodiesterase genes and activating mutations in the siaA phosphatase. These data highlight that airway environments select for traits associated with sessile lifestyles and suggest upper airway niches support emergence of phenotypes that promote establishment of lung infection.},
}
@article {pmid38643972,
year = {2024},
author = {Kogay, R and Wolf, YI and Koonin, EV},
title = {Defence systems and horizontal gene transfer in bacteria.},
journal = {Environmental microbiology},
volume = {26},
number = {4},
pages = {e16630},
pmid = {38643972},
issn = {1462-2920},
support = {Z01 LM000073/ImNIH/Intramural NIH HHS/United States ; },
mesh = {*Gene Transfer, Horizontal/genetics ; *Bacteria/classification/genetics ; Interspersed Repetitive Sequences/genetics ; CRISPR-Cas Systems/genetics ; Lysogeny/genetics ; Species Specificity ; Evolution, Molecular ; },
abstract = {Horizontal gene transfer (HGT) is a fundamental process in prokaryotic evolution, contributing significantly to diversification and adaptation. HGT is typically facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages, which often impose fitness costs on their hosts. However, a considerable number of bacterial genes are involved in defence mechanisms that limit the propagation of MGEs, suggesting they may actively restrict HGT. In our study, we investigated whether defence systems limit HGT by examining the relationship between the HGT rate and the presence of 73 defence systems across 12 bacterial species. We discovered that only six defence systems, three of which were different CRISPR-Cas subtypes, were associated with a reduced gene gain rate at the species evolution scale. Hosts of these defence systems tend to have a smaller pangenome size and fewer phage-related genes compared to genomes without these systems. This suggests that these defence mechanisms inhibit HGT by limiting prophage integration. We hypothesize that the restriction of HGT by defence systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and the fitness effect of HGT in bacterial populations.},
}
@article {pmid38643216,
year = {2024},
author = {Bartoš, O and Chmel, M and Swierczková, I},
title = {The overlooked evolutionary dynamics of 16S rRNA revises its role as the "gold standard" for bacterial species identification.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9067},
pmid = {38643216},
issn = {2045-2322},
support = {MO1012//Ministry of Defence, Czech Republic/ ; },
mesh = {RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Biological Evolution ; Sequence Analysis, DNA ; },
abstract = {The role of 16S rRNA has been and largely remains crucial for the identification of microbial organisms. Although 16S rRNA could certainly be described as one of the most studied sequences ever, the current view of it remains somewhat ambiguous. While some consider 16S rRNA to be a variable marker with resolution power down to the strain level, others consider them to be living fossils that carry information about the origin of domains of cellular life. We show that 16S rRNA is clearly an evolutionarily very rigid sequence, making it a largely unique and irreplaceable marker, but its applicability beyond the genus level is highly limited. Interestingly, it seems that the evolutionary rigidity is not driven by functional constraints of the sequence (RNA-protein interactions), but rather results from the characteristics of the host organism. Our results suggest that, at least in some lineages, Horizontal Gene Transfer (HGT) within genera plays an important role for the evolutionary non-dynamics (stasis) of 16S rRNA. Such genera exhibit an apparent lack of diversification at the 16S rRNA level in comparison to the rest of a genome. However, why it is limited specifically and solely to 16S rRNA remains enigmatic.},
}
@article {pmid38642082,
year = {2024},
author = {Singh, CK and Sodhi, KK and Shree, P and Nitin, V},
title = {Heavy Metals as Catalysts in the Evolution of Antimicrobial Resistance and the Mechanisms Underpinning Co-selection.},
journal = {Current microbiology},
volume = {81},
number = {6},
pages = {148},
pmid = {38642082},
issn = {1432-0991},
mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; *Metals, Heavy ; Bacteria/genetics ; *Environmental Pollutants ; },
abstract = {The menace caused by antibiotic resistance in bacteria is acknowledged on a global scale. Concerns over the same are increasing because of the selection pressure exerted by a huge number of different antimicrobial agents, including heavy metals. Heavy metals are non-metabolizable and recalcitrant to degradation, therefore the bacteria can expel the pollutants out of the system and make it less harmful via different mechanisms. The selection of antibiotic-resistant bacteria may be influenced by heavy metals present in environmental reservoirs. Through co-resistance and cross-resistance processes, the presence of heavy metals in the environment can act as co-selecting agents, hence increasing resistance to both heavy metals and antibiotics. The horizontal gene transfer or mutation assists in the selection of mutant bacteria resistant to the polluted environment. Hence, bioremediation and biodegradation are sustainable methods for the natural clean-up of pollutants. This review sheds light on the occurrence of metal and antibiotic resistance in the environment via the co-resistance and cross-resistance mechanisms underpinning co-selection emphasizing the dearth of studies that specifically examine the method of co-selection in clinical settings. Furthermore, it is advised that future research incorporate both culture- and molecular-based methodologies to further our comprehension of the mechanisms underlying bacterial co- and cross-resistance to antibiotics and heavy metals.},
}
@article {pmid38641304,
year = {2024},
author = {Sha, G and Wu, Z and Chen, T and Zhang, G and Shen, J and Zhao, X and Wang, L},
title = {Mechanisms for more efficient antibiotics and antibiotic resistance genes removal during industrialized treatment of over 200 tons of tylosin and spectinomycin mycelial dregs by integrated meta-omics.},
journal = {Bioresource technology},
volume = {401},
number = {},
pages = {130715},
doi = {10.1016/j.biortech.2024.130715},
pmid = {38641304},
issn = {1873-2976},
mesh = {*Tylosin/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Fermentation ; *Spectinomycin/pharmacology ; Mycelium/drug effects ; Drug Resistance, Microbial/genetics/drug effects ; Biodegradation, Environmental ; Genes, Bacterial ; },
abstract = {To mitigate the environmental risks posed by the accumulation of antibiotic mycelial dregs (AMDs), this study first attempted over 200 tons of mass production fermentation (MP) using tylosin and spectinomycin mycelial dregs alongside pilot-scale fermentation (PS) for comparison, utilizing the integrated-omics and qPCR approaches. Co-fermentation results showed that both antibiotics were effectively removed in all treatments, with an average removal rate of 92%. Antibiotic resistance gene (ARG)-related metabolic pathways showed that rapid degradation of antibiotics was associated with enzymes that inactivate macrolides and aminoglycosides (e.g., K06979, K07027, K05593). Interestingly, MP fermentations with optimized conditions had more efficient ARGs removal because homogenization permitted faster microbial succession, with more stable removal of antibiotic resistant bacteria and mobile genetic elements. Moreover, Bacillus reached 75% and secreted antioxidant enzymes that might inhibit horizontal gene transfer of ARGs. The findings confirmed the advantages of MP fermentation and provided a scientific basis for other AMDs.},
}
@article {pmid38641198,
year = {2024},
author = {Ouzounis, CA},
title = {The Net of Life, a short story: Intricate patterns of gene flows across hundreds of extant genomes, all the way to LUCA.},
journal = {Bio Systems},
volume = {239},
number = {},
pages = {105199},
doi = {10.1016/j.biosystems.2024.105199},
pmid = {38641198},
issn = {1872-8324},
mesh = {Animals ; Humans ; *Evolution, Molecular ; *Gene Flow ; Gene Transfer, Horizontal ; *Genome/genetics ; Models, Genetic ; Phylogeny ; },
abstract = {Over the past quarter-century, the field of evolutionary biology has been transformed by the emergence of complete genome sequences and the conceptual framework known as the 'Net of Life.' This paradigm shift challenges traditional notions of evolution as a tree-like process, emphasizing the complex, interconnected network of gene flow that may blur the boundaries between distinct lineages. In this context, gene loss, rather than horizontal gene transfer, is the primary driver of gene content, with vertical inheritance playing a principal role. The 'Net of Life' not only impacts our understanding of genome evolution but also has profound implications for classification systems, the rapid appearance of new traits, and the spread of diseases. Here, we explore the core tenets of the 'Net of Life' and its implications for genome-scale phylogenetic divergence, providing a comprehensive framework for further investigations in evolutionary biology.},
}
@article {pmid38641137,
year = {2024},
author = {De, R and Jani, M and Azad, RK},
title = {DICEP: An integrative approach to augmenting genomic island detection.},
journal = {Journal of biotechnology},
volume = {388},
number = {},
pages = {49-58},
doi = {10.1016/j.jbiotec.2024.04.011},
pmid = {38641137},
issn = {1873-4863},
mesh = {*Genomic Islands/genetics ; *Genome, Bacterial/genetics ; Bacteria/genetics ; Genomics/methods ; Phylogeny ; Software ; Computational Biology/methods ; },
abstract = {Mobilization of clusters of genes called genomic islands (GIs) across bacterial lineages facilitates dissemination of traits, such as, resistance against antibiotics, virulence or hypervirulence, and versatile metabolic capabilities. Robust delineation of GIs is critical to understanding bacterial evolution that has a vast impact on different life forms. Methods for identification of GIs exploit different evolutionary features or signals encoded within the genomes of bacteria, however, the current state-of-the-art in GI detection still leaves much to be desired. Here, we have taken a combinatorial approach that accounted for GI specific features such as compositional bias, aberrant phyletic pattern, and marker gene enrichment within an integrative framework to delineate GIs in bacterial genomes. Our GI prediction tool, DICEP, was assessed on simulated genomes and well-characterized bacterial genomes. DICEP compared favorably with current GI detection tools on real and synthetic datasets.},
}
@article {pmid38641096,
year = {2024},
author = {Liu, Y and Chu, K and Hua, Z and Li, Q and Lu, Y and Ye, F and Dong, Y and Li, X},
title = {Dynamics of antibiotic resistance genes in the sediments of a water-diversion lake and its human exposure risk behaviour.},
journal = {The Science of the total environment},
volume = {929},
number = {},
pages = {172563},
doi = {10.1016/j.scitotenv.2024.172563},
pmid = {38641096},
issn = {1879-1026},
mesh = {*Drug Resistance, Microbial/genetics ; Lakes/microbiology ; Environmental Monitoring/methods ; Humans ; *Environmental Exposure/statistics &amp; numerical data ; Geologic Sediments/microbiology ; Water Pollution/statistics &amp; numerical data ; Spatio-Temporal Analysis ; Gene Transfer, Horizontal ; China ; },
abstract = {The dynamics and exposure risk behaviours of antibiotic resistance genes (ARGs) in the sediments of water-diversion lakes remain poorly understood. In this study, spatiotemporal investigations of ARG profiles in sediments targeting non-water (NWDP) and water diversion periods (WDP) were conducted in Luoma Lake, a typical water-diversion lake, and an innovative dynamics-based risk assessment framework was constructed to evaluate ARG exposure risks to local residents. ARGs in sediments were significantly more abundant in the WDP than in the NWDP, but there was no significant variation in their spatial distribution in either period. Moreover, the pattern of ARG dissemination in sediments was unchanged between the WDP and NWDP, with horizontal gene transfer (HGT) and vertical gene transfer (VGT) contributing to ARG dissemination in both periods. However, water diversion altered the pattern in lake water, with HGT and VGT in the NWDP but only HGT in the WDP, which were critical pathways for the dissemination of ARGs. The significantly lower ARG sediment-water partition coefficient in the WDP indicated that water diversion could shift the fate of ARGs and facilitate their aqueous partitioning. Risk assessment showed that all age groups faced a higher human exposure risk of ARGs (HERA) in the WDP than in the NWDP, with the 45-59 age group having the highest risk. Furthermore, HERA increased overall with the bacterial carrying capacity in the local environment and peaked when the carrying capacity reached three (NWDP) or four (WDP) orders of magnitude higher than the observed bacterial population. HGT and VGT promoted, whereas ODF covering gene mutation and loss mainly reduced HERA in the lake. As the carrying capacity increased, the relative contribution of ODF to HERA remained relatively stable, whereas the dominant mechanism of HERA development shifted from HGT to VGT.},
}
@article {pmid38640666,
year = {2024},
author = {Xie, S and Hamid, N and Zhang, T and Zhang, Z and Peng, L},
title = {Unraveling the nexus: Microplastics, antibiotics, and ARGs interactions, threats and control in aquaculture - A review.},
journal = {Journal of hazardous materials},
volume = {471},
number = {},
pages = {134324},
doi = {10.1016/j.jhazmat.2024.134324},
pmid = {38640666},
issn = {1873-3336},
mesh = {*Aquaculture ; *Microplastics/toxicity ; *Anti-Bacterial Agents ; *Water Pollutants, Chemical/analysis ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Wastewater/chemistry ; },
abstract = {In recent years, aquaculture has expanded rapidly to address food scarcity and provides high-quality aquatic products. However, this growth has led to the release of significant effluents, containing emerging contaminants like antibiotics, microplastics (MPs), and antibiotic resistance genes (ARGs). This study investigated the occurrence and interactions of these pollutants in aquaculture environment. Combined pollutants, such as MPs and coexisting adsorbents, were widespread and could include antibiotics, heavy metals, resistance genes, and pathogens. Elevated levels of chemical pollutants on MPs could lead to the emergence of resistance genes under selective pressure, facilitated by bacterial communities and horizontal gene transfer (HGT). MPs acted as vectors, transferring pollutants into the food web. Various technologies, including membrane technology, coagulation, and advanced oxidation, have been trialed for pollutants removal, each with its benefits and drawbacks. Future research should focus on ecologically friendly treatment technologies for emerging contaminants in aquaculture wastewater. This review provided insights into understanding and addressing newly developing toxins, aiming to develop integrated systems for effective aquaculture wastewater treatment.},
}
@article {pmid38638913,
year = {2024},
author = {Liu, F and Luo, Y and Xu, T and Lin, H and Qiu, Y and Li, B},
title = {Current examining methods and mathematical models of horizontal transfer of antibiotic resistance genes in the environment.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1371388},
pmid = {38638913},
issn = {1664-302X},
abstract = {The increasing prevalence of antibiotic resistance genes (ARGs) in the environment has garnered significant attention due to their health risk to human beings. Horizontal gene transfer (HGT) is considered as an important way for ARG dissemination. There are four general routes of HGT, including conjugation, transformation, transduction and vesiduction. Selection of appropriate examining methods is crucial for comprehensively understanding characteristics and mechanisms of different HGT ways. Moreover, combined with the results obtained from different experimental methods, mathematical models could be established and serve as a powerful tool for predicting ARG transfer dynamics and frequencies. However, current reviews of HGT for ARG spread mainly focus on its influencing factors and mechanisms, overlooking the important roles of examining methods and models. This review, therefore, delineated four pathways of HGT, summarized the strengths and limitations of current examining methods, and provided a comprehensive summing-up of mathematical models pertaining to three main HGT ways of conjugation, transformation and transduction. Finally, deficiencies in current studies were discussed, and proposed the future perspectives to better understand and assess the risks of ARG dissemination through HGT.},
}
@article {pmid38638826,
year = {2024},
author = {Nasrollahian, S and Graham, JP and Halaji, M},
title = {A review of the mechanisms that confer antibiotic resistance in pathotypes of E. coli.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1387497},
pmid = {38638826},
issn = {2235-2988},
mesh = {Humans ; *Escherichia coli/genetics ; *Escherichia coli Infections/drug therapy ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology/therapeutic use ; beta-Lactamases/genetics ; Drug Resistance, Microbial ; },
abstract = {The dissemination of antibiotic resistance in Escherichia coli poses a significant threat to public health worldwide. This review provides a comprehensive update on the diverse mechanisms employed by E. coli in developing resistance to antibiotics. We primarily focus on pathotypes of E. coli (e.g., uropathogenic E. coli) and investigate the genetic determinants and molecular pathways that confer resistance, shedding light on both well-characterized and recently discovered mechanisms. The most prevalent mechanism continues to be the acquisition of resistance genes through horizontal gene transfer, facilitated by mobile genetic elements such as plasmids and transposons. We discuss the role of extended-spectrum β-lactamases (ESBLs) and carbapenemases in conferring resistance to β-lactam antibiotics, which remain vital in clinical practice. The review covers the key resistant mechanisms, including: 1) Efflux pumps and porin mutations that mediate resistance to a broad spectrum of antibiotics, including fluoroquinolones and aminoglycosides; 2) adaptive strategies employed by E. coli, including biofilm formation, persister cell formation, and the activation of stress response systems, to withstand antibiotic pressure; and 3) the role of regulatory systems in coordinating resistance mechanisms, providing insights into potential targets for therapeutic interventions. Understanding the intricate network of antibiotic resistance mechanisms in E. coli is crucial for the development of effective strategies to combat this growing public health crisis. By clarifying these mechanisms, we aim to pave the way for the design of innovative therapeutic approaches and the implementation of prudent antibiotic stewardship practices to preserve the efficacy of current antibiotics and ensure a sustainable future for healthcare.},
}
@article {pmid38626826,
year = {2024},
author = {Zhang, J and Zhao, L and Wang, W and Zhang, Q and Wang, XT and Xing, DF and Ren, NQ and Lee, DJ and Chen, C},
title = {Large language model for horizontal transfer of resistance gene: From resistance gene prevalence detection to plasmid conjugation rate evaluation.},
journal = {The Science of the total environment},
volume = {931},
number = {},
pages = {172466},
doi = {10.1016/j.scitotenv.2024.172466},
pmid = {38626826},
issn = {1879-1026},
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; Conjugation, Genetic ; Drug Resistance, Bacterial/genetics ; Pseudomonas/genetics ; },
abstract = {The burgeoning issue of plasmid-mediated resistance genes (ARGs) dissemination poses a significant threat to environmental integrity. However, the prediction of ARGs prevalence is overlooked, especially for emerging ARGs that are potentially evolving gene exchange hotspot. Here, we explored to classify plasmid or chromosome sequences and detect resistance gene prevalence by using DNABERT. Initially, the DNABERT fine-tuned in plasmid and chromosome sequences followed by multilayer perceptron (MLP) classifier could achieve 0.764 AUC (Area under curve) on external datasets across 23 genera, outperforming 0.02 AUC than traditional statistic-based model. Furthermore, Escherichia, Pseudomonas single genera based model were also be trained to explore its predict performance to ARGs prevalence detection. By integrating K-mer frequency attributes, our model could boost the performance to predict the prevalence of ARGs in an external dataset in Escherichia with 0.0281-0.0615 AUC and Pseudomonas with 0.0196-0.0928 AUC. Finally, we established a random forest model aimed at forecasting the relative conjugation transfer rate of plasmids with 0.7956 AUC, drawing on data from existing literature. It identifies the plasmid's repression status, cellular density, and temperature as the most important factors influencing transfer frequency. With these two models combined, they provide useful reference for quick and low-cost integrated evaluation of resistance gene transfer, accelerating the process of computer-assisted quantitative risk assessment of ARGs transfer in environmental field.},
}
@article {pmid38626743,
year = {2024},
author = {Sewell, HL and Criddle, CS and Woo, SG and Kim, S and Müller, JA and Kaster, AK},
title = {Pseudomonas stutzeri KC carries the pdt genes for carbon tetrachloride degradation on an integrative and conjugative element.},
journal = {Microbial physiology},
volume = {},
number = {},
pages = {},
doi = {10.1159/000538783},
pmid = {38626743},
issn = {2673-1673},
abstract = {Pseudomonas stutzeri KC can rapidly degrade carbon tetrachloride (CCl4) to CO2 by a fortuitous reaction with pyridine-2,6-bis(thiocarboxylic acid), a metal chelator encoded by pdt genes. These genes were first identified after a spontaneous mutant, strain CTN1, lost the ability to degrade CCl4. Here we report the complete genome of strain KC and show that these pdt genes are located on an integrative and conjugative element (ICE), designated ICEPsstKC. Comparative genome analyses revealed homologues of pdt genes in genomes of members of other gammaproteobacterial orders. Discrepancies between the tree topologies of the deduced pdt gene products and the host phylogeny based on 16S rRNA provided evidence for horizontal gene transfer (HGT) in several sequenced strains of these orders. In addition to ICEPsstKC, HGT may be have been facilitated by other mobile genetic elements, as indicated by the location of the pdt gene cluster adjacent to fragments of other ICEs and prophages in several genome assemblies. We could here show that the majority of cells from the culture collection DSMZ had lost the ICE. The presence of the pdt gene cluster on mobile genetic elements has important implications for the bioremediation of CCl4 for bioremediation of CCl4 and needs consideration when selecting suitable strains.},
}
@article {pmid38618896,
year = {2024},
author = {Peng, X and Zhou, J and Lan, Z and Tan, R and Chen, T and Shi, D and Li, H and Yang, Z and Zhou, S and Jin, M and Li, JW and Yang, D},
title = {Carbonaceous particulate matter promotes the horizontal transfer of antibiotic resistance genes.},
journal = {Environmental science. Processes &amp; impacts},
volume = {26},
number = {5},
pages = {915-927},
doi = {10.1039/d3em00547j},
pmid = {38618896},
issn = {2050-7895},
mesh = {*Particulate Matter/analysis ; *Gene Transfer, Horizontal ; *Air Pollutants/analysis ; Drug Resistance, Microbial/genetics ; Particle Size ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; },
abstract = {There is growing concern about the transfer of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in airborne particulate matter. In this study, we investigated the effects of various types of carbonaceous particulate matter (CPM) on the transfer of ARGs in vitro. The results showed that CPM promoted the transfer of ARGs, which was related to the concentration and particle size. Compared with the control group, the transfer frequency was 95.5, 74.7, 65.4, 14.7, and 3.8 times higher in G (graphene), CB (carbon black), NGP (nanographite powder), GP1.6 (graphite powder 1.6 micron), and GP45 (graphite powder 45 micron) groups, respectively. Moreover, the transfer frequency gradually increased with the increase in CPM concentration, while there was a negative relationship between the CPM particle size and conjugative transfer frequency. In addition, the results showed that CPM could promote the transfer of ARGs by increasing ROS, as well as activating the SOS response and expression of conjugative transfer-related genes (trbBp, trfAp, korA, kroB, and trbA). These findings are indicative of the potential risk of CPM for the transfer of ARGs in the environment, enriching our understanding of environmental pollution and further raising awareness of environmental protection.},
}
@article {pmid38618705,
year = {2024},
author = {Sarkar, S and Anyaso-Samuel, S and Qiu, P and Datta, S},
title = {Multiblock partial least squares and rank aggregation: Applications to detection of bacteriophages associated with antimicrobial resistance in the presence of potential confounding factors.},
journal = {Statistics in medicine},
volume = {43},
number = {13},
pages = {2527-2546},
doi = {10.1002/sim.10058},
pmid = {38618705},
issn = {1097-0258},
mesh = {*Bacteriophages/genetics ; Humans ; Least-Squares Analysis ; Metagenomics/methods ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Microbial/genetics ; Confounding Factors, Epidemiologic ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Microbiota/drug effects ; },
abstract = {Urban environments, characterized by bustling mass transit systems and high population density, host a complex web of microorganisms that impact microbial interactions. These urban microbiomes, influenced by diverse demographics and constant human movement, are vital for understanding microbial dynamics. We explore urban metagenomics, utilizing an extensive dataset from the Metagenomics &amp; Metadesign of Subways &amp; Urban Biomes (MetaSUB) consortium, and investigate antimicrobial resistance (AMR) patterns. In this pioneering research, we delve into the role of bacteriophages, or "phages"-viruses that prey on bacteria and can facilitate the exchange of antibiotic resistance genes (ARGs) through mechanisms like horizontal gene transfer (HGT). Despite their potential significance, existing literature lacks a consensus on their significance in ARG dissemination. We argue that they are an important consideration. We uncover that environmental variables, such as those on climate, demographics, and landscape, can obscure phage-resistome relationships. We adjust for these potential confounders and clarify these relationships across specific and overall antibiotic classes with precision, identifying several key phages. Leveraging machine learning tools and validating findings through clinical literature, we uncover novel associations, adding valuable insights to our comprehension of AMR development.},
}
@article {pmid38617843,
year = {2024},
author = {Guinet, B and Leobold, M and Herniou, EA and Bloin, P and Burlet, N and Bredlau, J and Navratil, V and Ravallec, M and Uzbekov, R and Kester, K and Gundersen Rindal, D and Drezen, JM and Varaldi, J and Bézier, A},
title = {A novel and diverse family of filamentous DNA viruses associated with parasitic wasps.},
journal = {Virus evolution},
volume = {10},
number = {1},
pages = {veae022},
pmid = {38617843},
issn = {2057-1577},
abstract = {Large dsDNA viruses from the Naldaviricetes class are currently composed of four viral families infecting insects and/or crustaceans. Since the 1970s, particles described as filamentous viruses (FVs) have been observed by electronic microscopy in several species of Hymenoptera parasitoids but until recently, no genomic data was available. This study provides the first comparative morphological and genomic analysis of these FVs. We analyzed the genomes of seven FVs, six of which were newly obtained, to gain a better understanding of their evolutionary history. We show that these FVs share all genomic features of the Naldaviricetes while encoding five specific core genes that distinguish them from their closest relatives, the Hytrosaviruses. By mining public databases, we show that FVs preferentially infect Hymenoptera with parasitoid lifestyle and that these viruses have been repeatedly integrated into the genome of many insects, particularly Hymenoptera parasitoids, overall suggesting a long-standing specialization of these viruses to parasitic wasps. Finally, we propose a taxonomical revision of the class Naldaviricetes in which FVs related to the Leptopilina boulardi FV constitute a fifth family. We propose to name this new family, Filamentoviridae.},
}
@article {pmid38617331,
year = {2024},
author = {Lyulina, AS and Liu, Z and Good, BH},
title = {Linkage equilibrium between rare mutations.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38617331},
issn = {2692-8205},
support = {R35 GM146949/GM/NIGMS NIH HHS/United States ; },
abstract = {Recombination breaks down genetic linkage by reshuffling existing variants onto new genetic backgrounds. These dynamics are traditionally quantified by examining the correlations between alleles, and how they decay as a function of the recombination rate. However, the magnitudes of these correlations are strongly influenced by other evolutionary forces like natural selection and genetic drift, making it difficult to tease out the effects of recombination. Here we introduce a theoretical framework for analyzing an alternative family of statistics that measure the homoplasy produced by recombination. We derive analytical expressions that predict how these statistics depend on the rates of recombination and recurrent mutation, the strength of negative selection and genetic drift, and the present-day frequencies of the mutant alleles. We find that the degree of homoplasy can strongly depend on this frequency scale, which reflects the underlying timescales over which these mutations occurred. We show how these scaling properties can be used to isolate the effects of recombination, and discuss their implications for the rates of horizontal gene transfer in bacteria.},
}
@article {pmid38615644,
year = {2024},
author = {Fu, X and Gao, J and Wang, Q and Chen, H and Liu, Y and Zeng, L and Yuan, Y and Xu, H},
title = {Mechanisms on the removal of gram-negative/positive antibiotic resistant bacteria and inhibition of horizontal gene transfer by ferrate coupled with peroxydisulfate or peroxymonosulfate.},
journal = {Journal of hazardous materials},
volume = {470},
number = {},
pages = {134254},
doi = {10.1016/j.jhazmat.2024.134254},
pmid = {38615644},
issn = {1873-3336},
mesh = {*Peroxides/chemistry ; *Gene Transfer, Horizontal ; *Iron/chemistry ; Water Purification/methods ; Escherichia coli/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; Disinfection/methods ; Sulfates/chemistry ; Anti-Bacterial Agents/pharmacology/chemistry ; Bacillus/genetics/drug effects/metabolism ; },
abstract = {The existence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) has been a global public environment and health issue. Due to the different cell structures, gram-positive/negative ARB exhibit various inactivation mechanisms in water disinfection. In this study, a gram-negative ARB Escherichia coli DH5α (E. coli DH5α) was used as a horizontal gene transfer (HGT) donor, while a gram-positive ARB Bacillus as a recipient. To develop an efficient and engineering applicable method in water disinfection, ARB and ARGs removal efficiency of Fe(VI) coupled peroxydisulfate (PDS) or peroxymonosulfate (PMS) was compared, wherein hydroxylamine (HA) was added as a reducing agent. The results indicated that Fe(VI)/PMS/HA showed higher disinfection efficiency than Fe(VI)/PDS/HA. When the concentration of each Fe(VI), PMS, HA was 0.48 mM, 5.15 log E. coli DH5α and 3.57 log Bacillus lost cultivability, while the proportion of recovered cells was 0.0017 % and 0.0566 %, respectively, and HGT was blocked. Intracellular tetA was reduced by 2.49 log. Fe(IV) and/or Fe(V) were proved to be the decisive reactive species. Due to the superiority of low cost as well as high efficiency and practicality, Fe(VI)/PMS/HA has significant application potential in ARB, ARGs removal and HGT inhibition, offering a new insight for wastewater treatment.},
}
@article {pmid38609370,
year = {2024},
author = {Quinones-Olvera, N and Owen, SV and McCully, LM and Marin, MG and Rand, EA and Fan, AC and Martins Dosumu, OJ and Paul, K and Sanchez Castaño, CE and Petherbridge, R and Paull, JS and Baym, M},
title = {Diverse and abundant phages exploit conjugative plasmids.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3197},
pmid = {38609370},
issn = {2041-1723},
support = {T32 GM135014/GM/NIGMS NIH HHS/United States ; R35 GM133700/GM/NIGMS NIH HHS/United States ; },
mesh = {*Bacteriophages/genetics ; Wastewater ; Biological Evolution ; Biotechnology ; Cell Membrane ; },
abstract = {Phages exert profound evolutionary pressure on bacteria by interacting with receptors on the cell surface to initiate infection. While the majority of phages use chromosomally encoded cell surface structures as receptors, plasmid-dependent phages exploit plasmid-encoded conjugation proteins, making their host range dependent on horizontal transfer of the plasmid. Despite their unique biology and biotechnological significance, only a small number of plasmid-dependent phages have been characterized. Here we systematically search for new plasmid-dependent phages targeting IncP and IncF plasmids using a targeted discovery platform, and find that they are common and abundant in wastewater, and largely unexplored in terms of their genetic diversity. Plasmid-dependent phages are enriched in non-canonical types of phages, and all but one of the 65 phages we isolated were non-tailed, and members of the lipid-containing tectiviruses, ssDNA filamentous phages or ssRNA phages. We show that plasmid-dependent tectiviruses exhibit profound differences in their host range which is associated with variation in the phage holin protein. Despite their relatively high abundance in wastewater, plasmid-dependent tectiviruses are missed by metaviromic analyses, underscoring the continued importance of culture-based phage discovery. Finally, we identify a tailed phage dependent on the IncF plasmid, and find related structural genes in phages that use the orthogonal type 4 pilus as a receptor, highlighting the evolutionarily promiscuous use of these distinct contractile structures by multiple groups of phages. Taken together, these results indicate plasmid-dependent phages play an under-appreciated evolutionary role in constraining horizontal gene transfer via conjugative plasmids.},
}
@article {pmid38608575,
year = {2024},
author = {Xu, Z and Hu, S and Zhao, D and Xiong, J and Li, C and Ma, Y and Li, S and Huang, B and Pan, X},
title = {Molybdenum disulfide nanosheets promote the plasmid-mediated conjugative transfer of antibiotic resistance genes.},
journal = {Journal of environmental management},
volume = {358},
number = {},
pages = {120827},
doi = {10.1016/j.jenvman.2024.120827},
pmid = {38608575},
issn = {1095-8630},
mesh = {*Molybdenum/chemistry ; *Plasmids/genetics ; *Disulfides/chemistry ; *Escherichia coli/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; Conjugation, Genetic ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; },
abstract = {The environmental safety of nanoscale molybdenum disulfide (MoS2) has attracted considerable attention, but its influence on the horizontal migration of antibiotic resistance genes and the ecological risks entailed have not been reported. This study addressed the influence of exposure to MoS2 at different concentrations up to 100 mg/L on the conjugative transfer of antibiotic resistance genes carried by RP4 plasmids with two strains of Escherichia coli. As a result, MoS2 facilitated RP4 plasmid-mediated conjugative transfer in a dose-dependent manner. The conjugation of RP4 plasmids was enhanced as much as 7-fold. The promoting effect is mainly attributable to increased membrane permeability, oxidative stress induced by reactive oxygen species, changes in extracellular polymer secretion and differential expression of the genes involved in horizontal gene transfer. The data highlight the distinct dose dependence of the conjugative transfer of antibiotic resistance genes and the need to improve awareness of the ecological and health risks of nanoscale transition metal dichalcogenides.},
}
@article {pmid38608246,
year = {2024},
author = {Yi, S and Zhou, K and Xu, X},
title = {Characterization of erm(B)-Carrying Integrative and Conjugative Elements Transferred from Streptococcus anginosus to Other Streptococci and Enterococci.},
journal = {Microbial drug resistance (Larchmont, N.Y.)},
volume = {30},
number = {6},
pages = {243-253},
doi = {10.1089/mdr.2023.0342},
pmid = {38608246},
issn = {1931-8448},
mesh = {*Streptococcus anginosus/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Gene Transfer, Horizontal ; *Enterococcus/genetics/drug effects ; *Conjugation, Genetic ; Streptococcus/genetics/drug effects ; Microbial Sensitivity Tests ; Humans ; Bacterial Proteins/genetics ; Drug Resistance, Bacterial/genetics ; },
abstract = {Integrative and conjugative elements (ICEs) are important vectors of lateral gene transfer and contribute to the evolution of bacterial pathogens. However, studies on the transfer among species and the physiological consequences of ICEs are rare. The objective of this study was to investigate the cross-species transferability of newly identified erm(B)-carried ICE in Streptococcus anginosus San95 and its physiological consequences after transfer. The erm(B)-carried ICE, characterized by a triple serine integrase module, integrated into hsdM genes, thus designated ICESan95_hsdM. Analysis of ICESan95_hsdM revealed 32 additional ICESan95-like ICEs in the available NCBI genome (n = 24) and sequence of clinical isolates (n = 8). Polymerase chain reaction (PCR) was used to evaluate the 467 clinical isolates, of which 84 were positive for core genes (integrase, relaxase, and T4SS genes) of ICESan95_hsdM. Cross-species transfer experiments demonstrated that ICESan95_hsdM could transfer from S. anginosus to different streptococcal and enterococcal recipients. Growth and competitive culture assays showed acquisition of ICESan95_hsdM incurred no fitness cost. Our work discovered a group of ICEs in Streptococci and Enterococci. For the first time, we demonstrated the broad cross-species transferability to different species or genera of ICEs with no fitness cost that enables commensal S. anginosus to deliver antimicrobial resistance genes to other streptococci and enterococci.},
}
@article {pmid38605260,
year = {2024},
author = {Rafiq, MS and Shabbir, MA and Raza, A and Irshad, S and Asghar, A and Maan, MK and Gondal, MA and Hao, H},
title = {CRISPR-Cas System: A New Dawn to Combat Antibiotic Resistance.},
journal = {BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy},
volume = {38},
number = {3},
pages = {387-404},
pmid = {38605260},
issn = {1179-190X},
support = {32172914//the National Natural Science Foundation of China/ ; 2021YFD1800600//Key Technology Research and Development Program of Shandong Province/ ; . 2662022DKYJC005//the Fundamental Research Funds for the Central Universities/ ; },
mesh = {*CRISPR-Cas Systems ; Humans ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacterial Infections/drug therapy ; Plasmids/genetics ; },
abstract = {Antimicrobial resistance (AMR) can potentially harm global public health. Horizontal gene transfer (HGT), which speeds up the emergence of AMR and increases the burden of drug resistance in mobile genetic elements (MGEs), is the primary method by which AMR genes are transferred across bacterial pathogens. New approaches are urgently needed to halt the spread of bacterial diseases and antibiotic resistance. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), an RNA-guided adaptive immune system, protects prokaryotes from foreign DNA like plasmids and phages. This approach may be essential in limiting horizontal gene transfer and halting the spread of antibiotic resistance. The CRISPR-Cas system has been crucial in identifying and understanding resistance mechanisms and developing novel therapeutic approaches. This review article investigates the CRISPR-Cas system's potential as a tool to combat bacterial AMR. Antibiotic-resistant bacteria can be targeted and eliminated by the CRISPR-Cas system. It has been proven to be an efficient method for removing carbapenem-resistant plasmids and regaining antibiotic susceptibility. The CRISPR-Cas system has enormous potential as a weapon against bacterial AMR. It precisely targets and eliminates antibiotic-resistant bacteria, facilitates resistance mechanism identification, and offers new possibilities in diagnostics and therapeutics.},
}
@article {pmid38605009,
year = {2024},
author = {Zorea, A and Pellow, D and Levin, L and Pilosof, S and Friedman, J and Shamir, R and Mizrahi, I},
title = {Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3147},
pmid = {38605009},
issn = {2041-1723},
support = {866530//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; ISF 1947/19//Israel Science Foundation (ISF)/ ; },
mesh = {Humans ; *Ecosystem ; Plasmids/genetics ; Bacteria/genetics ; Anti-Bacterial Agents ; Gene Transfer, Horizontal ; *Inflammatory Bowel Diseases/genetics ; },
abstract = {Plasmids are pivotal in driving bacterial evolution through horizontal gene transfer. Here, we investigated 3467 human gut microbiome samples across continents and disease states, analyzing 11,086 plasmids. Our analyses reveal that plasmid dispersal is predominantly stochastic, indicating neutral processes as the primary driver of their wide distribution. We find that only 20-25% of plasmid DNA is being selected in various disease states, constraining its distribution across hosts. Selective pressures shape specific plasmid segments with distinct ecological functions, influenced by plasmid mobilization lifestyle, antibiotic usage, and inflammatory gut diseases. Notably, these elements are more commonly shared within groups of individuals with similar health conditions, such as Inflammatory Bowel Disease (IBD), regardless of geographic location across continents. These segments contain essential genes such as iron transport mechanisms- a distinctive gut signature of IBD that impacts the severity of inflammation. Our findings shed light on mechanisms driving plasmid dispersal and selection in the human gut, highlighting their role as carriers of vital gene pools impacting bacterial hosts and ecosystem dynamics.},
}
@article {pmid38604355,
year = {2024},
author = {Yin, Z and Liang, J and Zhang, M and Chen, B and Yu, Z and Tian, X and Deng, X and Peng, L},
title = {Pan-genome insights into adaptive evolution of bacterial symbionts in mixed host-microbe symbioses represented by human gut microbiota Bacteroides cellulosilyticus.},
journal = {The Science of the total environment},
volume = {927},
number = {},
pages = {172251},
doi = {10.1016/j.scitotenv.2024.172251},
pmid = {38604355},
issn = {1879-1026},
mesh = {*Symbiosis ; *Gastrointestinal Microbiome/genetics ; *Bacteroides/genetics/physiology ; Humans ; *Genome, Bacterial ; Evolution, Molecular ; Gene Transfer, Horizontal ; },
abstract = {Animal hosts harbor diverse assemblages of microbial symbionts that play crucial roles in the host's lifestyle. The link between microbial symbiosis and host development remains poorly understood. In particular, little is known about the adaptive evolution of gut bacteria in host-microbe symbioses. Recently, symbiotic relationships have been categorized as open, closed, or mixed, reflecting their modes of inter-host transmission and resulting in distinct genomic features. Members of the genus Bacteroides are the most abundant human gut microbiota and possess both probiotic and pathogenic potential, providing an excellent model for studying pan-genome evolution in symbiotic systems. Here, we determined the complete genome of an novel clinical strain PL2022, which was isolated from a blood sample and performed pan-genome analyses on a representative set of Bacteroides cellulosilyticus strains to quantify the influence of the symbiotic relationship on the evolutionary dynamics. B. cellulosilyticus exhibited correlated genomic features with both open and closed symbioses, suggesting a mixed symbiosis. An open pan-genome is characterized by abundant accessory gene families, potential horizontal gene transfer (HGT), and diverse mobile genetic elements (MGEs), indicating an innovative gene pool, mainly associated with genomic islands and plasmids. However, massive parallel gene loss, weak purifying selection, and accumulation of positively selected mutations were the main drivers of genome reduction in B. cellulosilyticus. Metagenomic read recruitment analyses showed that B. cellulosilyticus members are globally distributed and active in human gut habitats, in line with predominant vertical transmission in the human gut. However, existence and/or high abundance were also detected in non-intestinal tissues, other animal hosts, and non-host environments, indicating occasional horizontal transmission to new niches, thereby creating arenas for the acquisition of novel genes. This case study of adaptive evolution under a mixed host-microbe symbiosis advances our understanding of symbiotic pan-genome evolution. Our results highlight the complexity of genetic evolution in this unusual intestinal symbiont.},
}
@article {pmid38601936,
year = {2024},
author = {Ortañez, J and Degnan, PH},
title = {Tracking and characterization of a novel conjugative transposon identified by shotgun transposon mutagenesis.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1241582},
pmid = {38601936},
issn = {1664-302X},
abstract = {The horizontal transfer of mobile genetic elements (MGEs) is an essential process determining the functional and genomic diversity of bacterial populations. MGEs facilitate the exchange of fitness determinant genes like antibiotic resistance and virulence factors. Various computational methods exist to identify potential MGEs, but confirming their ability to transfer requires additional experimental approaches. Here, we apply a transposon (Tn) mutagenesis technique for confirming mobilization without the need for targeted mutations. Using this method, we identified two MGEs, including a previously known conjugative transposon (CTn) called BoCTn found in Bacteroides ovatus and a novel CTn, PvCTn, identified in Phocaeicola vulgatus. In addition, Tn mutagenesis and subsequent genetic deletion enabled our characterization of a helix-turn-helix motif gene, BVU3433 which negatively regulates the conjugation efficiency of PvCTn in vitro. Furthermore, our transcriptomics data revealed that BVU3433 plays a crucial role in the repression of PvCTn genes, including genes involved in forming complete conjugation machinery [Type IV Secretion System (T4SS)]. Finally, analysis of individual strain genomes and community metagenomes identified the widespread prevalence of PvCTn-like elements with putative BVU3433 homologs among human gut-associated bacteria. In summary, this Tn mutagenesis mobilization method (TMMM) enables observation of transfer events in vitro and can ultimately be applied in vivo to identify a broader diversity of functional MGEs that may underly the transfer of important fitness determinants.},
}
@article {pmid38601791,
year = {2024},
author = {Babiker, A and Lohsen, S and Van Riel, J and Hjort, K and Weiss, DS and Andersson, DI and Satola, S},
title = {Heteroresistance to piperacillin/tazobactam in Klebsiella pneumoniae is mediated by increased copy number of multiple β-lactamase genes.},
journal = {JAC-antimicrobial resistance},
volume = {6},
number = {2},
pages = {dlae057},
pmid = {38601791},
issn = {2632-1823},
support = {U19 AI158080/AI/NIAID NIH HHS/United States ; UM1 AI104681/AI/NIAID NIH HHS/United States ; },
abstract = {BACKGROUND: Piperacillin/tazobactam is a β-lactam/β-lactamase inhibitor combination with a broad spectrum of activity that is often used as empirical and/or targeted therapy among hospitalized patients. Heteroresistance (HR) is a form of antibiotic resistance in which a minority population of resistant cells coexists with a majority susceptible population that has been found to be a cause of antibiotic treatment failure in murine models.<br><br>OBJECTIVES: To determine the prevalence of HR and mechanisms of HR to piperacillin/tazobactam among Klebsiella pneumoniae bloodstream infection (BSI) isolates.<br><br>MATERIALS: From July 2018 to June 2021, K. pneumoniae piperacillin/tazobactam-susceptible BSI isolates were collected from two tertiary hospitals in Atlanta, GA, USA. Only first isolates from each patient per calendar year were included. Population analysis profiling (PAP) and WGS were performed to identify HR and its mechanisms.<br><br>RESULTS: Among 423 K. pneumoniae BSI isolates collected during the study period, 6% (25/423) were found to be HR with a subpopulation surviving above the breakpoint. WGS of HR isolates grown in the presence of piperacillin/tazobactam at concentrations 8-fold that of the MIC revealed copy number changes of plasmid-located &#x3b2;-lactamase genes blaCTX-M-15, blaSHV33, blaOXA-1 and blaTEM-1 by tandem gene amplification or plasmid copy number increase.<br><br>CONCLUSIONS: Prevalence of HR to piperacillin/tazobactam among bloodstream isolates was substantial. The HR phenotype appears to be caused by tandem amplification of &#x3b2;-lactamase genes found on plasmids or plasmid copy number increase. This raises the possibility of dissemination of HR through horizontal gene transfer and requires further study.},
}
@article {pmid38601688,
year = {2024},
author = {Ma, X and Yin, Z and Li, H and Guo, J},
title = {Roles of herbivorous insects salivary proteins.},
journal = {Heliyon},
volume = {10},
number = {7},
pages = {e29201},
pmid = {38601688},
issn = {2405-8440},
abstract = {The intricate relationship between herbivorous insects and plants has evolved over millions of years, central to this dynamic interaction are salivary proteins (SPs), which mediate key processes ranging from nutrient acquisition to plant defense manipulation. SPs, sourced from salivary glands, intestinal regurgitation or acquired through horizontal gene transfer, exhibit remarkable functional versatility, influencing insect development, behavior, and adhesion mechanisms. Moreover, SPs play pivotal roles in modulating plant defenses, to induce or inhibit plant defenses as elicitors or effectors. In this review, we delve into the multifaceted roles of SPs in herbivorous insects, highlighting their diverse impacts on insect physiology and plant responses. Through a comprehensive exploration of SP functions, this review aims to deepen our understanding of plant-insect interactions and foster advancements in both fundamental research and practical applications in plant-insect interactions.},
}
@article {pmid38599270,
year = {2024},
author = {Thibodeau, AJ and Barret, M and Mouchet, F and Nguyen, VX and Pinelli, E},
title = {The potential contribution of aquatic wildlife to antibiotic resistance dissemination in freshwater ecosystems: A review.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {350},
number = {},
pages = {123894},
doi = {10.1016/j.envpol.2024.123894},
pmid = {38599270},
issn = {1873-6424},
mesh = {Animals ; *Fresh Water ; *Ecosystem ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; Bacteria/drug effects/genetics ; Fishes/microbiology ; Environmental Monitoring ; Water Pollutants, Chemical ; Gene Transfer, Horizontal ; Aquatic Organisms/genetics ; Animals, Wild/microbiology ; Drug Resistance, Bacterial/genetics ; },
abstract = {Antibiotic resistance (AR) is one of the major health threats of our time. The presence of antibiotics in the environment and their continuous release from sewage treatment plants, chemical manufacturing plants and animal husbandry, agriculture and aquaculture, result in constant selection pressure on microbial organisms. This presence leads to the emergence, mobilization, horizontal gene transfer and a selection of antibiotic resistance genes, resistant bacteria and mobile genetic elements. Under these circumstances, aquatic wildlife is impacted in all compartments, including freshwater organisms with partially impermeable microbiota. In this narrative review, recent advancements in terms of occurrence of antibiotics and antibiotic resistance genes in sewage treatment plant effluents source compared to freshwater have been examined, occurrence of antibiotic resistance in wildlife, as well as experiments on antibiotic exposure. Based on this current state of knowledge, we propose the hypothesis that freshwater aquatic wildlife may play a crucial role in the dissemination of antibiotic resistance within the environment. Specifically, we suggest that organisms with high bacterial density tissues, which are partially isolated from the external environment, such as fishes and amphibians, could potentially be reservoirs and amplifiers of antibiotic resistance in the environment, potentially favoring the increase of the abundance of antibiotic resistance genes and resistant bacteria. Potential avenues for further research (trophic transfer, innovative exposure experiment) and action (biodiversity eco-engineering) are finally proposed.},
}
@article {pmid38598950,
year = {2024},
author = {Lei, L and Chen, N and Chen, Z and Zhao, Y and Lin, H and Li, X and Hu, W and Zhang, H and Shi, J and Luo, Y},
title = {Dissemination of antibiotic resistance genes from aboveground sources to groundwater in livestock farms.},
journal = {Water research},
volume = {256},
number = {},
pages = {121584},
doi = {10.1016/j.watres.2024.121584},
pmid = {38598950},
issn = {1879-2448},
mesh = {*Groundwater/microbiology ; Animals ; *Livestock ; *Drug Resistance, Microbial/genetics ; Farms ; Swine ; China ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Wastewater/microbiology ; Drug Resistance, Bacterial/genetics ; },
abstract = {Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are prevalent in various environments on livestock farms, including livestock waste, soil, and groundwater. Contamination of groundwater by ARB and ARGs in livestock farms is a growing concern as it may have potentially huge risks to human health. However, the source of groundwater-borne ARB and ARGs in animal farms remains largely unknown. In this study, different types of samples including groundwater and its potential contamination sources from aboveground (pig feces, wastewater, and soil) from both working and abandoned swine feedlots in southern China were collected and subjected to metagenomic sequencing and ARB isolation. The source tracking based on metagenomic analysis revealed that 56-95 % of ARGs in groundwater was attributable to aboveground sources. Using metagenomic assembly, we found that 45 ARGs predominantly conferring resistance to aminoglycosides, sulfonamides, and tetracyclines could be transferred from the aboveground sources to groundwater, mostly through plasmid-mediated horizontal gene transfer. Furthermore, the full-length nucleotide sequences of sul1, tetA, and TEM-1 detected in ARB isolates exhibited the close evolutionary relationships between aboveground sources and groundwater. Some isolated strains of antibiotic-resistant Pseudomonas spp. from aboveground sources and groundwater had the high similarity (average nucleotide identity > 99 %). Notably, the groundwater-borne ARGs were identified as mainly carried by bacterial pathogens, potentially posing risks to human and animal health. Overall, this study underscores the dissemination of ARGs from aboveground sources to groundwater in animal farms and associated risks.},
}
@article {pmid38598855,
year = {2024},
author = {Hsieh, SC and Peters, JE},
title = {Natural and Engineered Guide RNA-Directed Transposition with CRISPR-Associated Tn7-Like Transposons.},
journal = {Annual review of biochemistry},
volume = {93},
number = {1},
pages = {139-161},
pmid = {38598855},
issn = {1545-4509},
support = {R01 GM129118/GM/NIGMS NIH HHS/United States ; R35 GM152260/GM/NIGMS NIH HHS/United States ; },
mesh = {*DNA Transposable Elements/genetics ; *CRISPR-Cas Systems ; *RNA, Guide, CRISPR-Cas Systems/genetics/metabolism ; *Transposases/metabolism/genetics ; Gene Editing/methods ; Bacteria/genetics ; Plasmids/metabolism/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; },
abstract = {CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated nuclease) defense systems have been naturally coopted for guide RNA-directed transposition on multiple occasions. In all cases, cooption occurred with diverse elements related to the bacterial transposon Tn7. Tn7 tightly controls transposition; the transposase is activated only when special targets are recognized by dedicated target-site selection proteins. Tn7 and the Tn7-like elements that coopted CRISPR-Cas systems evolved complementary targeting pathways: one that recognizes a highly conserved site in the chromosome and a second pathway that targets mobile plasmids capable of cell-to-cell transfer. Tn7 and Tn7-like elements deliver a single integration into the site they recognize and also control the orientation of the integration event, providing future potential for use as programmable gene-integration tools. Early work has shown that guide RNA-directed transposition systems can be adapted to diverse hosts, even within microbial communities, suggesting great potential for engineering these systems as powerful gene-editing tools.},
}
@article {pmid38598457,
year = {2024},
author = {Gao, X and Xu, L and Zhong, T and Song, X and Zhang, H and Liu, X and Jiang, Y},
title = {The proliferation of antibiotic resistance genes (ARGs) and microbial communities in industrial wastewater treatment plant treating N,N-dimethylformamide (DMF) by AAO process.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0299740},
pmid = {38598457},
issn = {1932-6203},
mesh = {*Anti-Bacterial Agents/pharmacology ; Dimethylformamide ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; *Microbiota/genetics ; Cell Proliferation ; },
abstract = {The excessive use of antibiotics has resulted in the contamination of the environment with antibiotic resistance genes (ARGs), posing a significant threat to public health. Wastewater treatment plants (WWTPs) are known to be reservoirs of ARGs and considered to be hotspots for horizontal gene transfer (HGT) between bacterial communities. However, most studies focused on the distribution and dissemination of ARGs in hospital and urban WWTPs, and little is known about their fate in industrial WWTPs. In this study, collected the 15 wastewater samples containing N,N-dimethylformamide (DMF) from five stages of the anaerobic anoxic aerobic (AAO) process in an industrial WWTPs. The findings revealed a stepwise decrease in DMF and chemical oxygen demand (COD) content with the progression of treatment. However, the number and abundances of ARGs increase in the effluents of biological treatments. Furthermore, the residues of DMF and the treatment process altered the structure of the bacterial community. The correlation analysis indicated that the shift in bacterial community structures might be the main driver for the dynamics change of ARGs. Interestingly, observed that the AAO process may acted as a microbial source and increased the total abundance of ARGs instead of attenuating it. Additionally, found that non-pathogenic bacteria had higher ARGs abundance than pathogenic bacteria in effluents. The study provides insights into the microbial community structure and the mechanisms that drive the variation in ARGs abundance in industrial WWTPs.},
}
@article {pmid38598029,
year = {2024},
author = {Ramnarine, SDBJ and Jayaraman, J and Ramsubhag, A},
title = {Crucifer Lesion-Associated Xanthomonas Strains Show Multi-Resistance to Heavy Metals and Antibiotics.},
journal = {Current microbiology},
volume = {81},
number = {5},
pages = {136},
pmid = {38598029},
issn = {1432-0991},
support = {CRP.5.APR17.45//University of the West Indies, St. Augustine Campus/ ; },
mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology ; Copper ; *Metals, Heavy/toxicity ; Ampicillin ; Chloramphenicol ; },
abstract = {Copper resistance in phytopathogens is a major challenge to crop production globally and is known to be driven by excessive use of copper-based pesticides. However, recent studies have shown co-selection of multiple heavy metal and antibiotic resistance genes in bacteria exposed to heavy metal and xenobiotics, which may impact the epidemiology of plant, animal, and human diseases. In this study, multi-resistance to heavy metals and antibiotics were evaluated in local Xanthomonas campestris pv. campestris (Xcc) and co-isolated Xanthomonas melonis (Xmel) strains from infected crucifer plants in Trinidad. Resistance to cobalt, cadmium, zinc, copper, and arsenic (V) was observed in both Xanthomonas species up to 25 mM. Heavy metal resistance (HMR) genes were found on a small plasmid-derived locus with ~ 90% similarity to a Stenotrophomonas spp. chromosomal locus and a X. perforans pLH3.1 plasmid. The co-occurrence of mobile elements in these regions implies their organization on a composite transposon-like structure. HMR genes in Xcc strains showed the lowest similarity to references, and the cus and ars operons appear to be unique among Xanthomonads. Overall, the similarity of HMR genes to Stenotrophomonas sp. chromosomal genomes suggest their origin in this genus or a related organism and subsequent spread through lateral gene transfer events. Further resistome characterization revealed the presence of small multidrug resistance (SMR), multidrug resistance (MDR) efflux pumps, and bla (Xcc) genes for broad biocide resistance in both species. Concurrently, resistance to antibiotics (streptomycin, kanamycin, tetracycline, chloramphenicol, and ampicillin) up to 1000 µg/mL was confirmed.},
}
@article {pmid38597658,
year = {2024},
author = {Schmid, N and Brandt, D and Walasek, C and Rolland, C and Wittmann, J and Fischer, D and Müsken, M and Kalinowski, J and Thormann, K},
title = {An autonomous plasmid as an inovirus phage satellite.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {5},
pages = {e0024624},
pmid = {38597658},
issn = {1098-5336},
mesh = {*Plasmids/genetics ; *Shewanella/virology/genetics ; Inovirus/genetics ; Satellite Viruses/genetics ; Genome, Viral ; Bacteriophages/genetics/classification/isolation &amp; purification ; },
abstract = {Bacterial viruses (phages) are potent agents of lateral gene transfer and thus are important drivers of evolution. A group of mobile genetic elements, referred to as phage satellites, exploits phages to disseminate their own genetic material. Here, we isolated a novel member of the family Inoviridae, Shewanella phage Dolos, along with an autonomously replicating plasmid, pDolos. Dolos causes a chronic infection in its host Shewanella oneidensis by phage production with only minor effects on the host cell proliferation. When present, plasmid pDolos hijacks Dolos functions to be predominantly packaged into phage virions and released into the environment and, thus, acts as a phage satellite. pDolos can disseminate further genetic material encoding, e.g., resistances or fluorophores to host cells sensitive to Dolos infection. Given the rather simple requirements of a plasmid for takeover of an inovirus and the wide distribution of phages of this group, we speculate that similar phage-satellite systems are common among bacteria.IMPORTANCEPhage satellites are mobile genetic elements, which hijack phages to be transferred to other host cells. The vast majority of these phage satellites integrate within the host's chromosome, and they all carry remaining phage genes. Here, we identified a novel phage satellite, pDolos, which uses an inovirus for dissemination. pDolos (i) remains as an autonomously replicating plasmid within its host, (ii) does not carry recognizable phage genes, and (iii) is smaller than any other phage satellites identified so far. Thus, pDolos is the first member of a new class of phage satellites, which resemble natural versions of phagemids.},
}
@article {pmid38593892,
year = {2024},
author = {Zheng, B and Wang, G and Qu, Z and Hu, J and Bao, Z and Wang, M},
title = {Glycosaminoglycan lyase: A new competition between bacteria and the pacific white shrimp Litopenaeus vannamei.},
journal = {Developmental and comparative immunology},
volume = {156},
number = {},
pages = {105177},
doi = {10.1016/j.dci.2024.105177},
pmid = {38593892},
issn = {1879-0089},
mesh = {Animals ; *Penaeidae/immunology/microbiology/genetics ; *Vibrio parahaemolyticus/physiology ; *Phylogeny ; *Gene Transfer, Horizontal ; Arthropod Proteins/genetics/metabolism ; Hepatopancreas/microbiology/immunology/metabolism ; Bacteria ; Immunity, Innate/genetics ; Polysaccharide-Lyases/genetics/metabolism ; Vibrio Infections/immunology ; },
abstract = {Horizontal gene transfer (HGT) is an important evolutionary force in the formation of prokaryotic and eukaryotic genomes. In recent years, many HGT genes horizontally transferred from prokaryotes to eukaryotes have been reported, and most of them are present in arthropods. The Pacific white shrimp Litopenaeus vannamei, an important economic species of arthropod, has close relationships with bacteria, providing a platform for horizontal gene transfer (HGT). In this study, we analyzed bacteria-derived HGT based on a high-quality genome of L. vannamei via a homology search and phylogenetic analysis, and six HGT genes were identified. Among these six horizontally transferred genes, we found one gene (LOC113799989) that contains a bacterial chondroitinase AC structural domain and encodes an unknown glycosaminoglycan (GAG) lyase in L. vannamei. The real-time quantitative PCR results showed that the mRNA expression level of LOC113799989 was highest in the hepatopancreas and heart, and after stimulation by Vibrio parahaemolyticus, its mRNA expression level was rapidly up-regulated within 12 h. Furthermore, after injecting si-RNA and stimulation by V. parahaemolyticus, we found that the experimental group had a higher cumulative mortality rate in 48 h than the control group, indicating that the bacteria-derived GAG lyase can reduce the mortality of shrimp with respect to infection by V. parahaemolyticus and might be related to the resistance of shrimp to bacterial diseases. Our findings contribute to the study of the function of GAGs and provide new insights into GAG-related microbial pathogenesis and host defense mechanisms in arthropods.},
}
@article {pmid38593473,
year = {2024},
author = {Paul, B and Siddaramappa, S},
title = {Comparative analysis of the diversity of trinucleotide repeats in bacterial genomes.},
journal = {Genome},
volume = {67},
number = {8},
pages = {281-291},
doi = {10.1139/gen-2023-0097},
pmid = {38593473},
issn = {1480-3321},
mesh = {*Genome, Bacterial ; *Trinucleotide Repeats ; Humans ; Genetic Variation ; Bacteria/genetics/classification ; },
abstract = {The human gut is the most favorable niche for microbial populations, and few studies have explored the possibilities of horizontal gene transfer between host and pathogen. Trinucleotide repeat (TNR) expansion in humans can cause more than 40 neurodegenerative diseases. Further, TNRs are a type of microsatellite that resides on coding regions can contribute to the synthesis of homopolymeric amino acids. Hence, the present study aims to estimate the occurrence and diversity of TNRs in bacterial genomes available in the NCBI Genome database. Genome-wide analyses revealed that several bacterial genomes contain different types of uninterrupted TNRs. It was found that TNRs are abundant in the genomes of Alcaligenes faecalis, Mycoplasma gallisepticum, Mycoplasma genitalium, Sorangium cellulosum, and Thermus thermophilus. Interestingly, the genome of Bacillus thuringiensis strain YBT-1518 contained 169 uninterrupted ATT repeats. The genome of Leclercia adecarboxylata had 46 uninterrupted CAG repeats, which potentially translate into polyglutamine. In some instances, the TNRs were present in genes that potentially encode essential functions. Similar occurrences in human genes are known to cause genetic disorders. Further analysis of the occurrence of TNRs in bacterial genomes is likely to provide a better understanding of mismatch repair, genetic disorders, host-pathogen interaction, and homopolymeric amino acids.},
}
@article {pmid38591887,
year = {2024},
author = {Ng, WL and Rego, EH},
title = {A nucleoid-associated protein is involved in the emergence of antibiotic resistance by promoting the frequent exchange of the replicative DNA polymerase in Mycobacterium smegmatis.},
journal = {mSphere},
volume = {9},
number = {5},
pages = {e0012224},
pmid = {38591887},
issn = {2379-5042},
support = {R01 AI148255/AI/NIAID NIH HHS/United States ; 100000875//Pew Charitable Trusts (PCT)/ ; 100014185//Searle Scholars Program (SSP)/ ; },
mesh = {*Mycobacterium smegmatis/genetics/drug effects/metabolism/enzymology ; *DNA Replication ; *DNA-Directed DNA Polymerase/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism ; *Drug Resistance, Bacterial/genetics ; DNA-Binding Proteins/genetics/metabolism ; Antigens, Bacterial ; },
abstract = {UNLABELLED: Antibiotic resistance in Mycobacterium tuberculosis exclusively originates from chromosomal mutations, either during normal DNA replication or under stress, when the expression of error-prone DNA polymerases increases to repair damaged DNA. To bypass DNA lesions and catalyze error-prone DNA synthesis, translesion polymerases must be able to access the DNA, temporarily replacing the high-fidelity replicative polymerase. The mechanisms that govern polymerase exchange are not well understood, especially in mycobacteria. Here, using a suite of quantitative fluorescence imaging techniques, we discover that in Mycobacterium smegmatis, as in other bacterial species, the replicative polymerase, DnaE1, exchanges at a timescale much faster than that of DNA replication. Interestingly, this fast exchange rate depends on an actinobacteria-specific nucleoid-associated protein (NAP), Lsr2. In cells missing lsr2, DnaE1 exchanges less frequently, and the chromosome is replicated more faithfully. Additionally, in conditions that damage DNA, cells lacking lsr2 load the complex needed to bypass DNA lesions less effectively and, consistently, replicate with higher fidelity but exhibit growth defects. Together, our results show that Lsr2 promotes dynamic flexibility of the mycobacterial replisome, which is critical for robust cell growth and lesion repair in conditions that damage DNA.<br><br>IMPORTANCE: Unlike many other pathogens, Mycobacterium tuberculosis has limited ability for horizontal gene transfer, a major mechanism for developing antibiotic resistance. Thus, the mechanisms that facilitate chromosomal mutagenesis are of particular importance in mycobacteria. Here, we show that Lsr2, a nucleoid-associated protein, has a novel role in DNA replication and mutagenesis in the model mycobacterium Mycobacterium smegmatis. We find that Lsr2 promotes the fast exchange rate of the replicative DNA polymerase, DnaE1, at the replication fork and is important for the effective loading of the DnaE2-ImuA'-ImuB translesion complex. Without lsr2, M. smegmatis replicates its chromosome more faithfully and acquires resistance to rifampin at a lower rate, but at the cost of impaired survival to DNA damaging agents. Together, our work establishes Lsr2 as a potential factor in the emergence of mycobacterial antibiotic resistance.},
}
@article {pmid38591882,
year = {2024},
author = {Xing, Y and Clark, JR and Chang, JD and Zulk, JJ and Chirman, DM and Piedra, F-A and Vaughan, EE and Hernandez Santos, HJ and Patras, KA and Maresso, AW},
title = {Progress toward a vaccine for extraintestinal pathogenic E. coli (ExPEC) II: efficacy of a toxin-autotransporter dual antigen approach.},
journal = {Infection and immunity},
volume = {92},
number = {5},
pages = {e0044023},
pmid = {38591882},
issn = {1098-5522},
support = {U19 AI144297/AI/NIAID NIH HHS/United States ; U19 AI157981/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; *Extraintestinal Pathogenic Escherichia coli/genetics/immunology ; *Escherichia coli Infections/prevention &amp; control/microbiology/immunology ; Mice ; *Hemolysin Proteins/immunology/genetics ; *Escherichia coli Proteins/genetics/immunology ; *Escherichia coli Vaccines/immunology ; Antigens, Bacterial/immunology/genetics ; Female ; Virulence Factors/genetics/immunology ; Type V Secretion Systems/immunology/genetics ; Disease Models, Animal ; Humans ; },
abstract = {Extraintestinal pathogenic Escherichia coli (ExPEC) is a leading cause of worldwide morbidity and mortality, the top cause of antimicrobial-resistant (AMR) infections, and the most frequent cause of life-threatening sepsis and urinary tract infections (UTI) in adults. The development of an effective and universal vaccine is complicated by this pathogen's pan-genome, its ability to mix and match virulence factors and AMR genes via horizontal gene transfer, an inability to decipher commensal from pathogens, and its intimate association and co-evolution with mammals. Using a pan virulome analysis of >20,000 sequenced E. coli strains, we identified the secreted cytolysin α-hemolysin (HlyA) as a high priority target for vaccine exploration studies. We demonstrate that a catalytically inactive pure form of HlyA, expressed in an autologous host using its own secretion system, is highly immunogenic in a murine host, protects against several forms of ExPEC infection (including lethal bacteremia), and significantly lowers bacterial burdens in multiple organ systems. Interestingly, the combination of a previously reported autotransporter (SinH) with HlyA was notably effective, inducing near complete protection against lethal challenge, including commonly used infection strains ST73 (CFT073) and ST95 (UTI89), as well as a mixture of 10 of the most highly virulent sequence types and strains from our clinical collection. Both HlyA and HlyA-SinH combinations also afforded some protection against UTI89 colonization in a murine UTI model. These findings suggest recombinant, inactive hemolysin and/or its combination with SinH warrant investigation in the development of an E. coli vaccine against invasive disease.},
}
@article {pmid38591037,
year = {2024},
author = {Giermasińska-Buczek, K and Gawor, J and Stefańczyk, E and Gągała, U and Żuchniewicz, K and Rekosz-Burlaga, H and Gromadka, R and Łobocka, M},
title = {Interaction of bacteriophage P1 with an epiphytic Pantoea agglomerans strain-the role of the interplay between various mobilome elements.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1356206},
pmid = {38591037},
issn = {1664-302X},
abstract = {P1 is a model, temperate bacteriophage of the 94 kb genome. It can lysogenize representatives of the Enterobacterales order. In lysogens, it is maintained as a plasmid. We tested P1 interactions with the biocontrol P. agglomerans L15 strain to explore the utility of P1 in P. agglomerans genome engineering. A P1 derivative carrying the Tn9 (cm[R]) transposon could transfer a plasmid from Escherichia coli to the L15 cells. The L15 cells infected with this derivative formed chloramphenicol-resistant colonies. They could grow in a liquid medium with chloramphenicol after adaptation and did not contain prophage P1 but the chromosomally inserted cm[R] marker of P1 Tn9 (cat). The insertions were accompanied by various rearrangements upstream of the Tn9 cat gene promoter and the loss of IS1 (IS1L) from the corresponding region. Sequence analysis of the L15 strain genome revealed a chromosome and three plasmids of 0.58, 0.18, and 0.07 Mb. The largest and the smallest plasmid appeared to encode partition and replication incompatibility determinants similar to those of prophage P1, respectively. In the L15 derivatives cured of the largest plasmid, P1 with Tn9 could not replace the smallest plasmid even if selected. However, it could replace the smallest and the largest plasmid of L15 if its Tn9 IS1L sequence driving the Tn9 mobility was inactivated or if it was enriched with an immobile kanamycin resistance marker. Moreover, it could develop lytically in the L15 derivatives cured of both these plasmids. Clearly, under conditions of selection for P1, the mobility of the P1 selective marker determines whether or not the incoming P1 can outcompete the incompatible L15 resident plasmids. Our results demonstrate that P. agglomerans can serve as a host for bacteriophage P1 and can be engineered with the help of this phage. They also provide an example of how antibiotics can modify the outcome of horizontal gene transfer in natural environments. Numerous plasmids of Pantoea strains appear to contain determinants of replication or partition incompatibility with P1. Therefore, P1 with an immobile selective marker may be a tool of choice in curing these strains from the respective plasmids to facilitate their functional analysis.},
}
@article {pmid38587657,
year = {2024},
author = {Gidhi, A and Jha, SK and Kumar, M and Mukhopadhyay, K},
title = {The F-box protein encoding genes of the leaf-rust fungi Puccinia triticina: genome-wide identification, characterization and expression dynamics during pathogenesis.},
journal = {Archives of microbiology},
volume = {206},
number = {5},
pages = {209},
pmid = {38587657},
issn = {1432-072X},
mesh = {Phylogeny ; Puccinia ; *Basidiomycota/genetics ; *F-Box Proteins/genetics ; },
abstract = {The F-box proteins in fungi perform diverse functions including regulation of cell cycle, circadian clock, development, signal transduction and nutrient sensing. Genome-wide analysis revealed 10 F-box genes in Puccinia triticina, the causal organism for the leaf rust disease in wheat and were characterized using in silico approaches for revealing phylogenetic relationships, gene structures, gene ontology, protein properties, sequence analysis and gene expression studies. Domain analysis predicted functional domains like WD40 and LRR at C-terminus along with the obvious presence of F-box motif in N-terminus. MSA showed amino acid replacements, which might be due to nucleotide substitution during replication. Phylogenetic analysis revealed the F-box proteins with similar domains to be clustered together while some sequences were spread out in different clades, which might be due to functional diversity. The clustering of Puccinia triticina GG705409 with Triticum aestivum TaAFB4/TaAFB5 in a single clade suggested the possibilities of horizontal gene transfer during the coevolution of P. triticina and wheat. Gene ontological annotation categorized them into three classes and were functionally involved in protein degradation through the protein ubiquitination pathway. Protein-protein interaction network revealed F-box proteins to interact with other components of the SCF complex involved in protein ubiquitination. Relative expression analysis of five F-box genes in a time course experiment denoted their involvement in leaf rust susceptible wheat plants. This study provides information on structure elucidation of F-box proteins of a basidiomycetes plant pathogenic fungi and their role during pathogenesis.},
}
@article {pmid38587426,
year = {2024},
author = {Bessen, DE and Beall, BW and Hayes, A and Huang, W and DiChiara, JM and Velusamy, S and Tettelin, H and Jolley, KA and Fallon, JT and Chochua, S and Alobaidallah, MSA and Higgs, C and Barnett, TC and Steemson, JT and Proft, T and Davies, MR},
title = {Recombinational exchange of M-fibril and T-pilus genes generates extensive cell surface diversity in the global group A Streptococcus population.},
journal = {mBio},
volume = {15},
number = {5},
pages = {e0069324},
pmid = {38587426},
issn = {2150-7511},
support = {R21 AI156226/AI/NIAID NIH HHS/United States ; R01 AI173565/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R03 AI148983/AI/NIAID NIH HHS/United States ; },
mesh = {*Streptococcus pyogenes/genetics/classification ; *Genetic Variation ; Humans ; *Genotype ; Recombination, Genetic ; Bacterial Outer Membrane Proteins/genetics ; Fimbriae Proteins/genetics ; Gene Transfer, Horizontal ; Antigens, Bacterial/genetics ; Streptococcal Infections/microbiology/epidemiology ; Impetigo/microbiology/epidemiology ; Pharyngitis/microbiology ; Fimbriae, Bacterial/genetics ; Carrier Proteins ; },
abstract = {Among genes present in all group A streptococci (GAS), those encoding M-fibril and T-pilus proteins display the highest levels of sequence diversity, giving rise to the two primary serological typing schemes historically used to define strain. A new genotyping scheme for the pilin adhesin and backbone genes is developed and, when combined with emm typing, provides an account of the global GAS strain population. Cluster analysis based on nucleotide sequence similarity assigns most T-serotypes to discrete pilin backbone sequence clusters, yet the established T-types correspond to only half the clusters. The major pilin adhesin and backbone sequence clusters yield 98 unique combinations, defined as "pilin types." Numerous horizontal transfer events that involve pilin or emm genes generate extensive antigenic and functional diversity on the bacterial cell surface and lead to the emergence of new strains. Inferred pilin genotypes applied to a meta-analysis of global population-based collections of pharyngitis and impetigo isolates reveal highly significant associations between pilin genotypes and GAS infection at distinct ecological niches, consistent with a role for pilin gene products in adaptive evolution. Integration of emm and pilin typing into open-access online tools (pubmlst.org) ensures broad utility for end-users wanting to determine the architecture of M-fibril and T-pilus genes from genome assemblies.IMPORTANCEPrecision in defining the variant forms of infectious agents is critical to understanding their population biology and the epidemiology of associated diseases. Group A Streptococcus (GAS) is a global pathogen that causes a wide range of diseases and displays a highly diverse cell surface due to the antigenic heterogeneity of M-fibril and T-pilus proteins which also act as virulence factors of varied functions. emm genotyping is well-established and highly utilized, but there is no counterpart for pilin genes. A global GAS collection provides the basis for a comprehensive pilin typing scheme, and online tools for determining emm and pilin genotypes are developed. Application of these tools reveals the expansion of structural-functional diversity among GAS via horizontal gene transfer, as evidenced by unique combinations of surface protein genes. Pilin and emm genotype correlations with superficial throat vs skin infection provide new insights on the molecular determinants underlying key ecological and epidemiological trends.},
}
@article {pmid38585972,
year = {2024},
author = {Marin, MG and Wippel, C and Quinones-Olvera, N and Behruznia, M and Jeffrey, BM and Harris, M and Mann, BC and Rosenthal, A and Jacobson, KR and Warren, RM and Li, H and Meehan, CJ and Farhat, MR},
title = {Analysis of the limited M. tuberculosis accessory genome reveals potential pitfalls of pan-genome analysis approaches.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.03.21.586149},
pmid = {38585972},
issn = {2692-8205},
support = {R01 AI155765/AI/NIAID NIH HHS/United States ; T15 LM007092/LM/NLM NIH HHS/United States ; },
abstract = {Pan-genome analysis is a fundamental tool for studying bacterial genome evolution; however, the variety of methods used to define and measure the pan-genome poses challenges to the interpretation and reliability of results. To quantify sources of bias and error related to common pan-genome analysis approaches, we evaluated different approaches applied to curated collection of 151 Mycobacterium tuberculosis (Mtb) isolates. Mtb is characterized by its clonal evolution, absence of horizontal gene transfer, and limited accessory genome, making it an ideal test case for this study. Using a state-of-the-art graph-genome approach, we found that a majority of the structural variation observed in Mtb originates from rearrangement, deletion, and duplication of redundant nucleotide sequences. In contrast, we found that pan-genome analyses that focus on comparison of coding sequences (at the amino acid level) can yield surprisingly variable results, driven by differences in assembly quality and the softwares used. Upon closer inspection, we found that coding sequence annotation discrepancies were a major contributor to inflated Mtb accessory genome estimates. To address this, we developed panqc, a software that detects annotation discrepancies and collapses nucleotide redundancy in pan-genome estimates. When applied to Mtb and E. coli pan-genomes, panqc exposed distinct biases influenced by the genomic diversity of the population studied. Our findings underscore the need for careful methodological selection and quality control to accurately map the evolutionary dynamics of a bacterial species.},
}
@article {pmid38585963,
year = {2024},
author = {Maier, JL and Gin, C and Callahan, B and Sheriff, EK and Duerkop, BA and Kleiner, M},
title = {Pseudo-pac site sequences used by phage P22 in generalized transduction of Salmonella.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38585963},
issn = {2692-8205},
support = {R01 AI141479/AI/NIAID NIH HHS/United States ; R35 GM138362/GM/NIGMS NIH HHS/United States ; },
abstract = {Salmonella enterica Serovar Typhimurium (Salmonella) and its bacteriophage P22 are a model system for the study of horizontal gene transfer by generalized transduction. Typically, the P22 DNA packaging machinery initiates packaging when a short sequence of DNA, known as the pac site, is recognized on the P22 genome. However, sequences similar to the pac site in the host genome, called pseudo-pac sites, lead to erroneous packaging and subsequent generalized transduction of Salmonella DNA. While the general genomic locations of the Salmonella pseudo-pac sites are known, the sequences themselves have not been determined. We used visualization of P22 sequencing reads mapped to host Salmonella genomes to define regions of generalized transduction initiation and the likely locations of pseudo-pac sites. We searched each genome region for the sequence with the highest similarity to the P22 pac site and aligned the resulting sequences. We built a regular expression (sequence match pattern) from the alignment and used it to search the genomes of two P22-susceptible Salmonella strains- LT2 and 14028S- for sequence matches. The final regular expression successfully identified pseudo-pac sites in both LT2 and 14028S that correspond with generalized transduction initiation sites in mapped read coverages. The pseudo-pac site sequences identified in this study can be used to predict locations of generalized transduction in other P22-susceptible hosts or to initiate generalized transduction at specific locations in P22-susceptible hosts with genetic engineering. Furthermore, the bioinformatics approach used to identify the Salmonella pseudo-pac sites in this study could be applied to other phage-host systems.},
}
@article {pmid38579360,
year = {2024},
author = {Whitfield, GB and Brun, YV},
title = {The type IVc pilus: just a Tad different.},
journal = {Current opinion in microbiology},
volume = {79},
number = {},
pages = {102468},
doi = {10.1016/j.mib.2024.102468},
pmid = {38579360},
issn = {1879-0364},
mesh = {*Fimbriae, Bacterial/metabolism/genetics/physiology ; Caulobacter crescentus/genetics/metabolism/physiology ; Bacteria/genetics/metabolism ; Bacterial Adhesion/genetics ; Gene Transfer, Horizontal ; Fimbriae Proteins/genetics/metabolism ; Bacterial Proteins/metabolism/genetics ; Myxococcus xanthus/genetics/physiology/metabolism ; },
abstract = {Bacteria utilize type IV pili (T4P) to interact with their environment, where they facilitate processes including motility, adherence, and DNA uptake. T4P require multisubunit, membrane-spanning nanomachines for assembly. The tight adherence (Tad) pili are an Archaea-derived T4P subgroup whose machinery exhibits significant mechanistic and architectural differences from bacterial type IVa and IVb pili. Most Tad biosynthetic genes are encoded in a single locus that is widespread in bacteria due to facile acquisition via horizontal gene transfer. These loci experience extensive structural rearrangements, including the acquisition of novel regulatory or biosynthetic genes, which fine-tune their function. This has permitted their integration into many different bacterial lifestyles, including the Caulobacter crescentus cell cycle, Myxococcus xanthus predation, and numerous plant and mammalian pathogens and symbionts.},
}
@article {pmid38578105,
year = {2024},
author = {Darby, EM and Moran, RA and Holden, E and Morris, T and Harrison, F and Clough, B and McInnes, RS and Schneider, L and Frickel, EM and Webber, MA and Blair, JMA},
title = {Differential development of antibiotic resistance and virulence between Acinetobacter species.},
journal = {mSphere},
volume = {9},
number = {5},
pages = {e0010924},
pmid = {38578105},
issn = {2379-5042},
support = {/WT_/Wellcome Trust/United Kingdom ; 222386/Z/21/Z//Wellcome Trust (WT)/ ; },
mesh = {*Acinetobacter/genetics/drug effects/pathogenicity ; Virulence/genetics ; *Acinetobacter Infections/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Biofilms/drug effects/growth &amp; development ; *Microbial Sensitivity Tests ; Animals ; Humans ; Drug Resistance, Bacterial/genetics ; Acinetobacter baumannii/genetics/drug effects/pathogenicity ; Mice ; Gene Transfer, Horizontal ; United Kingdom ; Female ; Plasmids/genetics ; },
abstract = {UNLABELLED: The two species that account for most cases of Acinetobacter-associated bacteremia in the United Kingdom are Acinetobacter lwoffii, often a commensal but also an emerging pathogen, and Acinetobacter baumannii, a well-known antibiotic-resistant species. While these species both cause similar types of human infection and occupy the same niche, A. lwoffii (unlike A. baumannii) has thus far remained susceptible to antibiotics. Comparatively little is known about the biology of A. lwoffii, and this is the largest study on it conducted to date, providing valuable insights into its behaviour and potential threat to human health. This study aimed to explain the antibiotic susceptibility, virulence, and fundamental biological differences between these two species. The relative susceptibility of A. lwoffii was explained as it encoded fewer antibiotic resistance and efflux pump genes than A. baumannii (9 and 30, respectively). While both species had markers of horizontal gene transfer, A. lwoffii encoded more DNA defense systems and harbored a far more restricted range of plasmids. Furthermore, A. lwoffii displayed a reduced ability to select for antibiotic resistance mutations, form biofilm, and infect both in vivo and in in vitro models of infection. This study suggests that the emerging pathogen A. lwoffii has remained susceptible to antibiotics because mechanisms exist to make it highly selective about the DNA it acquires, and we hypothesize that the fact that it only harbors a single RND system restricts the ability to select for resistance mutations. This provides valuable insights into how development of resistance can be constrained in Gram-negative bacteria.<br><br>IMPORTANCE: Acinetobacter lwoffii is often a harmless commensal but is also an emerging pathogen and is the most common cause of Acinetobacter-derived bloodstream infections in England and Wales. In contrast to the well-studied and often highly drug-resistant A. baumannii, A. lwoffii has remained susceptible to antibiotics. This study explains why this organism has not evolved resistance to antibiotics. These new insights are important to understand why and how some species develop antibiotic resistance, while others do not, and could inform future novel treatment strategies.},
}
@article {pmid38574109,
year = {2024},
author = {Samson, S and Lord, &#xc9; and Makarenkov, V},
title = {Assessing the emergence time of SARS-CoV-2 zoonotic spillover.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0301195},
pmid = {38574109},
issn = {1932-6203},
mesh = {Animals ; Humans ; SARS-CoV-2/genetics ; Phylogeny ; *Chiroptera ; Pangolins/genetics ; *COVID-19/epidemiology ; Bayes Theorem ; Zoonoses/epidemiology ; },
abstract = {Understanding the evolution of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) and its relationship to other coronaviruses in the wild is crucial for preventing future virus outbreaks. While the origin of the SARS-CoV-2 pandemic remains uncertain, mounting evidence suggests the direct involvement of the bat and pangolin coronaviruses in the evolution of the SARS-CoV-2 genome. To unravel the early days of a probable zoonotic spillover event, we analyzed genomic data from various coronavirus strains from both human and wild hosts. Bayesian phylogenetic analysis was performed using multiple datasets, using strict and relaxed clock evolutionary models to estimate the occurrence times of key speciation, gene transfer, and recombination events affecting the evolution of SARS-CoV-2 and its closest relatives. We found strong evidence supporting the presence of temporal structure in datasets containing SARS-CoV-2 variants, enabling us to estimate the time of SARS-CoV-2 zoonotic spillover between August and early October 2019. In contrast, datasets without SARS-CoV-2 variants provided mixed results in terms of temporal structure. However, they allowed us to establish that the presence of a statistically robust clade in the phylogenies of gene S and its receptor-binding (RBD) domain, including two bat (BANAL) and two Guangdong pangolin coronaviruses (CoVs), is due to the horizontal gene transfer of this gene from the bat CoV to the pangolin CoV that occurred in the middle of 2018. Importantly, this clade is closely located to SARS-CoV-2 in both phylogenies. This phylogenetic proximity had been explained by an RBD gene transfer from the Guangdong pangolin CoV to a very recent ancestor of SARS-CoV-2 in some earlier works in the field before the BANAL coronaviruses were discovered. Overall, our study provides valuable insights into the timeline and evolutionary dynamics of the SARS-CoV-2 pandemic.},
}
@article {pmid38572613,
year = {2024},
author = {Moore, KA and Petersen, AP and Zierden, HC},
title = {Microorganism-derived extracellular vesicles: emerging contributors to female reproductive health.},
journal = {Nanoscale},
volume = {16},
number = {17},
pages = {8216-8235},
doi = {10.1039/d3nr05524h},
pmid = {38572613},
issn = {2040-3372},
mesh = {*Extracellular Vesicles/metabolism ; Female ; Humans ; *Vagina/microbiology/metabolism ; *Microbiota ; *Reproductive Health ; Bacteria/metabolism ; },
abstract = {Extracellular vesicles (EVs) are cell-derived nanoparticles that carry small molecules, nucleic acids, and proteins long distances in the body facilitating cell-cell communication. Microorganism-derived EVs mediate communication between parent cells and host cells, with recent evidence supporting their role in biofilm formation, horizontal gene transfer, and suppression of the host immune system. As lipid-bound bacterial byproducts, EVs demonstrate improved cellular uptake and distribution in vivo compared to cell-free nucleic acids, proteins, or small molecules, allowing these biological nanoparticles to recapitulate the effects of parent cells and contribute to a range of human health outcomes. Here, we focus on how EVs derived from vaginal microorganisms contribute to gynecologic and obstetric outcomes. As the composition of the vaginal microbiome significantly impacts women's health, we discuss bacterial EVs from both healthy and dysbiotic vaginal microbiota. We also examine recent work done to evaluate the role of EVs from common vaginal bacterial, fungal, and parasitic pathogens in pathogenesis of female reproductive tract disease. We highlight evidence for the role of EVs in women's health, gaps in current knowledge, and opportunities for future work. Finally, we discuss how leveraging the innate interactions between microorganisms and mammalian cells may establish EVs as a novel therapeutic modality for gynecologic and obstetric indications.},
}
@article {pmid38568420,
year = {2024},
author = {Hamrick, GS and Maddamsetti, R and Son, HI and Wilson, ML and Davis, HM and You, L},
title = {Programming Dynamic Division of Labor Using Horizontal Gene Transfer.},
journal = {ACS synthetic biology},
volume = {13},
number = {4},
pages = {1142-1151},
doi = {10.1021/acssynbio.3c00615},
pmid = {38568420},
issn = {2161-5063},
support = {R01 EB031869/EB/NIBIB NIH HHS/United States ; },
mesh = {*Microbial Consortia ; Gene Transfer, Horizontal ; *Microbiota ; Metabolic Engineering ; Genomics ; },
abstract = {The metabolic engineering of microbes has broad applications, including biomanufacturing, bioprocessing, and environmental remediation. The introduction of a complex, multistep pathway often imposes a substantial metabolic burden on the host cell, restraining the accumulation of productive biomass and limiting pathway efficiency. One strategy to alleviate metabolic burden is the division of labor (DOL) in which different subpopulations carry out different parts of the pathway and work together to convert a substrate into a final product. However, the maintenance of different engineered subpopulations is challenging due to competition and convoluted interstrain population dynamics. Through modeling, we show that dynamic division of labor (DDOL), which we define as the DOL between indiscrete populations capable of dynamic and reversible interchange, can overcome these limitations and enable the robust maintenance of burdensome, multistep pathways. We propose that DDOL can be mediated by horizontal gene transfer (HGT) and use plasmid genomics to uncover evidence that DDOL is a strategy utilized by natural microbial communities. Our work suggests that bioengineers can harness HGT to stabilize synthetic metabolic pathways in microbial communities, enabling the development of robust engineered systems for deployment in a variety of contexts.},
}
@article {pmid38568247,
year = {2024},
author = {Fu, S and Iqbal, B and Li, G and Alabbosh, KF and Khan, KA and Zhao, X and Raheem, A and Du, D},
title = {The role of microbial partners in heavy metal metabolism in plants: a review.},
journal = {Plant cell reports},
volume = {43},
number = {4},
pages = {111},
pmid = {38568247},
issn = {1432-203X},
support = {BK20220030//Open Project of the Carbon Peak and Carbon Neutrality Technology Innovation Foundation of Jiangsu Province/ ; 32271587//National Natural Science Foundation of China/ ; 3235041400//National Natural Science Foundation of China/ ; 18JDG039//Senior Talent Foundation of Jiangsu University/ ; RGP2/360/44//Deanship of Scientific Research at King Khalid University Saudi Arabia for funding this work through Large Groups Project/ ; },
mesh = {*Herb-Drug Interactions ; *Metals, Heavy/toxicity ; Protein Processing, Post-Translational ; Soil ; },
abstract = {Heavy metal pollution threatens plant growth and development as well as ecological stability. Here, we synthesize current research on the interplay between plants and their microbial symbionts under heavy metal stress, highlighting the mechanisms employed by microbes to enhance plant tolerance and resilience. Several key strategies such as bioavailability alteration, chelation, detoxification, induced systemic tolerance, horizontal gene transfer, and methylation and demethylation, are examined, alongside the genetic and molecular basis governing these plant-microbe interactions. However, the complexity of plant-microbe interactions, coupled with our limited understanding of the associated mechanisms, presents challenges in their practical application. Thus, this review underscores the necessity of a more detailed understanding of how plants and microbes interact and the importance of using a combined approach from different scientific fields to maximize the benefits of these microbial processes. By advancing our knowledge of plant-microbe synergies in the metabolism of heavy metals, we can develop more effective bioremediation strategies to combat the contamination of soil by heavy metals.},
}
@article {pmid38565359,
year = {2024},
author = {Medeiros, P and Canato, D and Braz, ASK and Paulino, LC},
title = {Phylogenetic analyses reveal insights into interdomain horizontal gene transfer of microbial lipases.},
journal = {Molecular phylogenetics and evolution},
volume = {195},
number = {},
pages = {108069},
doi = {10.1016/j.ympev.2024.108069},
pmid = {38565359},
issn = {1095-9513},
mesh = {Humans ; Phylogeny ; *Gene Transfer, Horizontal ; *Evolution, Molecular ; Bacteria/genetics ; Gene Duplication ; },
abstract = {Microbial lipases play a pivotal role in a wide range of biotechnological processes and in the human skin microbiome. However, their evolution remains poorly understood. Accessing the evolutionary process of lipases could contribute to future applications in health and biotechnology. We investigated genetic events associated with the evolutionary trajectory of the microbial family LIP lipases. Using phylogenetic analysis, we identified two distinct horizontal gene transfer (HGT) events from Bacteria to Fungi. Further analysis of human cutaneous mycobiome members such as the lipophilic Malassezia yeasts and CUG-Ser-1 clade (including Candida sp. and other microorganisms associated with cutaneous mycobiota) revealed recent evolutionary processes, with multiple gene duplication events. The Lid region of fungal lipases, crucial for substrate interaction, exhibits varying degrees of conservation among different groups. Our findings suggest the adaptability of the fungal LIP family in various genetic and metabolic contexts and its potential role in niche exploration.},
}
@article {pmid38565354,
year = {2024},
author = {Li, X and Chen, T and Ren, Q and Lu, J and Cao, S and Liu, C and Li, Y},
title = {Phages in sludge from the A/O wastewater treatment process play an important role in the transmission of ARGs.},
journal = {The Science of the total environment},
volume = {926},
number = {},
pages = {172111},
doi = {10.1016/j.scitotenv.2024.172111},
pmid = {38565354},
issn = {1879-1026},
mesh = {Humans ; Swine ; Animals ; Sewage/microbiology ; Wastewater ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; *Bacteriophages/genetics ; Drug Resistance, Microbial/genetics ; *Water Purification ; },
abstract = {Phages can influence the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) through transduction, but their profiles and effects on the transmission of ARGs are unclear, especially in complex swine sludge. In this study, we investigated the characterization of phage and ARG profiles in sludge generated from anoxic/oxic (A/O) wastewater treatment processes on swine farms using metagenomes and viromes. The results demonstrated that 205-221 subtypes of ARGs could be identified in swine sludge, among which sul1, tet(M), and floR were the dominant ARGs, indicating that sludge is an important reservoir of ARGs, especially in sludge (S) tanks. The greater abundance of mobile genetic elements (MGEs) in the S tank could significantly contribute to the greater abundance of ARGs there compared to the anoxic (A) and oxic (O) tanks (P < 0.05). However, when we compared the abundances of ARGs and MGEs in the A and O tanks, we observed opposite significant differences (P < 0.05), suggesting that MGEs are not the only factor influencing the abundance of ARGs. The high proportion of lysogenic phages in sludge from the S tank can also have a major impact on the ARG profile. Siphoviridae, Myoviridae, and Podoviridae were the dominant phage families in sludge, and a network diagram of bacteria-ARG-phages revealed that dominant phages and bacteria acted simultaneously as potential hosts for ARGs, which may have led to phage-mediated HGT of ARGs. Therefore, the risk of phage-mediated HGT of ARGs cannot be overlooked.},
}
@article {pmid38564675,
year = {2024},
author = {Lehman, SS and Verhoeve, VI and Driscoll, TP and Beckmann, JF and Gillespie, JJ},
title = {Metagenome diversity illuminates the origins of pathogen effectors.},
journal = {mBio},
volume = {15},
number = {5},
pages = {e0075923},
pmid = {38564675},
issn = {2150-7511},
support = {R21 AI156762/AI/NIAID NIH HHS/United States ; R21 AI166832/AI/NIAID NIH HHS/United States ; },
mesh = {*Metagenome ; *Rickettsia/genetics/classification ; *Phylogeny ; *Genome, Bacterial ; Evolution, Molecular ; Rickettsiales/genetics/classification ; Genetic Variation ; Type IV Secretion Systems/genetics/metabolism ; Gene Transfer, Horizontal ; Humans ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Recent metagenome-assembled genome (MAG) analyses have profoundly impacted Rickettsiology systematics. The discovery of basal lineages (novel families Mitibacteraceae and Athabascaceae) with predicted extracellular lifestyles exposed an evolutionary timepoint for the transition to host dependency, which seemingly occurred independent of mitochondrial evolution. Notably, these basal rickettsiae carry the Rickettsiales vir homolog (rvh) type IV secretion system and purportedly use rvh to kill congener microbes rather than parasitize host cells as described for later-evolving rickettsial pathogens. MAG analysis also substantially increased diversity for the genus Rickettsia and delineated a sister lineage (the novel genus Tisiphia) that stands to inform on the emergence of human pathogens from protist and invertebrate endosymbionts. Herein, we probed Rickettsiales MAG and genomic diversity for the distribution of Rickettsia rvh effectors to ascertain their origins. A sparse distribution of most Rickettsia rvh effectors outside of Rickettsiaceae lineages illuminates unique rvh evolution from basal extracellular species and other rickettsial families. Remarkably, nearly every effector was found in multiple divergent forms with variable architectures, indicating profound roles for gene duplication and recombination in shaping effector repertoires in Rickettsia pathogens. Lateral gene transfer plays a prominent role in shaping the rvh effector landscape, as evinced by the discovery of many effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchange between Rickettsia and Legionella species. Our study exemplifies how MAGs can yield insight into pathogen effector origins, particularly how effector architectures might become tailored to the discrete host cell functions of different eukaryotic hosts.IMPORTANCEWhile rickettsioses are deadly vector-borne human diseases, factors distinguishing Rickettsia pathogens from the innumerable bevy of environmental rickettsial endosymbionts remain lacking. Recent metagenome-assembled genome (MAG) studies revealed evolutionary timepoints for rickettsial transitions to host dependency. The rvh type IV secretion system was likely repurposed from congener killing in basal extracellular species to parasitizing host cells in later-evolving pathogens. Our analysis of MAG diversity for over two dozen rvh effectors unearthed their presence in some non-pathogens. However, most effectors were found in multiple divergent forms with variable architectures, indicating gene duplication and recombination-fashioned effector repertoires of Rickettsia pathogens. Lateral gene transfer substantially shaped pathogen effector arsenals, evinced by the discovery of effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchanges between Rickettsia and Legionella species. Our study exemplifies how MAGs yield insight into pathogen effector origins and evolutionary processes tailoring effectors to eukaryotic host cell biology.},
}
@article {pmid38561802,
year = {2024},
author = {Lanoizelet, M and Elkhoury Youhanna, C and Roure, A and Darras, S},
title = {Molecular control of cellulosic fin morphogenesis in ascidians.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {74},
pmid = {38561802},
issn = {1741-7007},
support = {Emergence 2021//Sorbonne Universit&#xe9;/ ; DBM2020//Institut des sciences biologiques/ ; DBM2022//Institut des sciences biologiques/ ; },
mesh = {Animals ; *Urochordata/genetics ; Morphogenesis/genetics ; Epidermis ; Peripheral Nervous System ; Larva/genetics ; Cellulose ; },
abstract = {BACKGROUND: The tunicates form a group of filter-feeding marine animals closely related to vertebrates. They share with them a number of features such as a notochord and a dorsal neural tube in the tadpole larvae of ascidians, one of the three groups that make tunicates. However, a number of typical chordate characters have been lost in different branches of tunicates, a diverse and fast-evolving phylum. Consequently, the tunic, a sort of exoskeleton made of extracellular material including cellulose secreted by the epidermis, is the unifying character defining the tunicate phylum. In the larva of ascidians, the tunic differentiates in the tail into a median fin (with dorsal and ventral extended blades) and a caudal fin.<br><br>RESULTS: Here we have performed experiments in the ascidian Phallusia mammillata to address the molecular control of tunic 3D morphogenesis. We have demonstrated that the tail epidermis medio-lateral patterning essential for peripheral nervous system specification also controls tunic elongation into fins. More specifically, when tail epidermis midline identity was abolished by BMP signaling inhibition, or CRISPR/Cas9 inactivation of the transcription factor coding genes Msx or Klf1/2/4/17, median fin did not form. We postulated that this genetic program should regulate effectors of tunic secretion. We thus analyzed the expression and regulation in different ascidian species of two genes acquired by horizontal gene transfer (HGT) from bacteria, CesA coding for a cellulose synthase and Gh6 coding for a cellulase. We have uncovered an unexpected dynamic history of these genes in tunicates and high levels of variability in gene expression and regulation among ascidians. Although, in Phallusia, Gh6 has a regionalized expression in the epidermis compatible with an involvement in fin elongation, our functional studies indicate a minor function during caudal fin formation only.<br><br>CONCLUSIONS: Our study constitutes an important step in the study of the integration of HGT-acquired genes into developmental networks and a cellulose-based morphogenesis of extracellular material in animals.},
}
@article {pmid38561223,
year = {2024},
author = {LeBleu, VS and Kanasaki, K and Lovisa, S and Alge, JL and Kim, J and Chen, Y and Teng, Y and Gerami-Naini, B and Sugimoto, H and Kato, N and Revuelta, I and Grau, N and Sleeman, JP and Taduri, G and Kizu, A and Rafii, S and Hochedlinger, K and Quaggin, SE and Kalluri, R},
title = {Genetic reprogramming with stem cells regenerates glomerular epithelial podocytes in Alport syndrome.},
journal = {Life science alliance},
volume = {7},
number = {6},
pages = {},
pmid = {38561223},
issn = {2575-1077},
support = {P30 CA016672/CA/NCI NIH HHS/United States ; R01 DK055001/DK/NIDDK NIH HHS/United States ; T32 DK007760/DK/NIDDK NIH HHS/United States ; T32 HL007374/HL/NHLBI NIH HHS/United States ; },
mesh = {Mice ; Animals ; *Nephritis, Hereditary/genetics/metabolism ; *Podocytes/metabolism ; Collagen Type IV/genetics/metabolism ; Glomerular Basement Membrane/metabolism ; Stem Cells/metabolism ; },
abstract = {Glomerular filtration relies on the type IV collagen (ColIV) network of the glomerular basement membrane, namely, in the triple helical molecules containing the α3, α4, and α5 chains of ColIV. Loss of function mutations in the genes encoding these chains (Col4a3, Col4a4, and Col4a5) is associated with the loss of renal function observed in Alport syndrome (AS). Precise understanding of the cellular basis for the patho-mechanism remains unknown and a specific therapy for this disease does not currently exist. Here, we generated a novel allele for the conditional deletion of Col4a3 in different glomerular cell types in mice. We found that podocytes specifically generate α3 chains in the developing glomerular basement membrane, and that its absence is sufficient to impair glomerular filtration as seen in AS. Next, we show that horizontal gene transfer, enhanced by TGFβ1 and using allogenic bone marrow-derived mesenchymal stem cells and induced pluripotent stem cells, rescues Col4a3 expression and revive kidney function in Col4a3-deficient AS mice. Our proof-of-concept study supports that horizontal gene transfer such as cell fusion enables cell-based therapy in Alport syndrome.},
}
@article {pmid38560215,
year = {2024},
author = {Comba-González, NB and Chaves-Moreno, D and Santamaría-Vanegas, J and Montoya-Castaño, D},
title = {A pan-genomic assessment: Delving into the genome of the marine epiphyte Bacillus altitudinis strain 19_A and other very close Bacillus strains from multiple environments.},
journal = {Heliyon},
volume = {10},
number = {7},
pages = {e27820},
pmid = {38560215},
issn = {2405-8440},
abstract = {Marine macroalgae are the habitat of epiphytic bacteria and provide several conditions for a beneficial biological interaction to thrive. Although Bacillus is one of the most abundant epiphytic genera, genomic information on marine macroalgae-associated Bacillus species remains scarce. In this study, we further investigated our previously published genome of the epiphytic strain Bacillus altitudinis 19_A to find features that could be translated to potential metabolites produced by this microorganism, as well as genes that play a role in its interaction with its macroalgal host. To achieve this goal, we performed a pan-genome analysis of Bacillus sp. and a codon bias assessment, including the genome of the strain Bacillus altitudinis 19_A and 29 complete genome sequences of closely related Bacillus strains isolated from soil, marine environments, plants, extreme environments, air, and food. This genomic analysis revealed that Bacillus altitudinis 19_A possessed unique genes encoding proteins involved in horizontal gene transfer, DNA repair, transcriptional regulation, and bacteriocin biosynthesis. In this comparative analysis, codon bias was not associated with the habitat of the strains studied. Some accessory genes were identified in the Bacillus altitudinis 19_A genome that could be related to its epiphytic lifestyle, as well as gene clusters for the biosynthesis of a sporulation-killing factor and a bacteriocin, showing their potential as a source of antimicrobial peptides. Our results provide a comprehensive view of the Bacillus altitudinis 19_A genome to understand its adaptation to the marine environment and its potential as a producer of bioactive compounds.},
}
@article {pmid38555673,
year = {2024},
author = {Sun, H and Chang, H and Zhu, Y and Li, X and Yang, X and Zhou, X and Wu, D and Ding, J and Liu, Y},
title = {Strong suppression of silver nanoparticles on antibiotic resistome in anammox process.},
journal = {Journal of hazardous materials},
volume = {470},
number = {},
pages = {134128},
doi = {10.1016/j.jhazmat.2024.134128},
pmid = {38555673},
issn = {1873-3336},
mesh = {*Silver/chemistry/pharmacology ; *Metal Nanoparticles/chemistry/toxicity ; *Drug Resistance, Microbial/genetics/drug effects ; Anti-Bacterial Agents/pharmacology/chemistry ; Gene Transfer, Horizontal ; Sewage/microbiology ; Nitrogen/chemistry/metabolism ; Bacteria/drug effects/genetics/metabolism ; Anaerobiosis ; Microbiota/drug effects ; Oxidation-Reduction ; },
abstract = {This study comprehensively deciphered the effect of silver nanoparticles (AgNPs) on anammox flocculent sludge, including nitrogen removal performance, microbial community structure, functional enzyme abundance, antibiotic resistance gene (ARGs) dissemination, and horizontal gene transfer (HGT) mechanisms. After long-term exposure to 0-2.5 mg/L AgNPs for 200 cycles, anammox performance significantly decreased (P < 0.05), while the relative abundances of dominant Ca. Kuenenia and anammox-related enzymes (hzsA, nirK) increased compared to the control (P < 0.05). For antibiotic resistome, ARG abundance hardly changed with 0-0.5 mg/L AgNPs but decreased by approximately 90% with 1.5-2.5 mg/L AgNPs. More importantly, AgNPs effectively inhibited MGE-mediated HGT of ARGs. Additionally, structural equation model (SEM) disclosed the underlying relationship between AgNPs, the antibiotic resistome, and the microbial community. Overall, AgNPs suppressed the anammox-driven nitrogen cycle, regulated the microbial community, and prevented the spread of ARGs in anammox flocs. This study provides a theoretical baseline for an advanced understanding of the ecological roles of nanoparticles and resistance elements in engineered ecosystems.},
}
@article {pmid38554973,
year = {2024},
author = {Song, H and Yoo, JS and Unno, T},
title = {Discerning the dissemination mechanisms of antibiotic resistance genes through whole genome sequencing of extended-spectrum beta-lactamase (ESBL)-producing E. coli isolated from veterinary clinics and farms in South Korea.},
journal = {The Science of the total environment},
volume = {926},
number = {},
pages = {172068},
doi = {10.1016/j.scitotenv.2024.172068},
pmid = {38554973},
issn = {1879-1026},
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Escherichia coli ; Farms ; *Escherichia coli Infections/microbiology ; Hospitals, Animal ; beta-Lactamases/genetics ; Drug Resistance, Microbial ; Republic of Korea ; Plasmids/genetics ; Whole Genome Sequencing ; },
abstract = {Extended-spectrum beta-lactamase (ESBL)-producing bacteria are resistant to most beta-lactams, including third-generation cephalosporins, limiting the treatment methods against the infections they cause. In this study, we performed whole genome sequencing of ESBL-producing E. coli to determine the mechanisms underlying the dissemination of antibiotic resistance genes. We analyzed 141 ESBL-producing isolates which had been collected from 16 veterinary clinics and 16 farms in South Korea. Long- and short-read sequencing platforms were used to obtain high-quality assemblies. The results showed that blaCTX-M is the dominant ESBL gene type found in South Korea. The spread of blaCTX-M appears to have been facilitated by both clonal spread between different host species and conjugation. Most blaCTX-M genes were found associated with diverse mobile genetic elements that may contribute to the chromosomal integration of the genes. Diverse incompatibility groups of blaCTX-M-harboring plasmids were also observed, which allows their spread among a variety of bacteria. Comprehensive whole genome sequence analysis was useful for the identification of the most prevalent types of ESBL genes and their dissemination mechanisms. The results of this study suggest that the propagation of ESBL genes can occur through clonal spread and plasmid-mediated dissemination, and that suitable action plans should be developed to prevent further propagation of these genes.},
}
@article {pmid38554512,
year = {2024},
author = {Qin, J and Qi, X and Li, Y and Tang, Z and Zhang, X and Ru, S and Xiong, JQ},
title = {Bisphenols can promote antibiotic resistance by inducing metabolic adaptations and natural transformation.},
journal = {Journal of hazardous materials},
volume = {470},
number = {},
pages = {134149},
doi = {10.1016/j.jhazmat.2024.134149},
pmid = {38554512},
issn = {1873-3336},
mesh = {*Phenols/toxicity/metabolism ; *Acinetobacter/drug effects/genetics/metabolism ; *Benzhydryl Compounds/toxicity/metabolism ; Animals ; Plasmids ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Water Pollutants, Chemical/toxicity/metabolism ; Adaptation, Physiological ; Plasticizers/toxicity ; Anti-Bacterial Agents/pharmacology/toxicity ; *Sulfones ; },
abstract = {Whether bisphenols, as plasticizers, can influence bacterial uptake of antibiotic resistance genes (ARGs) in natural environment, as well as the underlying mechanism remains largely unknown. Our results showed that four commonly used bisphenols (bisphenol A, S, F, and AF) at their environmental relative concentrations can significantly promote transmission of ARGs by 2.97-3.56 times in Acinetobacter baylyi ADP1. Intriguingly, we observed ADP1 acquired resistance by integrating plasmids uptake and cellular metabolic adaptations other than through reactive oxygen species mediated pathway. Metabolic adaptations including upregulation of capsules polysaccharide biosynthesis and intracellularly metabolic enzymes, which enabled formation of thicker capsules for capturing free plasmids, and degradation of accumulated compounds. Simultaneously, genes encoding DNA uptake and translocation machinery were incorporated to enhance natural transformation of antibiotic resistance carrying plasmids. We further exposed aquatic fish to bisphenols for 120 days to monitor their long-term effects in aquatic environment, which showed that intestinal bacteria communities were dominated by a drug resistant microbiome. Our study provides new insight into the mechanism of enhanced natural transformation of ARGs by bisphenols, and highlights the investigations for unexpectedly-elevated antibiotic-resistant risks by structurally related environmental chemicals.},
}
@article {pmid38552150,
year = {2024},
author = {Howard-Varona, C and Lindback, MM and Fudyma, JD and Krongauz, A and Solonenko, NE and Zayed, AA and Andreopoulos, WB and Olson, HM and Kim, YM and Kyle, JE and Glavina Del Rio, T and Adkins, JN and Tfaily, MM and Paul, S and Sullivan, MB and Duhaime, MB},
title = {Environment-specific virocell metabolic reprogramming.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38552150},
issn = {1751-7370},
support = {2149505//NSF Advances in Biological Informatics/ ; DE-AC05-76RL0-1830//U.S. Department of Energy/ ; //Joint Genome Institute/ ; //U.S. Department of Energy/ ; 1536989//National Science Foundation/ ; //University of Michigan/ ; 034//C-CoMP/ ; //Department of Energy/ ; T32 AI112542/AI/NIAID NIH HHS/United States ; 2055455//NSF Polar Programs/ ; 1-T32-AI-112542//National Institutes of Health (NIH)/National Institute of Allergy and Infectious Diseases (NIAID)/ ; //Facilities Integrating Collaborations for User Science/ ; 3790//Gordon and Betty Moore Foundation/ ; //EMSL/ ; //Office of Science/ ; DGE1256260//NSF Graduate Research Fellowship/ ; DE-AC02-05CH11231//Biological and Environmental Research/ ; C-CoMP NSF-STC 2019589//NSF Center for Chemical Currencies of a Microbial Planet/ ; //Environmental Molecular Sciences Laboratory/ ; DE-SC0020173//Office of Biological and Environmental Research/ ; },
mesh = {*Bacteriophages/genetics/physiology ; Proteomics ; Phosphates/metabolism ; Metabolomics ; Systems Biology ; Transcriptome ; Metabolic Reprogramming ; },
abstract = {Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a "virocell," is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.},
}
@article {pmid38551849,
year = {2024},
author = {Masuda, T and Mareš, J and Shiozaki, T and Inomura, K and Fujiwara, A and Prášil, O},
title = {Crocosphaera watsonii - A widespread nitrogen-fixing unicellular marine cyanobacterium.},
journal = {Journal of phycology},
volume = {60},
number = {3},
pages = {604-620},
doi = {10.1111/jpy.13450},
pmid = {38551849},
issn = {1529-8817},
support = {23-06593S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; JP23H02301//Japan Society for the Promotion of Science/ ; JPMJPR23GA//JST, PRESTO/ ; },
mesh = {*Cyanobacteria/genetics/metabolism/physiology ; *Nitrogen Fixation ; *Phylogeny ; },
abstract = {Crocosphaera watsonii is a unicellular N2-fixing (diazotrophic) cyanobacterium observed in tropical and subtropical oligotrophic oceans. As a diazotroph, it can be a source of bioavailable nitrogen (N) to the microbial community in N-limited environments, and this may fuel primary production in the regions where it occurs. Crocosphaera watsonii has been the subject of intense study, both in culture and in field populations. Here, we summarize the current understanding of the phylogenetic and physiological diversity of C. watsonii, its distribution, and its ecological niche. Analysis of the relationships among the individual Crocosphaera species and related free-living and symbiotic lineages of diazotrophs based on the nifH gene have shown that the C. watsonii group holds a basal position and that its sequence is more similar to Rippkaea and Zehria than to other Crocosphaera species. This finding warrants further scrutiny to determine if the placement is related to a horizontal gene transfer event. Here, the nifH UCYN-B gene copy number from a recent synthesis effort was used as a proxy for relative C. watsonii abundance to examine patterns of C. watsonii distribution as a function of environmental factors, like iron and phosphorus concentration, and complimented with a synthesis of C. watsonii physiology. Furthermore, we have summarized the current knowledge of C. watsonii with regards to N2 fixation, photosynthesis, and quantitative modeling of physiology. Because N availability can limit primary production, C. watsonii is widely recognized for its importance to carbon and N cycling in ocean ecosystems, and we conclude this review by highlighting important topics for further research on this important species.},
}
@article {pmid38548766,
year = {2024},
author = {Pratt, CJ and Meili, CH and Jones, AL and Jackson, DK and England, EE and Wang, Y and Hartson, S and Rogers, J and Elshahed, MS and Youssef, NH},
title = {Anaerobic fungi in the tortoise alimentary tract illuminate early stages of host-fungal symbiosis and Neocallimastigomycota evolution.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {2714},
pmid = {38548766},
issn = {2041-1723},
support = {2029478//National Science Foundation (NSF)/ ; 2029478//National Science Foundation (NSF)/ ; },
mesh = {Humans ; Animals ; *Neocallimastigomycota/genetics/metabolism ; *Turtles/genetics ; Phylogeny ; Anaerobiosis ; Symbiosis/genetics ; Mammals ; Fungi/genetics ; },
abstract = {Anaerobic gut fungi (AGF, Neocallimastigomycota) reside in the alimentary tract of herbivores. While their presence in mammals is well documented, evidence for their occurrence in non-mammalian hosts is currently sparse. Culture-independent surveys of AGF in tortoises identified a unique community, with three novel deep-branching genera representing >90% of sequences in most samples. Representatives of all genera were successfully isolated under strict anaerobic conditions. Transcriptomics-enabled phylogenomic and molecular dating analyses indicated an ancient, deep-branching position in the AGF tree for these genera, with an evolutionary divergence time estimate of 104-112 million years ago (Mya). Such estimates push the establishment of animal-Neocallimastigomycota symbiosis from the late to the early Cretaceous. Further, tortoise-associated isolates (T-AGF) exhibited limited capacity for plant polysaccharides metabolism and lacked genes encoding several carbohydrate-active enzyme (CAZyme) families. Finally, we demonstrate that the observed curtailed degradation capacities and reduced CAZyme repertoire is driven by the paucity of horizontal gene transfer (HGT) in T-AGF genomes, compared to their mammalian counterparts. This reduced capacity was reflected in an altered cellulosomal production capacity in T-AGF. Our findings provide insights into the phylogenetic diversity, ecological distribution, evolutionary history, evolution of fungal-host nutritional symbiosis, and dynamics of genes acquisition in Neocallimastigomycota.},
}
@article {pmid38546735,
year = {2024},
author = {Klose, SM and Legione, AR and Bushell, RN and Browning, GF and Vaz, PK},
title = {Unveiling genome plasticity and a novel phage in Mycoplasma felis: Genomic investigations of four feline isolates.},
journal = {Microbial genomics},
volume = {10},
number = {3},
pages = {},
pmid = {38546735},
issn = {2057-5858},
mesh = {Cats ; Animals ; Horses ; Australia ; Genomics ; *Mycoplasma/genetics ; *Felis ; *Bacteriophages ; },
abstract = {Mycoplasma felis has been isolated from diseased cats and horses, but to date only a single fully assembled genome of this species, of an isolate from a horse, has been characterized. This study aimed to characterize and compare the completely assembled genomes of four clinical isolates of M. felis from three domestic cats, assembled with the aid of short- and long-read sequencing methods. The completed genomes encoded a median of 759 ORFs (range 743-777) and had a median average nucleotide identity of 98.2 % with the genome of the available equid origin reference strain. Comparative genomic analysis revealed the occurrence of multiple horizontal gene transfer events and significant genome reassortment. This had resulted in the acquisition or loss of numerous genes within the Australian felid isolate genomes, encoding putative proteins involved in DNA transfer, metabolism, DNA replication, host cell interaction and restriction modification systems. Additionally, a novel mycoplasma phage was detected in one Australian felid M. felis isolate by genomic analysis and visualized using cryo-transmission electron microscopy. This study has highlighted the complex genomic dynamics in different host environments. Furthermore, the sequences obtained in this work will enable the development of new diagnostic tools, and identification of future infection control and treatment options for the respiratory disease complex in cats.},
}
@article {pmid38543613,
year = {2024},
author = {Mei, L and Song, Y and Liu, X and Li, K and Guo, X and Liu, L and Liu, Y and Kozlakidis, Z and Cheong, IH and Wang, D and Wei, Q},
title = {Characterization and Implications of IncP-2A Plasmid pMAS152 Harboring Multidrug Resistance Genes in Extensively Drug-Resistant Pseudomonas aeruginosa.},
journal = {Microorganisms},
volume = {12},
number = {3},
pages = {},
pmid = {38543613},
issn = {2076-2607},
support = {001/WHO_/World Health Organization/International ; },
abstract = {Bacterial antimicrobial resistance (AMR) poses a significant global public health challenge. The escalation of AMR is primarily attributed to the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs), often facilitated by plasmids. This underscores the critical need for a comprehensive understanding of the resistance mechanisms and transmission dynamics of these plasmids. In this study, we utilized in vitro drug sensitivity testing, conjugation transfer assays, and whole-genome sequencing to investigate the resistance mechanism of an extensively drug-resistant (XDR) Pseudomonas aeruginosa clinical isolate, MAS152. We specifically focused on analyzing the drug-resistant plasmid pMAS152 it harbors and its potential for widespread dissemination. Bioinformatics analysis revealed that MAS152 carries a distinct IncpP-2A plasmid, pMAS152, characterized by a 44.8 kb multidrug resistance (MDR) region. This region houses a 16S rRNA methyltransferase (16S-RMTase) gene, rmtB, conferring high-level resistance to aminoglycoside antibiotics. Notably, this region also contains an extended-spectrum β-Lactamase (ESBL) gene, blaPER-1, and an efflux pump operon, tmexCD-oprJ, which mediate resistance to β-Lactams and quinolone antibiotics, respectively. Such a combination of ARGs, unprecedented in reported plasmids, could significantly undermine the effectiveness of first-line antibiotics in treating P. aeruginosa infections. Investigation into the genetic environment of the MDR region suggests that Tn2 and IS91 elements may be instrumental in the horizontal transfer of rmtB. Additionally, a complex Class I integron with an ISCR1 structure, along with TnAs1, seems to facilitate the horizontal transfer of blaPER-1. The conjugation transfer assay, coupled with the annotation of conjugation-related genes and phylogenetic analysis, indicates that the plasmid pMAS152 functions as a conjugative plasmid, with other genus Pseudomonas species as potential hosts. Our findings provide vital insights into the resistance mechanisms and transmission potential of the XDR P. aeruginosa isolate MAS152, underlining the urgent need for novel strategies to combat the spread of AMR. This study highlights the complex interplay of genetic elements contributing to antibiotic resistance and underscores the importance of continuous surveillance of emerging ARGs in clinical isolates.},
}
@article {pmid38543545,
year = {2024},
author = {Skwor, T and Jones, DC and Cahak, C and Newton, RJ},
title = {First Report and Characterization of a Plasmid-Encoded blaSFO-1 in a Multi-Drug-Resistant Aeromonas hydrophila Clinical Isolate.},
journal = {Microorganisms},
volume = {12},
number = {3},
pages = {},
pmid = {38543545},
issn = {2076-2607},
abstract = {Antibiotic resistance remains one of the most pressing public health issues facing the world today. At the forefront of this battle lies the ever-increasing identification of extended-spectrum beta-lactamases and carbapenemases within human pathogens, conferring resistance towards broad-spectrum and last-resort antimicrobials. This study was prompted due to the identification of a pathogenic Aeromonas hydrophila isolate (strain MAH-4) collected from abdominal fluid, which presented a robust resistance pattern against second-, third-, and fourth-generation cephalosporins, ertapenem, ciprofloxacin, gentamicin, levofloxacin and moxifloxacin, and beta lactam/beta-lactamase inhibitor combinations. Whole genome sequencing was performed and identified a 328 kb plasmid (pMAH4) encoding 10 antibiotic resistance genes, including blaSFO-1, blaTEM-1, and blaOXA-1 of A. hydrophia MAH-4. This is the first report of beta-lactamase SFO-1 within a clinical strain of Aeromonas. Due to the remarkable sequence identity of pMAH4 to plasmids associated with Enterobacterales genera like Klebsiella and the extensive capabilities of Aeromonas for horizontal gene transfer, our identification of a clinical isolate encoding SFO-1 on a plasmid suggests antibiotic resistance gene mobility between Enterobacterales and non-Enterobacterales species.},
}
@article {pmid38542054,
year = {2024},
author = {Barathan, M and Ng, SL and Lokanathan, Y and Ng, MH and Law, JX},
title = {Unseen Weapons: Bacterial Extracellular Vesicles and the Spread of Antibiotic Resistance in Aquatic Environments.},
journal = {International journal of molecular sciences},
volume = {25},
number = {6},
pages = {},
pmid = {38542054},
issn = {1422-0067},
support = {DIP-2023-011//National University of Malaysia/ ; FF-2021-518//Faculty of Medicine, Universiti Kebangsaan Malaysia/ ; },
mesh = {*Ecosystem ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Multiple, Bacterial ; *Extracellular Vesicles ; Genes, Bacterial ; },
abstract = {This paper sheds light on the alarming issue of antibiotic resistance (ABR) in aquatic environments, exploring its detrimental effects on ecosystems and public health. It examines the multifaceted role of antibiotic use in aquaculture, agricultural runoff, and industrial waste in fostering the development and dissemination of resistant bacteria. The intricate interplay between various environmental factors, horizontal gene transfer, and bacterial extracellular vesicles (BEVs) in accelerating the spread of ABR is comprehensively discussed. Various BEVs carrying resistance genes like blaCTX-M, tetA, floR, and sul/I, as well as their contribution to the dominance of multidrug-resistant bacteria, are highlighted. The potential of BEVs as both a threat and a tool in combating ABR is explored, with promising strategies like targeted antimicrobial delivery systems and probiotic-derived EVs holding significant promise. This paper underscores the urgency of understanding the intricate interplay between BEVs and ABR in aquatic environments. By unraveling these unseen weapons, we pave the way for developing effective strategies to mitigate the spread of ABR, advocating for a multidisciplinary approach that includes stringent regulations, enhanced wastewater treatment, and the adoption of sustainable practices in aquaculture.},
}
@article {pmid38539090,
year = {2024},
author = {Kumar, G and Balakrishna, K and Mukhopadhyay, C and Kalwaje Eshwara, V},
title = {Comparison of integron mediated antimicrobial resistance in clinical isolates of Escherichia coli from urinary and bacteremic sources.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {102},
pmid = {38539090},
issn = {1471-2180},
mesh = {Humans ; *Escherichia coli ; Anti-Bacterial Agents/pharmacology ; Integrons/genetics ; *Escherichia coli Infections/microbiology ; Drug Resistance, Bacterial/genetics ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a global threat driven mainly by horizontal gene transfer (HGT) mechanisms through mobile genetic elements (MGEs) including integrons. The variable region (VR) of an integron can acquire or excise gene cassettes (GCs) that confer resistance to antibiotics based on the selection pressure. Escherichia coli plays a significant role in the genetic transfer of resistance determinants to other Gram-negative bacteria. Current study is aimed to detect and compare integron-mediated resistance in clinical isolates of E. coli. Unique isolates of E. coli from urine or blood cultures were studied for their antimicrobial resistance patterns and integrons were detected using polymerase chain reaction assays followed by Sanger sequencing of GCs.<br><br>RESULTS: During the study period, a total of 470 E. coli isolates were obtained, 361 (76.8%) from urinary and 109 (23.1%) from bacteremic sources. Class 1 integrons were detected in 66 (18.2%) and 26 (23.8%) isolates respectively. Urinary isolates of E. coli harbouring Class 1 integrons demonstrated significantly higher rates of resistance (p&#x2009;<&#x2009;0.05) for most antibiotics (12/16, 75%) compared to integron negative isolates. Although not statistically significant, similar differences were observed in bacteremic isolates. Among the urinary isolates, 27 (40.9%) had a VR, in which the most common GC array detected was DfrA17-AadA5 (n&#x2009;=&#x2009;14), followed by DfrA5 (n&#x2009;=&#x2009;4) and DfrA12 (n&#x2009;=&#x2009;3). Among bacteremic isolates, only 4 (15.3%) had a VR, all of which were carrying DfrA17. The detected GC array correlated with the respective isolates' phenotypic resistance patterns.<br><br>CONCLUSION: We found a strong correlation between integron positivity and trimethoprim resistance among E. coli from urinary sources. Although higher rates of resistance were observed in bacteremic isolates, they mostly carried empty integrons.},
}
@article {pmid38538528,
year = {2024},
author = {Chiquito-Contreras, CJ and Meza-Menchaca, T and Guzmán-López, O and Vásquez, EC and Ricaño-Rodríguez, J},
title = {Molecular Insights into Plant-Microbe Interactions: A Comprehensive Review of Key Mechanisms.},
journal = {Frontiers in bioscience (Elite edition)},
volume = {16},
number = {1},
pages = {9},
doi = {10.31083/j.fbe1601009},
pmid = {38538528},
issn = {1945-0508},
mesh = {*Ecosystem ; *Epigenesis, Genetic ; Plants ; Symbiosis ; Bacteria ; },
abstract = {In most ecosystems, plants establish complex symbiotic relationships with organisms, such as bacteria and fungi, which significantly influence their health by promoting or inhibiting growth. These relationships involve biochemical exchanges at the cellular level that affect plant physiology and have evolutionary implications, such as species diversification, horizontal gene transfer, symbiosis and mutualism, environmental adaptation, and positive impacts on community structure and biodiversity. For these reasons, contemporary research, moving beyond observational studies, seeks to elucidate the molecular basis of these interactions; however, gaps in knowledge remain. This is particularly noticeable in understanding how plants distinguish between beneficial and antagonistic microorganisms. In light of the above, this literature review aims to address some of these gaps by exploring the key mechanisms in common interspecies relationships. Thus, our study presents novel insights into these evolutionary archetypes, focusing on the antibiosis process and microbial signaling, including chemotaxis and quorum sensing. Additionally, it examined the biochemical basis of endophytism, pre-mRNA splicing, and transcriptional plasticity, highlighting the roles of transcription factors and epigenetic regulation in the functions of the interacting organisms. These findings emphasize the importance of understanding these confluences in natural environments, which are crucial for future theoretical and practical applications, such as improving plant nutrition, protecting against pathogens, developing transgenic crops, sustainable agriculture, and researching disease mechanisms. It was concluded that because of the characteristics of the various biomolecules involved in these biological interactions, there are interconnected molecular networks in nature that give rise to different ecological scaffolds. These networks integrate a myriad of functionally organic units that belong to various kingdoms. This interweaving underscores the complexity and multidisciplinary integration required to understand plant-microbe interactions at the molecular level. Regarding the limitations inherent in this study, it is recognized that researchers face significant obstacles. These include technical difficulties in experimentation and fieldwork, as well as the arduous task of consolidating and summarizing findings for academic articles. Challenges range from understanding complex ecological and molecular dynamics to unbiased and objective interpretation of diverse and ever-changing literature.},
}
@article {pmid38537404,
year = {2024},
author = {Cui, J and Dong, Y and Chen, Q and Zhang, C and He, K and Hu, G and He, D and Yuan, L},
title = {Horizontal transfer characterization of ColV plasmids in blaCTX-M-bearing avian Escherichia coli.},
journal = {Poultry science},
volume = {103},
number = {5},
pages = {103631},
pmid = {38537404},
issn = {1525-3171},
mesh = {*Escherichia coli/genetics/drug effects ; Animals ; *Escherichia coli Infections/veterinary/microbiology ; *Gene Transfer, Horizontal ; *Poultry Diseases/microbiology ; *Plasmids/genetics ; *Chickens ; *beta-Lactamases/genetics/metabolism ; Drug Resistance, Multiple, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Extended-spectrum-β-lactamases (ESBLs)-producing Escherichia coli conferred resistance to most β-lactams, except for carbapenems. To date, the transmission mechanism of blaCTX-M, as the most common ESBLs subtype, in E. coli has received sustained attention around the worldwide, but the research on the pathogenicity of blaCTX-M-bearing E. coli is still scarce. The aims of this study were to discern the spread characteristics of ColV (encoding colicin V) plasmids in blaCTX-M-positive E. coli. The multi-drug resistance traits, phylogroups, and ColV plasmid profilings were screened in 76 blaCTX-M-positive E. coli. Thereafter, the genetic profiles of E. coli G12 and GZM7 were determined by whole genome sequencing, conjugation and S1-pulsed-field gel electrophoresis. The median lethal dose was analyzed in E. coli G12 and TG12A, the ColV-plasmid transconjugant of G12. Of all 76 blaCTX-M-bearing E. coli, 67.11% exhibited resistance to at least 2 drugs in addition to ceftiofur, 14.47% carried ColV-positive plasmids, and 53.95% were phylogroup C. Further studies demonstrated that the blaCTX-M-bearing E. coli G12 was assigned to the predominant lineage O78:H4-ST117 of phylogroup G. In addition, its ColV-positive plasmid simultaneously carried multiple resistance genes, and could be independently transferred to confer partial pathogenicity on its host by plasmid mating. E. coli GZM7 was O53:H9-ST23 of phylogroup C, which belonged to another representative lineage of APEC (avian pathogenic E. coli). Its ColV-positive plasmid could complete conjugation with the help of the other coexisting-resistance conjugative plasmid, although it failed to transfer alone. Our findings highlight the flexibly horizontal transfer of ColV plasmids along with multidrug-resistant genes among blaCTX-M-bearing E. coli poses a threat to poultry health and food safety, which contributes to elucidate the concept of "One Health" and deserves particular concern.},
}
@article {pmid38536216,
year = {2024},
author = {Dechêne-Tempier, M and de Boisséson, C and Lucas, P and Bougeard, S and Libante, V and Marois-Créhan, C and Payot, S},
title = {Virulence genes, resistome and mobilome of Streptococcus suis strains isolated in France.},
journal = {Microbial genomics},
volume = {10},
number = {3},
pages = {},
pmid = {38536216},
issn = {2057-5858},
mesh = {Humans ; Animals ; Swine ; *Streptococcus suis ; Virulence ; France ; Virulence Factors ; DNA ; },
abstract = {Streptococcus suis is a leading cause of infection in pigs, causing extensive economic losses. In addition, it can also infect wild fauna, and can be responsible for severe infections in humans. Increasing antimicrobial resistance (AMR) has been described in S. suis worldwide and most of the AMR genes are carried by mobile genetic elements (MGEs). This contributes to their dissemination by horizontal gene transfer. A collection of 102 strains isolated from humans, pigs and wild boars in France was subjected to whole genome sequencing in order to: (i) study their genetic diversity, (ii) evaluate their content in virulence-associated genes, (iii) decipher the mechanisms responsible for their AMR and their association with MGEs, and (iv) study their ability to acquire extracellular DNA by natural transformation. Analysis by hierarchical clustering on principal components identified a few virulence-associated factors that distinguish invasive CC1 strains from the other strains. A plethora of AMR genes (n=217) was found in the genomes. Apart from the frequently reported erm(B) and tet(O) genes, more recently described AMR genes were identified [vga(F)/sprA, vat(D)]. Modifications in PBPs/MraY and GyrA/ParC were detected in the penicillin- and fluoroquinolone-resistant isolates respectively. New AMR gene-MGE associations were detected. The majority of the strains have the full set of genes required for competence, i.e for the acquisition of extracellular DNA (that could carry AMR genes) by natural transformation. Hence the risk of dissemination of these AMR genes should not be neglected.},
}
@article {pmid38534711,
year = {2024},
author = {Li, Q and Li, J and He, T and Ji, X and Wei, R and Yu, M and Wang, R},
title = {Sub-MIC Antibiotics Modulate Productions of Outer Membrane Vesicles in Tigecycline-Resistant Escherichia coli.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {3},
pages = {},
pmid = {38534711},
issn = {2079-6382},
support = {32102728//National Natural Science Foundation of China/ ; ZX(21)1224//Exploration and Disruptive Innovation Projects of Jiangsu Academy of Agricultural Sciences/ ; GJFP20230305//National Agricultural Product Quality and Safety Risk Assessment/ ; },
abstract = {Antimicrobial resistance (AMR) has been recognized as one of the most important crises affecting global human health in the 21st century. Tigecycline is one of the last resort antibiotics for treating severe infections caused by multi-drug resistant Enterobacteriaceae. However, the mobile resistance gene tet(X4), which could mediate high-level tigecycline resistance, was discovered in 2019. The outer membrane vesicle (OMV) has been recognized as a new route for horizontal gene transfer; antimicrobial resistant bacteria also have the ability to secret OMVs, while little is known about the impact of antibiotics on the secretion and characteristics of OMVs from tigecycline resistant bacteria till now. This study aimed to investigate the effects of antibiotics on the production and traits of a tigecycline resistant Escherichia coli strain of 47EC. The results showed that sub-inhibitory (1/2 MIC or 1/4 MIC) concentrations of gentamicin, meropenem, ceftazidime, chloramphenicol, tigecycline, ciprofloxacin, polymycin, rifaximin and mitomycin C could significantly increase the secretion of OMVs (0.713 ± 0.05~6.333 ± 0.15 mg/mL) from E. coli 47EC compared to the respective untreated control (0.709 ± 0.03 mg/mL). In addition, the particle sizes of OMVs were generally larger, and the zeta potential were lower in the antibiotics-treated groups than those of the antibiotic-free group. The copy numbers of the tigecycline resistance gene of tet(X4) in the OMVs of most antimicrobial-treated groups were higher than that of the control group. Moreover, transcriptome analysis on ciprofloxacin-treated E. coli 47EC indicated that the SOS response and prophage activation might participate in the ciprofloxacin-induced OMV formation. In conclusion, the clinical application of antibiotics in treating bacterial infections, especially multi-drug resistant bacteria, might lead to the increased secretion of bacterial OMVs and the enrichment of antimicrobial-resistant genes in the OMVs.},
}
@article {pmid38534448,
year = {2024},
author = {Duwor, S and Brites, D and Mäser, P},
title = {Phylogenetic Analysis of Pyruvate-Ferredoxin Oxidoreductase, a Redox Enzyme Involved in the Pharmacological Activation of Nitro-Based Prodrugs in Bacteria and Protozoa.},
journal = {Biology},
volume = {13},
number = {3},
pages = {},
pmid = {38534448},
issn = {2079-7737},
abstract = {The present frontrunners in the chemotherapy of infections caused by protozoa are nitro-based prodrugs that are selectively activated by PFOR-mediated redox reactions. This study seeks to analyze the distribution of PFOR in selected protozoa and bacteria by applying comparative genomics to test the hypothesis that PFOR in eukaryotes was acquired through horizontal gene transfer (HGT) from bacteria. Furthermore, to identify other putatively acquired genes, proteome-wide and gene enrichment analyses were used. A plausible explanation for the patchy occurrence of PFOR in protozoa is based on the hypothesis that bacteria are potential sources of genes that enhance the adaptation of protozoa in hostile environments. Comparative genomics of Entamoeba histolytica and the putative gene donor, Desulfovibrio vulgaris, identified eleven candidate genes for HGT involved in intermediary metabolism. If these results can be reproduced in other PFOR-possessing protozoa, it would provide more validated evidence to support the horizontal transfer of pfor from bacteria.},
}
@article {pmid38533399,
year = {2024},
author = {Peng, D and Wang, Z and Tian, J and Wang, W and Guo, S and Dai, X and Yin, H and Li, L},
title = {Phyllosphere bacterial community dynamics in response to bacterial wildfire disease: succession and interaction patterns.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1331443},
pmid = {38533399},
issn = {1664-462X},
abstract = {Plants interact with complex microbial communities in which microorganisms play different roles in plant development and health. While certain microorganisms may cause disease, others promote nutrient uptake and resistance to stresses through a variety of mechanisms. Developing plant protection measures requires a deeper comprehension of the factors that influence multitrophic interactions and the organization of phyllospheric communities. High-throughput sequencing was used in this work to investigate the effects of climate variables and bacterial wildfire disease on the bacterial community's composition and assembly in the phyllosphere of tobacco (Nicotiana tabacum L.). The samples from June (M1), July (M2), August (M3), and September (M4) formed statistically separate clusters. The assembly of the whole bacterial population was mostly influenced by stochastic processes. PICRUSt2 predictions revealed genes enriched in the M3, a period when the plant wildfire disease index reached climax, were associated with the development of the wildfire disease (secretion of virulence factor), the enhanced metabolic capacity and environmental adaption. The M3 and M4 microbial communities have more intricate molecular ecological networks (MENs), bursting with interconnections within a densely networked bacterial population. The relative abundances of plant-beneficial and antagonistic microbes Clostridiales, Bacillales, Lactobacillales, and Sphingobacteriales, showed significant decrease in severally diseased sample (M3) compared to the pre-diseased samples (M1/M2). Following the results of MENs, we further test if the correlating bacterial pairs within the MEN have the possibility to share functional genes and we have unraveled 139 entries of such horizontal gene transfer (HGT) events, highlighting the significance of HGT in shaping the adaptive traits of plant-associated bacteria across the MENs, particularly in relation to host colonization and pathogenicity.},
}
@article {pmid38530969,
year = {2024},
author = {Nasser, F and Gaudreau, A and Lubega, S and Zaker, A and Xia, X and Mer, AS and D'Costa, VM},
title = {Characterization of the diversity of type IV secretion system-encoding plasmids in Acinetobacter.},
journal = {Emerging microbes &amp; infections},
volume = {13},
number = {1},
pages = {2320929},
pmid = {38530969},
issn = {2222-1751},
mesh = {Humans ; *Type IV Secretion Systems ; Escherichia coli/genetics ; Plasmids ; Anti-Bacterial Agents/pharmacology ; *Acinetobacter baumannii ; beta-Lactamases/genetics ; Microbial Sensitivity Tests ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {The multi-drug resistant pathogen Acinetobacter baumannii has gained global attention as an important clinical challenge. Owing to its ability to survive on surfaces, its capacity for horizontal gene transfer, and its resistance to front-line antibiotics, A. baumannii has established itself as a successful pathogen. Bacterial conjugation is a central mechanism for pathogen evolution. The epidemic multidrug-resistant A. baumannii ACICU harbours a plasmid encoding a Type IV Secretion System (T4SS) with homology to the E. coli F-plasmid, and plasmids with homologous gene clusters have been identified in several A. baumannii sequence types. However the genetic and host strain diversity, global distribution, and functional ability of this group of plasmids is not fully understood. Using systematic analysis, we show that pACICU2 belongs to a group of almost 120 T4SS-encoding plasmids within four different species of Acinetobacter and one strain of Klebsiella pneumoniae from human and environmental origin, and globally distributed across 20 countries spanning 4 continents. Genetic diversity was observed both outside and within the T4SS-encoding cluster, and 47% of plasmids harboured resistance determinants, with two plasmids harbouring eleven. Conjugation studies with an extensively drug-resistant (XDR) strain showed that the XDR plasmid could be successfully transferred to a more divergent A. baumanii, and transconjugants exhibited the resistance phenotype of the plasmid. Collectively, this demonstrates that these T4SS-encoding plasmids are globally distributed and more widespread among Acinetobacter than previously thought, and that they represent an important potential reservoir for future clinical concern.},
}
@article {pmid38529905,
year = {2024},
author = {Crowley, C and Selvaraj, A and Hariharan, A and Healy, CM and Moran, GP},
title = {Fusobacterium nucleatum subsp. polymorphum recovered from malignant and potentially malignant oral disease exhibit heterogeneity in adhesion phenotypes and adhesin gene copy number, shaped by inter-subspecies horizontal gene transfer and recombination-derived mosaicism.},
journal = {Microbial genomics},
volume = {10},
number = {3},
pages = {},
pmid = {38529905},
issn = {2057-5858},
mesh = {Humans ; *Mosaicism ; Phylogeny ; *Gene Transfer, Horizontal ; Fusobacterium/genetics ; Phenotype ; Gene Dosage ; },
abstract = {Fusobacterium nucleatum is an anaerobic commensal of the oral cavity associated with periodontitis and extra-oral diseases, including colorectal cancer. Previous studies have shown an increased relative abundance of this bacterium associated with oral dysplasia or within oral tumours. Using direct culture, we found that 75 % of Fusobacterium species isolated from malignant or potentially malignant oral mucosa were F. nucleatum subsp. polymorphum. Whole genome sequencing and pangenome analysis with Panaroo was carried out on 76 F. nucleatum subsp. polymorphum genomes. F. nucleatum subsp. polymorphum was shown to possesses a relatively small core genome of 1604 genes in a pangenome of 7363 genes. Phylogenetic analysis based on the core genome shows the isolates can be separated into three main clades with no obvious genotypic associations with disease. Isolates recovered from healthy and diseased sites in the same patient are generally highly related. A large repertoire of adhesins belonging to the type V secretion system (TVSS) could be identified with major variation in repertoire and copy number between strains. Analysis of intergenic recombination using fastGEAR showed that adhesin complement is shaped by horizontal gene transfer and recombination. Recombination events at TVSS adhesin genes were not only common between lineages of subspecies polymorphum, but also between different subspecies of F. nucleatum. Strains of subspecies polymorphum with low copy numbers of TVSS adhesin encoding genes tended to have the weakest adhesion to oral keratinocytes. This study highlights the genetic heterogeneity of F. nucleatum subsp. polymorphum and provides a new framework for defining virulence in this organism.},
}
@article {pmid38527381,
year = {2024},
author = {Ferilli, F and Lione, G and Gonthier, P and Turina, M and Forgia, M},
title = {First detection of mycoviruses in Gnomoniopsis castaneae suggests a putative horizontal gene transfer event between negative-sense and double-strand RNA viruses.},
journal = {Virology},
volume = {594},
number = {},
pages = {110057},
doi = {10.1016/j.virol.2024.110057},
pmid = {38527381},
issn = {1096-0341},
mesh = {*Fungal Viruses/genetics ; Double Stranded RNA Viruses/genetics ; Gene Transfer, Horizontal ; Genome, Viral ; Plant Diseases ; Phylogeny ; *RNA Viruses/genetics ; *Viruses/genetics ; RNA, Viral/genetics ; RNA, Double-Stranded/genetics ; *Ascomycota ; },
abstract = {Gnomoniopsis castaneae is an ascomycetous fungus mainly known as a major pathogen of chestnut causing nut rots, although it is often found as an endophyte in chestnut tissues. To date, no virus has been reported as associated with to this fungus. Here, a collection of G. castaneae isolates from several European countries was screened to detect mycoviruses infecting the fungus: for the first time we report the identification and prevalence of mitovirus Gnomoniopsis castaneae mitovirus 1 (GcMV1) and the chrysovirus Gnomoniopsis castaneae chrysovirus 1 (GcCV1). Interestingly, we provide evidence supporting a putative horizontal gene transfer between members of the phyla Negarnaviricota and Duplornaviricota: a small putative protein of unknown function encoded on the RNA3 of GcCV1 (Chrysoviridae) has homologs in the genome of viruses of the family Mymonaviridae.},
}
@article {pmid38521802,
year = {2024},
author = {Asad, A and Jahan, I and Munni, MA and Begum, R and Mukta, MA and Saif, K and Faruque, SN and Hayat, S and Islam, Z},
title = {Multidrug-resistant conjugative plasmid carrying mphA confers increased antimicrobial resistance in Shigella.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {6947},
pmid = {38521802},
issn = {2045-2322},
support = {D43 TW010540/TW/FIC NIH HHS/United States ; K43 TW011447/TW/FIC NIH HHS/United States ; K43TW011447/TW/FIC NIH HHS/United States ; NIH FIC TW010540/TW/FIC NIH HHS/United States ; },
mesh = {Child ; Humans ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Dysentery, Bacillary/drug therapy/epidemiology ; Macrolides/pharmacology/therapeutic use ; Drug Resistance, Bacterial/genetics ; *Shigella ; Azithromycin/pharmacology/therapeutic use ; Ciprofloxacin/pharmacology/therapeutic use ; Ceftriaxone/pharmacology ; Microbial Sensitivity Tests ; Protein Synthesis Inhibitors/pharmacology ; Plasmids/genetics ; },
abstract = {Shigellosis remains a common gastrointestinal disease mostly in children < 5 years of age in developing countries. Azithromycin (AZM), a macrolide, is currently the first-line treatment for shigellosis in Bangladesh; ciprofloxacin (CIP) and ceftriaxone (CRO) are also used frequently. We aimed to evaluate the current epidemiology of antimicrobial resistance (AMR) and mechanism(s) of increasing macrolide resistance in Shigella in Bangladesh. A total of 2407 clinical isolates of Shigella from 2009 to 2016 were studied. Over the study period, Shigella sonnei was gradually increasing and become predominant (55%) over Shigella flexneri (36%) by 2016. We used CLSI-guided epidemiological cut-off value (ECV) for AZM in Shigella to set resistance breakpoints (zone-diameter ≤ 15 mm for S. flexneri and ≤ 11 mm for S. sonnei). Between 2009 and 2016, AZM resistance increased from 22% to approximately 60%, CIP resistance increased by 40%, and CRO resistance increased from zero to 15%. The mphA gene was the key macrolide resistance factor in Shigella; a 63MDa conjugative middle-range plasmid was harboring AZM and CRO resistance factors. Our findings show that, especially after 2014, there has been a rapid increase in resistance to the three most effective antibiotics. The rapid spread of macrolide (AZM) resistance genes among Shigella are driven by horizontal gene transfer rather than direct lineage.},
}
@article {pmid38521276,
year = {2024},
author = {Liu, Q and Peng, Y and Liao, J and Liu, X and Peng, J and Wang, JH and Shao, Z},
title = {Broad-spectrum hydrocarbon-degrading microbes in the global ocean metagenomes.},
journal = {The Science of the total environment},
volume = {926},
number = {},
pages = {171746},
doi = {10.1016/j.scitotenv.2024.171746},
pmid = {38521276},
issn = {1879-1026},
mesh = {*Metagenome ; Hydrocarbons/metabolism ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Oceans and Seas ; *Petroleum/metabolism ; },
abstract = {Understanding the diversity and functions of hydrocarbon-degrading microorganisms in marine environments is crucial for both advancing knowledge of biogeochemical processes and improving bioremediation methods. In this study, we leveraged nearly 20,000 metagenome-assembled genomes (MAGs), recovered from a wide array of marine samples across the global oceans, to map the diversity of aerobic hydrocarbon-degrading microorganisms. A broad bacterial diversity was uncovered, with a notable preference for degrading aliphatic hydrocarbons over aromatic ones, primarily within Proteobacteria and Actinobacteriota. Three types of broad-spectrum hydrocarbon-degrading bacteria were identified for their ability to degrade various hydrocarbons and possession of multiple copies of hydrocarbon biodegradation genes. These bacteria demonstrate extensive metabolic versatility, aiding their survival and adaptability in diverse environmental conditions. Evidence of gene duplication and horizontal gene transfer in these microbes suggested a potential enhancement in the diversity of hydrocarbon-degrading bacteria. Positive correlations were observed between the abundances of hydrocarbon-degrading genes and environmental parameters such as temperature (-5 to 35 °C) and salinity (20 to 42 PSU). Overall, our findings offer valuable insights into marine hydrocarbon-degrading microorganisms and suggest considerations for selecting microbial strains for oil pollution remediation.},
}
@article {pmid38519541,
year = {2024},
author = {Baker, BA and Gutiérrez-Preciado, A and Rodríguez Del Río, &#xc1; and McCarthy, CGP and López-García, P and Huerta-Cepas, J and Susko, E and Roger, AJ and Eme, L and Moreira, D},
title = {Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments.},
journal = {Nature microbiology},
volume = {9},
number = {4},
pages = {964-975},
pmid = {38519541},
issn = {2058-5276},
support = {787904//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 803151//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {Phylogeny ; *Salinity ; Archaea/genetics ; *Euryarchaeota/genetics ; Metagenome ; },
abstract = {Extremely halophilic archaea (Haloarchaea, Nanohaloarchaeota, Methanonatronarchaeia and Halarchaeoplasmatales) thrive in saturating salt concentrations where they must maintain osmotic equilibrium with their environment. The evolutionary history of adaptations enabling salt tolerance remains poorly understood, in particular because the phylogeny of several lineages is conflicting. Here we present a resolved phylogeny of extremely halophilic archaea obtained using improved taxon sampling and state-of-the-art phylogenetic approaches designed to cope with the strong compositional biases of their proteomes. We describe two uncultured lineages, Afararchaeaceae and Asbonarchaeaceae, which break the long branches at the base of Haloarchaea and Nanohaloarchaeota, respectively. We obtained 13 metagenome-assembled genomes (MAGs) of these archaea from metagenomes of hypersaline aquatic systems of the Danakil Depression (Ethiopia). Our phylogenomic analyses including these taxa show that at least four independent adaptations to extreme halophily occurred during archaeal evolution. Gene-tree/species-tree reconciliation suggests that gene duplication and horizontal gene transfer played an important role in this process, for example, by spreading key genes (such as those encoding potassium transporters) across extremely halophilic lineages.},
}
@article {pmid38518756,
year = {2024},
author = {Gàlvez-Morante, A and Guéguen, L and Natsidis, P and Telford, MJ and Richter, DJ},
title = {Dollo Parsimony Overestimates Ancestral Gene Content Reconstructions.},
journal = {Genome biology and evolution},
volume = {16},
number = {4},
pages = {},
pmid = {38518756},
issn = {1759-6653},
support = {/ERC_/European Research Council/International ; 949745/ERC_/European Research Council/International ; },
mesh = {Phylogeny ; Likelihood Functions ; *Evolution, Molecular ; },
abstract = {Ancestral reconstruction is a widely used technique that has been applied to understand the evolutionary history of gain and loss of gene families. Ancestral gene content can be reconstructed via different phylogenetic methods, but many current and previous studies employ Dollo parsimony. We hypothesize that Dollo parsimony is not appropriate for ancestral gene content reconstruction inferences based on sequence homology, as Dollo parsimony is derived from the assumption that a complex character cannot be regained. This premise does not accurately model molecular sequence evolution, in which false orthology can result from sequence convergence or lateral gene transfer. The aim of this study is to test Dollo parsimony's suitability for ancestral gene content reconstruction and to compare its inferences with a maximum likelihood-based approach that allows a gene family to be gained more than once within a tree. We first compared the performance of the two approaches on a series of artificial data sets each of 5,000 genes that were simulated according to a spectrum of evolutionary rates without gene gain or loss, so that inferred deviations from the true gene count would arise only from errors in orthology inference and ancestral reconstruction. Next, we reconstructed protein domain evolution on a phylogeny representing known eukaryotic diversity. We observed that Dollo parsimony produced numerous ancestral gene content overestimations, especially at nodes closer to the root of the tree. These observations led us to the conclusion that, confirming our hypothesis, Dollo parsimony is not an appropriate method for ancestral reconstruction studies based on sequence homology.},
}
@article {pmid38517978,
year = {2024},
author = {Sheinman, M and Arndt, PF and Massip, F},
title = {Modeling the mosaic structure of bacterial genomes to infer their evolutionary history.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {13},
pages = {e2313367121},
pmid = {38517978},
issn = {1091-6490},
mesh = {Phylogeny ; *Models, Genetic ; *Genome, Bacterial/genetics ; Genomics/methods ; Bacteria/genetics ; Evolution, Molecular ; },
abstract = {The chronology and phylogeny of bacterial evolution are difficult to reconstruct due to a scarce fossil record. The analysis of bacterial genomes remains challenging because of large sequence divergence, the plasticity of bacterial genomes due to frequent gene loss, horizontal gene transfer, and differences in selective pressure from one locus to another. Therefore, taking advantage of the rich and rapidly accumulating genomic data requires accurate modeling of genome evolution. An important technical consideration is that loci with high effective mutation rates may diverge beyond the detection limit of the alignment algorithms used, biasing the genome-wide divergence estimates toward smaller divergences. In this article, we propose a novel method to gain insight into bacterial evolution based on statistical properties of genome comparisons. We find that the length distribution of sequence matches is shaped by the effective mutation rates of different loci, by the horizontal transfers, and by the aligner sensitivity. Based on these inputs, we build a model and show that it accounts for the empirically observed distributions, taking the Enterobacteriaceae family as an example. Our method allows to distinguish segments of vertical and horizontal origins and to estimate the time divergence and exchange rate between any pair of taxa from genome-wide alignments. Based on the estimated time divergences, we construct a time-calibrated phylogenetic tree to demonstrate the accuracy of the method.},
}
@article {pmid38511257,
year = {2025},
author = {Fogg, PCM},
title = {Gene transfer agents: The ambiguous role of selfless viruses in genetic exchange and bacterial evolution.},
journal = {Molecular microbiology},
volume = {123},
number = {2},
pages = {124-131},
pmid = {38511257},
issn = {1365-2958},
support = {/WT_/Wellcome Trust/United Kingdom ; BB/V016288/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 109363/Z/15/A/WT_/Wellcome Trust/United Kingdom ; 109363/Z/15/A//Royal Society/ ; },
mesh = {*Gene Transfer, Horizontal/genetics ; *Bacteriophages/genetics ; *Bacteria/genetics/virology ; Evolution, Molecular ; },
abstract = {Gene transfer agents (GTAs) are genetic elements derived from ancestral bacteriophages that have become domesticated by the host. GTAs are present in diverse prokaryotic organisms, where they can facilitate horizontal gene transfer under certain conditions. Unlike typical bacteriophages, GTAs do not exhibit any preference for the replication or transfer of the genes encoding them; instead, they exhibit a remarkable capacity to package chromosomal, and sometimes extrachromosomal, DNA into virus-like capsids and disseminate it to neighboring cells. Because GTAs resemble defective prophages, identification of novel GTAs is not trivial. The detection of candidates relies on the genetic similarity to known GTAs, which has been fruitful in α-proteobacterial lineages but challenging in more distant bacteria. Here we consider several fundamental questions: What is the true prevalence of GTAs in prokaryote genomes? Given there are high costs for GTA production, what advantage do GTAs provide to the bacterial host to justify their maintenance? How is the bacterial chromosome recognized and processed for inclusion in GTA particles? This article highlights the challenges in comprehensively understanding GTAs' prevalence, function and DNA packaging method. Going forward, broad study of atypical GTAs and use of ecologically relevant conditions are required to uncover their true impact on bacterial chromosome evolution.},
}
@article {pmid38510031,
year = {2024},
author = {Liu, X and Zhao, H and Wong, A},
title = {Accounting for the health risk of probiotics.},
journal = {Heliyon},
volume = {10},
number = {6},
pages = {e27908},
pmid = {38510031},
issn = {2405-8440},
abstract = {Probiotics have long been associated with a myriad of health benefits, so much so that their adverse effects whether mild or severe, are often neglected or overshadowed by the enormous volume of articles describing their beneficial effects in the current literature. Recent evidence has demonstrated several health risks of probiotics that warrant serious reconsideration of their applications and further investigations. This review aims to highlight studies that report on how probiotics might cause opportunistic systemic and local infections, detrimental immunological effects, metabolic disturbance, allergic reactions, and facilitating the spread of antimicrobial resistance. To offer a recent account of the literature, articles within the last five years were prioritized. The narration of these evidence was based on the nature of the studies in the following order of preference: clinical studies or human samples, in vivo or animal models, in situ, in vitro and/or in silico. We hope that this review will inform consumers, food scientists, and medical practitioners, on the health risks, while also encouraging research that will focus on and clarify the adverse effects of probiotics.},
}
@article {pmid38508537,
year = {2024},
author = {Yang, W and Tang, C and Shen, S and Shi, Q and Hu, F},
title = {Spread and evolution of blaKPC-plasmid between Serratia marcescens and Klebsiella pneumoniae.},
journal = {International journal of antimicrobial agents},
volume = {63},
number = {5},
pages = {107149},
doi = {10.1016/j.ijantimicag.2024.107149},
pmid = {38508537},
issn = {1872-7913},
mesh = {*Serratia marcescens/genetics/drug effects/isolation &amp; purification/enzymology ; *Klebsiella pneumoniae/genetics/drug effects ; Humans ; *Plasmids/genetics ; *Microbial Sensitivity Tests ; *beta-Lactamases/genetics ; *Serratia Infections/microbiology/epidemiology ; *Anti-Bacterial Agents/pharmacology ; *Klebsiella Infections/microbiology/epidemiology ; *Whole Genome Sequencing ; Ceftazidime/pharmacology ; Drug Combinations ; Drug Resistance, Multiple, Bacterial/genetics ; Azabicyclo Compounds/pharmacology ; Sputum/microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Carbapenems/pharmacology ; },
abstract = {OBJECTIVES: blaKPC-carrying Enterobacterales have post great challenges to global healthcare systems. In this study, we reported the evolution and spread of blaKPC between Serratia marcescens and Klebsiella pneumoniae.<br><br>METHODS: Four S. marcescens and one K. pneumoniae strains were isolated from the sputum samples of the patient. Antimicrobial susceptibility tests and whole genome sequencing were performed to investigate the phenotype &amp; genotype of strains. Conjugation assays, cloning experiment and kinetic parameters measuring were performed to explore the spread and antimicrobial resistance mechanisms.<br><br>RESULTS: The evolution and transmission of blaKPC-2 occurred during the treatment of ceftazidime-avibactam and trimethoprim-sulfamethoxazole. Analysis of the antimicrobial susceptibility and genetic profiles of the clinical strains showed that blaKPC-2 evolved into blaKPC-71 and blaKPC-44, together with resistance to ceftazidime-avibactam and carbapenems susceptibility recovery under antimicrobial pressure. Cloning and expression of blaKPC-44 &amp; blaKPC-71 in E. coli DH5&#x3b1; showed that KPC-44 and KPC-71 resulted in a 64&#x223c;128-fold increase in the MIC value for ceftazidime-avibactam. Meanwhile, the kinetic assays also showed that the enzyme activity of KPC-44 and KPC-71 towards carbapenems was destroyed and couldn't be inhibited by avibactam. Based on the conjugation assay and whole genome sequence analyses, we provided evolutionary insights into the transmission pathway trace of blaKPC-bearing plasmids between S. marcescens and K. pneumoniae.<br><br>CONCLUSIONS: Mixed-species co-infection is one of the risk factors leading to the spread of plasmids carrying carbapenem-resistant genes, and increased surveillance of multidrug-resistant Enterobacterales is urgently needed.},
}
@article {pmid38507447,
year = {2024},
author = {Kehlet-Delgado, H and Montoya, AP and Jensen, KT and Wendlandt, CE and Dexheimer, C and Roberts, M and Torres Martínez, L and Friesen, ML and Griffitts, JS and Porter, SS},
title = {The evolutionary genomics of adaptation to stress in wild rhizobium bacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {13},
pages = {e2311127121},
pmid = {38507447},
issn = {1091-6490},
support = {IOS-1755454//National Science Foundation (NSF)/ ; DEB-1943239//National Science Foundation (NSF)/ ; },
mesh = {Humans ; *Rhizobium/genetics ; Nickel ; *Metals, Heavy/toxicity ; Genomics ; Soil ; },
abstract = {Microbiota comprise the bulk of life's diversity, yet we know little about how populations of microbes accumulate adaptive diversity across natural landscapes. Adaptation to stressful soil conditions in plants provides seminal examples of adaptation in response to natural selection via allelic substitution. For microbes symbiotic with plants however, horizontal gene transfer allows for adaptation via gene gain and loss, which could generate fundamentally different evolutionary dynamics. We use comparative genomics and genetics to elucidate the evolutionary mechanisms of adaptation to physiologically stressful serpentine soils in rhizobial bacteria in western North American grasslands. In vitro experiments demonstrate that the presence of a locus of major effect, the nre operon, is necessary and sufficient to confer adaptation to nickel, a heavy metal enriched to toxic levels in serpentine soil, and a major axis of environmental soil chemistry variation. We find discordance between inferred evolutionary histories of the core genome and nreAXY genes, which often reside in putative genomic islands. This suggests that the evolutionary history of this adaptive variant is marked by frequent losses, and/or gains via horizontal acquisition across divergent rhizobium clades. However, different nre alleles confer distinct levels of nickel resistance, suggesting allelic substitution could also play a role in rhizobium adaptation to serpentine soil. These results illustrate that the interplay between evolution via gene gain and loss and evolution via allelic substitution may underlie adaptation in wild soil microbiota. Both processes are important to consider for understanding adaptive diversity in microbes and improving stress-adapted microbial inocula for human use.},
}
@article {pmid38506281,
year = {2024},
author = {Adeyelu, OO and Essien, EN and Adebote, V and Ajayi, A and Essiet, UU and Adeleye, AI and Smith, SI},
title = {Antimicrobial resistance genetic determinants and susceptibility profile of Pseudomonas aeruginosa isolated from clinical samples in a tertiary hospital in Ogun State, Nigeria.},
journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene},
volume = {118},
number = {7},
pages = {474-476},
doi = {10.1093/trstmh/trae012},
pmid = {38506281},
issn = {1878-3503},
mesh = {*Pseudomonas aeruginosa/genetics/drug effects/isolation &amp; purification ; Humans ; *Pseudomonas Infections/microbiology/epidemiology ; *Microbial Sensitivity Tests ; *Tertiary Care Centers ; *Anti-Bacterial Agents/pharmacology ; *beta-Lactamases/genetics ; Nigeria/epidemiology ; *Plasmids/genetics ; Female ; Integrons/genetics ; Male ; Adult ; Drug Resistance, Multiple, Bacterial/genetics ; Middle Aged ; beta-Lactams/pharmacology ; Drug Resistance, Bacterial/genetics ; },
abstract = {BACKGROUND: Genetic determinants are known to promote antibiotic resistance through horizontal gene transfer.<br><br>METHODS: We molecularly characterized integrons, plasmid replicon types and metallo-&#x3b2;-lactamase-encoding genes of 38 Pseudomonas aeruginosa strains isolated from clinical samples.<br><br>RESULTS: The P. aeruginosa isolates displayed high resistance (97.4%) to &#x3b2;-lactams. Seventeen (44.74%) of them possessed plasmids. Of the 17 isolates that possessed plasmids, 11 (64.7%) of them harboured IncFIA plasmid replicon type, while 6 (35.3%), 5 (29.4%) and 5 (29.4%) were of the IncFIB, IncF and IncW types, respectively. The intI1 gene was detected in 19 (50%) of the isolates. The blaNDM-A, blaNDM-B and blaVIM genes were detected in 14 (35.9%), 4 (10.3%) and 5 (12.8%) of the isolates, respectively.<br><br>CONCLUSIONS: High resistance to &#x3b2;-lactams was observed among P. aeruginosa strains of clinical origin in this study. They possessed transmissible genetic elements indicating the potential for continuous dissemination, thus continuous surveillance is advocated.},
}
@article {pmid38504610,
year = {2024},
author = {Tekle, YI and Tefera, H},
title = {A Small Genome amidst the Giants: Evidence of Genome Reduction in a Small Tubulinid Free-Living Amoeba.},
journal = {Genome biology and evolution},
volume = {16},
number = {3},
pages = {},
pmid = {38504610},
issn = {1759-6653},
support = {R15 GM116103/GM/NIGMS NIH HHS/United States ; 1R15GM116103-02/NH/NIH HHS/United States ; },
mesh = {*Amoeba/genetics ; Phylogeny ; Genome ; *Amoebozoa/genetics ; Genomics ; },
abstract = {This study investigates the genomic characteristics of Echinamoeba silvestris, a small-sized amoeba within the Tubulinea clade of the Amoebozoa supergroup. Despite Tubulinea's significance in various fields, genomic data for this clade have been scarce. E. silvestris presents the smallest free-living amoeba genome within Tubulinea and Amoebozoa to date. Comparative analysis reveals intriguing parallels with parasitic lineages in terms of genome size and predicted gene numbers, emphasizing the need to understand the consequences of reduced genomes in free-living amoebae. Functional categorization of predicted genes in E. silvestris shows similar percentages of ortholog groups to other amoebae in various categories, but a distinctive feature is the extensive gene contraction in orphan (ORFan) genes and those involved in biological processes. Notably, among the few genes that underwent expansion, none are related to cellular components, suggesting adaptive processes that streamline biological processes and cellular components for efficiency and energy conservation. Additionally, our investigation into noncoding and repetitive elements sheds light on the evolution of genome size in amoebae, with E. silvestris distinguished by low percentage of repetitive elements. Furthermore, the analysis reveals that E. silvestris has the lowest mean number of introns per gene among the species studied, providing further support for its observed compact genome. Overall, this research underscores the diversity within Tubulinea, highlights knowledge gaps in Amoebozoa genomics, and positions E. silvestris as a valuable addition to genomic data sets, prompting further exploration of complexities in Amoebozoa diversity and genome evolution.},
}
@article {pmid38498548,
year = {2024},
author = {Bernabeu, M and Manzano-Morales, S and Gabaldón, T},
title = {On the impact of incomplete taxon sampling on the relative timing of gene transfer events.},
journal = {PLoS biology},
volume = {22},
number = {3},
pages = {e3002460},
pmid = {38498548},
issn = {1545-7885},
mesh = {Phylogeny ; *Gene Flow ; *Biological Evolution ; Gene Transfer, Horizontal ; },
abstract = {A recent study questioned the use of branch length methods to assess the relative timing of horizontal gene transfers because of the effects of so-called "ghost" lineages. This Formal Comment discusses key considerations regarding the potential effect of missing lineages when assessing relative timing of evolutionary events.},
}
@article {pmid38497713,
year = {2024},
author = {Tang, X-F and Sun, Y-F and Liang, Y-S and Yang, K-Y and Chen, P-T and Li, H-S and Huang, Y-H and Pang, H},
title = {Metabolism, digestion, and horizontal transfer: potential roles and interaction of symbiotic bacteria in the ladybird beetle Novius pumilus and their prey Icerya aegyptiaca.},
journal = {Microbiology spectrum},
volume = {12},
number = {5},
pages = {e0295523},
pmid = {38497713},
issn = {2165-0497},
support = {2023YFD1400600//National Key Research and Development Program of China/ ; 32172472//National Natural Science Foundation of China/ ; 31970439//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Coleoptera/microbiology ; *Symbiosis ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Gene Transfer, Horizontal ; Phylogeny ; Female ; Microbiota ; },
abstract = {In this study, we first time sequenced and analyzed the 16S rRNA gene data of predator ladybird beetles Novius pumilus and globally distributed invasive pest Icerya aegyptiaca at different stages, and combined data with bacterial genome sequences in N. pumilus to explored the taxonomic distribution, alpha and beta diversity, differentially abundant bacteria, co-occurrence network, and putative functions of their microbial community. Our finding revealed that Candidatus Walczuchella, which exhibited a higher abundance in I. aegyptiaca, possessed several genes in essential amino acid biosynthesis and seemed to perform roles in providing nutrients to the host, similar to other obligate symbionts in scale insects. Lactococcus, Serratia, and Pseudomonas, more abundant in N. pumilus, were predicted to have genes related to hydrocarbon, fatty acids, and chitin degradation, which may assist their hosts in digesting the wax shell covering the scale insects. Notably, our result showed that Lactococcus had relatively higher abundances in adults and eggs compared to other stages in N. pumilus, indicating potential vertical transmission. Additionally, we found that Arsenophonus, known to influence sex ratios in whitefly and wasp, may also function in I. aegyptiaca, probably by influencing nutrient metabolism as it similarly had many genes corresponding to vitamin B and essential amino acid biosynthesis. Also, we observed a potential horizontal transfer of Arsenophonus between the scale insect and its predator, with a relatively high abundance in the ladybirds compared to other bacteria from the scale insects.IMPORTANCEThe composition and dynamic changes of microbiome in different developmental stages of ladybird beetles Novius pumilus with its prey Icerya aegyptiaca were detected. We found that Candidatus Walczuchella, abundant in I. aegyptiaca, probably provide nutrients to their host based on their amino acid biosynthesis-related genes. Abundant symbionts in N. pumilus, including Lactococcus, Serratia, and Pseudophonus, may help the host digest the scale insects with their hydrocarbon, fatty acid, and chitin degrading-related genes. A key endosymbiont Arsenophonus may play potential roles in the nutrient metabolisms and sex determination in I. aegyptiaca, and is possibly transferred from the scale insect to the predator.},
}
@article {pmid38497640,
year = {2024},
author = {Wang, P and Du, X and Zhao, Y and Wang, W and Cai, T and Tang, K and Wang, X},
title = {Combining CRISPR/Cas9 and natural excision for the precise and complete removal of mobile genetic elements in bacteria.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {4},
pages = {e0009524},
pmid = {38497640},
issn = {1098-5336},
support = {32070175//MOST | National Natural Science Foundation of China (NSFC)/ ; 42188102//MOST | National Natural Science Foundation of China (NSFC)/ ; 91951203//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022YFC3103600//MOST | National Key Research and Development Program of China (NKPs)/ ; 2019BT02Y262//Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program/ ; 2021345//Youth Innovation Promotion Association of the Chinese Academy of Sciences (CAS YIPA)/ ; },
mesh = {*CRISPR-Cas Systems ; *RNA, Guide, CRISPR-Cas Systems ; Bacteria/genetics ; Genomic Islands ; Gene Transfer, Horizontal ; Plasmids/genetics ; Interspersed Repetitive Sequences ; },
abstract = {Horizontal gene transfer, facilitated by mobile genetic elements (MGEs), is an adaptive evolutionary process that contributes to the evolution of bacterial populations and infectious diseases. A variety of MGEs not only can integrate into the bacterial genome but also can survive or even replicate like plasmids in the cytoplasm, thus requiring precise and complete removal for studying their strategies in benefiting host cells. Existing methods for MGE removal, such as homologous recombination-based deletion and excisionase-based methods, have limitations in effectively eliminating certain MGEs. To overcome these limitations, we developed the Cas9-NE method, which combines the CRISPR/Cas9 system with the natural excision of MGEs. In this approach, a specialized single guide RNA (sgRNA) element is designed with a 20-nucleotide region that pairs with the MGE sequence. This sgRNA is expressed from a plasmid that also carries the Cas9 gene. By utilizing the Cas9-NE method, both the integrative and circular forms of MGEs can be precisely and completely eliminated through Cas9 cleavage, generating MGE-removed cells. We have successfully applied the Cas9-NE method to remove four representative MGEs, including plasmids, prophages, and genomic islands, from Vibrio strains. This new approach not only enables various investigations on MGEs but also has significant implications for the rapid generation of strains for commercial purposes.IMPORTANCEMobile genetic elements (MGEs) are of utmost importance for bacterial adaptation and pathogenicity, existing in various forms and multiple copies within bacterial cells. Integrated MGEs play dual roles in bacterial hosts, enhancing the fitness of the host by delivering cargo genes and potentially modifying the bacterial genome through the integration/excision process. This process can lead to alterations in promoters or coding sequences or even gene disruptions at integration sites, influencing the physiological functions of host bacteria. Here, we developed a new approach called Cas9-NE, allowing them to maintain the natural sequence changes associated with MGE excision. Cas9-NE allows the one-step removal of integrated and circular MGEs, addressing the challenge of eliminating various MGE forms efficiently. This approach simplifies MGE elimination in bacteria, expediting research on MGEs.},
}
@article {pmid38494146,
year = {2024},
author = {Xu, H and Tan, C and Li, C and Li, J and Han, Y and Tang, Y and Lei, C and Wang, H},
title = {ESBL-Escherichia coli extracellular vesicles mediate bacterial resistance to β-lactam and mediate horizontal transfer of blaCTX-M-55.},
journal = {International journal of antimicrobial agents},
volume = {63},
number = {5},
pages = {107145},
doi = {10.1016/j.ijantimicag.2024.107145},
pmid = {38494146},
issn = {1872-7913},
mesh = {*Escherichia coli/drug effects/genetics ; *Extracellular Vesicles/metabolism ; *Gene Transfer, Horizontal ; *beta-Lactamases/genetics/metabolism ; *beta-Lactams/pharmacology ; *beta-Lactam Resistance/genetics ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Escherichia coli Infections/microbiology ; Animals ; },
abstract = {OBJECTIVES: Extracellular vesicles (EVs) have become the focus of research as an emerging method of horizontal gene transfer. In recent years, studies on the association between EVs and the spread of bacterial resistance have emerged, but there is a lack of research on the role of EVs secreted by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in the spread of β-lactam resistance. Therefore, the aim of this study was to investigate the role of EVs in the transmission of β-lactam resistance.<br><br>METHODS: In this study, the role of EVs in the transmission of &#x3b2;-lactam resistance in E. coli was evaluated by the EVs-mediated bacterial resistance to &#x3b2;-lactam antibiotics test and the EVs-mediated blaCTX-M-55 transfer experiments using EVs secreted by ESBL-E. coli.<br><br>RESULTS: The results showed that ESBL-EVs were protective against &#x3b2;-lactam antibiotic-susceptible bacteria, and this protective effect was dependent on the integrity of the EVs and showed dose- and time-dependent effects. At the same time, ESBL-EVs can also mediate the horizontal transmission of blaCTX-M-55, and EVs-mediated gene transfer is selective, preferring to transfer in more closely related species.<br><br>CONCLUSIONS: In this study, we demonstrated the important role of EVs in the transmission of &#x3b2;-lactam resistance in chicken ESBL-E. coli, and evaluated the risk of EVs-mediated horizontal gene transfer, which provided a theoretical basis for elucidating the mechanism of EVs-mediated resistance transmission.},
}
@article {pmid38493856,
year = {2024},
author = {You, Z and Wang, C and Yang, X and Liu, Z and Guan, Y and Mu, J and Shi, H and Zhao, Z},
title = {Effects of eutrophication on the horizontal transfer of antibiotic resistance genes in microalgal-bacterial symbiotic systems.},
journal = {Environmental research},
volume = {251},
number = {Pt 2},
pages = {118692},
doi = {10.1016/j.envres.2024.118692},
pmid = {38493856},
issn = {1096-0953},
mesh = {*Gene Transfer, Horizontal ; *Microalgae/genetics/drug effects ; *Eutrophication ; *Symbiosis ; *Bacteria/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; Chlorella/genetics/drug effects ; Nitrogen ; },
abstract = {Overloading of nutrients such as nitrogen causes eutrophication of freshwater bodies. The spread of antibiotic resistance genes (ARGs) poses a threat to ecosystems. However, studies on the enrichment and spread of ARGs from increased nitrogen loading in algal-bacterial symbiotic systems are limited. In this study, the transfer of extracellular kanamycin resistance (KR) genes from large (RP4) small (pEASY-T1) plasmids into the intracellular and extracellular DNA (iDNA, eDNA) of the inter-algal environment of Chlorella pyrenoidosa was investigated, along with the community structure of free-living (FL) and particle-attached (PA) bacteria under different nitrogen source concentrations (0-2.5 g/L KNO3). The results showed that KR gene abundance in the eDNA adsorbed on solid particles (D-eDNA) increased initially and then decreased with increasing nitrogen concentration, while the opposite was true for the rest of the free eDNA (E-eDNA). Medium nitrogen concentrations promoted the transfer of extracellular KR genes into the iDNA attached to algal microorganisms (A-iDNA), eDNA attached to algae (B-eDNA), and the iDNA of free microorganisms (C-iDNA); high nitrogen contributed to the transfer of KR genes into C-iDNA. The highest percentage of KR genes was found in B-eDNA with RP4 plasmid treatment (66.2%) and in C-iDNA with pEASY-T1 plasmid treatment (86.88%). In addition, dissolved oxygen (DO) significantly affected the bacterial PA and FL community compositions. Nephelometric turbidity units (NTU) reflected the abundance of ARGs in algae. Proteobacteria, Cyanobacteria, Bacteroidota, and Actinobacteriota were the main potential hosts of ARGs. These findings provide new insights into the distribution and dispersal of ARGs in the phytoplankton inter-algal environment.},
}
@article {pmid38486809,
year = {2024},
author = {Novikova, PV and Bhanu Busi, S and Probst, AJ and May, P and Wilmes, P},
title = {Functional prediction of proteins from the human gut archaeome.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycad014},
pmid = {38486809},
issn = {2730-6151},
abstract = {The human gastrointestinal tract contains diverse microbial communities, including archaea. Among them, Methanobrevibacter smithii represents a highly active and clinically relevant methanogenic archaeon, being involved in gastrointestinal disorders, such as inflammatory bowel disease and obesity. Herein, we present an integrated approach using sequence and structure information to improve the annotation of M. smithii proteins using advanced protein structure prediction and annotation tools, such as AlphaFold2, trRosetta, ProFunc, and DeepFri. Of an initial set of 873 481 archaeal proteins, we found 707 754 proteins exclusively present in the human gut. Having analysed archaeal proteins together with 87 282 994 bacterial proteins, we identified unique archaeal proteins and archaeal-bacterial homologs. We then predicted and characterized functional domains and structures of 73 unique and homologous archaeal protein clusters linked the human gut and M. smithii. We refined annotations based on the predicted structures, extending existing sequence similarity-based annotations. We identified gut-specific archaeal proteins that may be involved in defense mechanisms, virulence, adhesion, and the degradation of toxic substances. Interestingly, we identified potential glycosyltransferases that could be associated with N-linked and O-glycosylation. Additionally, we found preliminary evidence for interdomain horizontal gene transfer between Clostridia species and M. smithii, which includes sporulation Stage V proteins AE and AD. Our study broadens the understanding of archaeal biology, particularly M. smithii, and highlights the importance of considering both sequence and structure for the prediction of protein function.},
}
@article {pmid38485028,
year = {2024},
author = {Liu, H and Zhang, Z and Li, X and Zhou, T and Wang, Z and Li, J and Li, Y and Wang, Q},
title = {Temperature-phased anaerobic sludge digestion effectively removes antibiotic resistance genes in a full-scale wastewater treatment plant.},
journal = {The Science of the total environment},
volume = {924},
number = {},
pages = {171555},
doi = {10.1016/j.scitotenv.2024.171555},
pmid = {38485028},
issn = {1879-1026},
mesh = {*Sewage/microbiology ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Anaerobiosis ; Temperature ; Drug Resistance, Microbial/genetics ; *Water Purification ; Digestion ; },
abstract = {Sludge is a major by-product and the final reservoir of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs). Temperature-phased anaerobic digestion (TPAD), consisting of thermophilic anaerobic digestion (AD) (55 °C) and mesophilic AD processes (37 °C), has been implemented in WWTPs for sludge reduction while improving the biomethane production. However, the impact of TPAD on the ARGs' fate is still undiscovered in lab-scale experiments and full-scale WWTPs. This study, for the first time, investigated the fate of ARGs during the TPAD process across three seasons in a full-size WWTP. Ten typical ARGs and one integrase gene of class 1 integron (intI1) involving ARGs horizontal gene transfer were examined in sludge before and after each step of the TPAD process. TPAD reduced aac(6')-Ib-cr, blaTEM, drfA1, sul1, sul2, ermb, mefA, tetA, tetB and tetX by 87.3-100.0 %. TPAD reduced the overall average absolute abundance of targeted ARGs and intI1 by 92.39 % and 92.50 %, respectively. The abundance of targeted ARGs in sludge was higher in winter than in summer and autumn before and after TPAD. During the TPAD processes, thermophilic AD played a major role in the removal of ARGs, contributing to >60 % removal of ARGs, while the subsequent mesophilic AD contributed to a further 31 % removal of ARGs. The microbial community analysis revealed that thermophilic AD reduced the absolute abundance of ARGs hosts, antibiotic resistant bacteria. In addition, thermophilic AD reduced the abundance of the intI1, while the intI1 did not reproduce during the mesophilic AD, also contributing to a decline in the absolute abundance of ARGs in TPAD. This study demonstrates that TPAD can effectively reduce the abundance of ARGs in sludge, which will suppress the transmission of ARGs from sludge into the natural environment and deliver environmental and health benefits to our society.},
}
@article {pmid38478693,
year = {2024},
author = {Keith, M and Park de la Torriente, A and Chalka, A and Vallejo-Trujillo, A and McAteer, SP and Paterson, GK and Low, AS and Gally, DL},
title = {Predictive phage therapy for Escherichia coli urinary tract infections: Cocktail selection for therapy based on machine learning models.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {12},
pages = {e2313574121},
pmid = {38478693},
issn = {1091-6490},
support = {BBS/E/D/20002173//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {Humans ; Animals ; Escherichia coli/genetics ; *Phage Therapy ; *Escherichia coli Infections/microbiology ; *Bacteriophages/genetics ; Anti-Bacterial Agents/pharmacology ; *Urinary Tract Infections/drug therapy ; },
abstract = {This study supports the development of predictive bacteriophage (phage) therapy: the concept of phage cocktail selection to treat a bacterial infection based on machine learning (ML) models. For this purpose, ML models were trained on thousands of measured interactions between a panel of phage and sequenced bacterial isolates. The concept was applied to Escherichia coli associated with urinary tract infections. This is an important common infection in humans and companion animals from which multidrug-resistant (MDR) bloodstream infections can originate. The global threat of MDR infection has reinvigorated international efforts into alternatives to antibiotics including phage therapy. E. coli exhibit extensive genome-level variation due to horizontal gene transfer via phage and plasmids. Associated with this, phage selection for E. coli is difficult as individual isolates can exhibit considerable variation in phage susceptibility due to differences in factors important to phage infection including phage receptor profiles and resistance mechanisms. The activity of 31 phage was measured on 314 isolates with growth curves in artificial urine. Random Forest models were built for each phage from bacterial genome features, and the more generalist phage, acting on over 20% of the bacterial population, exhibited F1 scores of >0.6 and could be used to predict phage cocktails effective against previously untested strains. The study demonstrates the potential of predictive ML models which integrate bacterial genomics with phage activity datasets allowing their use on data derived from direct sequencing of clinical samples to inform rapid and effective phage therapy.},
}
@article {pmid38477539,
year = {2024},
author = {Shang, Y and Zhang, Y and Wang, R and Peng, Y and Ding, B and Liu, Y and Li, C and Feng, L and Liu, H and Yang, C and Tang, Y},
title = {Deciphering the molecular and functional basis of TMexCD1: the plasmid-encoded efflux pump of resistance-nodulation-division superfamily.},
journal = {Antimicrobial agents and chemotherapy},
volume = {68},
number = {4},
pages = {e0167823},
pmid = {38477539},
issn = {1098-6596},
support = {2021YFC2101500//National Key Research and Development Program of China/ ; 42077214//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Animals ; *Escherichia coli/genetics/metabolism ; *Escherichia coli Proteins/metabolism ; Anti-Bacterial Agents/chemistry ; Molecular Docking Simulation ; Drug Resistance, Multiple, Bacterial/genetics ; Multidrug Resistance-Associated Proteins/genetics ; Microbial Sensitivity Tests ; },
abstract = {Horizontal gene transfer has been demonstrated to be an important driver for the emergency of multidrug-resistant pathogens. Recently, a transferable gene cluster tmexCD1-toprJ1 of the resistance-nodulation-division (RND) superfamily was identified in the plasmids of animal-derived Klebsiella pneumoniae strains, with a higher efflux capacity for various drugs than the Escherichia coli AcrAB-TolC homolog system. In this study, we focused on the differences in the inner membrane pump of these two systems and identified some key residues that contribute to the robust efflux activity of the TMexCD1 system. With the aid of homologous modeling and molecular docking, eight residues from the proximal binding pocket (PBP) and nine from the distal binding pocket (DBP) were selected and subjected to site-directed mutagenesis. Several of them, such as S134, I139, D181, and A290, were shown to be important for substrate binding in the DBP region, and all residues in PBP and DBP showed certain substrate preferences. Apart from the conservative switch loop (L613-623[TMexD1]) previously identified in the E. coli AcrB (EcAcrB), a relatively unconservative loop (L665-675[TMexD1]) at the bottom of PBP was proposed as a critical element for the robust activity of TMexD1, due to variations at sites E669, G670, N673, and S674 compared to EcAcrAB, and the significantly altered efflux activity due to their mutations. The conservation and flexibility of these key factors can contribute to the evolution of the RND efflux pumps and thus serve as potential targets for developing inhibitors to block the widespread of the TMexCD1 system.},
}
@article {pmid38471323,
year = {2024},
author = {Li, J and Liao, Q and Wang, Y and Wang, X and Liu, J and Zha, R and He, JZ and Zhang, M and Zhang, W},
title = {Involvement of functional metabolism promotes the enrichment of antibiotic resistome in drinking water: Based on the PICRUSt2 functional prediction.},
journal = {Journal of environmental management},
volume = {356},
number = {},
pages = {120544},
doi = {10.1016/j.jenvman.2024.120544},
pmid = {38471323},
issn = {1095-8630},
mesh = {*Anti-Bacterial Agents/pharmacology/analysis ; *Drinking Water ; Genes, Bacterial ; Angiotensin Receptor Antagonists/analysis ; Nitrites/analysis ; Drug Resistance, Microbial/genetics ; Angiotensin-Converting Enzyme Inhibitors/analysis ; Nitrogen/analysis ; },
abstract = {Biofilters are the important source and sink of antibiotic resistance genes (ARGs) and antibiotic resistance bacteria (ARB) in the drinking water. Current studies generally ascribed the prevalence of BAR in biofilter from the perspective of gene behavior, i.e. horizontal gene transfer (HGT), little attentions have been paid on the ARGs carrier- ARB. In this study, we proposed the hypothesis that ARB participating in pollutant metabolism processes and becoming dominant is an important way for the enrichment of ARGs. To verify this, the antibiotic resistome and bacterial functional metabolic pathways of a sand filter was profiled using heterotrophic bacterial plate counting method (HPC), high-throughput qPCR, Illumina Hiseq sequencing and PICRUSt2 functional prediction. The results illustrated a significant leakage of ARB in the effluent of the sand filter with an average absolute abundance of approximately 10[2]-10[3] CFU/mL. Further contribution analysis revealed that the dominant genera, such as Acinetobacter spp., Aeromonas spp., Elizabethkingia spp., and Bacillus spp., were primary ARGs hosts, conferring resistance to multiple antibiotics including sulfamethoxazole, tetracycline and β-lactams. Notably, these ARGs hosts were involved in nitrogen metabolism, including extracellular nitrate/nitrite transport and nitrite reduction, which are crucial in nitrification and denitrification in biofilters. For example, Acinetobacter spp., the dominant bacteria in the filter (relative abundance 69.97 %), contributed the majority of ARGs and 53.79 % of nitrite reduction function. That is, ARB can predominate by participating in the nitrogen metabolism pathways, facilitating the enrichment of ARGs. These findings provide insights into the stable presence of ARGs in biofilters from a functional metabolism perspective, offering a significant supplementary to the mechanisms of the emergence, maintenance, and transmission of BARin drinking water.},
}
@article {pmid38470054,
year = {2024},
author = {Beck, C and Krusche, J and Notaro, A and Walter, A and Kränkel, L and Vollert, A and Stemmler, R and Wittmann, J and Schaller, M and Slavetinsky, C and Mayer, C and De Castro, C and Peschel, A},
title = {Wall teichoic acid substitution with glucose governs phage susceptibility of Staphylococcus epidermidis.},
journal = {mBio},
volume = {15},
number = {4},
pages = {e0199023},
pmid = {38470054},
issn = {2150-7511},
support = {ID 246807620, ID 410190180, ID 39083813//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Humans ; *Staphylococcus epidermidis/genetics/metabolism ; Staphylococcus aureus/genetics ; Coagulase/metabolism ; Glucose/metabolism ; Teichoic Acids/metabolism ; Staphylococcus/metabolism ; Staphylococcus Phages/genetics ; DNA/metabolism ; Cell Wall/metabolism ; *Staphylococcal Infections/metabolism ; },
abstract = {The species- and clone-specific susceptibility of Staphylococcus cells for bacteriophages is governed by the structures and glycosylation patterns of wall teichoic acid (WTA) glycopolymers. The glycosylation-dependent phage-WTA interactions in the opportunistic pathogen Staphylococcus epidermidis and in other coagulase-negative staphylococci (CoNS) have remained unknown. We report a new S. epidermidis WTA glycosyltransferase TagE whose deletion confers resistance to siphoviruses such as ΦE72 but enables binding of otherwise unbound podoviruses. S. epidermidis glycerolphosphate WTA was found to be modified with glucose in a tagE-dependent manner. TagE is encoded together with the enzymes PgcA and GtaB providing uridine diphosphate-activated glucose. ΦE72 transduced several other CoNS species encoding TagE homologs, suggesting that WTA glycosylation via TagE is a frequent trait among CoNS that permits interspecies horizontal gene transfer. Our study unravels a crucial mechanism of phage-Staphylococcus interaction and horizontal gene transfer, and it will help in the design of anti-staphylococcal phage therapies.IMPORTANCEPhages are highly specific for certain bacterial hosts, and some can transduce DNA even across species boundaries. How phages recognize cognate host cells remains incompletely understood. Phages infecting members of the genus Staphylococcus bind to wall teichoic acid (WTA) glycopolymers with highly variable structures and glycosylation patterns. How WTA is glycosylated in the opportunistic pathogen Staphylococcus epidermidis and in other coagulase-negative staphylococci (CoNS) species has remained unknown. We describe that S. epidermidis glycosylates its WTA backbone with glucose, and we identify a cluster of three genes responsible for glucose activation and transfer to WTA. Their inactivation strongly alters phage susceptibility patterns, yielding resistance to siphoviruses but susceptibility to podoviruses. Many different CoNS species with related glycosylation genes can exchange DNA via siphovirus ΦE72, suggesting that glucose-modified WTA is crucial for interspecies horizontal gene transfer. Our finding will help to develop antibacterial phage therapies and unravel routes of genetic exchange.},
}
@article {pmid38466360,
year = {2024},
author = {Kim, YH and Lee, DH and Seo, HS and Eun, SH and Lee, DS and Choi, YK and Lee, SH and Kim, TY},
title = {Genome-based taxonomic identification and safety assessment of an Enterococcus strain isolated from a homemade dairy product.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {27},
number = {5},
pages = {1513-1525},
pmid = {38466360},
issn = {1618-1905},
mesh = {*Enterococcus/genetics/isolation &amp; purification/classification/drug effects/pathogenicity ; *Genome, Bacterial ; *Virulence Factors/genetics ; *Anti-Bacterial Agents/pharmacology ; *Whole Genome Sequencing ; *Cheese/microbiology ; Food Microbiology ; Republic of Korea ; Virulence/genetics ; Drug Resistance, Bacterial/genetics ; Dairy Products/microbiology ; Microbial Sensitivity Tests ; },
abstract = {The aim of this study was to explore the taxonomic identification and evaluate the safety of a bacterium, Enterococcus lactis IDCC 2105, isolated from homemade cheese in Korea, using whole genome sequence (WGS) analysis. It sought to identify the species level of this Enterococcus spp., assess its antibiotic resistance, and evaluate its virulence potential. WGS analysis confirmed the bacterial strain IDCC 2105 as E. lactis and identified genes responsible for resistance to erythromycin and clindamycin, specifically msrC, and eatAv, which are chromosomally located, indicating a minimal risk for horizontal gene transfer. The absence of plasmids in E. lactis IDCC 2105 further diminishes the likelihood of resistance gene dissemination. Additionally, our investigation into seven virulence factors, including hemolysis, platelet aggregation, biofilm formation, hyaluronidase, gelatinase, ammonia production, and β-glucuronidase activity, revealed no detectable virulence traits. Although bioinformatic analysis suggested the presence of collagen adhesion genes acm and scm, these were not corroborated by phenotypic virulence assays. Based on these findings, E. lactis IDCC 2105 presents as a safe strain for potential applications, contributing valuable information on its taxonomy, antibiotic resistance profile, and lack of virulence factors, supporting its use in food products.},
}
@article {pmid38463488,
year = {2024},
author = {Simón, D and Ramos, N and Lamolle, G and Musto, H},
title = {Two decades ago, giant viruses were discovered: the fall of an old paradigm.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1356711},
pmid = {38463488},
issn = {1664-302X},
}
@article {pmid38458877,
year = {2024},
author = {Wilson, CG and Pieszko, T and Nowell, RW and Barraclough, TG},
title = {Recombination in bdelloid rotifer genomes: asexuality, transfer and stress.},
journal = {Trends in genetics : TIG},
volume = {40},
number = {5},
pages = {422-436},
doi = {10.1016/j.tig.2024.02.001},
pmid = {38458877},
issn = {0168-9525},
mesh = {Animals ; *Rotifera/genetics/physiology ; *Gene Transfer, Horizontal/genetics ; *Recombination, Genetic ; *Stress, Physiological/genetics ; Reproduction, Asexual/genetics ; Genome/genetics ; Genome, Helminth ; Phylogeny ; Male ; },
abstract = {Bdelloid rotifers constitute a class of microscopic animals living in freshwater habitats worldwide. Several strange features of bdelloids have drawn attention: their ability to tolerate desiccation and other stresses, a lack of reported males across the clade despite centuries of study, and unusually high numbers of horizontally acquired, non-metazoan genes. Genome sequencing is transforming our understanding of their lifestyle and its consequences, while in turn providing wider insights about recombination and genome organisation in animals. Many questions remain, not least how to reconcile apparent genomic signatures of sex with the continued absence of reported males, why bdelloids have so many horizontally acquired genes, and how their remarkable ability to survive stress interacts with recombination and other genomic processes.},
}
@article {pmid38457521,
year = {2024},
author = {Colombi, E and Bertels, F and Doulcier, G and McConnell, E and Pichugina, T and Sohn, KH and Straub, C and McCann, HC and Rainey, PB},
title = {Rapid dissemination of host metabolism-manipulating genes via integrative and conjugative elements.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {11},
pages = {e2309263121},
pmid = {38457521},
issn = {1091-6490},
support = {MAU1709//Royal Society of New Zealand | Marsden Fund (Royal Society of New Zealand Marsden Fund)/ ; SFB1182 Project C4//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {Phylogeny ; *Conjugation, Genetic ; *Gene Transfer, Horizontal/genetics ; Biological Evolution ; DNA Transposable Elements/genetics ; },
abstract = {Integrative and conjugative elements (ICEs) are self-transmissible mobile elements that transfer functional genetic units across broad phylogenetic distances. Accessory genes shuttled by ICEs can make significant contributions to bacterial fitness. Most ICEs characterized to date encode readily observable phenotypes contributing to symbiosis, pathogenicity, and antimicrobial resistance, yet the majority of ICEs carry genes of unknown function. Recent observations of rapid acquisition of ICEs in a pandemic lineage of Pseudomonas syringae pv. actinidae led to investigation of the structural and functional diversity of these elements. Fifty-three unique ICE types were identified across the P. syringae species complex. Together they form a distinct family of ICEs (PsICEs) that share a distant relationship to ICEs found in Pseudomonas aeruginosa. PsICEs are defined by conserved backbone genes punctuated by an array of accessory cargo genes, are highly recombinogenic, and display distinct evolutionary histories compared to their bacterial hosts. The most common cargo is a recently disseminated 16-kb mobile genetic element designated Tn6212. Deletion of Tn6212 did not alter pathogen growth in planta, but mutants displayed fitness defects when grown on tricarboxylic acid (TCA) cycle intermediates. RNA-seq analysis of a set of nested deletion mutants showed that a Tn6212-encoded LysR regulator has global effects on chromosomal gene expression. We show that Tn6212 responds to preferred carbon sources and manipulates bacterial metabolism to maximize growth.},
}
@article {pmid38453913,
year = {2024},
author = {Hayashi, N and Lai, Y and Fuerte-Stone, J and Mimee, M and Lu, TK},
title = {Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {2096},
pmid = {38453913},
issn = {2041-1723},
support = {R25 GM109439/GM/NIGMS NIH HHS/United States ; R35 GM147478/GM/NIGMS NIH HHS/United States ; T32 GM007183/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *CRISPR-Cas Systems/genetics ; *Containment of Biohazards ; Genetic Engineering ; Bacteria/genetics ; Thymidine ; },
abstract = {Sophisticated gene circuits built by synthetic biology can enable bacteria to sense their environment and respond predictably. Engineered biosensing bacteria outfitted with such circuits can potentially probe the human gut microbiome to prevent, diagnose, or treat disease. To provide robust biocontainment for engineered bacteria, we devised a Cas9-assisted auxotrophic biocontainment system combining thymidine auxotrophy, an Engineered Riboregulator (ER) for controlled gene expression, and a CRISPR Device (CD). The CD prevents the engineered bacteria from acquiring thyA via horizontal gene transfer, which would disrupt the biocontainment system, and inhibits the spread of genetic elements by killing bacteria harboring the gene cassette. This system tunably controlled gene expression in the human gut commensal bacterium Bacteroides thetaiotaomicron, prevented escape from thymidine auxotrophy, and blocked transgene dissemination. These capabilities were validated in vitro and in vivo. This biocontainment system exemplifies a powerful strategy for bringing genetically engineered microorganisms safely into biomedicine.},
}
@article {pmid38453092,
year = {2024},
author = {Wang, YC and Mao, Y and Fu, HM and Wang, J and Weng, X and Liu, ZH and Xu, XW and Yan, P and Fang, F and Guo, JS and Shen, Y and Chen, YP},
title = {New insights into functional divergence and adaptive evolution of uncultured bacteria in anammox community by complete genome-centric analysis.},
journal = {The Science of the total environment},
volume = {924},
number = {},
pages = {171530},
doi = {10.1016/j.scitotenv.2024.171530},
pmid = {38453092},
issn = {1879-1026},
mesh = {*Anaerobic Ammonia Oxidation ; Oxidation-Reduction ; *Sewage/microbiology ; Bacteria/genetics/metabolism ; Nitrogen/metabolism ; Bioreactors/microbiology ; },
abstract = {Anaerobic ammonium-oxidation (anammox) bacteria play a crucial role in global nitrogen cycling and wastewater nitrogen removal, but they share symbiotic relationships with various other microorganisms. Functional divergence and adaptive evolution of uncultured bacteria in anammox community remain underexplored. Although shotgun metagenomics based on short reads has been widely used in anammox research, metagenome-assembled genomes (MAGs) are often discontinuous and highly contaminated, which limits in-depth analyses of anammox communities. Here, for the first time, we performed Pacific Biosciences high-fidelity (HiFi) long-read sequencing on the anammox granule sludge sample from a lab-scale bioreactor, and obtained 30 accurate and complete metagenome-assembled genomes (cMAGs). These cMAGs were obtained by selecting high-quality circular contigs from initial assemblies of long reads generated by HiFi sequencing, eliminating the need for Illumina short reads, binning, and reassembly. One new anammox species affiliated with Candidatus Jettenia and three species affiliated with novel families were found in this anammox community. cMAG-centric analysis revealed functional divergence in general and nitrogen metabolism among the anammox community members, and they might adopt a cross-feeding strategy in organic matter, cofactors, and vitamins. Furthermore, we identified 63 mobile genetic elements (MGEs) and 50 putative horizontal gene transfer (HGT) events within these cMAGs. The results suggest that HGT events and MGEs related to phage and integration or excision, particularly transposons containing tnpA in anammox bacteria, might play important roles in the adaptive evolution of this anammox community. The cMAGs generated in the present study could be used to establish of a comprehensive database for anammox bacteria and associated microorganisms. These findings highlight the advantages of HiFi sequencing for the studies of complex mixed cultures and advance the understanding of anammox communities.},
}
@article {pmid38452676,
year = {2024},
author = {Xie, X and Chen, B and Zhu, S and Yang, R and Yuan, K and Yang, Y and Chen, R and Lin, L and Chen, B},
title = {Comparative analysis of characteristics of antibiotic resistomes between Arctic soils and representative contaminated samples using metagenomic approaches.},
journal = {Journal of hazardous materials},
volume = {469},
number = {},
pages = {133943},
doi = {10.1016/j.jhazmat.2024.133943},
pmid = {38452676},
issn = {1873-3336},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Soil ; Bacteria/genetics ; Ampicillin ; },
abstract = {Antibiotic resistance is one of the most concerned global health issues. However, comprehensive profiles of antibiotic resistance genes (ARGs) in various environmental settings are still needed to address modern antibiotic resistome. Here, Arctic soils and representative contaminated samples from ARG pollution sources were analyzed using metagenomic approaches. The diversity and abundance of ARGs in Arctic soils were significantly lower than those in contaminated samples (p < 0.01). ARG profiles in Arctic soils were featured with the dominance of vanF, ceoB, and bacA related to multidrug and bacitracin, whereas those from ARG pollution sources were characterized by prevalent resistance to anthropogenic antibiotics such as sulfonamides, tetracyclines, and beta-lactams. Mobile genetic elements (MGEs) were found in all samples, and their abundance and relatedness to ARGs were both lower in Arctic soils than in polluted samples. Significant relationships between bacterial communities and ARGs were observed (p < 0.01). Cultural bacteria in Arctic soils had clinically-concerned resistance to erythromycin, vancomycin, ampicillin, etc., but ARGs relevant to those antibiotics were undetectable in their genomes. Our results suggested that Arctic environment could be an important reservoir of novel ARGs, and antibiotic stresses could cause ARG pollution via horizontal gene transfer and enrichment of resistant bacteria.},
}
@article {pmid38449530,
year = {2024},
author = {Franceus, J and Rivas-Fernández, JP and Lormans, J and Rovira, C and Desmet, T},
title = {Evolution of Phosphorylase Activity in an Ancestral Glycosyltransferase.},
journal = {ACS catalysis},
volume = {14},
number = {5},
pages = {3103-3114},
pmid = {38449530},
issn = {2155-5435},
abstract = {The reconstruction of ancestral sequences can offer a glimpse into the fascinating process of molecular evolution by exposing the adaptive pathways that shape the proteins found in nature today. Here, we track the evolution of the carbohydrate-active enzymes responsible for the synthesis and turnover of mannogen, a critical carbohydrate reserve in Leishmania parasites. Biochemical characterization of resurrected enzymes demonstrated that mannoside phosphorylase activity emerged in an ancestral bacterial mannosyltransferase, and later disappeared in the process of horizontal gene transfer and gene duplication in Leishmania. By shuffling through plausible historical sequence space in an ancestral mannosyltransferase, we found that mannoside phosphorylase activity could be toggled on through various combinations of mutations at positions outside of the active site. Molecular dynamics simulations showed that such mutations can affect loop rigidity and shield the active site from water molecules that disrupt key interactions, allowing α-mannose 1-phosphate to adopt a catalytically productive conformation. These findings highlight the importance of subtle distal mutations in protein evolution and suggest that the vast collection of natural glycosyltransferases may be a promising source of engineering templates for the design of tailored phosphorylases.},
}
@article {pmid38448399,
year = {2024},
author = {Haudiquet, M and Le Bris, J and Nucci, A and Bonnin, RA and Domingo-Calap, P and Rocha, EPC and Rendueles, O},
title = {Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {2032},
pmid = {38448399},
issn = {2041-1723},
support = {ANR 18 CE12 0001 01 ENCAPSULATION//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR 16 CE15 0022 03 PREDIRES//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-LABX-62- IBEID//Agence Nationale de la Recherche (French National Research Agency)/ ; PIA/ANR-16- CONV-0005//Agence Nationale de la Recherche (French National Research Agency)/ ; EQU201903007835//Fondation pour la Recherche M&#xe9;dicale (Foundation for Medical Research in France)/ ; },
mesh = {Phenotype ; Plasmids/genetics ; Serogroup ; *Genome, Bacterial ; *Bacteriophages/genetics ; },
abstract = {Bacterial evolution is affected by mobile genetic elements like phages and conjugative plasmids, offering new adaptive traits while incurring fitness costs. Their infection is affected by the bacterial capsule. Yet, its importance has been difficult to quantify because of the high diversity of confounding mechanisms in bacterial genomes such as anti-viral systems and surface receptor modifications. Swapping capsule loci between Klebsiella pneumoniae strains allowed us to quantify their impact on plasmid and phage infection independently of genetic background. Capsule swaps systematically invert phage susceptibility, revealing serotypes as key determinants of phage infection. Capsule types also influence conjugation efficiency in both donor and recipient cells, a mechanism shaped by capsule volume and conjugative pilus structure. Comparative genomics confirmed that more permissive serotypes in the lab correspond to the strains acquiring more conjugative plasmids in nature. The least capsule-sensitive pili (F-like) are the most frequent in the species' plasmids, and are the only ones associated with both antibiotic resistance and virulence factors, driving the convergence between virulence and antibiotics resistance in the population. These results show how traits of cellular envelopes define slow and fast lanes of infection by mobile genetic elements, with implications for population dynamics and horizontal gene transfer.},
}
@article {pmid38447655,
year = {2024},
author = {Shi, X and Shen, Z and Shao, B and Shen, J and Wu, Y and Wang, S},
title = {Antibiotic resistance genes profile in the surface sediments of typical aquaculture areas across 15 major lakes in China.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {347},
number = {},
pages = {123709},
doi = {10.1016/j.envpol.2024.123709},
pmid = {38447655},
issn = {1873-6424},
mesh = {Humans ; *Lakes/microbiology ; *Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Aquaculture ; China ; Anti-Bacterial Agents/pharmacology/analysis ; },
abstract = {Aquatic farming is considered as a major source of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) for the natural environment of the lakes. ARB and ARGs in the natural environment have increased quickly because of the human activities. Here, we have profiled the diversity and abundance of ARGs in sediments from the typical aquaculture areas around 15 major lakes in China using PCR and qPCR, and further assessed the risk factor shaping the occurrence and distribution of ARGs. And class 1, 2 and 3 integrons were initially detected by PCR with specific primers. ARGs were widely distributed in the lakes: Weishan Lake and Poyang Lake showed high diversity of ARGs, followed by Dongting Lake, Chao Lake and Tai Lake. Generally, the ARGs in the Middle-Lower Yangtze Plain were more abundant than those in the Qinghai-Tibet Plateau. Tetracycline resistance genes (tet(C), tet(A) &amp; tet(M)) were prominent in sediments, and the next was AmpC β-lactamase gene group BIL/LAT/CMY, and the last was the genes resistance to aminoglycoside (strA-strB). Partial least squares path modeling analysis (PLS-PMA) revealed that livestock had a significant direct effect on the distribution of ARGs in lakes, and population might indirectly influence the profiles of ARGs by affecting the scale of livestock and aquaculture. The detectable rate of class 1, 2 and 3 integrons were 80%, 100% and 46.67%, respectively. The prevalence of integrons might play a key role in promoting more frequent horizontal gene transfer (HGT) events, resulting in the environmental mobilization and dissemination of ARGs between bacteria.},
}
@article {pmid38447371,
year = {2024},
author = {Wang, Y and Zhang, Z and Kang, J and Chen, B and Hong, W and Lv, B and Wang, T and Qian, H},
title = {Phages in different habitats and their ability to carry antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {469},
number = {},
pages = {133941},
doi = {10.1016/j.jhazmat.2024.133941},
pmid = {38447371},
issn = {1873-3336},
mesh = {Humans ; *Bacteriophages/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Ecosystem ; Biodiversity ; Genes, Bacterial ; },
abstract = {As the most abundant organisms on Earth, phages play a key role in the evolution of bacterial antibiotic resistance. Although previous studies have demonstrated the molecular mechanisms of horizontal gene transfer mediated by mobile genetic elements, our understanding of the intertwined relationships between antibiotic resistance genes (ARGs) and phages is limited. In this study, we analysed 2781 metagenomic samples to reveal the composition and species interactions of phage communities in different habitats as well as their capacity to carry ARGs with health risks. The composition of phage communities varies in different habitats and mainly depends on environmental conditions. Terrestrial habitats display more complex and robust interactions between phages than aquatic and human-associated habitats, resulting in the highest biodiversity of phages. Several types of phages in certain taxa (4.95-7.67%, mainly belonging to Caudoviricetes) have the capacity to carry specific ARGs and display a high potential risk to human health, especially in human-associated habitats. Overall, our results provide insights into the assembly mechanisms of phage communities and their effects on the dissemination of antibiotic resistance.},
}
@article {pmid38445859,
year = {2024},
author = {Sharma, DK and Rajpurohit, YS},
title = {Multitasking functions of bacterial extracellular DNA in biofilms.},
journal = {Journal of bacteriology},
volume = {206},
number = {4},
pages = {e0000624},
pmid = {38445859},
issn = {1098-5530},
support = {RBA4031//DAE | Bhabha Atomic Research Centre (BARC)/ ; },
mesh = {Humans ; DNA, Bacterial/genetics ; *Ecosystem ; *Biofilms ; Bacteria/genetics ; Extracellular Matrix ; },
abstract = {Bacterial biofilms are intricate ecosystems of microbial communities that adhere to various surfaces and are enveloped by an extracellular matrix composed of polymeric substances. Within the context of bacterial biofilms, extracellular DNA (eDNA) originates from cell lysis or is actively secreted, where it exerts a significant influence on the formation, stability, and resistance of biofilms to environmental stressors. The exploration of eDNA within bacterial biofilms holds paramount importance in research, with far-reaching implications for both human health and the environment. An enhanced understanding of the functions of eDNA in biofilm formation and antibiotic resistance could inspire the development of strategies to combat biofilm-related infections and improve the management of antibiotic resistance. This comprehensive review encapsulates the latest discoveries concerning eDNA, encompassing its origins, functions within bacterial biofilms, and significance in bacterial pathogenesis.},
}
@article {pmid38443606,
year = {2024},
author = {Dmitrijeva, M and Tackmann, J and Matias Rodrigues, JF and Huerta-Cepas, J and Coelho, LP and von Mering, C},
title = {A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer.},
journal = {Nature ecology &amp; evolution},
volume = {8},
number = {5},
pages = {986-998},
pmid = {38443606},
issn = {2397-334X},
support = {51NF40_180575//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 310030-192569//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 2018SHZDZX01//Science and Technology Commission of Shanghai Municipality (Shanghai Municipal Science and Technology Commission)/ ; },
mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics ; Genome, Bacterial ; Ecosystem ; Archaea/genetics ; Genome, Archaeal ; Evolution, Molecular ; },
abstract = {Horizontal gene transfer, the exchange of genetic material through means other than reproduction, is a fundamental force in prokaryotic genome evolution. Genomic persistence of horizontally transferred genes has been shown to be influenced by both ecological and evolutionary factors. However, there is limited availability of ecological information about species other than the habitats from which they were isolated, which has prevented a deeper exploration of ecological contributions to horizontal gene transfer. Here we focus on transfers detected through comparison of individual gene trees to the species tree, assessing the distribution of gene-exchanging prokaryotes across over a million environmental sequencing samples. By analysing detected horizontal gene transfer events, we show distinct functional profiles for recent versus old events. Although most genes transferred are part of the accessory genome, genes transferred earlier in evolution tend to be more ubiquitous within present-day species. We find that co-occurring, interacting and high-abundance species tend to exchange more genes. Finally, we show that host-associated specialist species are most likely to exchange genes with other host-associated specialist species, whereas species found across different habitats have similar gene exchange rates irrespective of their preferred habitat. Our study covers an unprecedented scale of integrated horizontal gene transfer and environmental information, highlighting broad eco-evolutionary trends.},
}
@article {pmid38442604,
year = {2024},
author = {Zhang, Y and Li, W and Wu, Y and Tian, X and Li, G and Zhou, Y and Sun, J and Liao, X and Liu, Y and Wang, Y and Yu, Y},
title = {Chitosan oligosaccharide accelerates the dissemination of antibiotic resistance genes through promoting conjugative plasmid transfer.},
journal = {Journal of hazardous materials},
volume = {469},
number = {},
pages = {133922},
doi = {10.1016/j.jhazmat.2024.133922},
pmid = {38442604},
issn = {1873-3336},
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Escherichia coli/genetics ; *Chitosan/pharmacology ; Drug Resistance, Bacterial/genetics ; Plasmids/genetics ; Gene Transfer, Horizontal ; Oligosaccharides/pharmacology ; },
abstract = {The dissemination of antibiotic resistance genes (ARGs), especially via plasmid-mediated horizontal gene transfer, poses a pervasive threat to global health. Chitosan-oligosaccharide (COS) is extensively utilized in medicine, plant and animal husbandry. However, their impact on microflora implies the potential to exert selective pressure on plasmid transfer. To explore the role of COS in facilitating the dissemination of ARGs via plasmid conjugation, we established in vitro mating models. The addition of COS to conjugation mixtures significantly enhanced the transfer of RP4 plasmid and mcr-1 positive IncX4 plasmid in both intra- and inter-specific. Phenotypic and transcriptome analysis revealed that COS enhanced intercellular contact by neutralizing cell surface charge and increasing cell surface hydrophobicity. Additionally, COS increased membrane permeability by inhibiting the Tol-Pal system, thereby facilitating plasmid conjugative transfer. Furthermore, COS served as the carbon source and was metabolized by E. coli, providing energy for plasmid conjugation through regulating the expression of ATPase and global repressor factor-related genes in RP4 plasmid. Overall, these findings improve our awareness of the potential risks associated with the presence of COS and the spread of bacterial antibiotic resistance, emphasizing the need to establish guidelines for the prudent use of COS and its discharge into the environment.},
}
@article {pmid38441061,
year = {2024},
author = {Gschwind, R and Petitjean, M and Fournier, C and Lao, J and Clermont, O and Nordmann, P and Mellmann, A and Denamur, E and Poirel, L and Ruppé, E},
title = {Inter-phylum circulation of a beta-lactamase-encoding gene: a rare but observable event.},
journal = {Antimicrobial agents and chemotherapy},
volume = {68},
number = {4},
pages = {e0145923},
pmid = {38441061},
issn = {1098-6596},
support = {FNS-407240_177381/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Humans ; *Escherichia coli ; beta-Lactamases/genetics/metabolism ; *Escherichia coli Infections/microbiology ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; },
abstract = {Beta-lactamase-mediated degradation of beta-lactams is the most common mechanism of beta-lactam resistance in Gram-negative bacteria. Beta-lactamase-encoding genes can be transferred between closely related bacteria, but spontaneous inter-phylum transfers (between distantly related bacteria) have never been reported. Here, we describe an extended-spectrum beta-lactamase (ESBL)-encoding gene (blaMUN-1) shared between the Pseudomonadota and Bacteroidota phyla. An Escherichia coli strain was isolated from a patient in Münster (Germany). Its genome was sequenced. The ESBL-encoding gene (named blaMUN-1) was cloned, and the corresponding enzyme was characterized. The distribution of the gene among bacteria was investigated using the RefSeq Genomes database. The frequency and relative abundance of its closest homolog in the global microbial gene catalog (GMGC) were analyzed. The E. coli strain exhibited two distinct morphotypes. Each morphotype possessed two chromosomal copies of the blaMUN-1 gene, with one morphotype having two additional copies located on a phage-plasmid p0111. Each copy was located within a 7.6-kb genomic island associated with mobility. blaMUN-1 encoded for an extended-spectrum Ambler subclass A2 beta-lactamase with 43.0% amino acid identity to TLA-1. blaMUN-1 was found in species among the Bacteroidales order and in Sutterella wadsworthensis (Pseudomonadota). Its closest homolog in GMGC was detected frequently in human fecal samples. This is, to our knowledge, the first reported instance of inter-phylum transfer of an ESBL-encoding gene, between the Bacteroidota and Pseudomonadota phyla. Although the gene was frequently detected in the human gut, inter-phylum transfer was rare, indicating that inter-phylum barriers are effective in impeding the spread of ESBL-encoding genes, but not entirely impenetrable.},
}
@article {pmid38436469,
year = {2024},
author = {van der Gulik, PTS and Hoff, WD and Speijer, D},
title = {The contours of evolution: In defence of Darwin's tree of life paradigm.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {46},
number = {5},
pages = {e2400012},
doi = {10.1002/bies.202400012},
pmid = {38436469},
issn = {1521-1878},
mesh = {Animals ; *Biological Evolution ; *Gene Transfer, Horizontal ; *Phylogeny ; },
abstract = {Both the concept of a Darwinian tree of life (TOL) and the possibility of its accurate reconstruction have been much criticized. Criticisms mostly revolve around the extensive occurrence of lateral gene transfer (LGT), instances of uptake of complete organisms to become organelles (with the associated subsequent gene transfer to the nucleus), as well as the implications of more subtle aspects of the biological species concept. Here we argue that none of these criticisms are sufficient to abandon the valuable TOL concept and the biological realities it captures. Especially important is the need to conceptually distinguish between organismal trees and gene trees, which necessitates incorporating insights of widely occurring LGT into modern evolutionary theory. We demonstrate that all criticisms, while based on important new findings, do not invalidate the TOL. After considering the implications of these new insights, we find that the contours of evolution are best represented by a TOL.},
}
@article {pmid38436262,
year = {2024},
author = {Harmer, CJ and Hall, RM},
title = {IS26 and the IS26 family: versatile resistance gene movers and genome reorganizers.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {88},
number = {2},
pages = {e0011922},
pmid = {38436262},
issn = {1098-5557},
support = {GNT1194879//DHAC | National Health and Medical Research Council (NHMRC)/ ; },
mesh = {*DNA Transposable Elements/genetics ; *Gram-Negative Bacteria/genetics ; Genome, Bacterial ; Drug Resistance, Bacterial/genetics ; Transposases/metabolism/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; },
abstract = {SUMMARYIn Gram-negative bacteria, the insertion sequence IS26 is highly active in disseminating antibiotic resistance genes. IS26 can recruit a gene or group of genes into the mobile gene pool and support their continued dissemination to new locations by creating pseudo-compound transposons (PCTs) that can be further mobilized by the insertion sequence (IS). IS26 can also enhance expression of adjacent potential resistance genes. IS26 encodes a DDE transposase but has unique properties. It forms cointegrates between two separate DNA molecules using two mechanisms. The well-known copy-in (replicative) route generates an additional IS copy and duplicates the target site. The recently discovered and more efficient and targeted conservative mechanism requires an IS in both participating molecules and does not generate any new sequence. The unit of movement for PCTs, known as a translocatable unit or TU, includes only one IS26. TU formed by homologous recombination between the bounding IS26s can be reincorporated via either cointegration route. However, the targeted conservative reaction is key to generation of arrays of overlapping PCTs seen in resistant pathogens. Using the copy-in route, IS26 can also act on a site in the same DNA molecule, either inverting adjacent DNA or generating an adjacent deletion plus a circular molecule carrying the DNA segment lost and an IS copy. If reincorporated, these circular molecules create a new PCT. IS26 is the best characterized IS in the IS26 family, which includes IS257/IS431, ISSau10, IS1216, IS1006, and IS1008 that are also implicated in spreading resistance genes in Gram-positive and Gram-negative pathogens.},
}
@article {pmid38435906,
year = {2024},
author = {Satija, K and Anjankar, VP},
title = {Molecular Characterization of Multidrug-Resistant Shigella flexneri.},
journal = {Cureus},
volume = {16},
number = {1},
pages = {e53276},
pmid = {38435906},
issn = {2168-8184},
abstract = {Due to their propensity for causing diarrheal illnesses and their rising susceptibility to antimicrobials, Shigella infections constitute a serious threat to global public health. This extensive study explores the frequency, antibiotic resistance, genetic evolution, and effects of Shigella infections on vulnerable groups. The research covers a wide range of geographical areas and sheds information on how the prevalence of Shigella species is evolving. Shigella strain antimicrobial resistance patterns are thoroughly examined. Multidrug resistance (MDR) has been found to often occur in investigations, especially when older antimicrobials are used. The improper use of antibiotics in China is blamed for the quick emergence of resistance, and variations in resistance rates have been seen across different geographical areas. Shigella strains' genetic makeup can be used to identify emerging trends and horizontal gene transfer's acquisition of resistance genes. Notably, S. sonnei exhibits the capacity to obtain resistance genes from nearby bacteria, increasing its capacity for infection. The study also emphasizes the difficulties in accurately serotyping Shigella strains due to inconsistencies between molecular and conventional serology. These results highlight the necessity of reliable diagnostic methods for monitoring Shigella infections. In conclusion, this study emphasizes how dynamic Shigella infections are, with varying patterns of occurrence, changing resistance landscapes, and genetic adaptability. In addition to tackling the rising problem of antibiotic resistance in Shigella infections, these findings are essential for guiding efforts for disease surveillance, prevention, and treatment.},
}
@article {pmid38434434,
year = {2024},
author = {Xiao, Y and Zhang, S and Li, H and Teng, K and Wu, S and Liu, Y and Yu, F and He, Z and Li, L and Li, L and Meng, D and Yin, H and Wang, Y},
title = {Metagenomic insights into the response of soil microbial communities to pathogenic Ralstonia solanacearum.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1325141},
pmid = {38434434},
issn = {1664-462X},
abstract = {Understanding the response of soil microbial communities to pathogenic Ralstonia solanacearum is crucial for preventing bacterial wilt outbreaks. In this study, we investigated the soil physicochemical and microbial community to assess their impact on the pathogenic R.solanacearum through metagenomics. Our results revealed that certain archaeal taxa were the main contributors influencing the health of plants. Additionally, the presence of the pathogen showed a strong negative correlation with soil phosphorus levels, while soil phosphorus was significantly correlated with bacterial and archaeal communities. We found that the network of microbial interactions in healthy plant rhizosphere soils was more complex compared to diseased soils. The diseased soil network had more linkages, particularly related to the pathogen occurrence. Within the network, the family Comamonadaceae, specifically Ramlibacter_tataouinensis, was enriched in healthy samples and showed a significantly negative correlation with the pathogen. In terms of archaea, Halorubrum, Halorussus_halophilus (family: Halobacteriaceae), and Natronomonas_pharaonis (family: Haloarculaceae) were enriched in healthy plant rhizosphere soils and showed negative correlations with R.solanacearum. These findings suggested that the presence of these archaea may potentially reduce the occurrence of bacterial wilt disease. On the other hand, Halostagnicola_larseniia and Haloterrigena_sp._BND6 (family: Natrialbaceae) had higher relative abundance in diseased plants and exhibited significantly positive correlations with R.solanacearum, indicating their potential contribution to the pathogen's occurrence. Moreover, we explored the possibility of functional gene sharing among the correlating bacterial pairs within the Molecular Ecological Network. Our analysis revealed 468 entries of horizontal gene transfer (HGT) events, emphasizing the significance of HGT in shaping the adaptive traits of plant-associated bacteria, particularly in relation to host colonization and pathogenicity. Overall, this work revealed key factors, patterns and response mechanisms underlying the rhizosphere soil microbial populations. The findings offer valuable guidance for effectively controlling soil-borne bacterial diseases and developing sustainable agriculture practices.},
}
@article {pmid38431762,
year = {2024},
author = {Huang, HJ and Li, LL and Ye, ZX and Lu, JB and Lou, YH and Wei, ZY and Sun, ZT and Chen, JP and Li, JM and Zhang, CX},
title = {Salivary proteins potentially derived from horizontal gene transfer are critical for salivary sheath formation and other feeding processes.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {257},
pmid = {38431762},
issn = {2399-3642},
support = {32001987//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Gene Transfer, Horizontal ; Insect Proteins/genetics/metabolism ; *Heteroptera/genetics/metabolism ; Salivary Proteins and Peptides/genetics/metabolism ; },
abstract = {Herbivorous insects employ an array of salivary proteins to aid feeding. However, the mechanisms behind the recruitment and evolution of these genes to mediate plant-insect interactions remain poorly understood. Here, we report a potential horizontal gene transfer (HGT) event from bacteria to an ancestral bug of Eutrichophora. The acquired genes subsequently underwent duplications and evolved through co-option. We annotated them as horizontal-transferred, Eutrichophora-specific salivary protein (HESPs) according to their origin and function. In Riptortus pedestris (Coreoidea), all nine HESPs are secreted into plants during feeding. The RpHESP4 to RpHESP8 are recently duplicated and found to be indispensable for salivary sheath formation. Silencing of RpHESP4-8 increases the difficulty of R. pedestris in probing the soybean, and the treated insects display a decreased survivability. Although silencing the other RpHESPs does not affect the salivary sheath formation, negative effects are also observed. In Pyrrhocoris apterus (Pyrrhocoroidea), five out of six PaHESPs are secretory salivary proteins, with PaHESP3 being critical for insect survival. The PaHESP5, while important for insects, no longer functions as a salivary protein. Our results provide insight into the potential origin of insect saliva and shed light on the evolution of salivary proteins.},
}
@article {pmid38431327,
year = {2024},
author = {Wiśniewski, P and Zakrzewski, A and Chajęcka-Wierzchowska, W and Zadernowska, A},
title = {Possibility of transfer and activation of 'silent' tetracycline resistance genes among Enterococcus faecalis under high-pressure processing.},
journal = {Food microbiology},
volume = {120},
number = {},
pages = {104481},
doi = {10.1016/j.fm.2024.104481},
pmid = {38431327},
issn = {1095-9998},
mesh = {*Enterococcus faecalis/genetics ; *Tetracycline Resistance/genetics ; Anti-Bacterial Agents/pharmacology ; Tetracycline/pharmacology ; Tetracyclines/pharmacology ; Microbial Sensitivity Tests ; },
abstract = {In this study, the tetracycline resistance of Enterococcus faecalis strains isolated from food was determined and molecular analyses of the resistance background were performed by determining the frequency of selected tetracycline resistance genes. In addition, the effect of high-pressure stress (400 and 500 MPa) on the expression of selected genes encoding tetracycline resistance was determined, as well as changes in the frequency of transfer of these genes in isolates showing sensitivity to tetracyclines. In our study, we observed an increase in the expression of genes encoding tetracyclines, especially the tet(L) gene, mainly under 400 MPa pressure. The study confirmed the possibility of transferring genes encoding tetracyclines such as tet(M), tet(L), tet(K), tet(W) and tet(O) by horizontal gene transfer in both control strains and exposed to high-pressure. Exposure of the strains to 400 MPa pressure had a greater effect on the possibility of gene transfer and expression than the application of a higher-pressure. To our knowledge, this study for the first time determined the effect of high-pressure stress on the expression of selected genes encoding tetracycline resistance, as well as the possibility and changes in the frequency of transfer of these genes in Enterococcus faecalis isolates showing sensitivity to tetracyclines and possessing silent genes. Due to the observed possibility of increased expression of some of the genes encoding tetracycline resistance and the possibility of their spread by horizontal gene transfer to other microorganisms in the food environment, under the influence of high-pressure processing in strains phenotypically susceptible to this antibiotic, it becomes necessary to monitor this ability in isolates derived from foods.},
}
@article {pmid38428395,
year = {2024},
author = {Fogarty, EC and Schechter, MS and Lolans, K and Sheahan, ML and Veseli, I and Moore, RM and Kiefl, E and Moody, T and Rice, PA and Yu, MK and Mimee, M and Chang, EB and Ruscheweyh, HJ and Sunagawa, S and Mclellan, SL and Willis, AD and Comstock, LE and Eren, AM},
title = {A cryptic plasmid is among the most numerous genetic elements in the human gut.},
journal = {Cell},
volume = {187},
number = {5},
pages = {1206-1222.e16},
pmid = {38428395},
issn = {1097-4172},
support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; RC2 DK122394/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Bacteria/genetics ; Bacteroidetes/genetics ; Feces/microbiology ; *Metagenome ; *Plasmids/genetics ; *Gastrointestinal Tract ; },
abstract = {Plasmids are extrachromosomal genetic elements that often encode fitness-enhancing features. However, many bacteria carry "cryptic" plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes and is 14 times as numerous as crAssphage, currently established as the most abundant extrachromosomal genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales, and although it does not appear to impact bacterial host fitness in vivo, it can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an alternative approach to track human colonic inflammatory states.},
}
@article {pmid38427560,
year = {2024},
author = {Workman, RE and Stoltzfus, MJ and Keith, NC and Euler, CW and Bondy-Denomy, J and Modell, JW},
title = {Anti-CRISPR proteins trigger a burst of CRISPR-Cas9 expression that enhances phage defense.},
journal = {Cell reports},
volume = {43},
number = {3},
pages = {113849},
pmid = {38427560},
issn = {2211-1247},
support = {R35 GM142731/GM/NIGMS NIH HHS/United States ; },
mesh = {*Bacteriophages/physiology ; CRISPR-Cas Systems/genetics ; Bacteria/metabolism ; Lysogeny ; Viral Proteins/genetics/metabolism ; },
abstract = {CRISPR-Cas immune systems provide bacteria with adaptive immunity against bacteriophages, but they are often transcriptionally repressed to mitigate auto-immunity. In some cases, CRISPR-Cas expression increases in response to a phage infection, but the mechanisms of induction are largely unknown, and it is unclear whether induction occurs strongly and quickly enough to benefit the bacterial host. In S. pyogenes, Cas9 is both an immune effector and auto-repressor of CRISPR-Cas expression. Here, we show that phage-encoded anti-CRISPR proteins relieve Cas9 auto-repression and trigger a rapid increase in CRISPR-Cas levels during a single phage infective cycle. As a result, fewer cells succumb to lysis, leading to a striking survival benefit after multiple rounds of infection. CRISPR-Cas induction also reduces lysogeny, thereby limiting a route for horizontal gene transfer. Altogether, we show that Cas9 is not only a CRISPR-Cas effector and repressor but also a phage sensor that can mount an anti-anti-CRISPR transcriptional response.},
}
@article {pmid38421146,
year = {2024},
author = {Wong, TKF and Cherryh, C and Rodrigo, AG and Hahn, MW and Minh, BQ and Lanfear, R},
title = {MAST: Phylogenetic Inference with Mixtures Across Sites and Trees.},
journal = {Systematic biology},
volume = {73},
number = {2},
pages = {375-391},
pmid = {38421146},
issn = {1076-836X},
support = {DP200103151//Australian Research Council Discovery Project/ ; DEB-1936187//National Science Foundation/ ; //Chan-Zuckerberg Initiative Grant/ ; //Moore-Simons Foundation/ ; },
mesh = {*Phylogeny ; *Classification/methods ; Models, Genetic ; Computer Simulation ; Software ; Animals ; },
abstract = {Hundreds or thousands of loci are now routinely used in modern phylogenomic studies. Concatenation approaches to tree inference assume that there is a single topology for the entire dataset, but different loci may have different evolutionary histories due to incomplete lineage sorting (ILS), introgression, and/or horizontal gene transfer; even single loci may not be treelike due to recombination. To overcome this shortcoming, we introduce an implementation of a multi-tree mixture model that we call mixtures across sites and trees (MAST). This model extends a prior implementation by Boussau et al. (2009) by allowing users to estimate the weight of each of a set of pre-specified bifurcating trees in a single alignment. The MAST model allows each tree to have its own weight, topology, branch lengths, substitution model, nucleotide or amino acid frequencies, and model of rate heterogeneity across sites. We implemented the MAST model in a maximum-likelihood framework in the popular phylogenetic software, IQ-TREE. Simulations show that we can accurately recover the true model parameters, including branch lengths and tree weights for a given set of tree topologies, under a wide range of biologically realistic scenarios. We also show that we can use standard statistical inference approaches to reject a single-tree model when data are simulated under multiple trees (and vice versa). We applied the MAST model to multiple primate datasets and found that it can recover the signal of ILS in the Great Apes, as well as the asymmetry in minor trees caused by introgression among several macaque species. When applied to a dataset of 4 Platyrrhine species for which standard concatenated maximum likelihood (ML) and gene tree approaches disagree, we observe that MAST gives the highest weight (i.e., the largest proportion of sites) to the tree also supported by gene tree approaches. These results suggest that the MAST model is able to analyze a concatenated alignment using ML while avoiding some of the biases that come with assuming there is only a single tree. We discuss how the MAST model can be extended in the future.},
}
@article {pmid38417645,
year = {2024},
author = {Jeong, GJ and Khan, F and Tabassum, N and Cho, KJ and Kim, YM},
title = {Bacterial extracellular vesicles: Modulation of biofilm and virulence properties.},
journal = {Acta biomaterialia},
volume = {178},
number = {},
pages = {13-23},
doi = {10.1016/j.actbio.2024.02.029},
pmid = {38417645},
issn = {1878-7568},
mesh = {Humans ; Virulence ; *Biofilms ; Bacteria/metabolism ; Virulence Factors/metabolism ; Polysaccharides ; DNA ; *Nucleic Acids ; Disease Progression ; Lipids ; },
abstract = {Microbial pathogens cause persistent infections by forming biofilms and producing numerous virulence factors. Bacterial extracellular vesicles (BEVs) are nanostructures produced by various bacterial species vital for molecular transport. BEVs include various components, including lipids (glycolipids, LPS, and phospholipids), nucleic acids (genomic DNA, plasmids, and short RNA), proteins (membrane proteins, enzymes, and toxins), and quorum-sensing signaling molecules. BEVs play a major role in forming extracellular polymeric substances (EPS) in biofilms by transporting EPS components such as extracellular polysaccharides, proteins, and extracellular DNA. BEVs have been observed to carry various secretory virulence factors. Thus, BEVs play critical roles in cell-to-cell communication, biofilm formation, virulence, disease progression, and resistance to antimicrobial treatment. In contrast, BEVs have been shown to impede early-stage biofilm formation, disseminate mature biofilms, and reduce virulence. This review summarizes the current status in the literature regarding the composition and role of BEVs in microbial infections. Furthermore, the dual functions of BEVs in eliciting and suppressing biofilm formation and virulence in various microbial pathogens are thoroughly discussed. This review is expected to improve our understanding of the use of BEVs in determining the mechanism of biofilm development in pathogenic bacteria and in developing drugs to inhibit biofilm formation by microbial pathogens. STATEMENT OF SIGNIFICANCE: Bacterial extracellular vesicles (BEVs) are nanostructures formed by membrane blebbing and explosive cell lysis. It is essential for transporting lipids, nucleic acids, proteins, and quorum-sensing signaling molecules. BEVs play an important role in the formation of the biofilm's extracellular polymeric substances (EPS) by transporting its components, such as extracellular polysaccharides, proteins, and extracellular DNA. Furthermore, BEVs shield genetic material from nucleases and thermodegradation by packaging it during horizontal gene transfer, contributing to the transmission of bacterial adaptation determinants like antibiotic resistance. Thus, BEVs play a critical role in cell-to-cell communication, biofilm formation, virulence enhancement, disease progression, and drug resistance. In contrast, BEVs have been shown to prevent early-stage biofilm, disperse mature biofilm, and reduce virulence characteristics.},
}
@article {pmid38417454,
year = {2024},
author = {Kfoury, B and Rodrigues, WFC and Kim, SJ and Brandizzi, F and Del-Bem, LE},
title = {Multiple horizontal gene transfer events have shaped plant glycosyl hydrolase diversity and function.},
journal = {The New phytologist},
volume = {242},
number = {2},
pages = {809-824},
doi = {10.1111/nph.19595},
pmid = {38417454},
issn = {1469-8137},
support = {Serra-1812-26691//Instituto Serrapilheira/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; DE-FG02-91ER20021//Chemical Sciences, Geosciences, and Biosciences Division/ ; DE-SC0018409//Great Lakes Bioenergy Research Center/ ; MICL02598//AgBioResearch, Michigan State University/ ; },
mesh = {Humans ; *Hydrolases ; Phylogeny ; *Gene Transfer, Horizontal/genetics ; Evolution, Molecular ; Plants/genetics ; },
abstract = {Plant glycosyl hydrolases (GHs) play a crucial role in selectively breaking down carbohydrates and glycoconjugates during various cellular processes, such as reserve mobilization, pathogen defense, and modification/disassembly of the cell wall. In this study, we examined the distribution of GH genes in the Archaeplastida supergroup, which encompasses red algae, glaucophytes, and green plants. We identified that the GH repertoire expanded from a few tens of genes in early archaeplastidians to over 400 genes in modern angiosperms, spanning 40 GH families in land plants. Our findings reveal that major evolutionary transitions were accompanied by significant changes in the GH repertoire. Specifically, we identified at least 23 GH families acquired by green plants through multiple horizontal gene transfer events, primarily from bacteria and fungi. We found a significant shift in the subcellular localization of GH activity during green plant evolution, with a marked increase in extracellular-targeted GH proteins associated with the diversification of plant cell wall polysaccharides and defense mechanisms against pathogens. In conclusion, our study sheds light on the macroevolutionary processes that have shaped the GH repertoire in plants, highlighting the acquisition of GH families through horizontal transfer and the role of GHs in plant adaptation and defense mechanisms.},
}
@article {pmid38415983,
year = {2024},
author = {Zhang, M and Yang, B and Shi, J and Wang, Z and Liu, Y},
title = {Host defense peptides mitigate the spread of antibiotic resistance in physiologically relevant condition.},
journal = {Antimicrobial agents and chemotherapy},
volume = {68},
number = {4},
pages = {e0126123},
pmid = {38415983},
issn = {1098-6596},
support = {32222084, 32172907//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Animals ; Cattle ; Humans ; *Conjugation, Genetic ; Plasmids/genetics ; Drug Resistance, Microbial ; *Genes, Bacterial ; Gene Transfer, Horizontal ; Antimicrobial Cationic Peptides/pharmacology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Antibiotic resistance represents a significant challenge to public health and human safety. The primary driver behind the dissemination of antibiotic resistance is the horizontal transfer of plasmids. Current conjugative transfer assay is generally performed in a standardized manner, ignoring the effect of the host environment. Host defense peptides (HDPs) possess a wide range of biological targets and play an essential role in the innate immune system. Herein, we reveal that sub-minimum inhibitory concentrations of HDPs facilitate the conjugative transfer of RP4-7 plasmid in the Luria Broth medium, and this observation is reversed in the RPMI medium, designed to simulate the host environment. Out of these HDPs, indolicidin (Ind), a cationic tridecapeptide from bovine neutrophils, significantly inhibits the conjugation of multidrug resistance plasmids in a dose-dependent manner, including blaNDM- and tet(X4)-bearing plasmids. We demonstrate that the addition of Ind to RPMI medium as the incubation substrate downregulates the expression of conjugation-related genes. In addition, Ind weakens the tricarboxylic acid cycle, impedes the electron transport chain, and disrupts the proton motive force, consequently diminishing the synthesis of adenosine triphosphate and limiting the energy supply. Our findings highlight the importance of the host-like environments for the development of horizontal transfer inhibitors and demonstrate the potential of HDPs in preventing the spread of resistance plasmids.},
}
@article {pmid38415839,
year = {2024},
author = {Sun, L and David, KT and Wolters, JF and Karlen, SD and Gonçalves, C and Opulente, DA and LaBella, AL and Groenewald, M and Zhou, X and Shen, XX and Rokas, A and Hittinger, CT},
title = {Functional and Evolutionary Integration of a Fungal Gene With a Bacterial Operon.},
journal = {Molecular biology and evolution},
volume = {41},
number = {4},
pages = {},
pmid = {38415839},
issn = {1537-1719},
support = {R01 AI153356/AI/NIAID NIH HHS/United States ; /NH/NIH HHS/United States ; },
mesh = {*Operon ; *Enterobactin/metabolism/genetics ; *Phylogeny ; *Evolution, Molecular ; Siderophores/metabolism/genetics ; Genes, Fungal ; Saccharomycetales/genetics/metabolism ; Gene Transfer, Horizontal ; },
abstract = {Siderophores are crucial for iron-scavenging in microorganisms. While many yeasts can uptake siderophores produced by other organisms, they are typically unable to synthesize siderophores themselves. In contrast, Wickerhamiella/Starmerella (W/S) clade yeasts gained the capacity to make the siderophore enterobactin following the remarkable horizontal acquisition of a bacterial operon enabling enterobactin synthesis. Yet, how these yeasts absorb the iron bound by enterobactin remains unresolved. Here, we demonstrate that Enb1 is the key enterobactin importer in the W/S-clade species Starmerella bombicola. Through phylogenomic analyses, we show that ENB1 is present in all W/S clade yeast species that retained the enterobactin biosynthetic genes. Conversely, it is absent in species that lost the ent genes, except for Starmerella stellata, making this species the only cheater in the W/S clade that can utilize enterobactin without producing it. Through phylogenetic analyses, we infer that ENB1 is a fungal gene that likely existed in the W/S clade prior to the acquisition of the ent genes and subsequently experienced multiple gene losses and duplications. Through phylogenetic topology tests, we show that ENB1 likely underwent horizontal gene transfer from an ancient W/S clade yeast to the order Saccharomycetales, which includes the model yeast Saccharomyces cerevisiae, followed by extensive secondary losses. Taken together, these results suggest that the fungal ENB1 and bacterial ent genes were cooperatively integrated into a functional unit within the W/S clade that enabled adaptation to iron-limited environments. This integrated fungal-bacterial circuit and its dynamic evolution determine the extant distribution of yeast enterobactin producers and cheaters.},
}
@article {pmid38413855,
year = {2024},
author = {Wang, H and Xia, F and Xia, Y and Li, J and Hu, Y and Deng, Y and Zou, M},
title = {Pangenome analysis of Shewanella xiamenensis revealed important genetic traits concerning genetic diversity, pathogenicity and antibiotic resistance.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {216},
pmid = {38413855},
issn = {1471-2164},
support = {No. 2023JJ30942//Natural Science Foundation of&#xa0;Hunan Province/ ; },
mesh = {Animals ; Humans ; *Genome, Bacterial ; Virulence/genetics ; Phylogeny ; Drug Resistance, Microbial ; *Genetic Variation ; *Shewanella ; },
abstract = {BACKGROUND: Shewanella xiamenensis, widely distributed in natural environments, has long been considered as opportunistic pathogen. Recently, significant changes in the resistance spectrum have been observed in S. xiamenensis, due to acquired antibiotic resistance genes. Therefore, a pan-genome analysis was conducted to illuminate the genomic changes in S. xiamenensis.<br><br>RESULTS: Phylogenetic analysis revealed three major clusters and three singletons, among which close relationship between several strains was discovered, regardless of their host and niches. The "open" genomes with diversity of accessory and strain-specific genomes took advantage towards diversity environments. The purifying selection pressure was the main force on genome evolution, especially in conservative genes. Only 53 gene families were under positive selection pressure. Phenotypic resistance analysis revealed 21 strains were classified as multi-drug resistance (MDR). Ten types of antibiotic resistance genes and two heavy metal resistance operons were discovered in S. xiamenensis. Mobile genetic elements and horizontal gene transfer increased genome diversity and were closely related to MDR strains. S. xiamenensis carried a variety of virulence genes and macromolecular secretion systems, indicating their important roles in pathogenicity and adaptability. Type IV secretion system was discovered in 15 genomes with various sequence structures, indicating it was originated from different donors through horizontal gene transfer.<br><br>CONCLUSIONS: This study provided with a detailed insight into the changes in the pan-genome of S. xiamenensis, highlighting its capability to acquire new mobile genetic elements and resistance genes for its adaptation to environment and pathogenicity to human and animals.},
}
@article {pmid38412971,
year = {2024},
author = {Dewar, AE and Belcher, LJ and Scott, TW and West, SA},
title = {Genes for cooperation are not more likely to be carried by plasmids.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2017},
pages = {20232549},
pmid = {38412971},
issn = {1471-2954},
mesh = {Plasmids/genetics ; *Genome, Bacterial ; *Bacteria/genetics ; Genomics ; Gene Transfer, Horizontal ; },
abstract = {Cooperation is prevalent across bacteria, but risks being exploited by non-cooperative cheats. Horizontal gene transfer, particularly via plasmids, has been suggested as a mechanism to stabilize cooperation. A key prediction of this hypothesis is that genes which are more likely to be transferred, such as those on plasmids, should be more likely to code for cooperative traits. Testing this prediction requires identifying all genes for cooperation in bacterial genomes. However, previous studies used a method which likely misses some of these genes for cooperation. To solve this, we used a new genomics tool, SOCfinder, which uses three distinct modules to identify all kinds of genes for cooperation. We compared where these genes were located across 4648 genomes from 146 bacterial species. In contrast to the prediction of the hypothesis, we found no evidence that plasmid genes are more likely to code for cooperative traits. Instead, we found the opposite-that genes for cooperation were more likely to be carried on chromosomes. Overall, the vast majority of genes for cooperation are not located on plasmids, suggesting that the more general mechanism of kin selection is sufficient to explain the prevalence of cooperation across bacteria.},
}
@article {pmid38412361,
year = {2024},
author = {Crippen, TL and Sullivan, JP and Anderson, RC},
title = {Bacterial proximity effects on the transfer of antibiotic resistance genes within the alimentary tract of yellow mealworm larvae.},
journal = {Journal of economic entomology},
volume = {117},
number = {2},
pages = {417-426},
doi = {10.1093/jee/toae019},
pmid = {38412361},
issn = {1938-291X},
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; *Tenebrio/genetics/microbiology ; Larva ; Plasmids ; Bacteria/genetics ; Insecta/genetics ; Drug Resistance, Microbial ; Escherichia coli/genetics ; },
abstract = {The arthropod intestinal tract and other anatomical parts naturally carry microorganisms. Some of which are pathogens, secrete toxins, or carry transferable antibiotic-resistance genes. The risks associated with the production and consumption of edible arthropods are dependent on indigenous microbes, as well as microbes introduced during the processes of rearing. This mass arthropod production puts individual arthropods in close proximity, which increases the possibility of their exposure to antibiotic-resistant bacteria carried by bacteria from fellow insects, industry workers, or rearing hardware and substrates. The purpose of this study was to determine if the alimentary tract of the yellow mealworm provided an environment permitting horizontal gene transfer between bacteria. The effect of the concentration of bacterial exposure was also assessed. Antibiotic resistance gene transfer between marker Salmonella Lignières (Enterobacterales: Enterobacteriaceae) and Escherichia coli (Migula) (Enterobacterales: Enterobacteriaceae) introduced into the larval gut demonstrated that the nutrient-rich environment of the yellow mealworm gut provided favorable conditions for the transfer of antibiotic resistance genes. Conjugation frequencies were similar across inoculum concentrations; however, transconjugant production correlated positively to increased exposure concentration. The lowest concentration of bacterial exposure required enrichment to detect and thus may have been approaching a threshold level for the 2 bacteria to colocate within the expanse of the larval gut. While many factors can affect this transfer, the simple factor of the proximity of donor and recipient bacteria, as defined by the concentration of bacteria within the volume of the insect gut, likely primarily contributed to the efficiency of antibiotic gene transfer.},
}
@article {pmid38410456,
year = {2024},
author = {Kogay, R and Wolf, YI and Koonin, EV},
title = {Defense systems and horizontal gene transfer in bacteria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38410456},
issn = {2692-8205},
abstract = {Horizontal gene transfer (HGT) is a fundamental process in the evolution of prokaryotes, making major contributions to diversification and adaptation. Typically, HGT is facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages that generally impose fitness costs on their hosts. However, a substantial fraction of bacterial genes is involved in defense mechanisms that limit the propagation of MGEs, raising the possibility that they can actively restrict HGT. Here we examine whether defense systems curb HGT by exploring the connections between HGT rate and the presence of 73 defense systems in 12 bacterial species. We found that only 6 defense systems, 3 of which are different CRISPR-Cas subtypes, are associated with the reduced gene gain rate on the scale of species evolution. The hosts of such defense systems tend to have a smaller pangenome size and harbor fewer phage-related genes compared to genomes lacking these systems, suggesting that these defense mechanisms inhibit HGT by limiting the integration of prophages. We hypothesize that restriction of HGT by defense systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and fitness effect of HGT in bacterial populations.},
}
@article {pmid38402936,
year = {2024},
author = {Rzymski, P and Gwenzi, W and Poniedziałek, B and Mangul, S and Fal, A},
title = {Climate warming, environmental degradation and pollution as drivers of antibiotic resistance.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {346},
number = {},
pages = {123649},
doi = {10.1016/j.envpol.2024.123649},
pmid = {38402936},
issn = {1873-6424},
mesh = {Humans ; *Plastics ; Environmental Pollution ; Drug Resistance, Microbial/genetics ; Bacteria ; Metals ; Anti-Bacterial Agents/pharmacology ; *Pesticides ; Genes, Bacterial ; },
abstract = {Antibiotic resistance is a major challenge to public health, but human-caused environmental changes have not been widely recognized as its drivers. Here, we provide a comprehensive overview of the relationships between environmental degradation and antibiotic resistance, demonstrating that the former can potentially fuel the latter with significant public health outcomes. We describe that (i) global warming favors horizontal gene transfer, bacterial infections, the spread of drug-resistant pathogens due to water scarcity, and the release of resistance genes with wastewater; (ii) pesticide and metal pollution act as co-selectors of antibiotic resistance mechanisms; (iii) microplastics create conditions promoting and spreading antibiotic resistance and resistant bacteria; (iv) changes in land use, deforestation, and environmental pollution reduce microbial diversity, a natural barrier to antibiotic resistance spread. We argue that management of antibiotic resistance must integrate environmental goals, including mitigation of further increases in the Earth's surface temperature, better qualitative and quantitative protection of water resources, strengthening of sewage infrastructure and improving wastewater treatment, counteracting the microbial diversity loss, reduction of pesticide and metal emissions, and plastic use, and improving waste recycling. These actions should be accompanied by restricting antibiotic use only to clinically justified situations, developing novel treatments, and promoting prophylaxis. It is pivotal for health authorities and the medical community to adopt the protection of environmental quality as a part of public health measures, also in the context of antibiotic resistance management.},
}
@article {pmid38399658,
year = {2024},
author = {Ishola, OA and Kublik, S and Durai Raj, AC and Ohnmacht, C and Schulz, S and Foesel, BU and Schloter, M},
title = {Comparative Metagenomic Analysis of Bacteriophages and Prophages in Gnotobiotic Mouse Models.},
journal = {Microorganisms},
volume = {12},
number = {2},
pages = {},
pmid = {38399658},
issn = {2076-2607},
support = {Helmholtz Munich Allergy Program//Helmholtz Munich Allergy Program/ ; },
abstract = {Gnotobiotic murine models are important to understand microbiota-host interactions. Despite the role of bacteriophages as drivers for microbiome structure and function, there is no information about the structure and function of the gut virome in gnotobiotic models and the link between bacterial and bacteriophage/prophage diversity. We studied the virome of gnotobiotic murine Oligo-MM12 (12 bacterial species) and reduced Altered Schaedler Flora (ASF, three bacterial species). As reference, the virome of Specific Pathogen-Free (SPF) mice was investigated. A metagenomic approach was used to assess prophages and bacteriophages in the guts of 6-week-old female mice. We identified a positive correlation between bacteria diversity, and bacteriophages and prophages. Caudoviricetes (82.4%) were the most prominent class of phages in all samples with differing relative abundance. However, the host specificity of bacteriophages belonging to class Caudoviricetes differed depending on model bacterial diversity. We further studied the role of bacteriophages in horizontal gene transfer and microbial adaptation to the host's environment. Analysis of mobile genetic elements showed the contribution of bacteriophages to the adaptation of bacterial amino acid metabolism. Overall, our results implicate virome "dark matter" and interactions with the host system as factors for microbial community structure and function which determine host health. Taking the importance of the virome in the microbiome diversity and horizontal gene transfer, reductions in the virome might be an important factor driving losses of microbial biodiversity and the subsequent dysbiosis of the gut microbiome.},
}
@article {pmid38399642,
year = {2024},
author = {Lerner, A and Benzvi, C and Vojdani, A},
title = {The Potential Harmful Effects of Genetically Engineered Microorganisms (GEMs) on the Intestinal Microbiome and Public Health.},
journal = {Microorganisms},
volume = {12},
number = {2},
pages = {},
pmid = {38399642},
issn = {2076-2607},
abstract = {Gut luminal dysbiosis and pathobiosis result in compositional and biodiversified alterations in the microbial and host co-metabolites. The primary mechanism of bacterial evolution is horizontal gene transfer (HGT), and the acquisition of new traits can be achieved through the exchange of mobile genetic elements (MGEs). Introducing genetically engineered microbes (GEMs) might break the harmonized balance in the intestinal compartment. The present objectives are: 1. To reveal the role played by the GEMs' horizontal gene transfers in changing the landscape of the enteric microbiome eubiosis 2. To expand on the potential detrimental effects of those changes on the human genome and health. A search of articles published in PubMed/MEDLINE, EMBASE, and Scielo from 2000 to August 2023 using appropriate MeSH entry terms was performed. The GEMs' horizontal gene exchanges might induce multiple human diseases. The new GEMs can change the long-term natural evolution of the enteric pro- or eukaryotic cell inhabitants. The worldwide regulatory authority's safety control of GEMs is not enough to protect public health. Viability, biocontainment, and many other aspects are only partially controlled and harmful consequences for public health should be avoided. It is important to remember that prevention is the most cost-effective strategy and primum non nocere should be the focus.},
}
@article {pmid38397005,
year = {2024},
author = {Valenzuela, JA and Vázquez, L and Rodríguez, J and Flórez, AB and Vasek, OM and Mayo, B},
title = {Phenotypic, Technological, Safety, and Genomic Profiles of Gamma-Aminobutyric Acid-Producing Lactococcus lactis and Streptococcus thermophilus Strains Isolated from Cow's Milk.},
journal = {International journal of molecular sciences},
volume = {25},
number = {4},
pages = {},
pmid = {38397005},
issn = {1422-0067},
support = {PID2022-141271NB-I00//Agencia Estatal de Investigaci&#xf3;n/ ; },
mesh = {Animals ; Milk/microbiology ; *Lactococcus lactis/genetics ; Streptococcus thermophilus/genetics ; gamma-Aminobutyric Acid ; *Lactobacillales ; Genomics ; Fermentation ; *Cheese/microbiology ; },
abstract = {Gamma-aminobutyric acid (GABA)-producing lactic acid bacteria (LAB) can be used as starters in the development of GABA-enriched functional fermented foods. In this work, four GABA-producing strains each of Lactococcus lactis and Streptococcus thermophilus species were isolated from cow's milk, and their phenotypic, technological, and safety profiles determined. Genome analysis provided genetic support for the majority of the analyzed traits, namely, GABA production, growth in milk, and the absence of genes of concern. The operon harboring the glutamate decarboxylase gene (gadB) was chromosomally encoded in all strains and showed the same gene content and gene order as those reported, respectively, for L. lactis and S. thermophilus. In the latter species, the operon was flanked (as in most strains of this species) by complete or truncated copies of insertion sequences (IS), suggesting recent acquisition through horizontal gene transfer. The genomes of three L. lactis and two S. thermophilus strains showed a gene encoding a caseinolytic proteinase (PrtP in L. lactis and PrtS in S. thermophilus). Of these, all but one grew in milk, forming a coagulum of good appearance and an appealing acidic flavor and taste. They also produced GABA in milk supplemented with monosodium glutamate. Two L. lactis strains were identified as belonging to the biovar. diacetylactis, utilized citrate from milk, and produced significant amounts of acetoin. None of the strains showed any noticeable antibiotic resistance, nor did their genomes harbor transferable antibiotic resistance genes or genes involved in toxicity, virulence, or pathogenicity. Altogether these results suggest that all eight strains may be considered candidates for use as starters or components of mixed LAB cultures for the manufacture of GABA-enriched fermented dairy products.},
}
@article {pmid38394997,
year = {2024},
author = {Wang, H and Wu, P and Xiong, L and Kim, HS and Kim, JH and Ki, JS},
title = {Nuclear genome of dinoflagellates: Size variation and insights into evolutionary mechanisms.},
journal = {European journal of protistology},
volume = {93},
number = {},
pages = {126061},
doi = {10.1016/j.ejop.2024.126061},
pmid = {38394997},
issn = {1618-0429},
mesh = {Humans ; Phylogeny ; *Dinoflagellida/genetics ; Genome/genetics ; Biological Evolution ; DNA ; },
abstract = {Recent progress in high-throughput sequencing technologies has dramatically increased availability of genome data for prokaryotes and eukaryotes. Dinoflagellates have distinct chromosomes and a huge genome size, which make their genomic analysis complicated. Here, we reviewed the nuclear genomes of core dinoflagellates, focusing on the genome and cell size. Till now, the genome sizes of several dinoflagellates (more than 25) have been measured by certain methods (e.g., flow cytometry), showing a range of 3-250 pg of genomic DNA per cell. In contrast to their relatively small cell size, their genomes are huge (about 1-80 times the human haploid genome). In the present study, we collected the genome and cell size data of dinoflagellates and compared their relationships. We found that dinoflagellate genome size exhibits a positive correlation with cell size. On the other hand, we recognized that the genome size is not correlated with phylogenetic relatedness. These may be caused by genome duplication, increased gene copy number, repetitive non-coding DNA, transposon expansion, horizontal gene transfer, organelle-to-nucleus gene transfer, and/or mRNA reintegration into the genome. Ultimate verification of these factors as potential causative mechanisms would require sequencing of more dinoflagellate genomes in the future.},
}
@article {pmid38394893,
year = {2024},
author = {Chen, T and Mo, C and Yuan, Y and Li, S and Wu, Y and Liao, X and Yang, Y},
title = {Short-, long-read metagenome and virome reveal the profile of phage-mediated ARGs in anoxic-oxic processes for swine wastewater treatment.},
journal = {Journal of hazardous materials},
volume = {468},
number = {},
pages = {133789},
doi = {10.1016/j.jhazmat.2024.133789},
pmid = {38394893},
issn = {1873-3336},
mesh = {Animals ; Swine ; *Anti-Bacterial Agents/pharmacology ; Metagenome ; Wastewater ; *Bacteriophages/genetics ; Virome ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Genes, Bacterial ; },
abstract = {Phages are among the most widely spread viruses, but their profiles and the antibiotic resistance genes (ARGs) they carry in swine wastewater remain underexplored. The present study investigated the distribution characteristics of phages and their ARG risk in anoxic/oxic (A/O) wastewater treatment processes of swine farms using short- and long-read metagenome and virome. The results demonstrated that the virome could extract more phage sequences than the total metagenome; thus, it was more suited for studying phages in wastewater settings. Intriguingly, phages had significantly lower abundance of ARG than ARGs harbored by total microorganisms (P < 0.01). Eleven ARGs co-occurred with phages and bacteria (R > 0.6 and P < 0.05), with Siphoviridae being the phage co-occurring with the most ARGs (5). Horizontal gene transfer (HGT) events were observed between Proteobacteria and the major phyla except for Bacteroidota. Furthermore, there were prophage sequences and ARGs on the same contig in bacterial MAGs. These data strongly demonstrate that phages promote horizontal transfer of ARG between bacterial hosts in A/O processes for swine wastewater treatment. Therefore, the risk of phage-mediated horizontal transfer of ARGs cannot be overlooked despite the low abundance of phage ARGs (pARG).},
}
@article {pmid38393159,
year = {2024},
author = {Jiang, YN and Tamiya-Ishitsuka, H and Aoi, R and Okabe, T and Yokota, A and Noda, N},
title = {MazEF Homologs in Symbiobacterium thermophilum Exhibit Cross-Neutralization with Non-Cognate MazEFs.},
journal = {Toxins},
volume = {16},
number = {2},
pages = {},
pmid = {38393159},
issn = {2072-6651},
support = {KAKENHI JP19K06555//Japan Society for the Promotion of Science/ ; },
mesh = {*Escherichia coli Proteins/genetics ; *Bacterial Toxins/genetics/metabolism ; Escherichia coli/genetics ; *Lactobacillales/metabolism ; Endoribonucleases/metabolism ; Ribonucleotides ; Bacterial Proteins/genetics/metabolism ; DNA-Binding Proteins/genetics ; *Clostridiales ; },
abstract = {Toxin-antitoxin systems are preserved by nearly every prokaryote. The type II toxin MazF acts as a sequence-specific endoribonuclease, cleaving ribonucleotides at specific sequences that vary from three to seven bases, as has been reported in different host organisms to date. The present study characterized the MazEF module (MazEF-sth) conserved in the Symbiobacterium thermophilum IAM14863 strain, a Gram-negative syntrophic bacterium that can be supported by co-culture with multiple bacteria, including Bacillus subtilis. Based on a method combining massive parallel sequencing and the fluorometric assay, MazF-sth was determined to cleave ribonucleotides at the UACAUA motif, which is markedly similar to the motifs recognized by MazF from B. subtilis (MazF-bs), and by several MazFs from Gram-positive bacteria. MazF-sth, with mutations at conserved amino acid residues Arg29 and Thr52, lost most ribonuclease activity, indicating that these residues that are crucial for MazF-bs also play significant roles in MazF-sth catalysis. Further, cross-neutralization between MazF-sth and the non-cognate MazE-bs was discovered, and herein, the neutralization mechanism is discussed based on a protein-structure simulation via AlphaFold2 and multiple sequence alignment. The conflict between the high homology shared by these MazF amino acid sequences and the few genetic correlations among their host organisms may provide evidence of horizontal gene transfer.},
}
@article {pmid38391535,
year = {2024},
author = {Yaikhan, T and Chukamnerd, A and Singkhamanan, K and Nokchan, N and Chintakovid, N and Chusri, S and Pomwised, R and Wonglapsuwan, M and Surachat, K},
title = {Genomic Characterization of Mobile Genetic Elements Associated with Multidrug-Resistant Acinetobacter Non-baumannii Species from Southern Thailand.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {2},
pages = {},
pmid = {38391535},
issn = {2079-6382},
support = {MED6601319S//the National Science, Research and Innovation Fund (NSRF) and Prince of Songkla University, Thailand/ ; },
abstract = {This study investigated the genetic diversity, antimicrobial resistance profiles, and virulence characteristics of Acinetobacter non-baumannii isolates obtained from four hospitals in southern Thailand. Clinical data, genome information, and average nucleotide identity (ANI) were analyzed for eight isolates, revealing diverse genetic profiles and novel sequence types (STs). Minimum spanning tree analysis indicated potential clonal spread of certain STs across different geographic regions. Antimicrobial resistance genes (ARGs) were detected in all isolates, with a high prevalence of genes conferring resistance to carbapenems, highlighting the challenge of antimicrobial resistance in Acinetobacter spp. infections. Mobile genetic elements (MGEs) carrying ARGs were also identified, emphasizing the role of horizontal gene transfer in spreading resistance. Evaluation of virulence-associated genes revealed a diverse range of virulence factors, including those related to biofilm formation and antibiotic resistance. However, no direct correlation was found between virulence-associated genes in Acinetobacter spp. and specific clinical outcomes, such as infection severity or patient mortality. This complexity suggests that factors beyond gene presence may influence disease progression and outcomes. This study emphasizes the importance of continued surveillance and molecular epidemiological studies to combat the spread of multidrug-resistant (MDR) Acinetobacter non-baumannii strains. The findings provide valuable insights into the epidemiology and genetic characteristics of this bacteria in southern Thailand, with implications for infection control and antimicrobial management efforts.},
}
@article {pmid38384862,
year = {2024},
author = {Wu, Z and Solís-Lemus, C},
title = {Ultrafast learning of four-node hybridization cycles in phylogenetic networks using algebraic invariants.},
journal = {Bioinformatics advances},
volume = {4},
number = {1},
pages = {vbae014},
pmid = {38384862},
issn = {2635-0041},
abstract = {MOTIVATION: The abundance of gene flow in the Tree of Life challenges the notion that evolution can be represented with a fully bifurcating process which cannot capture important biological realities like hybridization, introgression, or horizontal gene transfer. Coalescent-based network methods are increasingly popular, yet not scalable for big data, because they need to perform a heuristic search in the space of networks as well as numerical optimization that can be NP-hard. Here, we introduce a novel method to reconstruct phylogenetic networks based on algebraic invariants. While there is a long tradition of using algebraic invariants in phylogenetics, our work is the first to define phylogenetic invariants on concordance factors (frequencies of four-taxon splits in the input gene trees) to identify level-1 phylogenetic networks under the multispecies coalescent model.<br><br>RESULTS: Our novel hybrid detection methodology is optimization-free as it only requires the evaluation of polynomial equations, and as such, it bypasses the traversal of network space, yielding a computational speed at least 10 times faster than the fastest-to-date network methods. We illustrate our method's performance on simulated and real data from the genus Canis.<br><br>We present an open-source publicly available Julia package PhyloDiamond.jl available at https://github.com/solislemuslab/PhyloDiamond.jl with broad applicability within the evolutionary community.},
}
@article {pmid38382161,
year = {2024},
author = {Mori, Y and Yamashita, E and Nakagawa, A and Matsuzawa, T and Inagaki, M and Aiba, Y and Tanaka, S and Hatori, S and Ayami, M and Takeda, S},
title = {Determination of the three-dimensional structure of bacteriophage Mu(-) tail fiber and its characterization.},
journal = {Virology},
volume = {593},
number = {},
pages = {110017},
doi = {10.1016/j.virol.2024.110017},
pmid = {38382161},
issn = {1096-0341},
mesh = {*Bacteriophage mu/chemistry/genetics ; *Bacteriophages/genetics ; Viral Tail Proteins/genetics ; },
abstract = {Bacteriophage Mu is a temperate phage known to infect various species of Enterobacteria, playing a role in bacterial mutation induction and horizontal gene transfer. The phage possesses two types of tail fibers important for host recognition, which enable it to expand its range of hosts. The alternate tail fibers are formed through the action of genes 49-50 or 52-51, allowing the Mu phage to recognize different surfaces of host cells. In a previous study, we presented the X-ray crystal structure of the C-terminal lipopolysaccharide (LPS)-binding domain of gene product (gp) 49, one of the subunits comprising the Mu tail fiber. In this study, we have determined the structure of the alternative tail fiber subunit, gp52, and compared it with other tail fibers. The results revealed that Mu phage employs different structural motifs for two individual tail fibers for recognizing different hosts.},
}
@article {pmid38381581,
year = {2024},
author = {Aggarwal, R and Mahajan, P and Pandiya, S and Bajaj, A and Verma, SK and Yadav, P and Kharat, AS and Khan, AU and Dua, M and Johri, AK},
title = {Antibiotic resistance: a global crisis, problems and solutions.},
journal = {Critical reviews in microbiology},
volume = {50},
number = {5},
pages = {896-921},
doi = {10.1080/1040841X.2024.2313024},
pmid = {38381581},
issn = {1549-7828},
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/genetics ; Bacterial Infections/microbiology/drug therapy ; Drug Resistance, Bacterial ; },
abstract = {Healthy state is priority in today's world which can be achieved using effective medicines. But due to overuse and misuse of antibiotics, a menace of resistance has increased in pathogenic microbes. World Health Organization (WHO) has announced ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) as the top priority pathogens as these have developed resistance against certain antibiotics. To combat such a global issue, it is utmost important to identify novel therapeutic strategies/agents as an alternate to such antibiotics. To name certain antibiotic adjuvants including: inhibitors of beta-lactamase, efflux pumps and permeabilizers for outer membrane can potentially solve the antibiotic resistance problems. In this regard, inhibitors of lytic domain of lytic transglycosylases provide a novel way to not only act as an alternate to antibiotics but also capable of restoring the efficiency of previously resistant antibiotics. Further, use of bacteriophages is another promising strategy to deal with antibiotic resistant pathogens. Taking in consideration the alternatives of antibiotics, a green synthesis nanoparticle-based therapy exemplifies a good option to combat microbial resistance. As horizontal gene transfer (HGT) in bacteria facilitates the evolution of new resistance strains, therefore identifying the mechanism of resistance and development of inhibitors against it can be a novel approach to combat such problems. In our perspective, host-directed therapy (HDT) represents another promising strategy in combating antimicrobial resistance (AMR). This approach involves targeting specific factors within host cells that pathogens rely on for their survival, either through replication or persistence. As many new drugs are under clinical trials it is advisable that more clinical data and antimicrobial stewardship programs should be conducted to fully assess the clinical efficacy and safety of new therapeutic agents.},
}
@article {pmid38381035,
year = {2024},
author = {Unitt, A and Maiden, M and Harrison, O},
title = {Characterizing the diversity and commensal origins of penA mosaicism in the genus Neisseria.},
journal = {Microbial genomics},
volume = {10},
number = {2},
pages = {},
pmid = {38381035},
issn = {2057-5858},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Mosaicism ; Neisseria/genetics ; Neisseria gonorrhoeae/genetics ; *Neisseria meningitidis ; *Gonorrhea ; },
abstract = {Mosaic penA alleles formed through horizontal gene transfer (HGT) have been instrumental to the rising incidence of ceftriaxone-resistant gonococcal infections. Although interspecies HGT of regions of the penA gene between Neisseria gonorrhoeae and commensal Neisseria species has been described, knowledge concerning which species are the most common contributors to mosaic penA alleles is limited, with most studies examining only a small number of alleles. Here, we investigated the origins of recombinant penA alleles through in silico analyses that incorporated 1700 penA alleles from 35 513 Neisseria isolates, comprising 15 different Neisseria species. We identified Neisseria subflava and Neisseria cinerea as the most common source of recombinant sequences in N. gonorrhoeae penA. This contrasted with Neisseria meningitidis penA, for which the primary source of recombinant DNA was other meningococci, followed by Neisseria lactamica. Additionally, we described the distribution of polymorphisms implicated in antimicrobial resistance in penA, and found that these are present across the genus. These results provide insight into resistance-related changes in the penA gene across human-associated Neisseria species, illustrating the importance of genomic surveillance of not only the pathogenic Neisseria, but also of the oral niche-associated commensals from which these pathogens are sourcing key genetic variation.},
}
@article {pmid38378896,
year = {2024},
author = {Pfeifer, E and Rocha, EPC},
title = {Phage-plasmids promote recombination and emergence of phages and plasmids.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {1545},
pmid = {38378896},
issn = {2041-1723},
mesh = {*Bacteriophages/genetics ; Plasmids/genetics ; Prophages/genetics ; Gene Transfer, Horizontal/genetics ; },
abstract = {Phages and plasmids are regarded as distinct types of mobile genetic elements that drive bacterial evolution by horizontal gene transfer. However, the distinction between both types is blurred by the existence of elements known as prophage-plasmids or phage-plasmids, which transfer horizontally between cells as viruses and vertically within cellular lineages as plasmids. Here, we study gene flow between the three types of elements. We show that the gene repertoire of phage-plasmids overlaps with those of phages and plasmids. By tracking recent recombination events, we find that phage-plasmids exchange genes more frequently with plasmids than with phages, and that direct gene exchange between plasmids and phages is less frequent in comparison. The results suggest that phage-plasmids can mediate gene flow between plasmids and phages, including exchange of mobile element core functions, defense systems, and antibiotic resistance. Moreover, a combination of gene transfer and gene inactivation may result in the conversion of elements. For example, gene loss turns P1-like phage-plasmids into integrative prophages or into plasmids (that are no longer phages). Remarkably, some of the latter have acquired conjugation-related functions to became mobilisable by conjugation. Thus, our work indicates that phage-plasmids can play a key role in the transfer of genes across mobile elements within their hosts, and can act as intermediates in the conversion of one type of element into another.},
}
@article {pmid38376265,
year = {2024},
author = {Saini, P and Bandsode, V and Singh, A and Mendem, SK and Semmler, T and Alam, M and Ahmed, N},
title = {Genomic insights into virulence, antimicrobial resistance, and adaptation acumen of Escherichia coli isolated from an urban environment.},
journal = {mBio},
volume = {15},
number = {3},
pages = {e0354523},
pmid = {38376265},
issn = {2150-7511},
support = {AMR/257/2021/ECD-II//ICMR/ ; IoE by MoE [F11/9/2019-U3A]//UoH/ ; //GAT-B Fellowship/ ; (PMRF-ID 3702547) MoE//Prime ministers Research Fellowship/ ; },
mesh = {Animals ; Humans ; *Escherichia coli/genetics ; Virulence/genetics ; Anti-Bacterial Agents/pharmacology ; *Escherichia coli Infections/microbiology ; Drug Resistance, Bacterial ; Genomics ; Soil ; Water ; },
abstract = {UNLABELLED: Populations of common commensal bacteria such as Escherichia coli undergo genetic changes by the acquisition of certain virulence and antimicrobial resistance (AMR) encoding genetic elements leading to the emergence of pathogenic strains capable of surviving in the previously uninhabited or protected niches. These bacteria are also reported to be prevalent in the environment where they survive by adopting various recombination strategies to counter microflora of the soil and water, under constant selection pressure(s). In this study, we performed molecular characterization, phenotypic AMR analysis, and whole genome sequencing (WGS) of E. coli (n = 37) isolated from soil and surface water representing the urban and peri-urban areas. The primary aim of this study was to understand the genetic architecture and pathogenic acumen exhibited by environmental E. coli. WGS-based analysis entailing resistome and virulome profiling indicated the presence of various virulence (adherence, iron uptake, and toxins) and AMR encoding genes, including blaNDM-5 in the environmental isolates. A majority of our isolates belonged to phylogroup B1 (73%). A few isolates in our collection were of sequence type(s) (ST) 58 and 224 that could have emerged recently as clonal lineages and might pose risk of infection/transmission. Mobile genetic elements (MGEs) such as plasmids (predominantly) of the IncF family, prophages, pipolins, and insertion elements such as IS1 and IS5 were also observed to exist, which may presumably aid in the propagation of genes encoding resistance against antimicrobial drugs. The observed high prevalence of MGEs associated with multidrug resistance in pathogenic E. coli isolates belonging to the phylogroup B1 underscores the need for extended surveillance to keep track of and prevent the transmission of the bacterium to certain vulnerable human and animal populations.<br><br>IMPORTANCE: Evolutionary patterns of E. coli bacteria convey that they evolve into highly pathogenic forms by acquiring fitness advantages, such as AMR, and various virulence factors through the horizontal gene transfer (HGT)-mediated acquisition of MGEs. However, limited research on the genetic profiles of environmental E. coli, particularly from India, hinders our understanding of their transition to pathogenic forms and impedes the adoption of a comprehensive approach to address the connection between environmentally dwelling E. coli populations and human and veterinary public health. This study focuses on high-resolution genomic analysis of the environmental E. coli isolates aiming to understand the genetic similarities and differences among isolates from different environmental niches and uncover the survival strategies employed by these bacteria to thrive in their surroundings. Our approach involved molecular characterization of environmental samples using PCR-based DNA fingerprinting and subsequent WGS analysis. This multidisciplinary approach is likely to provide valuable insights into the understanding of any potential spill-over to human and animal populations and locales. Investigating these environmental isolates has significant potential for developing epidemiological strategies against transmission and understanding niche-specific evolutionary patterns.},
}
@article {pmid38374083,
year = {2024},
author = {Fox, BW and Helf, MJ and Burkhardt, RN and Artyukhin, AB and Curtis, BJ and Palomino, DF and Schroeder, AF and Chaturbedi, A and Tauffenberger, A and Wrobel, CJJ and Zhang, YK and Lee, SS and Schroeder, FC},
title = {Evolutionarily related host and microbial pathways regulate fat desaturation in C. elegans.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {1520},
pmid = {38374083},
issn = {2041-1723},
support = {P40 OD010440/OD/NIH HHS/United States ; R35 GM131877/GM/NIGMS NIH HHS/United States ; T32 GM138826/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Caenorhabditis elegans/metabolism ; *Caenorhabditis elegans Proteins/metabolism ; PPAR alpha/metabolism ; Escherichia coli/genetics/metabolism ; Fatty Acids/metabolism ; Cyclopropanes/metabolism ; },
abstract = {Fatty acid desaturation is central to metazoan lipid metabolism and provides building blocks of membrane lipids and precursors of diverse signaling molecules. Nutritional conditions and associated microbiota regulate desaturase expression, but the underlying mechanisms have remained unclear. Here, we show that endogenous and microbiota-dependent small molecule signals promote lipid desaturation via the nuclear receptor NHR-49/PPARα in C. elegans. Untargeted metabolomics of a β-oxidation mutant, acdh-11, in which expression of the stearoyl-CoA desaturase FAT-7/SCD1 is constitutively increased, revealed accumulation of a β-cyclopropyl fatty acid, becyp#1, that potently activates fat-7 expression via NHR-49. Biosynthesis of becyp#1 is strictly dependent on expression of cyclopropane synthase by associated bacteria, e.g., E. coli. Screening for structurally related endogenous metabolites revealed a β-methyl fatty acid, bemeth#1, which mimics the activity of microbiota-dependent becyp#1 but is derived from a methyltransferase, fcmt-1, that is conserved across Nematoda and likely originates from bacterial cyclopropane synthase via ancient horizontal gene transfer. Activation of fat-7 expression by these structurally similar metabolites is controlled by distinct mechanisms, as microbiota-dependent becyp#1 is metabolized by a dedicated β-oxidation pathway, while the endogenous bemeth#1 is metabolized via α-oxidation. Collectively, we demonstrate that evolutionarily related biosynthetic pathways in metazoan host and associated microbiota converge on NHR-49/PPARα to regulate fat desaturation.},
}
@article {pmid38373236,
year = {2024},
author = {Zhao, S and Rogers, MJ and Ding, C and Xu, G and He, J},
title = {Interspecies Mobility of Organohalide Respiration Gene Clusters Enables Genetic Bioaugmentation.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {9},
pages = {4214-4225},
doi = {10.1021/acs.est.3c09171},
pmid = {38373236},
issn = {1520-5851},
mesh = {Ecosystem ; Bacteria/genetics ; *Environmental Pollutants ; Respiration ; Multigene Family ; Biodegradation, Environmental ; *Chloroflexi ; },
abstract = {Anthropogenic organohalide pollutants pose a severe threat to public health and ecosystems. In situ bioremediation using organohalide respiring bacteria (OHRB) offers an environmentally friendly and cost-efficient strategy for decontaminating organohalide-polluted sites. The genomic structures of many OHRB suggest that dehalogenation traits can be horizontally transferred among microbial populations, but their occurrence among anaerobic OHRB has not yet been demonstrated experimentally. This study isolates and characterizes a novel tetrachloroethene (PCE)-dechlorinating Sulfurospirillum sp. strain SP, distinguishing itself among anaerobic OHRB by showcasing a mechanism essential for horizontal dissemination of reductive dehalogenation capabilities within microbial populations. Its genetic characterization identifies a unique plasmid (pSULSP), harboring reductive dehalogenase and de novo corrinoid biosynthesis operons, functions critical to organohalide respiration, flanked by mobile elements. The active mobility of these elements was demonstrated through genetic analyses of spontaneously emerging nondehalogenating variants of strain SP. More importantly, bioaugmentation of nondehalogenating microcosms with pSULSP DNA triggered anaerobic PCE dechlorination in taxonomically diverse bacterial populations. Our results directly support the hypothesis that exposure to anthropogenic organohalide pollutants can drive the emergence of dehalogenating microbial populations via horizontal gene transfer and demonstrate a mechanism by which genetic bioaugmentation for remediation of organohalide pollutants could be achieved in anaerobic environments.},
}
@article {pmid38372324,
year = {2024},
author = {Lehnert, T and Gijs, MAM},
title = {Microfluidic systems for infectious disease diagnostics.},
journal = {Lab on a chip},
volume = {24},
number = {5},
pages = {1441-1493},
doi = {10.1039/d4lc00117f},
pmid = {38372324},
issn = {1473-0189},
mesh = {Humans ; Microfluidics ; Ecosystem ; *Viruses ; *Communicable Diseases/diagnosis ; Point-of-Care Systems ; },
abstract = {Microorganisms, encompassing both uni- and multicellular entities, exhibit remarkable diversity as omnipresent life forms in nature. They play a pivotal role by supplying essential components for sustaining biological processes across diverse ecosystems, including higher host organisms. The complex interactions within the human gut microbiota are crucial for metabolic functions, immune responses, and biochemical signalling, particularly through the gut-brain axis. Viruses also play important roles in biological processes, for example by increasing genetic diversity through horizontal gene transfer when replicating inside living cells. On the other hand, infection of the human body by microbiological agents may lead to severe physiological disorders and diseases. Infectious diseases pose a significant burden on global healthcare systems, characterized by substantial variations in the epidemiological landscape. Fast spreading antibiotic resistance or uncontrolled outbreaks of communicable diseases are major challenges at present. Furthermore, delivering field-proven point-of-care diagnostic tools to the most severely affected populations in low-resource settings is particularly important and challenging. New paradigms and technological approaches enabling rapid and informed disease management need to be implemented. In this respect, infectious disease diagnostics taking advantage of microfluidic systems combined with integrated biosensor-based pathogen detection offers a host of innovative and promising solutions. In this review, we aim to outline recent activities and progress in the development of microfluidic diagnostic tools. Our literature research mainly covers the last 5 years. We will follow a classification scheme based on the human body systems primarily involved at the clinical level or on specific pathogen transmission modes. Important diseases, such as tuberculosis and malaria, will be addressed more extensively.},
}
@article {pmid38370577,
year = {2023},
author = {Yuan, C and An, T and Li, X and Zou, J and Lin, Z and Gu, J and Hu, R and Fang, Z},
title = {Genomic analysis of Ralstonia pickettii reveals the genetic features for potential pathogenicity and adaptive evolution in drinking water.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1272636},
pmid = {38370577},
issn = {1664-302X},
abstract = {Ralstonia pickettii, the most critical clinical pathogen of the genus Ralstonia, has been identified as a causative agent of numerous harmful infections. Additionally, Ralstonia pickettii demonstrates adaptability to extreme environmental conditions, such as those found in drinking water. In this study, we conducted a comprehensive genomic analysis to investigate the genomic characteristics related to potential pathogenicity and adaptive evolution in drinking water environments of Ralstonia pickettii. Through phylogenetic analysis and population genetic analysis, we divided Ralstonia pickettii into five Groups, two of which were associated with drinking water environments. The open pan-genome with a large and flexible gene repertoire indicated a high genetic plasticity. Significant differences in functional enrichment were observed between the core- and pan-genome of different groups. Diverse mobile genetic elements (MGEs), extensive genomic rearrangements, and horizontal gene transfer (HGT) events played a crucial role in generating genetic diversity. In drinking water environments, Ralstonia pickettii exhibited strong adaptability, and the acquisition of specific adaptive genes was potentially facilitated by genomic islands (GIs) and HGT. Furthermore, environmental pressures drove the adaptive evolution of Ralstonia pickettii, leading to the accumulation of unique mutations in key genes. These mutations may have a significant impact on various physiological functions, particularly carbon metabolism and energy metabolism. The presence of virulence-related elements associated with macromolecular secretion systems, virulence factors, and antimicrobial resistance indicated the potential pathogenicity of Ralstonia pickettii, making it capable of causing multiple nosocomial infections. This study provides comprehensive insights into the potential pathogenicity and adaptive evolution of Ralstonia pickettii in drinking water environments from a genomic perspective.},
}
@article {pmid38368718,
year = {2024},
author = {Wang, T and Xu, Y and Ling, W and Mosa, A and Liu, S and Lin, Z and Wang, H and Hu, X},
title = {Dissemination of antibiotic resistance genes is regulated by iron oxides: Insight into the influence on bacterial transformation.},
journal = {Environment international},
volume = {185},
number = {},
pages = {108499},
doi = {10.1016/j.envint.2024.108499},
pmid = {38368718},
issn = {1873-6750},
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Transformation, Bacterial ; Escherichia coli/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Soil/chemistry ; Oxides ; Iron ; Soil Microbiology ; Manure/microbiology ; *Ferric Compounds ; },
abstract = {The transportation of antibiotic resistance genes (ARGs) in manure-soil-plant continuums poses risks to human health. Horizontal gene transfer, particularly for bacterial transformation, is an important way for ARG dissemination. As crucial components in soils, iron oxides impacted the fates of various abiotic and biotic contaminants due to their active properties. However, whether they can influence the transformation of ARGs is unknown, which waits to be figured out to boost the assessment and control of ARG spread risks. In this study, we have investigated the effects of goethite, hematite, and magnetite (0-250 mg/L, with sizes < 100 nm and > 100 nm) on the transfer of ampicillin resistance genes to Escherichia coli cells. At lower iron oxide concentrations, the transformation of ARGs was first facilitated (transformation frequency reached up to 3.38-fold higher), but the facilitating effects gradually weakened and eventually disappeared as concentrations further increased. Particle size and iron oxide type were not the universal determinants controlling the transformation. At lower concentrations, iron oxides interacted with proteins and phospholipids in E. coli envelope structures, and induced the overgeneration of intracellular reactive oxygen species. Consequently, they led to pore formation and permeability enhancement on the cell membrane, thus promoting the transformation. The facilitation was also associated with the carrier-like effect of iron oxides for antibiotic resistance plasmids. At higher concentrations, the weakened facilitations were attributed to the aggregation of iron oxides. In this study, we highlight the crucial roles of the concentrations (contents) of iron oxides on the dissemination of ARGs in soils; this study may serve as a reference for ARG pollution control in future agricultural production.},
}
@article {pmid38368638,
year = {2024},
author = {Zheng, W and Teng, X and Jiang, T and Tang, W and Jiang, L and Zhu, H and Yu, X and Chen, G and Wang, J and Zhang, J and Qu, M and Zhang, X},
title = {Genome analysis of a novel avian atadenovirus reveals a possible horizontal gene transfer.},
journal = {Virology},
volume = {593},
number = {},
pages = {109999},
doi = {10.1016/j.virol.2024.109999},
pmid = {38368638},
issn = {1096-0341},
mesh = {Animals ; *Atadenovirus/genetics ; Genome, Viral ; Phylogeny ; Gene Transfer, Horizontal ; Adenoviridae/genetics ; *Aviadenovirus/genetics ; Birds ; *Adenoviridae Infections/genetics ; },
abstract = {We report the discovery and characterization of a novel adenovirus, Zoothera dauma adenovirus (ZdAdV), from a wild bird species, Zoothera dauma (Scaly thrush). This new atadenovirus was discovered by metagenomic sequencing without virus cultivation. Analyses of the full genome sequence revealed that this new virus is a distinct member of the genus Atadenovirus and represents a novel species. ZdAdV has a genome of 34,760 bp with 28 predicted genes and 39% GC content. ZdAdV is the first atadenovirus to contain ORF19, a gene previously found only in aviadenoviruses. Phylogenetic analysis of ORF19 suggests that it was acquired by ZdAdV through horizontal gene transfer from an aviadenovirus. By analyzing all orthologous genes of aviadenovirus, mastadenovirus, atadenovirus, and siadenovirus, we also found potential horizontal gene transfer for the E4 gene in Pigeon aviadenovirus B. Our study widens our knowledge concerning the genetic diversity and evolutionary history of atadenoviruses and their potential for cross-species transmission.},
}
@article {pmid38367442,
year = {2024},
author = {Liu, Q and Jia, J and Hu, H and Li, X and Zhao, Y and Wu, C},
title = {Nitrogen and phosphorus limitations promoted bacterial nitrate metabolism and propagation of antibiotic resistome in the phycosphere of Auxenochlorella pyrenoidosa.},
journal = {Journal of hazardous materials},
volume = {468},
number = {},
pages = {133786},
doi = {10.1016/j.jhazmat.2024.133786},
pmid = {38367442},
issn = {1873-3336},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Nitrates ; Genes, Bacterial ; Nitrogen/pharmacology ; Bacteria/genetics ; },
abstract = {Despite that nitrogen (N) and phosphorus (P) play critical roles in the lifecycle of microalgae, how N and P further affect the distribution of bacteria and antibiotic resistance genes (ARGs) in the phycosphere is still poorly understood. In this study, the effects of N and P on the distribution of ARGs in the phycosphere of Auxenochlorella pyrenoidosa were investigated. Results showed that the growth and chlorophyll synthesis of microalgae were inhibited when N or P was limited, regardless of the N/P ratios, but the extracellular polymeric substances content and nitrate assimilation efficiency were enhanced in contrast. Metagenomic sequencing revealed that N or P limitation resulted in the recruitment of specific bacteria that highly contribute to the nitrate metabolism in the phycosphere. Besides, N or P limitation promoted the propagation of phycosphere ARGs, primarily through horizontal gene transfer mediated by mobile genetic elements. The enrichment of specific bacteria induced by changes in the algal physiology also contributed to the ARGs proliferation under nutrient limitation. Our results demonstrated that the reduction of algal cells caused by nutrient limitation could promote the propagation of ARGs, which provides new insights into the occurrence and spread of ARGs in the phycosphere.},
}
@article {pmid38366574,
year = {2024},
author = {Ko, I and Kranse, OP and Senatori, B and Eves-van den Akker, S},
title = {A Critical Appraisal of DNA Transfer from Plants to Parasitic Cyst Nematodes.},
journal = {Molecular biology and evolution},
volume = {41},
number = {2},
pages = {},
pmid = {38366574},
issn = {1537-1719},
support = {//British Society for Plant Pathology/ ; 125034/359149/3//University of Cambridge/ ; BB/R011311/1//BBSRC/ ; EP/X024008/1//UKRI/ ; },
mesh = {Animals ; *Plants/genetics ; DNA ; Genomics ; *Tylenchoidea/genetics ; Plant Diseases/parasitology ; },
abstract = {Plant-parasitic nematodes are one of the most economically important pests of crops. It is widely accepted that horizontal gene transfer-the natural acquisition of foreign genes in parasitic nematodes-contributes to parasitism. However, an apparent paradox has emerged from horizontal gene transfer analyses: On the one hand, distantly related organisms with very dissimilar genetic structures (i.e. bacteria), and only transient interactions with nematodes as far as we know, dominate the list of putative donors, while on the other hand, considerably more closely related organisms (i.e. the host plant), with similar genetic structure (i.e. introns) and documented long-term associations with nematodes, are rare among the list of putative donors. Given that these nematodes ingest cytoplasm from a living plant cell for several weeks, there seems to be a conspicuous absence of plant-derived cases. Here, we used comparative genomic approaches to evaluate possible plant-derived horizontal gene transfer events in plant parasitic nematodes. Our evidence supports a cautionary message for plant-derived horizontal gene transfer cases in the sugar beet cyst nematode, Heterodera schachtii. We propose a 4-step model for horizontal gene transfer from plant to parasite in order to evaluate why the absence of plant-derived horizontal gene transfer cases is observed. We find that the plant genome is mobilized by the nematode during infection, but that uptake of the said "mobilome" is the first major barrier to horizontal gene transfer from host to nematode. These results provide new insight into our understanding of the prevalence/role of nucleic acid exchange in the arms race between plants and plant parasites.},
}
@article {pmid38366248,
year = {2024},
author = {Zhao, D and Zhang, S and Chen, J and Zhao, J and An, P and Xiang, H},
title = {Members of the class Candidatus Ordosarchaeia imply an alternative evolutionary scenario from methanogens to haloarchaea.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38366248},
issn = {1751-7370},
support = {92251302//National Natural Science Foundation of China/ ; CAM202202//Central Asian Drug Discovery and Development Center of Chinese Academy of Sciences/ ; },
mesh = {Phylogeny ; *Methane/metabolism ; *Euryarchaeota/metabolism ; Archaea ; Metagenome ; },
abstract = {The origin of methanogenesis can be traced to the common ancestor of non-DPANN archaea, whereas haloarchaea (or Halobacteria) are believed to have evolved from a methanogenic ancestor through multiple evolutionary events. However, due to the accelerated evolution and compositional bias of proteins adapting to hypersaline habitats, Halobacteria exhibit substantial evolutionary divergence from methanogens, and the identification of the closest methanogen (either Methanonatronarchaeia or other taxa) to Halobacteria remains a subject of debate. Here, we obtained five metagenome-assembled genomes with high completeness from soda-saline lakes on the Ordos Plateau in Inner Mongolia, China, and we proposed the name Candidatus Ordosarchaeia for this novel class. Phylogenetic analyses revealed that Ca. Ordosarchaeia is firmly positioned near the median position between the Methanonatronarchaeia and Halobacteria-Hikarchaeia lineages. Functional predictions supported the transitional status of Ca. Ordosarchaeia with the metabolic potential of nonmethanogenic and aerobic chemoheterotrophy, as did remnants of the gene sequences of methylamine/dimethylamine/trimethylamine metabolism and coenzyme M biosynthesis. Based on the similarity of the methyl-coenzyme M reductase genes mcrBGADC in Methanonatronarchaeia with the phylogenetically distant methanogens, an alternative evolutionary scenario is proposed, in which Methanonatronarchaeia, Ca. Ordosarchaeia, Ca. Hikarchaeia, and Halobacteria share a common ancestor that initially lost mcr genes. However, certain members of Methanonatronarchaeia subsequently acquired mcr genes through horizontal gene transfer from distantly related methanogens. This hypothesis is supported by amalgamated likelihood estimation, phylogenetic analysis, and gene arrangement patterns. Altogether, Ca. Ordosarchaeia genomes clarify the sisterhood of Methanonatronarchaeia with Halobacteria and provide new insights into the evolution from methanogens to haloarchaea.},
}
@article {pmid38366209,
year = {2024},
author = {Wang, X and Zhang, H and Yu, S and Li, D and Gillings, MR and Ren, H and Mao, D and Guo, J and Luo, Y},
title = {Inter-plasmid transfer of antibiotic resistance genes accelerates antibiotic resistance in bacterial pathogens.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38366209},
issn = {1751-7370},
support = {41831287//Key Projects of the National Natural Science Foundation of China/ ; 2020YFC1806904//National Key R&amp;D Program of China/ ; 31870351//National Natural Science Foundation of China/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; Drug Resistance, Microbial/genetics ; *Bacteria/genetics ; Genes, Bacterial ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; },
abstract = {Antimicrobial resistance is a major threat for public health. Plasmids play a critical role in the spread of antimicrobial resistance via horizontal gene transfer between bacterial species. However, it remains unclear how plasmids originally recruit and assemble various antibiotic resistance genes (ARGs). Here, we track ARG recruitment and assembly in clinically relevant plasmids by combining a systematic analysis of 2420 complete plasmid genomes and experimental validation. Results showed that ARG transfer across plasmids is prevalent, and 87% ARGs were observed to potentially transfer among various plasmids among 8229 plasmid-borne ARGs. Interestingly, recruitment and assembly of ARGs occur mostly among compatible plasmids within the same bacterial cell, with over 88% of ARG transfers occurring between compatible plasmids. Integron and insertion sequences drive the ongoing ARG acquisition by plasmids, especially in which IS26 facilitates 63.1% of ARG transfer events among plasmids. In vitro experiment validated the important role of IS26 involved in transferring gentamicin resistance gene aacC1 between compatible plasmids. Network analysis showed four beta-lactam genes (blaTEM-1, blaNDM-4, blaKPC-2, and blaSHV-1) shuffling among 1029 plasmids and 45 clinical pathogens, suggesting that clinically alarming ARGs transferred accelerate the propagation of antibiotic resistance in clinical pathogens. ARGs in plasmids are also able to transmit across clinical and environmental boundaries, in terms of the high-sequence similarities of plasmid-borne ARGs between clinical and environmental plasmids. This study demonstrated that inter-plasmid ARG transfer is a universal mechanism for plasmid to recruit various ARGs, thus advancing our understanding of the emergence of multidrug-resistant plasmids.},
}
@article {pmid38366199,
year = {2024},
author = {Takeuchi, N and Fullmer, MS and Maddock, DJ and Poole, AM},
title = {The Constructive Black Queen hypothesis: new functions can evolve under conditions favouring gene loss.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38366199},
issn = {1751-7370},
support = {22-UOA-250//Royal Society of New Zealand Marsden Fund/ ; //School of Biological Sciences Academic Leaders' Fund, University of Auckland/ ; //Faculty of Science Faculty Research Development Fund, University of Auckland/ ; },
mesh = {*Prokaryotic Cells ; *Multigene Family ; Evolution, Molecular ; },
abstract = {Duplication is a major route for the emergence of new gene functions. However, the emergence of new gene functions via this route may be reduced in prokaryotes, as redundant genes are often rapidly purged. In lineages with compact, streamlined genomes, it thus appears challenging for novel function to emerge via duplication and divergence. A further pressure contributing to gene loss occurs under Black Queen dynamics, as cheaters that lose the capacity to produce a public good can instead acquire it from neighbouring producers. We propose that Black Queen dynamics can favour the emergence of new function because, under an emerging Black Queen dynamic, there is high gene redundancy spread across a community of interacting cells. Using computational modelling, we demonstrate that new gene functions can emerge under Black Queen dynamics. This result holds even if there is deletion bias due to low duplication rates and selection against redundant gene copies resulting from the high cost associated with carrying a locus. However, when the public good production costs are high, Black Queen dynamics impede the fixation of new functions. Our results expand the mechanisms by which new gene functions can emerge in prokaryotic systems.},
}
@article {pmid38365845,
year = {2024},
author = {Maddamsetti, R and Yao, Y and Wang, T and Gao, J and Huang, VT and Hamrick, GS and Son, HI and You, L},
title = {Duplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {1449},
pmid = {38365845},
issn = {2041-1723},
support = {R01 AI125604/AI/NIAID NIH HHS/United States ; R01 GM098642/GM/NIGMS NIH HHS/United States ; R01 EB031869/EB/NIBIB NIH HHS/United States ; },
mesh = {Humans ; *Genes, Bacterial/genetics ; *Gene Transfer, Horizontal/genetics ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Horizontal gene transfer (HGT) and gene duplication are often considered as separate mechanisms driving the evolution of new functions. However, the mobile genetic elements (MGEs) implicated in HGT can copy themselves, so positive selection on MGEs could drive gene duplications. Here, we use a combination of modeling and experimental evolution to examine this hypothesis and use long-read genome sequences of tens of thousands of bacterial isolates to examine its generality in nature. Modeling and experiments show that antibiotic selection can drive the evolution of duplicated antibiotic resistance genes (ARGs) through MGE transposition. A key implication is that duplicated ARGs should be enriched in environments associated with antibiotic use. To test this, we examined the distribution of duplicated ARGs in 18,938 complete bacterial genomes with ecological metadata. Duplicated ARGs are highly enriched in bacteria isolated from humans and livestock. Duplicated ARGs are further enriched in an independent set of 321 antibiotic-resistant clinical isolates. Our findings indicate that duplicated genes often encode functions undergoing positive selection and horizontal gene transfer in microbial communities.},
}
@article {pmid38365256,
year = {2024},
author = {Holert, J and Borker, A and Nübel, LL and Daniel, R and Poehlein, A and Philipp, B},
title = {Bacteria use a catabolic patchwork pathway of apparently recent origin for degradation of the synthetic buffer compound TRIS.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38365256},
issn = {1751-7370},
support = {//German Research Foundation/ ; //BioAug/ ; //University of M&#xfc;nster/ ; INST 211/646--1 FUGG//German Research Foundation/ ; },
mesh = {*Pseudomonas putida/genetics/metabolism ; Pseudomonas/genetics/metabolism ; Multigene Family ; Oxidation-Reduction ; Metabolic Networks and Pathways/genetics ; },
abstract = {The synthetic buffer compound TRIS (2-amino-2-(hydroxymethyl)propane-1,3-diol) is used in countless applications, and no detailed information on its degradation has been published so far. Herein, we describe the discovery of a complete bacterial degradation pathway for TRIS. By serendipity, a Pseudomonas strain was isolated from sewage sludge that was able to grow with TRIS as only carbon and nitrogen source. Genome and transcriptome analyses revealed two adjacent gene clusters embedded in a mobile genetic element on a conjugative plasmid to be involved in TRIS degradation. Heterologous gene expression revealed cluster I to encode a TRIS uptake protein, a TRIS alcohol dehydrogenase, and a TRIS aldehyde dehydrogenase, catalyzing the oxidation of TRIS into 2-hydroxymethylserine. Gene cluster II encodes a methylserine hydroxymethyltransferase (mSHMT) and a d-serine dehydratase that plausibly catalyze the conversion of 2-hydroxymethylserine into pyruvate. Conjugational plasmid transfer into Pseudomonas putida KT2440 enabled this strain to grow with TRIS and with 2-hydromethylserine, demonstrating that the complete TRIS degradation pathway can be transmitted by horizontal gene transfer. Subsequent enrichments from wastewater purification systems led to the isolation of further TRIS-degrading bacteria from the Pseudomonas and Shinella genera carrying highly similar TRIS degradation gene clusters. Our data indicate that TRIS degradation evolved recently via gene recruitment and enzyme adaptation from multiple independent metabolic pathways, and database searches suggest that the TRIS degradation pathway is now globally distributed. Overall, our study illustrates how engineered environments can enhance the emergence of new microbial metabolic pathways in short evolutionary time scales.},
}
@article {pmid38365232,
year = {2024},
author = {Zheng, Y and Wang, B and Gao, P and Yang, Y and Xu, B and Su, X and Ning, D and Tao, Q and Li, Q and Zhao, F and Wang, D and Zhang, Y and Li, M and Winkler, MH and Ingalls, AE and Zhou, J and Zhang, C and Stahl, DA and Jiang, J and Martens-Habbena, W and Qin, W},
title = {Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38365232},
issn = {1751-7370},
support = {548565//Simons Postdoctoral Fellowship in Marine Microbial Ecology/ ; //Florida Agricultural Experiment Station Hatch project/ ; //National Natural Science Foundation of China/ ; 2020Z01//Shanghai Sheshan National Geophysical Observatory/ ; 20200925173954005//Stable Support Plan Program of Shenzhen Natural Science Fund/ ; ZDSYS201802081843490//Southern University of Science and Technology/ ; //Shenzhen Key Laboratory of Marine Archaea Geo-Omics/ ; 2020KCXTD023//the Innovation Team Project of Universities/ ; //National Natural Science Foundation of China/ ; //Fundamental Research Funds for the Central Universities of China/ ; 92051114//National Natural Science Foundation of China/ ; },
mesh = {*Archaea ; *Ammonia/metabolism ; Ecosystem ; RNA, Ribosomal, 16S/genetics/metabolism ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.},
}
@article {pmid38365231,
year = {2024},
author = {Kolan, D and Cattan-Tsaushu, E and Enav, H and Freiman, Z and Malinsky-Rushansky, N and Ninio, S and Avrani, S},
title = {Tradeoffs between phage resistance and nitrogen fixation drive the evolution of genes essential for cyanobacterial heterocyst functionality.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38365231},
issn = {1751-7370},
support = {//Israel Water Authority/ ; 1386/20//Israel Science Foundation/ ; },
mesh = {Nitrogen Fixation/genetics ; *Bacteriophages/genetics ; Phylogeny ; *Nostoc/genetics ; Nitrogen ; },
abstract = {Harmful blooms caused by diazotrophic (nitrogen-fixing) Cyanobacteria are becoming increasingly frequent and negatively impact aquatic environments worldwide. Cyanophages (viruses infecting Cyanobacteria) can potentially regulate cyanobacterial blooms, yet Cyanobacteria can rapidly acquire mutations that provide protection against phage infection. Here, we provide novel insights into cyanophage:Cyanobacteria interactions by characterizing the resistance to phages in two species of diazotrophic Cyanobacteria: Nostoc sp. and Cylindrospermopsis raciborskii. Our results demonstrate that phage resistance is associated with a fitness tradeoff by which resistant Cyanobacteria have reduced ability to fix nitrogen and/or to survive nitrogen starvation. Furthermore, we use whole-genome sequence analysis of 58 Nostoc-resistant strains to identify several mutations associated with phage resistance, including in cell surface-related genes and regulatory genes involved in the development and function of heterocysts (cells specialized in nitrogen fixation). Finally, we employ phylogenetic analyses to show that most of these resistance genes are accessory genes whose evolution is impacted by lateral gene transfer events. Together, these results further our understanding of the interplay between diazotrophic Cyanobacteria and their phages and suggest that a tradeoff between phage resistance and nitrogen fixation affects the evolution of cell surface-related genes and of genes involved in heterocyst differentiation and nitrogen fixation.},
}
@article {pmid38361819,
year = {2024},
author = {Zhang, S and Yang, C and Qiu, Y and Liao, R and Xuan, Z and Ren, F and Dong, Y and Xie, X and Han, Y and Wu, D and Ramos-González, PL and Freitas-Astúa, J and Yang, H and Zhou, C and Cao, M},
title = {Conserved untranslated regions of multipartite viruses: Natural markers of novel viral genomic components and tags of viral evolution.},
journal = {Virus evolution},
volume = {10},
number = {1},
pages = {veae004},
pmid = {38361819},
issn = {2057-1577},
abstract = {Viruses with split genomes are classified as being either segmented or multipartite based on whether their genomic segments occur within a single virion or across different virions. Despite variations in number and sequence during evolution, the genomic segments of many viruses are conserved within the untranslated regions (UTRs). In this study, we present a methodology that combines RNA sequencing with iterative BLASTn of UTRs (https://github.com/qq371260/Iterative-blast-v.1.0) to identify new viral genomic segments. Some novel multipartite-like viruses related to the phylum Kitrinoviricota were annotated using sequencing data from field plant samples and public databases. We identified potentially plant-infecting jingmen-related viruses (order Amarillovirales) and jivi-related viruses (order Martellivirales) with at least six genomic components. The number of RNA molecules associated with a genome of the novel viruses in the families Closteroviridae, Kitaviridae, and Virgaviridae within the order Martellivirales reached five. Several of these viruses seem to represent new taxa at the subgenus, genus, and family levels. The diversity of novel genomic components and the multiple duplication of proteins or protein domains within single or multiple genomic components emphasize the evolutionary roles of genetic recombination (horizontal gene transfer), reassortment, and deletion. The relatively conserved UTRs at the genome level might explain the relationships between monopartite and multipartite viruses, as well as how subviral agents such as defective RNAs and satellite viruses can coexist with their helper viruses.},
}
@article {pmid38352454,
year = {2024},
author = {Curry, KD and Yu, FB and Vance, SE and Segarra, S and Bhaya, D and Chikhi, R and Rocha, EPC and Treangen, TJ},
title = {Reference-free Structural Variant Detection in Microbiomes via Long-read Coassembly Graphs.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38352454},
issn = {2692-8205},
support = {P01 AI152999/AI/NIAID NIH HHS/United States ; },
abstract = {Bacterial genome dynamics are vital for understanding the mechanisms underlying microbial adaptation, growth, and their broader impact on host phenotype. Structural variants (SVs), genomic alterations of 10 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to absence of clear reference genomes and presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing a single metagenome coassembly graph constructed from all samples in a series. The log fold change in graph coverage between subsequent samples is then calculated to call SVs that are thriving or declining throughout the series. We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, which is particularly noticeable as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between subsequent time and temperature samples, suggesting host advantage. Our innovative approach leverages raw read patterns rather than references or MAGs to include all sequencing reads in analysis, and thus provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial genome dynamics.},
}
@article {pmid38351266,
year = {2024},
author = {Arbulu, S and Kjos, M},
title = {Revisiting the Multifaceted Roles of Bacteriocins : The Multifaceted Roles of Bacteriocins.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {41},
pmid = {38351266},
issn = {1432-184X},
support = {101029099//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; 296906//Norges Forskningsr&#xe5;d/ ; },
mesh = {*Bacteriocins/pharmacology ; Biofilms ; Bacteria ; Peptides ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Bacteriocins are gene-encoded antimicrobial peptides produced by bacteria. These peptides are heterogeneous in terms of structure, antimicrobial activities, biosynthetic clusters, and regulatory mechanisms. Bacteriocins are widespread in nature and may contribute to microbial diversity due to their capacity to target specific bacteria. Primarily studied as food preservatives and therapeutic agents, their function in natural settings is however less known. This review emphasizes the ecological significance of bacteriocins as multifunctional peptides by exploring bacteriocin distribution, mobility, and their impact on bacterial population dynamics and biofilms.},
}
@article {pmid38349402,
year = {2024},
author = {Neil, B and Cheney, GL and Rosenzweig, JA and Sha, J and Chopra, AK},
title = {Antimicrobial resistance in aeromonads and new therapies targeting quorum sensing.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {205},
pmid = {38349402},
issn = {1432-0614},
support = {R21 AI135453/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Quorum Sensing ; Drug Resistance, Bacterial ; Agriculture ; *Cross Infection ; },
abstract = {Aeromonas species (spp.) are well-known fish pathogens, several of which have been recognized as emerging human pathogens. The organism is capable of causing a wide spectrum of diseases in humans, ranging from gastroenteritis, wound infections, and septicemia to devastating necrotizing fasciitis. The systemic form of infection is often fatal, particularly in patients with underlying chronic diseases. Indeed, recent trends demonstrate rising numbers of hospital-acquired Aeromonas infections, especially in immuno-compromised individuals. Additionally, Aeromonas-associated antibiotic resistance is an increasing challenge in combating both fish and human infections. The acquisition of antibiotic resistance is related to Aeromonas' innate transformative properties including its ability to share plasmids and integron-related gene cassettes between species and with the environment. As a result, alternatives to antibiotic treatments are desperately needed. In that vein, many treatments have been proposed and studied extensively in the fish-farming industry, including treatments that target Aeromonas quorum sensing. In this review, we discuss current strategies targeting quorum sensing inhibition and propose that such studies empower the development of novel chemotherapeutic approaches to combat drug-resistant Aeromonas spp. infections in humans. KEY POINTS: • Aeromonas notoriously acquires and maintains antimicrobial resistance, making treatment options limited. • Quorum sensing is an essential virulence mechanism in Aeromonas infections. • Inhibiting quorum sensing can be an effective strategy in combating Aeromonas infections in animals and humans.},
}
@article {pmid38349154,
year = {2024},
author = {Vargas-Gastélum, L and Romer, AS and Ghotbi, M and Dallas, JW and Alexander, NR and Moe, KC and McPhail, KL and Neuhaus, GF and Shadmani, L and Spatafora, JW and Stajich, JE and Tabima, JF and Walker, DM},
title = {Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria.},
journal = {mSphere},
volume = {9},
number = {3},
pages = {e0047523},
pmid = {38349154},
issn = {2379-5042},
mesh = {Bacteria/genetics ; Fungi/genetics ; *Gastrointestinal Microbiome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Animals ; },
abstract = {Reptiles and amphibians (herptiles) are some of the most endangered and threatened species on the planet and numerous conservation strategies are being implemented with the goal of ensuring species recovery. Little is known, however, about the gut microbiome of wild herptiles and how it relates to the health of these populations. Here, we report results from the gut microbiome characterization of both a broad survey of herptiles, and the correlation between the fungus Basidiobolus, and the bacterial community supported by a deeper, more intensive sampling of Plethodon glutinosus, known as slimy salamanders. We demonstrate that bacterial communities sampled from frogs, lizards, and salamanders are structured by the host taxonomy and that Basidiobolus is a common and natural component of these wild gut microbiomes. Intensive sampling of multiple hosts across the ecoregions of Tennessee revealed that geography and host:geography interactions are strong predictors of distinct Basidiobolus operational taxonomic units present within a given host. Co-occurrence analyses of Basidiobolus and bacterial community diversity support a correlation and interaction between Basidiobolus and bacteria, suggesting that Basidiobolus may play a role in structuring the bacterial community. We further the hypothesis that this interaction is advanced by unique specialized metabolism originating from horizontal gene transfer from bacteria to Basidiobolus and demonstrate that Basidiobolus is capable of producing a diversity of specialized metabolites including small cyclic peptides.IMPORTANCEThis work significantly advances our understanding of biodiversity and microbial interactions in herptile microbiomes, the role that fungi play as a structural and functional members of herptile gut microbiomes, and the chemical functions that structure microbiome phenotypes. We also provide an important observational system of how the gut microbiome represents a unique environment that selects for novel metabolic functions through horizontal gene transfer between fungi and bacteria. Such studies are needed to better understand the complexity of gut microbiomes in nature and will inform conservation strategies for threatened species of herpetofauna.},
}
@article {pmid38347627,
year = {2024},
author = {Behling, AH and Wilson, BC and Ho, D and Cutfield, WS and Vatanen, T and O'Sullivan, JM},
title = {Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {26},
pmid = {38347627},
issn = {2049-2618},
mesh = {Adolescent ; Humans ; Fecal Microbiota Transplantation/methods ; Gene Transfer, Horizontal ; *Pediatric Obesity ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics ; Feces/microbiology ; Treatment Outcome ; },
abstract = {BACKGROUND: Horizontal gene transfer (HGT) describes the transmission of DNA outside of direct ancestral lineages. The process is best characterised within the bacterial kingdom and can enable the acquisition of genetic traits that support bacterial adaptation to novel niches. The adaptation of bacteria to novel niches has particular relevance for faecal microbiota transplantation (FMT), a therapeutic procedure which aims to resolve gut-related health conditions of individuals, through transplanted gut microbiota from healthy donors.<br><br>RESULTS: Three hundred eighty-one stool metagenomic samples from a placebo-controlled FMT trial for obese adolescents (the Gut Bugs Trial) were analysed for HGT, using two complementary methodologies. First, all putative HGT events, including historical HGT signatures, were quantified using the bioinformatics application WAAFLE. Second, metagenomic assembly and gene clustering were used to assess and quantify donor-specific genes transferred to recipients following the intervention. Both methodologies found no difference between the level of putative HGT events in the gut microbiomes of FMT and placebo recipients, post-intervention. HGT events facilitated by engrafted donor species in the FMT recipient gut at 6&#xa0;weeks post-intervention were identified and characterised. Bacterial strains contributing to this subset of HGT events predominantly belonged to the phylum Bacteroidetes. Engraftment-dependent horizontally transferred genes were retained within recipient microbiomes at 12 and 26&#xa0;weeks post-intervention.<br><br>CONCLUSION: Our study suggests that novel microorganisms introduced into the recipient gut following FMT have no impact on the basal rate of HGT within the human gut microbiome. Analyses of further FMT studies are required to assess the generalisability of this conclusion across different FMT study designs and for the treatment of different gut-related conditions. Video Abstract.},
}
@article {pmid38344902,
year = {2024},
author = {Macesic, N and Dennis, A and Hawkey, J and Vezina, B and Wisniewski, JA and Cottingham, H and Blakeway, LV and Harshegyi, T and Pragastis, K and Badoordeen, GZ and Bass, P and Stewardson, AJ and Dennison, A and Spelman, DW and Jenney, AWJ and Peleg, AY},
title = {Genomic investigation of multispecies and multivariant blaNDM outbreak reveals key role of horizontal plasmid transmission.},
journal = {Infection control and hospital epidemiology},
volume = {45},
number = {6},
pages = {709-716},
pmid = {38344902},
issn = {1559-6834},
mesh = {Humans ; *beta-Lactamases/genetics ; *Plasmids/genetics ; *Disease Outbreaks ; Male ; Female ; Middle Aged ; Aged ; Australia/epidemiology ; Whole Genome Sequencing ; Adult ; Enterobacteriaceae Infections/epidemiology/transmission/microbiology ; Gene Transfer, Horizontal ; Aged, 80 and over ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Genome, Bacterial ; },
abstract = {OBJECTIVES: New Delhi metallo-β-lactamases (NDMs) are major contributors to the spread of carbapenem resistance globally. In Australia, NDMs were previously associated with international travel, but from 2019 we noted increasing incidence of NDM-positive clinical isolates. We investigated the clinical and genomic epidemiology of NDM carriage at a tertiary-care Australian hospital from 2016 to 2021.<br><br>METHODS: We identified 49 patients with 84 NDM-carrying isolates in an institutional database, and we collected clinical data from electronic medical record. Short- and long-read whole genome sequencing was performed on all isolates. Completed genome assemblies were used to assess the genetic setting of blaNDM genes and to compare NDM plasmids.<br><br>RESULTS: Of 49 patients, 38 (78%) were identified in 2019-2021 and only 11 (29%) of 38 reported prior travel, compared with 9 (82%) of 11 in 2016-2018 (P = .037). In patients with NDM infection, the crude 7-day mortality rate was 0% and the 30-day mortality rate was 14% (2 of 14 patients). NDMs were noted in 41 bacterial strains (ie, species and sequence type combinations). Across 13 plasmid groups, 4 NDM variants were detected: blaNDM-1, blaNDM-4, blaNDM-5, and blaNDM-7. We noted a change from a diverse NDM plasmid repertoire in 2016-2018 to the emergence of conserved blaNDM-1 IncN and blaNDM-7 IncX3 epidemic plasmids, with interstrain spread in 2019-2021. These plasmids were noted in 19 (50%) of 38 patients and 35 (51%) of 68 genomes in 2019-2021.<br><br>CONCLUSIONS: Increased NDM case numbers were due to local circulation of 2 epidemic plasmids with extensive interstrain transfer. Our findings underscore the challenges of outbreak detection when horizontal transmission of plasmids is the primary mode of spread.},
}
@article {pmid38341975,
year = {2024},
author = {Li, Z and Guo, X and Liu, B and Huang, T and Liu, R and Liu, X},
title = {Metagenome sequencing reveals shifts in phage-associated antibiotic resistance genes from influent to effluent in wastewater treatment plants.},
journal = {Water research},
volume = {253},
number = {},
pages = {121289},
doi = {10.1016/j.watres.2024.121289},
pmid = {38341975},
issn = {1879-2448},
mesh = {*Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Wastewater ; Metagenome ; Drug Resistance, Microbial/genetics ; *Water Purification ; },
abstract = {Antibiotic resistance poses a significant threat to global health, and the microbe-rich activated sludge environment may contribute to the dissemination of antibiotic resistance genes (ARGs). ARGs spread across various bacterial populations via multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages (phages). However, the potential role of phages in spreading ARGs in wastewater treatment systems remains unclear. This study characterized the core resistome, mobile genetic elements (MGEs), and virus-associated ARGs (vir_ARGs) in influents (Inf) and effluents (Eff) samples from nine WWTPs in eastern China. The abundance of ARGs in the Inf samples was higher than that in the Eff samples. A total of 21 core ARGs were identified, accounting for 38.70 %-83.70 % of the different samples. There was an increase in MGEs associated with phage-related processes from influents to effluents (from 12.68 % to 21.10 %). These MGEs showed strong correlations in relative abundance and composition with the core ARGs in the Eff samples. Across the Inf and Eff samples, 58 unique vir_ARGs were detected, with the Eff samples exhibiting higher diversity of vir_ARGs than the Inf samples. Statistical analyses indicated a robust relationship between core ARG profile, MGEs associated with phage-related processes, and vir_ARG composition in the Eff samples. Additionally, the co-occurrence of MGEs and ARGs in viral genomes was observed, ranging from 22.73 % to 68.75 %. This co-occurrence may exacerbate the persistence and spread of ARGs within WWTPs. The findings present new information on the changes in core ARGs, MGEs, and phage-associated ARGs from influents to effluents in WWTPs and provide new insights into the role of phage-associated ARGs in these systems.},
}
@article {pmid38340701,
year = {2024},
author = {Liu, Z and Heng, S and Dai, Q and Gao, Y and Han, Y and Hu, L and Liu, Y and Lu, X and Zhen, G},
title = {Simultaneous removal of antibiotic resistance genes and improved dewatering ability of waste activated sludge by Fe(II)-activated persulfate oxidation.},
journal = {Water research},
volume = {253},
number = {},
pages = {121265},
doi = {10.1016/j.watres.2024.121265},
pmid = {38340701},
issn = {1879-2448},
mesh = {*Sewage/chemistry ; *Anti-Bacterial Agents ; Waste Disposal, Fluid/methods ; Drug Resistance, Microbial/genetics ; Oxidation-Reduction ; Water/chemistry ; Ferrous Compounds/chemistry ; },
abstract = {Waste activated sludge properties vary widely with different regions due to the difference in living standards and geographical distribution, making a big challenge to developing a universally effective sludge dewatering technique. The Fe(II)-activated persulfate (S2O8[2-]) oxidation process shows excellent ability to disrupt sludge cells and extracellular polymeric substances (EPS), and release bound water from sludge flocs. In this study, the discrepancies in the physicochemical characteristics of sludge samples from seven representative cities in China (e.g., dewaterability, EPS composition, surface charge, microbial community, relative abundance of antibiotic resistance genes (ARGs), etc.) were investigated, and the role of Fe(II)-S2O8[2-] oxidation in enhancing removal of antibiotic resistance genes and dewatering ability were explored. The results showed significant differences between the EPS distribution and chemical composition of sludge samples due to different treatment processes, effluent sources, and regions. The Fe(II)-S2O8[2-] oxidation pretreatment had a good enhancement of sludge dewatering capacity (up to 76 %). Microbial analysis showed that the microbial community in each sludge varied significantly depending on the types of wastewater, the wastewater treatment processes, and the regions, but Fe(II)-S2O8[2-] oxidation was able to attack and rupture the sludge zoogloea indiscriminately. Genetic analysis further showed that a considerable number of ARGs were detected in all of these sludge samples and that Fe(II)-S2O8[2-] oxidation was effective in removing ARGs by higher than 90 %. The highly active radicals (e.g., SO4[-]·, ·OH) produced in this process caused drastic damage to sludge microbial cells and DNA stability while liberating the EPS/cell-bound water. Co-occurrence network analysis highlighted a positive correlation between population distribution and ARGs abundance, while variations in microbial communities were linked to regional differences in living standards and level of economic development. Despite these variations, the Fe(II)-S2O8[2-] oxidation consistently achieved excellent performance in both ARGs removal and sludge dewatering. The significant modularity of associations between different microbial communities also confirms its ability to reduce horizontal gene transfer (HGT) by scavenging microbes.},
}
@article {pmid38338856,
year = {2024},
author = {Zhao, Z and Li, Y and Zhai, JW and Liu, ZJ and Li, MH},
title = {Organelle Genomes of Epipogium roseum Provide Insight into the Evolution of Mycoheterotrophic Orchids.},
journal = {International journal of molecular sciences},
volume = {25},
number = {3},
pages = {},
pmid = {38338856},
issn = {1422-0067},
support = {2023YFD1000500//the National Key Research and Development Program of China/ ; 72202200205//the Forestry Peak Discipline Construction Project of Fujian Agriculture and Forestry University/ ; },
mesh = {Phylogeny ; Plastids ; *Genome, Plastid ; *Orchidaceae/genetics ; Asia ; Evolution, Molecular ; },
abstract = {Epipogium roseum, commonly known as one of the ghost orchids due to its rarity and almost transparent color, is a non-photosynthetic and fully mycoheterotrophic plant. Given its special nutritional strategies and evolutionary significance, the mitogenome was first characterized, and three plastomes sampled from Asia were assembled. The plastomes were found to be the smallest among Orchidaceae, with lengths ranging from 18,339 to 19,047 bp, and exhibited high sequence variety. For the mitogenome, a total of 414,552 bp in length, comprising 26 circular chromosomes, were identified. A total of 54 genes, including 38 protein-coding genes, 13 tRNA genes, and 3 rRNA genes, were annotated. Multiple repeat sequences spanning a length of 203,423 bp (45.47%) were discovered. Intriguingly, six plastid regions via intracellular gene transfer and four plastid regions via horizontal gene transfer to the mitogenome were observed. The phylogenomics, incorporating 90 plastomes and 56 mitogenomes, consistently revealed the sister relationship of Epipogium and Gastrodia, with a bootstrap percentage of 100%. These findings shed light on the organelle evolution of Orchidaceae and non-photosynthetic plants.},
}
@article {pmid38337962,
year = {2024},
author = {Zhang, J and Wang, J and Zhu, C and Singh, RP and Chen, W},
title = {Chickpea: Its Origin, Distribution, Nutrition, Benefits, Breeding, and Symbiotic Relationship with Mesorhizobium Species.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {3},
pages = {},
pmid = {38337962},
issn = {2223-7747},
support = {31970006//National Nature Science Foundation of China/ ; Yuzutong[2023]No.11//Central Plains youth top talent project/ ; },
abstract = {Chickpea (Cicer arietinum L.), encompassing the desi and kabuli varieties, is a beloved pulse crop globally. Its cultivation spans over fifty countries, from the Indian subcontinent and southern Europe to the Middle East, North Africa, the Americas, Australia, and China. With a rich composition of carbohydrates and protein, constituting 80% of its dry seed mass, chickpea is also touted for its numerous health benefits, earning it the title of a 'functional food'. In the past two decades, research has extensively explored the rhizobial diversity associated with chickpea and its breeding in various countries across Europe, Asia, and Oceania, aiming to understand its impact on the sustainable yield and quality of chickpea crops. To date, four notable species of Mesorhizobium-M. ciceri, M. mediterraneum, M. muleiense, and M. wenxiniae-have been reported, originally isolated from chickpea root nodules. Other species, such as M. amorphae, M. loti, M. tianshanense, M. oportunistum, M. abyssinicae, and M. shonense, have been identified as potential symbionts of chickpea, possibly acquiring symbiotic genes through lateral gene transfer. While M. ciceri and M. mediterraneum are widely distributed and studied across chickpea-growing regions, they remain absent in China, where M. muleiense and M. wenxiniae are the sole rhizobial species associated with chickpea. The geographic distribution of chickpea rhizobia is believed to be influenced by factors such as genetic characteristics, competitiveness, evolutionary adaptation to local soil conditions, and compatibility with native soil microbes. Inoculating chickpea with suitable rhizobial strains is crucial when introducing the crop to new regions lacking indigenous chickpea rhizobia. The introduction of a novel chickpea variety, coupled with the effective use of rhizobia for inoculation, offers the potential not only to boost the yield and seed quality of chickpeas, but also to enhance crop productivity within rotation and intercropped systems involving chickpea and other crops. Consequently, this advancement holds the promise to drive forward the cause of sustainable agriculture on a global scale.},
}
@article {pmid38335841,
year = {2024},
author = {Qiu, X and Wang, B and Ren, S and Liu, X and Wang, Y},
title = {Regulation of quorum sensing for the manipulation of conjugative transfer of antibiotic resistance genes in wastewater treatment system.},
journal = {Water research},
volume = {253},
number = {},
pages = {121222},
doi = {10.1016/j.watres.2024.121222},
pmid = {38335841},
issn = {1879-2448},
mesh = {*Quorum Sensing ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Escherichia coli ; Plasmids ; Gene Transfer, Horizontal ; *Benzaldehydes ; },
abstract = {The emergence and transmission of antibiotic resistance genes (ARGs) through plasmid-mediated conjugation has become a significant worldwide public health threat. Biofilms are widely recognized as the primary reservoirs for ARGs, providing favorable conditions for horizontal gene transfer. Quorum sensing (QS) plays a critical role in bacterial biofilm formation, which further influences the spread of bacterial resistance. In this study, we examined the effects of vanillin, a QS inhibitor (QSI), at subinhibitory concentrations (sub-MICs) ranging from 0 - 0.1 g/L, on the transfer of ARGs between Escherichia coli and Pseudomonas aeruginosa. Our findings indicated that vanillin at sub-MICs inhibited the conjugative transfer frequency of the RP4 plasmid. This inhibition was supported by the downregulation of plasmid transfer genes. The suppression of conjugation can mainly be attributed to the inhibition of biofilm formation, the synthesis of extracellular polymeric substances (EPS), and the secretion of virulence factors, all of which are regulated by the bacterial QS system. On the other hand, the levels of ROS and cell membrane permeability were not primary explanations for this phenomenon. Furthermore, vanillin also reduced the conjugative transfer frequency of ARGs in wastewater effluent, providing a potential approach to alleviate bacterial resistance in water environments. These findings underscore the regulatory role of QSI in controlling ARGs transfer and have significant implications for manipulating the dissemination of bacterial resistance in the environment.},
}
@article {pmid38330161,
year = {2024},
author = {Li, Q and Chan, YB and Galtier, N and Scornavacca, C},
title = {The Effect of Copy Number Hemiplasy on Gene Family Evolution.},
journal = {Systematic biology},
volume = {73},
number = {2},
pages = {355-374},
doi = {10.1093/sysbio/syae007},
pmid = {38330161},
issn = {1076-836X},
support = {ANR-19-CE45-0012//Agence Nationale de la Recherche/ ; },
mesh = {*Evolution, Molecular ; *Models, Genetic ; *Gene Dosage ; Gene Duplication ; Multigene Family ; Phylogeny ; Classification/methods ; Computer Simulation ; },
abstract = {The evolution of gene families is complex, involving gene-level evolutionary events such as gene duplication, horizontal gene transfer, and gene loss, and other processes such as incomplete lineage sorting (ILS). Because of this, topological differences often exist between gene trees and species trees. A number of models have been recently developed to explain these discrepancies, the most realistic of which attempts to consider both gene-level events and ILS. When unified in a single model, the interaction between ILS and gene-level events can cause polymorphism in gene copy number, which we refer to as copy number hemiplasy (CNH). In this paper, we extend the Wright-Fisher process to include duplications and losses over several species, and show that the probability of CNH for this process can be significant. We study how well two unified models-multilocus multispecies coalescent (MLMSC), which models CNH, and duplication, loss, and coalescence (DLCoal), which does not-approximate the Wright-Fisher process with duplication and loss. We then study the effect of CNH on gene family evolution by comparing MLMSC and DLCoal. We generate comparable gene trees under both models, showing significant differences in various summary statistics; most importantly, CNH reduces the number of gene copies greatly. If this is not taken into account, the traditional method of estimating duplication rates (by counting the number of gene copies) becomes inaccurate. The simulated gene trees are also used for species tree inference with the summary methods ASTRAL and ASTRAL-Pro, demonstrating that their accuracy, based on CNH-unaware simulations calibrated on real data, may have been overestimated.},
}
@article {pmid38329938,
year = {2024},
author = {Liu, Z and Good, BH},
title = {Dynamics of bacterial recombination in the human gut microbiome.},
journal = {PLoS biology},
volume = {22},
number = {2},
pages = {e3002472},
pmid = {38329938},
issn = {1545-7885},
support = {R35 GM146949/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Bacteria/genetics ; Gene Transfer, Horizontal/genetics ; },
abstract = {Horizontal gene transfer (HGT) is a ubiquitous force in microbial evolution. Previous work has shown that the human gut is a hotspot for gene transfer between species, but the more subtle exchange of variation within species-also known as recombination-remains poorly characterized in this ecosystem. Here, we show that the genetic structure of the human gut microbiome provides an opportunity to measure recent recombination events from sequenced fecal samples, enabling quantitative comparisons across diverse commensal species that inhabit a common environment. By analyzing recent recombination events in the core genomes of 29 human gut bacteria, we observed widespread heterogeneities in the rates and lengths of transferred fragments, which are difficult to explain by existing models of ecological isolation or homology-dependent recombination rates. We also show that natural selection helps facilitate the spread of genetic variants across strain backgrounds, both within individual hosts and across the broader population. These results shed light on the dynamics of in situ recombination, which can strongly constrain the adaptability of gut microbial communities.},
}
@article {pmid38326975,
year = {2024},
author = {Ma, D and Xu, J and Wu, M and Zhang, R and Hu, Z and Ji, CA and Wang, Y and Zhang, Z and Yu, R and Liu, X and Yang, L and Li, G and Shen, D and Liu, M and Yang, Z and Zhang, H and Wang, P and Zhang, Z},
title = {Phenazine biosynthesis protein MoPhzF regulates appressorium formation and host infection through canonical metabolic and noncanonical signaling function in Magnaporthe oryzae.},
journal = {The New phytologist},
volume = {242},
number = {1},
pages = {211-230},
pmid = {38326975},
issn = {1469-8137},
support = {R03 AI156254/AI/NIAID NIH HHS/United States ; R21 AI168867/AI/NIAID NIH HHS/United States ; },
mesh = {Fungal Proteins/genetics/metabolism ; *Magnaporthe ; *Oryza/metabolism ; Phenazines/metabolism ; Plant Diseases/genetics ; *Ascomycota ; },
abstract = {Microbe-produced secondary metabolite phenazine-1-carboxylic acid (PCA) facilitates pathogen virulence and defense mechanisms against competitors. Magnaporthe oryzae, a causal agent of the devastating rice blast disease, needs to compete with other phyllosphere microbes and overcome host immunity for successful colonization and infection. However, whether M. oryzae produces PCA or it has any other functions remains unknown. Here, we found that the MoPHZF gene encodes the phenazine biosynthesis protein MoPhzF, synthesizes PCA in M. oryzae, and regulates appressorium formation and host virulence. MoPhzF is likely acquired through an ancient horizontal gene transfer event and has a canonical function in PCA synthesis. In addition, we found that PCA has a role in suppressing the accumulation of host-derived reactive oxygen species (ROS) during infection. Further examination indicated that MoPhzF recruits both the endoplasmic reticulum membrane protein MoEmc2 and the regulator of G-protein signaling MoRgs1 to the plasma membrane (PM) for MoRgs1 phosphorylation, which is a critical regulatory mechanism in appressorium formation and pathogenicity. Collectively, our studies unveiled a canonical function of MoPhzF in PCA synthesis and a noncanonical signaling function in promoting appressorium formation and host infection.},
}
@article {pmid38323496,
year = {2024},
author = {Sabino, YNV and de Melo, MD and da Silva, GC and Mantovani, HC},
title = {Unraveling the diversity and dissemination dynamics of antimicrobial resistance genes in Enterobacteriaceae plasmids across diverse ecosystems.},
journal = {Journal of applied microbiology},
volume = {135},
number = {2},
pages = {},
doi = {10.1093/jambio/lxae028},
pmid = {38323496},
issn = {1365-2672},
support = {//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; //Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; },
mesh = {Animals ; Humans ; *Enterobacteriaceae/genetics ; *Anti-Bacterial Agents/pharmacology ; Phylogeny ; Ecosystem ; Drug Resistance, Bacterial/genetics ; Plasmids/genetics ; Escherichia coli/genetics ; },
abstract = {AIM: The objective of this study was to investigate the antimicrobial resistance genes (ARGs) in plasmids of Enterobacteriaceae from soil, sewage, and feces of food-producing animals and humans.<br><br>METHODS AND RESULTS: The plasmid sequences were obtained from the NCBI database. For the identification of ARG, comprehensive antibiotic resistance database (CARD), and ResFinder were used. Gene conservation and evolution were investigated using DnaSP v.6. The transfer potential of the plasmids was evaluated using oriTfinder and a MOB-based phylogenetic tree was reconstructed using Fastree. We identified a total of 1064 ARGs in all plasmids analyzed, conferring resistance to 15 groups of antibiotics, mostly aminoglycosides, beta-lactams, and sulfonamides. The greatest number of ARGs per plasmid was found in enterobacteria from chicken feces. Plasmids from Escherichia coli carrying multiple ARGs were found in all ecosystems. Some of the most abundant genes were shared among all ecosystems, including aph(6)-Id, aph(3'')-Ib, tet(A), and sul2. A high level of sequence conservation was found among these genes, and tet(A) and sul2 are under positive selective pressure. Approximately 62% of the plasmids carrying at least one ARG were potentially transferable. Phylogenetic analysis indicated a potential co-evolution of Enterobacteriaceae plasmids in nature.<br><br>CONCLUSION: The high abundance of Enterobacteriaceae plasmids from diverse ecosystems carrying ARGs reveals their widespread distribution and importance.},
}
@article {pmid38321476,
year = {2024},
author = {López Sánchez, A and Lafond, M},
title = {Predicting horizontal gene transfers with perfect transfer networks.},
journal = {Algorithms for molecular biology : AMB},
volume = {19},
number = {1},
pages = {6},
pmid = {38321476},
issn = {1748-7188},
abstract = {BACKGROUND: Horizontal gene transfer inference approaches are usually based on gene sequences: parametric methods search for patterns that deviate from a particular genomic signature, while phylogenetic methods use sequences to reconstruct the gene and species trees. However, it is well-known that sequences have difficulty identifying ancient transfers since mutations have enough time to erase all evidence of such events. In this work, we ask whether character-based methods can predict gene transfers. Their advantage over sequences is that homologous genes can have low DNA similarity, but still have retained enough important common motifs that allow them to have common character traits, for instance the same functional or expression profile. A phylogeny that has two separate clades that acquired the same character independently might indicate the presence of a transfer even in the absence of sequence similarity.<br><br>OUR CONTRIBUTIONS: We introduce perfect transfer networks, which are phylogenetic networks that can explain the character diversity of a set of taxa under the assumption that characters have unique births, and that once a character is gained it is rarely lost. Examples of such traits include transposable elements, biochemical markers and emergence of organelles, just to name a few. We study the differences between our model and two similar models: perfect phylogenetic networks and ancestral recombination networks. Our goals are to initiate a study on the structural and algorithmic properties of perfect transfer networks. We then show that in polynomial time, one can decide whether a given network is a valid explanation for a set of taxa, and show how, for a given tree, one can add transfer edges to it so that it explains a set of taxa. We finally provide lower and upper bounds on the number of transfers required to explain a set of taxa, in the worst case.},
}
@article {pmid38321410,
year = {2024},
author = {Orel, N and Fadeev, E and Herndl, GJ and Turk, V and Tinta, T},
title = {Recovering high-quality bacterial genomes from cross-contaminated cultures: a case study of marine Vibrio campbellii.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {146},
pmid = {38321410},
issn = {1471-2164},
mesh = {Animals ; *Ecosystem ; Sequence Analysis, DNA ; RNA, Ribosomal, 16S/genetics ; *Vibrio/genetics ; Genome, Bacterial ; Phylogeny ; },
abstract = {BACKGROUND: Environmental monitoring of bacterial pathogens is critical for disease control in coastal marine ecosystems to maintain animal welfare and ecosystem function and to prevent significant economic losses. This requires accurate taxonomic identification of environmental bacterial pathogens, which often cannot be achieved by commonly used genetic markers (e.g., 16S rRNA gene), and an understanding of their pathogenic potential based on the information encoded in their genomes. The decreasing costs of whole genome sequencing (WGS), combined with newly developed bioinformatics tools, now make it possible to unravel the full potential of environmental pathogens, beyond traditional microbiological approaches. However, obtaining a high-quality bacterial genome, requires initial cultivation in an axenic culture, which is a bottleneck in environmental microbiology due to cross-contamination in the laboratory or isolation of non-axenic strains.<br><br>RESULTS: We applied WGS to determine the pathogenic potential of two Vibrio isolates from coastal seawater. During the analysis, we identified cross-contamination of one of the isolates and decided to use this dataset to evaluate the possibility of bioinformatic contaminant removal and recovery of bacterial genomes from a contaminated culture. Despite the contamination, using an appropriate bioinformatics workflow, we were able to obtain high quality and highly identical genomes (Average Nucleotide Identity value 99.98%) of one of the Vibrio isolates from both the axenic and the contaminated culture. Using the assembled genome, we were able to determine that this isolate belongs to a sub-lineage of Vibrio campbellii associated with several diseases in marine organisms. We also found that the genome of the isolate contains a novel Vibrio plasmid associated with bacterial defense mechanisms and horizontal gene transfer, which may offer a competitive advantage to this putative pathogen.<br><br>CONCLUSIONS: Our study shows that, using state-of-the-art bioinformatics tools and a sufficient sequencing effort, it is possible to obtain high quality genomes of the bacteria of interest and perform in-depth genomic analyses even in the case of a contaminated culture. With the new isolate and its complete genome, we are providing new insights into the genomic characteristics and functional potential of this sub-lineage of V. campbellii. The approach described here also highlights the possibility of recovering complete bacterial genomes in the case of non-axenic cultures or obligatory co-cultures.},
}
@article {pmid38315121,
year = {2024},
author = {Han, K and Li, J and Yang, D and Zhuang, Q and Zeng, H and Rong, C and Yue, J and Li, N and Gu, C and Chen, L and Chen, C},
title = {Detecting horizontal gene transfer with metagenomics co-barcoding sequencing.},
journal = {Microbiology spectrum},
volume = {12},
number = {3},
pages = {e0360223},
pmid = {38315121},
issn = {2165-0497},
support = {2021YFF0703805//MOST | National Key Research and Development Program of China (NKPs)/ ; 82102447//MOST | National Natural Science Foundation of China (NSFC)/ ; DFL20191801//Beijing Hospital Authority/ ; Z201100005520040//Beijing Municipal Science and Technology Commission, Adminitrative Commission of Zhongguancun Science Park/ ; QML20230701//Beijing Hospitals Authority Youth Programme/ ; },
mesh = {Animals ; Humans ; Mice ; *Gene Transfer, Horizontal ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; Bacteria/genetics ; DNA ; },
abstract = {Horizontal gene transfer (HGT) is the process through which genetic information is transferred between different genomes and that played a crucial role in bacterial evolution. HGT can enable bacteria to rapidly acquire antibiotic resistance and bacteria that have acquired resistance is spreading within the microbiome. Conventional methods of characterizing HGT patterns include short-read metagenomic sequencing (short-reads mNGS), long-read sequencing, and single-cell sequencing. These approaches present several limitations, such as short-read fragments, high amounts of input DNA, and sequencing costs, respectively. Here, we attempt to circumvent present limitations to detect HGT by developing a metagenomics co-barcode sequencing workflow (MECOS) and applying it to the human and mouse gut microbiomes. In addition to that, we have over 10-fold increased contig length compared to short-reads mNGS; we also obtained exceeding 30 million paired reads with co-barcode information. Applying the novel bioinformatic pipeline, we integrated this co-barcoding information and the context information from long reads, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Specifically, we detected approximately 3,000 HGT blocks in individual samples, encompassing ~6,000 genes and ~100 taxonomic groups, including loci conferring tetracycline resistance through ribosomal protection. MECOS provides a valuable tool for investigating HGT and advance our understanding on the evolution of natural microbial communities within hosts.IMPORTANCEIn this study, to better identify horizontal gene transfer (HGT) in individual samples, we introduce a new co-barcoding sequencing system called metagenomics co-barcoding sequencing (MECOS), which has three significant improvements: (i) long DNA fragment extraction, (ii) a special transposome insertion, (iii) hybridization of DNA to barcode beads, and (4) an integrated bioinformatic pipeline. Using our approach, we have over 10-fold increased contig length compared to short-reads mNGS, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Our results indicate the presence of approximately 3,000 HGT blocks, involving roughly 6,000 genes and 100 taxonomic groups in individual samples. Notably, these HGT events are predominantly enriched in genes that confer tetracycline resistance via ribosomal protection. MECOS is a useful tool for investigating HGT and the evolution of natural microbial communities within hosts, thereby advancing our understanding of microbial ecology and evolution.},
}
@article {pmid38313259,
year = {2024},
author = {Babajanyan, SG and Garushyants, SK and Wolf, YI and Koonin, EV},
title = {Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38313259},
issn = {2692-8205},
abstract = {Microbiomes are generally characterized by high diversity of coexisting microbial species and strains that remains stable within a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis obtained, namely, pure competition, host-parasite relationship and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environments. These findings show that basic phenomena that are universal in microbial communities, environmental variation and HGT, provide for stabilization of microbial diversity and ecological complexity.},
}
@article {pmid38310066,
year = {2024},
author = {Stein, AM and Biller, SJ},
title = {An ocean of diffusible information.},
journal = {Trends in genetics : TIG},
volume = {40},
number = {3},
pages = {209-210},
doi = {10.1016/j.tig.2024.01.007},
pmid = {38310066},
issn = {0168-9525},
mesh = {*DNA/genetics ; Bacteria/genetics ; *Extracellular Vesicles/genetics ; Gene Transfer, Horizontal/genetics ; Oceans and Seas ; },
abstract = {In the ocean, free-living bacteria exist in a dilute world where direct physical interactions between cells are relatively rare. How then do they exchange genetic information via horizontal gene transfer (HGT)? Lücking et al. have explored the world of marine 'protected extracellular DNA' (peDNA), and find that extracellular vesicles (EVs) are likely to play an important role.},
}
@article {pmid38309275,
year = {2024},
author = {Roisné-Hamelin, F and Liu, HW and Taschner, M and Li, Y and Gruber, S},
title = {Structural basis for plasmid restriction by SMC JET nuclease.},
journal = {Molecular cell},
volume = {84},
number = {5},
pages = {883-896.e7},
doi = {10.1016/j.molcel.2024.01.009},
pmid = {38309275},
issn = {1097-4164},
mesh = {*DNA/metabolism ; Plasmids/genetics ; *Endonucleases ; Prokaryotic Cells ; Cell Cycle Proteins/metabolism ; },
abstract = {DNA loop-extruding SMC complexes play crucial roles in chromosome folding and DNA immunity. Prokaryotic SMC Wadjet (JET) complexes limit the spread of plasmids through DNA cleavage, yet the mechanisms for plasmid recognition are unresolved. We show that artificial DNA circularization renders linear DNA susceptible to JET nuclease cleavage. Unlike free DNA, JET cleaves immobilized plasmid DNA at a specific site, the plasmid-anchoring point, showing that the anchor hinders DNA extrusion but not DNA cleavage. Structures of plasmid-bound JetABC reveal two presumably stalled SMC motor units that are drastically rearranged from the resting state, together entrapping a U-shaped DNA segment, which is further converted to kinked V-shaped cleavage substrate by JetD nuclease binding. Our findings uncover mechanical bending of residual unextruded DNA as molecular signature for plasmid recognition and non-self DNA elimination. We moreover elucidate key elements of SMC loop extrusion, including the motor direction and the structure of a DNA-holding state.},
}
@article {pmid38309246,
year = {2024},
author = {Banks, EJ and Le, TBK},
title = {Co-opting bacterial viruses for DNA exchange: structure and regulation of gene transfer agents.},
journal = {Current opinion in microbiology},
volume = {78},
number = {},
pages = {102431},
doi = {10.1016/j.mib.2024.102431},
pmid = {38309246},
issn = {1879-0364},
mesh = {*Rhodobacter capsulatus/genetics ; *Bacteriophages/genetics ; Bacteria/genetics ; DNA ; Gene Transfer, Horizontal ; DNA, Bacterial/genetics ; },
abstract = {Horizontal gene transfer occurs via a range of mechanisms, including transformation, conjugation and bacteriophage transduction. Gene transfer agents (GTAs) are an alternative, less-studied route for interbacterial DNA exchange. Encoded within bacterial or archaeal genomes, GTAs assemble into phage-like particles that selflessly package and transmit host DNA to recipient bacteria. Several unique features distinguish GTAs from canonical phages such as an inability to self-replicate, thus producing non-infectious particles. GTAs are also deeply integrated into the physiology of the host cell and are maintained under tight host-regulatory control. Recent advances in understanding the structure and regulation of GTAs have provided further insights into a DNA transfer mechanism that is proving increasingly widespread across the bacterial tree of life.},
}
@article {pmid38306427,
year = {2024},
author = {Yang, Z and Guo, Z and Gong, C and Xia, J and Hu, Y and Zhong, J and Yang, X and Xie, W and Wang, S and Wu, Q and Ye, W and Liu, B and Zhou, X and Turlings, TCJ and Zhang, Y},
title = {Two horizontally acquired bacterial genes steer the exceptionally efficient and flexible nitrogenous waste cycling in whiteflies.},
journal = {Science advances},
volume = {10},
number = {5},
pages = {eadi3105},
pmid = {38306427},
issn = {2375-2548},
mesh = {Animals ; *Hemiptera/genetics/metabolism/microbiology ; Genes, Bacterial ; Plants/genetics ; Nitrogen/metabolism ; },
abstract = {Nitrogen is an essential element for all life on earth. Nitrogen metabolism, including excretion, is essential for growth, development, and survival of plants and animals alike. Several nitrogen metabolic processes have been described, but the underlying molecular mechanisms are unclear. Here, we reveal a unique process of nitrogen metabolism in the whitefly Bemisia tabaci, a global pest. We show that it has acquired two bacterial uricolytic enzyme genes, B. tabaci urea carboxylase (BtUCA) and B. tabaci allophanate hydrolase (BtAtzF), through horizontal gene transfer. These genes operate in conjunction to not only coordinate an efficient way of metabolizing nitrogenous waste but also control B. tabaci's exceptionally flexible nitrogen recycling capacity. Its efficient nitrogen processing explains how this important pest can feed on a vast spectrum of plants. This finding provides insight into how the hijacking of microbial genes has allowed whiteflies to develop a highly economic and stable nitrogen metabolism network and offers clues for pest management strategies.},
}
@article {pmid38305416,
year = {2024},
author = {Phillips, D and Noble, D},
title = {Reply from Daniel Phillips and Denis Noble.},
journal = {The Journal of physiology},
volume = {602},
number = {11},
pages = {2669-2672},
doi = {10.1113/JP286224},
pmid = {38305416},
issn = {1469-7793},
}
@article {pmid38304712,
year = {2024},
author = {Chen, P and Wang, S and Li, H and Qi, X and Hou, Y and Ma, T},
title = {Comparative genomic analyses of Cutibacterium granulosum provide insights into genomic diversity.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1343227},
pmid = {38304712},
issn = {1664-302X},
abstract = {Cutibacterium granulosum, a commensal bacterium found on human skin, formerly known as Propionibacterium granulosum, rarely causes infections and is generally considered non-pathogenic. Recent research has revealed the transferability of the multidrug-resistant plasmid pTZC1 between C. granulosum and Cutibacterium acnes, the latter being an opportunistic pathogen in surgical site infections. However, there is a noticeable lack of research on the genome of C. granulosum, and the genetic landscape of this species remains largely uncharted. We investigated the genomic features and evolutionary structure of C. granulosum by analyzing a total of 30 Metagenome-Assembled Genomes (MAGs) and isolate genomes retrieved from public databases, as well as those generated in this study. A pan-genome of 6,077 genes was identified for C. granulosum. Remarkably, the 'cloud genes' constituted 62.38% of the pan-genome. Genes associated with mobilome: prophages, transposons [X], defense mechanisms [V] and replication, recombination and repair [L] were enriched in the cloud genome. Phylogenomic analysis revealed two distinct mono-clades, highlighting the genomic diversity of C. granulosum. The genomic diversity was further confirmed by the distribution of Average Nucleotide Identity (ANI) values. The functional profiles analysis of C. granulosum unveiled a wide range of potential Antibiotic Resistance Genes (ARGs) and virulence factors, suggesting its potential tolerance to various environmental challenges. Subtype I-E of the CRISPR-Cas system was the most abundant in these genomes, a feature also detected in C. acnes genomes. Given the widespread distribution of C. granulosum strains within skin microbiome, our findings make a substantial contribution to our broader understanding of the genetic diversity, which may open new avenues for investigating the mechanisms and treatment of conditions such as acne vulgaris.},
}
@article {pmid38299814,
year = {2024},
author = {Yu, S and Ma, Q and Huang, J and Liu, Y and Li, J and Wang, Y and Gong, T and Zhang, Q and Zou, J and Li, Y},
title = {SMU_1361c regulates the oxidative stress response of Streptococcus mutans.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {2},
pages = {e0187123},
pmid = {38299814},
issn = {1098-5336},
support = {2022NSFSC1482//Sichuan Science and Technology Program/ ; 2023NSFSC1509//Sichuan Science and Technology Program/ ; 82170947//MOST | National Natural Science Foundation of China (NSFC)/ ; 32170046//MOST | National Natural Science Foundation of China (NSFC)/ ; RD-02-202402//Fundamental Research Funds for the Central Universities, Research and Develop Program, West China Hospital of Stomatology Sichuan University/ ; RD-02-202406//Fundamental Research Funds for the Central Universities, Research and Develop Program, West China Hospital of Stomatology Sichuan University/ ; RCDWJS2023-10//Research Funding from West China School/Hospital of Stomatology Sichuan University/ ; },
mesh = {Humans ; *Streptococcus mutans/metabolism ; Bacterial Proteins/genetics/metabolism ; *Dental Caries ; Biofilms ; Oxidative Stress ; Tetracyclines ; Deoxyribonuclease I/metabolism ; },
abstract = {Dental caries is the most common chronic infectious disease around the world and disproportionately affects the marginalized socioeconomic group. Streptococcus mutans, considered a primary etiological agent of caries, depends on the coordinated physiological response to tolerate the oxidative stress generated by commensal species within dental plaque, which is a critical aspect of its pathogenicity. Here, we identified and characterized a novel tetracycline repressor family regulator, SMU_1361c, which appears to be acquired by the bacteria via horizontal gene transfer. Surprisingly, smu_1361c functions as a negative transcriptional regulator to regulate gene expression outside its operon and is involved in the oxidative stress response of S. mutans. The smu_1361c overexpression strain UA159/pDL278-1361c was more susceptible to oxidative stress and less competitive against hydrogen peroxide generated by commensal species Streptococcus gordonii and Streptococcus sanguinis. Transcriptomics analysis revealed that smu_1361c overexpression resulted in the significant downregulation of 22 genes, mainly belonging to three gene clusters responsible for the oxidative stress response. The conversed DNA binding motif of SMU_1361c was determined by electrophoretic mobility shift and DNase I footprinting assay with purified SMU_1361c protein; therefore, smu_1361c is directly involved in gene transcription related to the oxidative stress response. Crucially, our finding provides a new understanding of how S. mutans deals with the oxidative stress that is required for pathogenesis and will facilitate the development of new and improved therapeutic approaches for dental caries.IMPORTANCEStreptococcus mutans is the major organism associated with the development of dental caries, which globally is the most common chronic disease. To persist and survive in biofilms, S. mutans must compete with commensal species that occupy the same ecological niche. Here, we uncover a novel molecular mechanism of how tetracycline repressor family regulator smu_1361c is involved in the oxidative stress response through transcriptomics analysis, electrophoretic mobility shift assay, and DNase I footprinting assay. Furthermore, we demonstrated that smu_1361c mediates S. mutans sensitivity to oxidative stress and competitiveness with commensal streptococci. Therefore, this study has revealed a previously unknown regulation between smu_1361c and genes outside its operon and demonstrated the importance of smu_1361c in the oxidative stress response and the fitness of S. mutans within the plaque biofilms, which can be exploited as a new therapy to modulate ecological homeostasis and prevent dental caries.},
}
@article {pmid38296951,
year = {2024},
author = {Bálint, B and Merényi, Z and Hegedüs, B and Grigoriev, IV and Hou, Z and Földi, C and Nagy, LG},
title = {ContScout: sensitive detection and removal of contamination from annotated genomes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {936},
pmid = {38296951},
issn = {2041-1723},
support = {758161//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; LP2019-13/2019//Magyar Tudom&#x00E1;nyos Akad&#x00E9;mia (Hungarian Academy of Sciences)/ ; },
mesh = {*Genome ; *Genomics ; Phylogeny ; Biological Evolution ; Metagenomics ; Evolution, Molecular ; },
abstract = {Contamination of genomes is an increasingly recognized problem affecting several downstream applications, from comparative evolutionary genomics to metagenomics. Here we introduce ContScout, a precise tool for eliminating foreign sequences from annotated genomes. It achieves high specificity and sensitivity on synthetic benchmark data even when the contaminant is a closely related species, outperforms competing tools, and can distinguish horizontal gene transfer from contamination. A screen of 844 eukaryotic genomes for contamination identified bacteria as the most common source, followed by fungi and plants. Furthermore, we show that contaminants in ancestral genome reconstructions lead to erroneous early origins of genes and inflate gene loss rates, leading to a false notion of complex ancestral genomes. Taken together, we offer here a tool for sensitive removal of foreign proteins, identify and remove contaminants from diverse eukaryotic genomes and evaluate their impact on phylogenomic analyses.},
}
@article {pmid38295970,
year = {2024},
author = {Wei, J and Luo, J and Peng, T and Zhou, P and Zhang, J and Yang, F},
title = {Comparative genomic analysis and functional investigations for MCs catabolism mechanisms and evolutionary dynamics of MCs-degrading bacteria in ecology.},
journal = {Environmental research},
volume = {248},
number = {},
pages = {118336},
doi = {10.1016/j.envres.2024.118336},
pmid = {38295970},
issn = {1096-0953},
mesh = {Humans ; *Ecosystem ; Microcystins ; Biodegradation, Environmental ; *Sphingomonadaceae/genetics/metabolism ; Genomics ; },
abstract = {Microcystins (MCs) significantly threaten the ecosystem and public health. Biodegradation has emerged as a promising technology for removing MCs. Many MCs-degrading bacteria have been identified, including an indigenous bacterium Sphingopyxis sp. YF1 that could degrade MC-LR and Adda completely. Herein, we gained insight into the MCs biodegradation mechanisms and evolutionary dynamics of MCs-degrading bacteria, and revealed the toxic risks of the MCs degradation products. The biochemical characteristics and genetic repertoires of strain YF1 were explored. A comparative genomic analysis was performed on strain YF1 and six other MCs-degrading bacteria to investigate their functions. The degradation products were investigated, and the toxicity of the intermediates was analyzed through rigorous theoretical calculation. Strain YF1 might be a novel species that exhibited versatile substrate utilization capabilities. Many common genes and metabolic pathways were identified, shedding light on shared functions and catabolism in the MCs-degrading bacteria. The crucial genes involved in MCs catabolism mechanisms, including mlr and paa gene clusters, were identified successfully. These functional genes might experience horizontal gene transfer events, suggesting the evolutionary dynamics of these MCs-degrading bacteria in ecology. Moreover, the degradation products for MCs and Adda were summarized, and we found most of the intermediates exhibited lower toxicity to different organisms than the parent compound. These findings systematically revealed the MCs catabolism mechanisms and evolutionary dynamics of MCs-degrading bacteria. Consequently, this research contributed to the advancement of green biodegradation technology in aquatic ecology, which might protect human health from MCs.},
}
@article {pmid38295006,
year = {2024},
author = {Anantharajah, A and Goormaghtigh, F and Nguvuyla Mantu, E and Güler, B and Bearzatto, B and Momal, A and Werion, A and Hantson, P and Kabamba-Mukadi, B and Van Bambeke, F and Rodriguez-Villalobos, H and Verroken, A},
title = {Long-term intensive care unit outbreak of carbapenemase-producing organisms associated with contaminated sink drains.},
journal = {The Journal of hospital infection},
volume = {143},
number = {},
pages = {38-47},
doi = {10.1016/j.jhin.2023.10.010},
pmid = {38295006},
issn = {1532-2939},
mesh = {Adult ; Humans ; *Cross Infection/epidemiology/prevention &amp; control ; beta-Lactamases/genetics ; Bacterial Proteins/genetics ; Disease Outbreaks ; Anti-Bacterial Agents ; *Disinfectants ; Intensive Care Units ; },
abstract = {BACKGROUND: Between 2018 and 2022, a Belgian tertiary care hospital faced a growing issue with acquiring carbapenemase-producing organisms (CPO), mainly VIM-producing P. aeruginosa (PA-VIM) and NDM-producing Enterobacterales (CPE-NDM) among hospitalized patients in the adult intensive care unit (ICU).<br><br>AIM: To investigate this ICU long-term CPO outbreak involving multiple species and a persistent environmental reservoir.<br><br>METHODS: Active case finding, environmental sampling, whole-genome sequencing (WGS) analysis of patient and environmental strains, and implemented control strategies were described in this study.<br><br>FINDINGS: From 2018 to 2022, 37 patients became colonized or infected with PA-VIM and/or CPE-NDM during their ICU stay. WGS confirmed the epidemiological link between clinical and environmental strains collected from the sink drains with clonal strain dissemination and horizontal gene transfer mediated by plasmid conjugation and/or transposon jumps. Environmental disinfection by quaternary ammonium-based disinfectant and replacement of contaminated equipment failed to eradicate environmental sources. Interestingly, efflux pump genes conferring resistance to quaternary ammonium compounds were widespread in the isolates. As removing sinks was not feasible, a combination of a foaming product degrading the biofilm and foaming disinfectant based on peracetic acid and hydrogen peroxide has been evaluated and has so far prevented recolonization of the proximal sink drain by CPO.<br><br>CONCLUSION: The persistence in the hospital environment of antibiotic- and disinfectant-resistant bacteria with the ability to transfer mobile genetic elements poses a serious threat to ICU patients with a risk of shifting towards an endemicity scenario. Innovative strategies are needed to address persistent environmental reservoirs and prevent CPO transmission.},
}
@article {pmid38290350,
year = {2024},
author = {Wen, X and Chen, M and Ma, B and Xu, J and Zhu, T and Zou, Y and Liao, X and Wang, Y and Worrich, A and Wu, Y},
title = {Removal of antibiotic resistance genes during swine manure composting is strongly impaired by high levels of doxycycline residues.},
journal = {Waste management (New York, N.Y.)},
volume = {177},
number = {},
pages = {76-85},
doi = {10.1016/j.wasman.2024.01.037},
pmid = {38290350},
issn = {1879-2456},
mesh = {Animals ; Swine ; *Doxycycline ; Anti-Bacterial Agents/pharmacology ; *Composting ; Manure ; Drug Resistance, Microbial/genetics ; Livestock ; },
abstract = {Antibiotic resistance genes (ARGs) are emerging pollutants that enter the farm and surrounding environment via the manure of antibiotic-treated animals. Pretreatment of livestock manure by composting decreases ARGs abundance, but how antibiotic residues affect ARGs removal efficiency remains poorly understood. Here, we explored the fate of the resistome under different doxycycline residue levels during aerobic swine manure composting. Metagenomic sequencing showed that the presence of high levels of doxycycline generally had a higher abundance of tetracycline ARGs, and their dominant host bacteria of Firmicutes, especially Clostridium and Streptococcus, also had limited elimination in composting under high levels of doxycycline stress. Moreover, high levels of doxycycline impaired the removal of the total ARGs number in finished composts, with a removal rate of 51.74 % compared to 63.70 % and 71.52 % for the control and low-level doxycycline manure, respectively. Horizontal gene transfer and strengthened correlations among the bacterial community fostered ARGs preservation at high doxycycline levels during composting. In addition, ARGs carried by both plasmids and chromosomes, such as multidrug ARGs, showed wide host characteristics and rebound during compost maturation. Compared with chromosomes, a greater variety of ARGs on plasmids suggested that the majority of ARGs were characterized by horizontal mobility during composting, and the cross-host characteristics of ARGs during composting deserve further attention. This study provided deep insight into the fate of ARGs under residual antibiotic stress during manure composting and reminded the associated risk for environmental and public health.},
}
@article {pmid38289113,
year = {2024},
author = {Abdulkadir, N and Saraiva, JP and Zhang, J and Stolte, S and Gillor, O and Harms, H and Rocha, U},
title = {Genome-centric analyses of 165 metagenomes show that mobile genetic elements are crucial for the transmission of antimicrobial resistance genes to pathogens in activated sludge and wastewater.},
journal = {Microbiology spectrum},
volume = {12},
number = {3},
pages = {e0291823},
pmid = {38289113},
issn = {2165-0497},
support = {VH-NG-1248 Micro' Big Data'//Helmholtz Association ()/ ; 460129525//Deutsche Forschungsgemeinschaft (DFG)/ ; 91717355//German Academic Exchange Service (DAAD)/ ; },
mesh = {Animals ; Humans ; *Wastewater ; Sewage/microbiology ; Anti-Bacterial Agents/pharmacology ; Metagenome ; Genes, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Bacteria ; *Microbiota ; Interspersed Repetitive Sequences ; },
abstract = {UNLABELLED: Wastewater is considered a reservoir of antimicrobial resistance genes (ARGs), where the abundant antimicrobial-resistant bacteria and mobile genetic elements facilitate horizontal gene transfer. However, the prevalence and extent of these phenomena in different taxonomic groups that inhabit wastewater are still not fully understood. Here, we determined the presence of ARGs in metagenome-assembled genomes (MAGs) and evaluated the risks of MAG-carrying ARGs in potential human pathogens. The potential of these ARGs to be transmitted horizontally or vertically was also determined. A total of 5,916 MAGs (completeness >50%, contamination <10%) were recovered, covering 68 phyla and 279 genera. MAGs were dereplicated into 1,204 genome operational taxonomic units (gOTUs) as a proxy for species (average nucleotide identity >0.95). The dominant ARG classes detected were bacitracin, multi-drug, macrolide-lincosamide-streptogramin (MLS), glycopeptide, and aminoglycoside, and 10.26% of them were located on plasmids. The main hosts of ARGs belonged to Escherichia, Klebsiella, Acinetobacter, Gresbergeria, Mycobacterium, and Thauera. Our data showed that 253 MAGs carried virulence factor genes (VFGs) divided into 44 gOTUs, of which 45 MAGs were carriers of ARGs, indicating that potential human pathogens carried ARGs. Alarmingly, the MAG assigned as Escherichia coli contained 159 VFGs, of which 95 were located on chromosomes and 10 on plasmids. In addition to shedding light on the prevalence of ARGs in individual genomes recovered from activated sludge and wastewater, our study demonstrates a workflow that can identify antimicrobial-resistant pathogens in complex microbial communities.<br><br>IMPORTANCE: Antimicrobial resistance (AMR) threatens the health of humans, animals, and natural ecosystems. In our study, an analysis of 165 metagenomes from wastewater revealed antibiotic-targeted alteration, efflux, and inactivation as the most prevalent AMR mechanisms. We identified several genera correlated with multiple ARGs, including Klebsiella, Escherichia, Acinetobacter, Nitrospira, Ottowia, Pseudomonas, and Thauera, which could have significant implications for AMR transmission. The abundance of bacA, mexL, and aph(3")-I in the genomes calls for their urgent management in wastewater. Our approach could be applied to different ecosystems to assess the risk of potential pathogens containing ARGs. Our findings highlight the importance of managing AMR in wastewater and can help design measures to reduce the transmission and evolution of AMR in these systems.},
}
@article {pmid38288414,
year = {2023},
author = {Kuo, LY and Su, HJ and Koubínová, D and Xie, PJ and Whitehouse, C and Ebihara, A and Grant, JR},
title = {Organellar phylogenomics of Ophioglossaceae fern genera.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1294716},
pmid = {38288414},
issn = {1664-462X},
abstract = {Previous phylogenies showed conflicting relationships among the subfamilies and genera within the fern family Ophioglossaceae. However, their classification remains unsettled where contrasting classifications recognize four to 15 genera. Since these treatments are mostly based on phylogenetic evidence using limited, plastid-only loci, a phylogenomic understanding is actually necessary to provide conclusive insight into the systematics of the genera. In this study, we have therefore compiled datasets with the broadest sampling of Ophioglossaceae genera to date, including all fifteen currently recognized genera, especially for the first time the South African endemic genus Rhizoglossum. Notably, our comprehensive phylogenomic matrix is based on both plastome and mitogenome genes. Inferred from the coding sequences of 83 plastid and 37 mitochondrial genes, a strongly supported topology for these subfamilies is presented, and is established by analyses using different partitioning approaches and substitution models. At the generic level, most relationships are well resolved except for few within the subfamily Ophioglossoideae. With this new phylogenomic scheme, key morphological and genomic changes were further identified along this backbone. In addition, we confirmed numerous horizontally transferred (HGT) genes in the genera Botrypus, Helminthostachys, Mankyua, Sahashia, and Sceptridium. These HGT genes are most likely located in mitogenomes and are predominately donated from angiosperm Santalales or non-Ophioglossaceae ferns. By our in-depth searches of the organellar genomes, we also provided phylogenetic overviews for the plastid and mitochondrial MORFFO genes found in these Ophioglossaceae ferns.},
}
@article {pmid38286289,
year = {2024},
author = {Hazra, M and Watts, JEM and Williams, JB and Joshi, H},
title = {An evaluation of conventional and nature-based technologies for controlling antibiotic-resistant bacteria and antibiotic-resistant genes in wastewater treatment plants.},
journal = {The Science of the total environment},
volume = {917},
number = {},
pages = {170433},
doi = {10.1016/j.scitotenv.2024.170433},
pmid = {38286289},
issn = {1879-1026},
mesh = {Humans ; *Wastewater ; Anti-Bacterial Agents/analysis ; Genes, Bacterial ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria/genetics ; Soil ; Water ; *Water Purification ; },
abstract = {Antibiotic resistance is a globally recognized health concern which leads to longer hospital stays, increased morbidity, increased mortality, and higher medical costs. Understanding how antibiotic resistance persists and exchanges in environmental systems like soil, water, and wastewater are critically important for understanding the emergence of pathogens with new resistance profiles and the subsequent exposure of people who indirectly/directly come in contact with these pathogens. There are concerns about the widespread application of prophylactic antibiotics in the clinical and agriculture sectors, as well as chemicals/detergents used in food and manufacturing industries, especially the quaternary ammonium compounds which have been found responsible for the generation of resistant genes in water and soil. The rates of horizontal gene transfer increase where there is a lack of proper water/wastewater infrastructure, high antibiotic manufacturing industries, or endpoint users - such as hospitals and intensive agriculture. Conventional wastewater treatment technologies are often inefficient in the reduction of ARB/ARGs and provide the perfect combination of conditions for the development of antibiotic resistance. The wastewater discharged from municipal facilities may therefore be enriched with bacterial communities/pathogens and provide a suitable environment (due to the presence of nutrients and other pollutants) to enhance the transfer of antibiotic resistance. However, facilities with tertiary treatment (either traditional/emerging technologies) provide higher rates of reduction. This review provides a synthesis of the current understanding of wastewater treatment and antibiotic resistance, examining the drivers that may accelerate their possible transmission to a different environment, and highlighting the need for tertiary technologies used in treatment plants for the reduction of resistant bacteria/genes.},
}
@article {pmid38285528,
year = {2024},
author = {Wu, Y and Zhang, L},
title = {Computing the Bounds of the Number of Reticulations in a Tree-Child Network That Displays a Set of Trees.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {31},
number = {4},
pages = {345-359},
doi = {10.1089/cmb.2023.0309},
pmid = {38285528},
issn = {1557-8666},
mesh = {*Phylogeny ; *Algorithms ; Models, Genetic ; Evolution, Molecular ; Computational Biology/methods ; Computer Simulation ; Gene Transfer, Horizontal ; },
abstract = {Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e.g., hybrid speciation or horizontal gene transfer) occurred. Tree-child network is a kind of phylogenetic network with structural constraints. Existing approaches for tree-child network reconstruction can be slow for large data. In this study, we present several computational approaches for bounding from below the number of reticulations in a tree-child network that displays a given set of rooted binary phylogenetic trees. In addition, we also present some theoretical results on bounding from above the number of reticulations. Through simulation, we demonstrate that the new lower bounds on the reticulation number for tree-child networks can practically be computed for large tree data. The bounds can provide estimates of reticulation for relatively large data.},
}
@article {pmid38281357,
year = {2024},
author = {Kang, Y and Wang, J and Li, Z},
title = {Meta-analysis addressing the characterization of antibiotic resistome in global hospital wastewater.},
journal = {Journal of hazardous materials},
volume = {466},
number = {},
pages = {133577},
doi = {10.1016/j.jhazmat.2024.133577},
pmid = {38281357},
issn = {1873-3336},
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Wastewater ; Genes, Bacterial ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; },
abstract = {Hospital wastewater (HWW) is a significant environmental reservoir of antibiotic resistance genes (ARGs). However, currently, no comprehensive understanding exists of the antibiotic resistome in global HWW. In this study, we attempted to address this knowledge gap through an in silico reanalysis of publicly accessible global HWW metagenomic data. We reanalyzed ARGs in 338 HWW samples from 13 countries in Africa, Asia, and Europe. In total, 2420 ARG subtypes belonging to 30 ARG types were detected, dominated by multidrug, beta-lactam, and aminoglycoside resistance genes. ARG composition in Europe differed from that in Asia and Africa. Notably, the ARGs presented co-occurrence with mobile genetic elements (MGEs), metal resistance genes (MRGs), and human bacterial pathogens (HBP), indicating a potential dissemination risk of ARGs in the HWW. Multidrug resistance genes presented co-occurrence with MGEs, MRGs, and HBP, is particularly pronounced. The abundance of contigs that contained ARG, contigs that contained ARG and HBP, contigs that contained ARG and MGE, contigs that contained ARG and MRG were used for health and transmission risk assessment of antibiotic resistome and screened out 40 high risk ARGs in the global HWW. This study first provides a comprehensive characterization and risk of the antibiotic resistome in global HWW.},
}
@article {pmid38280843,
year = {2024},
author = {Zhu, S and Hong, J and Wang, T},
title = {Horizontal gene transfer is predicted to overcome the diversity limit of competing microbial species.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {800},
pmid = {38280843},
issn = {2041-1723},
mesh = {*Ecosystem ; *Gene Transfer, Horizontal ; Biodiversity ; },
abstract = {Natural microbial ecosystems harbor substantial diversity of competing species. Explaining such diversity is challenging, because in classic theories it is extremely infeasible for a large community of competing species to stably coexist in homogeneous environments. One important aspect mostly overlooked in these theories, however, is that microbes commonly share genetic materials with their neighbors through horizontal gene transfer (HGT), which enables the dynamic change of species growth rates due to the fitness effects of the mobile genetic elements (MGEs). Here, we establish a framework of species competition by accounting for the dynamic gene flow among competing microbes. Combining theoretical derivation and numerical simulations, we show that in many conditions HGT can surprisingly overcome the biodiversity limit predicted by the classic model and allow the coexistence of many competitors, by enabling dynamic neutrality of competing species. In contrast with the static neutrality proposed by previous theories, the diversity maintained by HGT is highly stable against random perturbations of microbial fitness. Our work highlights the importance of considering gene flow when addressing fundamental ecological questions in the world of microbes and has broad implications for the design and engineering of complex microbial consortia.},
}
@article {pmid38280464,
year = {2024},
author = {Kim, H and Yoo, K},
title = {Marine plastisphere selectively enriches microbial assemblages and antibiotic resistance genes during long-term cultivation periods.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {344},
number = {},
pages = {123450},
doi = {10.1016/j.envpol.2024.123450},
pmid = {38280464},
issn = {1873-6424},
mesh = {Humans ; *Plastics ; *Anti-Bacterial Agents/pharmacology ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Drug Resistance, Microbial/genetics ; Microplastics ; Bacteria ; Genes, Bacterial ; Polyethylene ; },
abstract = {Several studies have focused on identifying and quantifying suspended plastics in surface and subsurface seawater. Microplastics (MPs) have attracted attention as carriers of antibiotic resistance genes (ARGs) in the marine environment. Plastispheres, specific biofilms on MP, can provide an ideal niche to spread more widely through horizontal gene transfer (HGT), thereby increasing risks to ecosystems and human health. However, the microbial communities formed on different plastic types and ARG abundances during exposure time in natural marine environments remain unclear. Four types of commonly used MPs (polyethylene (PE), polypropylene (PP), polystyrene (PS), and polyvinyl chloride (PVC)) were periodically cultured (46, 63, and 102 d) in a field-based marine environment to study the co-selection of ARGs and microbial communities in marine plastispheres. After the first 63 d of incubation (p < 0.05), the initial 16S rRNA gene abundance of microorganisms in the plastisphere increased significantly, and the biomass subsequently decreased. These results suggest that MPs can serve as vehicles for various microorganisms to travel to different environments and eventually provide a niche for a variety of microorganisms. Additionally, the qPCR results showed that MPs selectively enriched ARGs. In particular, tetA, tetQ, sul1, and qnrS were selectively enriched in the PVC-MPs. The abundances of intl1, a mobile genetic element, was measured in all MP types for 46 d (5.22 × 10[-5] ± 8.21 × 10[-6] copies/16s rRNA gene copies), 63 d (5.90 × 10[-5] ± 2.49 × 10[-6] copies/16s rRNA gene copies), and 102 d (4.00 × 10[-5] ± 5.11 × 10[-6] copies/16s rRNA gene copies). Network analysis indicated that ARG profiles co-occurred with key biofilm-forming bacteria. This study suggests that the selection of ARGs and their co-occurring bacteria in MPs could potentially accelerate their transmission through HGT in natural marine plastics.},
}
@article {pmid38277437,
year = {2024},
author = {Goldstein, SA and Elde, NC},
title = {Recurrent viral capture of cellular phosphodiesterases that antagonize OAS-RNase L.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {5},
pages = {e2312691121},
pmid = {38277437},
issn = {1091-6490},
support = {F32 AI152341/AI/NIAID NIH HHS/United States ; R35 GM134936/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Phosphoric Diester Hydrolases/genetics/metabolism ; Phylogeny ; *Middle East Respiratory Syndrome Coronavirus ; Mammals/metabolism ; Diethylstilbestrol/*analogs &amp; derivatives ; *Endoribonucleases ; *Rotavirus ; },
abstract = {Phosphodiesterases (PDEs) encoded by viruses are putatively acquired by horizontal transfer of cellular PDE ancestor genes. Viral PDEs inhibit the OAS-RNase L antiviral pathway, a key effector component of the innate immune response. Although the function of these proteins is well-characterized, the origins of these gene acquisitions are less clear. Phylogenetic analysis revealed at least five independent PDE acquisition events by ancestral viruses. We found evidence that PDE-encoding genes were horizontally transferred between coronaviruses belonging to different genera. Three clades of viruses within Nidovirales: merbecoviruses (MERS-CoV), embecoviruses (HCoV-OC43), and toroviruses encode independently acquired PDEs, and a clade of rodent alphacoronaviruses acquired an embecovirus PDE via recent horizontal transfer. Among rotaviruses, the PDE of rotavirus A was acquired independently from rotavirus B and G PDEs, which share a common ancestor. Conserved motif analysis suggests a link between all viral PDEs and a similar ancestor among the mammalian AKAP7 proteins despite low levels of sequence conservation. Additionally, we used ancestral sequence reconstruction and structural modeling to reveal that sequence and structural divergence are not well-correlated among these proteins. Specifically, merbecovirus PDEs are as structurally divergent from the ancestral protein and the solved structure of human AKAP7 PDE as they are from each other. In contrast, comparisons of rotavirus B and G PDEs reveal virtually unchanged structures despite evidence for loss of function in one, suggesting impactful changes that lie outside conserved catalytic sites. These findings highlight the complex and volatile evolutionary history of viral PDEs and provide a framework to facilitate future studies.},
}
@article {pmid38276173,
year = {2023},
author = {Lücking, D and Alarcón-Schumacher, T and Erdmann, S},
title = {Distribution and Implications of Haloarchaeal Plasmids Disseminated in Self-Encoded Plasmid Vesicles.},
journal = {Microorganisms},
volume = {12},
number = {1},
pages = {},
pmid = {38276173},
issn = {2076-2607},
support = {Max-Planck Research Group Archaeal Virology//Max-Planck Society/ ; 98 190//Volkswagen Foundation/ ; },
abstract = {Even though viruses and plasmids are both drivers of horizontal gene transfer, they differ fundamentally in their mode of transfer. Virus genomes are enclosed in virus capsids and are not dependent on cell-to-cell contacts for their dissemination. In contrast, the transfer of plasmids most often requires physical contact between cells. However, plasmid pR1SE of Halorubrum lacusprofundi is disseminated between cells, independent of cell-cell contacts, in specialized membrane vesicles that contain plasmid proteins. In this study, we searched for pR1SE-like elements in public databases and a metagenomics dataset from Australian salt lakes and identified 40 additional pR1SE-like elements in hypersaline environments worldwide. Herein, these elements are named apHPVs (archaeal plasmids of haloarchaea potentially transferred in plasmid vesicles). They share two sets of closely related proteins with conserved synteny, strongly indicating an organization into different functional clusters. We find that apHPVs, besides transferring themselves, have the potential to transfer large fragments of DNA between host cells, including virus defense systems. Most interestingly, apHPVs likely play an important role in the evolution of viruses and plasmids in haloarchaea, as they appear to recombine with both of them. This further supports the idea that plasmids and viruses are not distinct but closely related mobile genetic elements.},
}
@article {pmid38275928,
year = {2024},
author = {Gong, J and Zeng, X and Xu, J and Zhang, D and Dou, X and Lin, J and Wang, C},
title = {Genomic Characterization of a Plasmid-Free and Highly Drug-Resistant Salmonella enterica Serovar Indiana Isolate in China.},
journal = {Veterinary sciences},
volume = {11},
number = {1},
pages = {},
pmid = {38275928},
issn = {2306-7381},
support = {31772758//National Natural Science 291 Foundation of China/ ; CX(23)3005//Jiangsu agricultural science and technology 292 innovation fund/ ; },
abstract = {The emergence of multi-drug resistant (MDR) Salmonella enterica serovar Indiana (S. Indiana) strains in China is commonly associated with the presence of one or more resistance plasmids harboring integrons pivotal in acquiring antimicrobial resistance (AMR). This study aims to elucidate the genetic makeup of this plasmid-free, highly drug-resistant S. Indiana S1467 strain. Genomic sequencing was performed using Illumina HiSeq 2500 sequencer and PacBio RS II System. Prodigal software predicted putative protein-coding sequences while BLASTP analysis was conducted. The S1467 genome comprises a circular 4,998,300 bp chromosome with an average GC content of 51.81%, encompassing 4709 open reading frames (ORFs). Fifty-four AMR genes were identified, conferring resistance across 16 AMR categories, aligning closely with the strain's antibiotic susceptibility profile. Genomic island prediction unveiled an approximately 51 kb genomic island housing a unique YeeVU toxin-antitoxin system (TAS), a rarity in Salmonella species. This suggests that the AMR gene cluster on the S1467 genomic island may stem from the integration of plasmids originating from other Enterobacteriaceae. This study contributes not only to the understanding of the genomic characteristics of a plasmid-free, highly drug-resistant S. Indiana strain but also sheds light on the intricate mechanisms underlying antimicrobial resistance. The implications of our findings extend to the broader context of horizontal gene transfer between bacterial species, emphasizing the need for continued surveillance and research to address the evolving challenges posed by drug-resistant pathogens.},
}
@article {pmid38273225,
year = {2024},
author = {Liu, D and Zhang, Z and Hao, Y and Li, M and Yu, H and Zhang, X and Mi, H and Cheng, L and Zhao, Y},
title = {Decoding the complete organelle genomic architecture of Stewartia gemmata: an early-diverging species in Theaceae.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {114},
pmid = {38273225},
issn = {1471-2164},
support = {21HASTIT040//Program for Science &amp; Technology Innovation Talents in Universities of Henan Province/ ; 21HASTIT040//Program for Science &amp; Technology Innovation Talents in Universities of Henan Province/ ; 212102110447//Scientific and Technological Project in Henan Province/ ; 212102110447//Scientific and Technological Project in Henan Province/ ; Qian-Jiao-Ji [2023]007//Key Laboratory of Functional Agriculture within Guizhou Province's Higher Education Institutions/ ; Qian-Jiao-Ji [2023]007//Key Laboratory of Functional Agriculture within Guizhou Province's Higher Education Institutions/ ; },
mesh = {Phylogeny ; *Theaceae/genetics ; Genomics ; Codon/genetics ; Chloroplasts/genetics ; RNA, Transfer/genetics ; Tea ; *Genome, Chloroplast ; },
abstract = {BACKGROUND: Theaceae, comprising 300 + species, holds significance in biodiversity, economics, and culture, notably including the globally consumed tea plant. Stewartia gemmata, a species of the earliest diverging tribe Stewartieae, is critical to offer insights into Theaceae's origin and evolutionary history.<br><br>RESULT: We sequenced the complete organelle genomes of Stewartia gemmata using short/long reads sequencing technologies. The chloroplast genome (158,406&#xa0;bp) exhibited a quadripartite structure including the large single-copy region (LSC), a small single-copy region (SSC), and a pair of inverted repeat regions (IRs); 114 genes encoded 80 proteins, 30 tRNAs, and four rRNAs. The mitochondrial genome (681,203&#xa0;bp) exhibited alternative conformations alongside a monocyclic structure: 61 genes encoding 38 proteins, 20 tRNAs, three rRNAs, and RNA editing-impacting genes, including ATP6, RPL16, COX2, NAD4L, NAD5, NAD7, and RPS1. Comparative analyses revealed frequent recombination events and apparent rRNA gene gains and losses in the mitochondrial genome of Theaceae. In organelle genomes, the protein-coding genes exhibited a strong A/U bias at codon endings; ENC-GC3 analysis implies selection-driven codon bias. Transposable elements might facilitate interorganelle sequence transfer. Phylogenetic analysis confirmed Stewartieae's early divergence within Theaceae, shedding light on organelle genome characteristics and evolution in Theaceae.<br><br>CONCLUSIONS: We studied the detailed characterization of organelle genomes, including genome structure, composition, and repeated sequences, along with the identification of lateral gene transfer (LGT) events and complexities. The discovery of a large number of repetitive sequences and simple sequence repeats (SSRs) has led to new insights into molecular phylogenetic markers. Decoding the Stewartia gemmata organellar genome provides valuable genomic resources for further studies in tea plant phylogenomics and evolutionary biology.},
}
@article {pmid38271287,
year = {2024},
author = {Harada, R and Hirakawa, Y and Yabuki, A and Kim, E and Yazaki, E and Kamikawa, R and Nakano, K and Eliáš, M and Inagaki, Y},
title = {Encyclopedia of Family A DNA Polymerases Localized in Organelles: Evolutionary Contribution of Bacteria Including the Proto-Mitochondrion.},
journal = {Molecular biology and evolution},
volume = {41},
number = {2},
pages = {},
pmid = {38271287},
issn = {1537-1719},
support = {18KK0203//Japan Society for Promotion of Sciences projects/ ; 21-19664S//Czech Science Foundation/ ; //National Institute for Environmental Studies/ ; //Ministry of Education, Culture, Sports, Science and Technology/ ; //National Institute of Genetics/ ; //University of Tsukuba/ ; },
mesh = {*Organelles/genetics ; Phylogeny ; DNA-Directed DNA Polymerase/genetics ; Plastids/genetics ; Mitochondria ; *Cyanobacteria/genetics ; Symbiosis ; },
abstract = {DNA polymerases synthesize DNA from deoxyribonucleotides in a semiconservative manner and serve as the core of DNA replication and repair machinery. In eukaryotic cells, there are 2 genome-containing organelles, mitochondria, and plastids, which were derived from an alphaproteobacterium and a cyanobacterium, respectively. Except for rare cases of genome-lacking mitochondria and plastids, both organelles must be served by nucleus-encoded DNA polymerases that localize and work in them to maintain their genomes. The evolution of organellar DNA polymerases has yet to be fully understood because of 2 unsettled issues. First, the diversity of organellar DNA polymerases has not been elucidated in the full spectrum of eukaryotes. Second, it is unclear when the DNA polymerases that were used originally in the endosymbiotic bacteria giving rise to mitochondria and plastids were discarded, as the organellar DNA polymerases known to date show no phylogenetic affinity to those of the extant alphaproteobacteria or cyanobacteria. In this study, we identified from diverse eukaryotes 134 family A DNA polymerase sequences, which were classified into 10 novel types, and explored their evolutionary origins. The subcellular localizations of selected DNA polymerases were further examined experimentally. The results presented here suggest that the diversity of organellar DNA polymerases has been shaped by multiple transfers of the PolI gene from phylogenetically broad bacteria, and their occurrence in eukaryotes was additionally impacted by secondary plastid endosymbioses. Finally, we propose that the last eukaryotic common ancestor may have possessed 2 mitochondrial DNA polymerases, POP, and a candidate of the direct descendant of the proto-mitochondrial DNA polymerase I, rdxPolA, identified in this study.},
}
@article {pmid38267392,
year = {2024},
author = {Zhang, J and Lu, T and Song, Y and Rocha, UND and Liu, J and Nikolausz, M and Wei, Y and Richnow, HH},
title = {Viral Communities Contribute More to the Lysis of Antibiotic-Resistant Bacteria than the Transduction of Antibiotic Resistance Genes in Anaerobic Digestion Revealed by Metagenomics.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {5},
pages = {2346-2359},
pmid = {38267392},
issn = {1520-5851},
mesh = {*Anti-Bacterial Agents/pharmacology ; Anaerobiosis ; Angiotensin Receptor Antagonists ; Genes, Bacterial ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; *Bacteriophages/genetics ; Metagenomics ; },
abstract = {Ecological role of the viral community on the fate of antibiotic resistance genes (ARGs) (reduction vs proliferation) remains unclear in anaerobic digestion (AD). Metagenomics revealed a dominance of Siphoviridae and Podoviridae among 13,895 identified viral operational taxonomic units (vOTUs) within AD, and only 21 of the vOTUs carried ARGs, which only accounted for 0.57 ± 0.43% of AD antibiotic resistome. Conversely, ARGs locating on plasmids and integrative and conjugative elements accounted for above 61.0%, indicating a substantial potential for conjugation in driving horizontal gene transfer of ARGs within AD. Virus-host prediction based on CRISPR spacer, tRNA, and homology matches indicated that most viruses (80.2%) could not infect across genera. Among 480 high-quality metagenome assembly genomes, 95 carried ARGs and were considered as putative antibiotic-resistant bacteria (pARB). Furthermore, lytic phages of 66 pARBs were identified and devoid of ARGs, and virus/host abundance ratios with an average value of 71.7 indicated extensive viral activity and lysis. The infectivity of lytic phage was also elucidated through laboratory experiments concerning changes of the phage-to-host ratio, pH, and temperature. Although metagenomic evidence for dissemination of ARGs by phage transduction was found, the higher proportion of lytic phages infecting pARBs suggested that the viral community played a greater role in reducing ARB numbers than spreading ARGs in AD.},
}
@article {pmid38266895,
year = {2024},
author = {Zhang, C and You, Z and Li, S and Zhang, C and Zhao, Z and Zhou, D},
title = {NO3[-] as an electron acceptor elevates antibiotic resistance gene and human bacterial pathogen risks in managed aquifer recharge (MAR): A comparison with O2.},
journal = {Environmental research},
volume = {248},
number = {},
pages = {118277},
doi = {10.1016/j.envres.2024.118277},
pmid = {38266895},
issn = {1096-0953},
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Electrons ; Bacteria ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Oxygen ; *Groundwater/microbiology ; },
abstract = {Managed aquifer recharge (MAR) stands out as a promising strategy for ensuring water resource sustainability. This study delves into the comparative impact of nitrate (NO3[-]) and oxygen (O2) as electron acceptors in MAR on water quality and safety. Notably, NO3[-], acting as an electron acceptor, has the potential to enrich denitrifying bacteria, serving as hosts for antibiotic resistance genes (ARGs) and enriching human bacterial pathogens (HBPs) compared to O2. However, a direct comparison between NO3[-] and O2 remains unexplored. This study assessed risks in MAR effluent induced by NO3[-] and O2, alongside the presence of the typical refractory antibiotic sulfamethoxazole. Key findings reveal that NO3[-] as an electron acceptor resulted in a 2 times reduction in dissolved organic carbon content compared to O2, primarily due to a decrease in soluble microbial product production. Furthermore, NO3[-] significantly enriched denitrifying bacteria, the primary hosts of major ARGs, by 747%, resulting in a 66% increase in the overall abundance of ARGs in the effluent of NO3[-] MAR compared to O2. This escalation was predominantly attributed to horizontal gene transfer mechanisms, as evidenced by a notable 78% increase in the relative abundance of mobile ARGs, alongside a minor 27% rise in chromosomal ARGs. Additionally, the numerous denitrifying bacteria enriched under NO3[-] influence also belong to the HBP category, resulting in a significant 114% increase in the abundance of all HBPs. The co-occurrence of ARGs and HBPs was also observed to intensify under NO3[-] influence. Thus, NO3[-] as an electron acceptor in MAR elevates ARG and HBP risks compared to O2, potentially compromising groundwater quality and safety.},
}
@article {pmid38263430,
year = {2024},
author = {Keeling, PJ},
title = {Horizontal gene transfer in eukaryotes: aligning theory with data.},
journal = {Nature reviews. Genetics},
volume = {25},
number = {6},
pages = {416-430},
pmid = {38263430},
issn = {1471-0064},
mesh = {*Gene Transfer, Horizontal ; Eukaryota/genetics ; Symbiosis/genetics ; Eukaryotic Cells/metabolism ; Animals ; Phagocytosis/genetics ; Archaea/genetics ; Evolution, Molecular ; Models, Genetic ; },
abstract = {Horizontal gene transfer (HGT), or lateral gene transfer, is the non-sexual movement of genetic information between genomes. It has played a pronounced part in bacterial and archaeal evolution, but its role in eukaryotes is less clear. Behaviours unique to eukaryotic cells - phagocytosis and endosymbiosis - have been proposed to increase the frequency of HGT, but nuclear genomes encode fewer HGTs than bacteria and archaea. Here, I review the existing theory in the context of the growing body of data on HGT in eukaryotes, which suggests that any increased chance of acquiring new genes through phagocytosis and endosymbiosis is offset by a reduced need for these genes in eukaryotes, because selection in most eukaryotes operates on variation not readily generated by HGT.},
}
@article {pmid38262510,
year = {2024},
author = {Sajjad, W and Ilahi, N and Haq, A and Shang, Z and Nabi, G and Rafiq, M and Bahadur, A and Banerjee, A and Kang, S},
title = {Bacteria populating freshly appeared supraglacial lake possess metals and antibiotic-resistant genes.},
journal = {Environmental research},
volume = {247},
number = {},
pages = {118288},
doi = {10.1016/j.envres.2024.118288},
pmid = {38262510},
issn = {1096-0953},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Lakes/microbiology ; Metals ; },
abstract = {Antibiotic resistance (AR) has been extensively studied in natural habitats and clinical applications. AR is mainly reported with the use and misuse of antibiotics; however, little is known about its presence in antibiotic-free remote supraglacial lake environments. This study evaluated bacterial strains isolated from supraglacial lake debris and meltwater in Dook Pal Glacier, northern Pakistan, for antibiotic-resistant genes (ARGs) and metal-tolerant genes (MTGs) using conventional PCR. Several distinct ARGs were reported in the bacterial strains isolated from lake debris (92.5%) and meltwater (100%). In lake debris, 57.5% of isolates harbored the blaTEM gene, whereas 58.3% of isolates in meltwater possessed blaTEM and qnrA each. Among the ARGs, qnrA was dominant in debris isolates (19%), whereas in meltwater isolates, qnrA (15.2%) and blaTEM (15.2%) were dominant. ARGs were widely distributed among the bacterial isolates and different bacteria shared similar types of ARGs. Relatively greater number of ARGs were reported in Gram-negative bacterial strains. In addition, 92.5% of bacterial isolates from lake debris and 83.3% of isolates from meltwater harbored MTGs. Gene copA was dominant in meltwater isolates (50%), whereas czcA was greater in debris bacterial isolates (45%). Among the MTGs, czcA (18.75%) was dominant in debris strains, whereas copA (26.0%) was greater in meltwater isolates. This presents the co-occurrence and co-selection of MTGs and ARGs in a freshly appeared supraglacial lake. The same ARGs and MTGs were present in different bacteria, exhibiting horizontal gene transfer (HGT). Both positive and negative correlations were determined between ARGs and MTGs. The research provides insights into the existence of MTGs and ARGs in bacterial strains isolated from remote supraglacial lake environments, signifying the need for a more detailed study of bacteria harboring ARGs and MTGs in supraglacial lakes.},
}
@article {pmid38261993,
year = {2024},
author = {Teyssonniere, EM and Shichino, Y and Mito, M and Friedrich, A and Iwasaki, S and Schacherer, J},
title = {Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast.},
journal = {Nucleic acids research},
volume = {52},
number = {5},
pages = {2434-2445},
pmid = {38261993},
issn = {1362-4962},
support = {S10 OD018174/OD/NIH HHS/United States ; S10 OD018174/CD/ODCDC CDC HHS/United States ; 772505/ERC_/European Research Council/International ; },
mesh = {Humans ; *Saccharomyces cerevisiae/genetics ; *Transcriptome ; Gene Expression Profiling ; Ribosomes/genetics ; Genetic Background ; Genetic Variation ; },
abstract = {Gene expression is known to vary among individuals, and this variability can impact the phenotypic diversity observed in natural populations. While the transcriptome and proteome have been extensively studied, little is known about the translation process itself. Here, we therefore performed ribosome and transcriptomic profiling on a genetically and ecologically diverse set of natural isolates of the Saccharomyces cerevisiae yeast. Interestingly, we found that the Euclidean distances between each profile and the expression fold changes in each pairwise isolate comparison were higher at the transcriptomic level. This observation clearly indicates that the transcriptional variation observed in the different isolates is buffered through a phenomenon known as post-transcriptional buffering at the translation level. Furthermore, this phenomenon seemed to have a specific signature by preferentially affecting essential genes as well as genes involved in complex-forming proteins, and low transcribed genes. We also explored the translation of the S. cerevisiae pangenome and found that the accessory genes related to introgression events displayed similar transcription and translation levels as the core genome. By contrast, genes acquired through horizontal gene transfer events tended to be less efficiently translated. Together, our results highlight both the extent and signature of the post-transcriptional buffering.},
}
@article {pmid38261836,
year = {2024},
author = {Kaur, J and Kaur, J},
title = {Comparative genomics of seven genomes of genus Idiomarina reveals important halo adaptations and genes for stress response.},
journal = {3 Biotech},
volume = {14},
number = {2},
pages = {40},
pmid = {38261836},
issn = {2190-572X},
abstract = {UNLABELLED: The genus Idiomarina consists of halophilic and/or haloalkaliphilic organisms. We compared the complete genomes of seven strains of the genus Idiomarina to investigate its adaptation to saline environment. A total of 1,313 core genes related to salinity tolerance, stress response, antibiotic resistance genes, virulence factors, and drug targets were found. Comparative genomics revealed various genes involved in halo adaptations of these organisms, including transporters and influx or efflux systems for elements such as Fe, Cu, Zn, Pb, and Cd. In agreement with their isolation sources (such as hydrothermal vents and marine sediments) and environments abundant in heavy metals, various resistance proteins and transporters associated with metal tolerance were also identified. These included copper resistance proteins, zinc uptake transcriptional repressor Zur, MerC domain-containing protein, Cd(II)/Pb(II)-responsive transcriptional regulator, Co/Zn/Cd efflux system protein, and mercuric transporter. Interestingly, we observed that the carbohydrate metabolism pathways were incomplete in all the strains and transporters used for absorption of small sugars were also not found in them. Also, the presence of higher proportion of genes involved in protein metabolism than carbohydrate metabolism indicates that proteinaceous substrates act as the major food substrates for these bacterial strains than carbohydrates. Genomic islands were detected in some species, highlighting the role of horizontal gene transfer for acquisition in novel genes. Genomic rearrangements in terms of partially palindromic regions were detected in all strains. To our knowledge, this is the first comprehensive comparative genomics study among the genus Idiomarina revealing unique genomic features within bacterial species inhabiting different ecological niches.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-023-03887-3.},
}
@article {pmid38259350,
year = {2024},
author = {Allman, ES and Baños, H and Garrote-Lopez, M and Rhodes, JA},
title = {IDENTIFIABILITY OF LEVEL-1 SPECIES NETWORKS FROM GENE TREE QUARTETS.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {38259350},
issn = {2331-8422},
support = {P20 GM103395/GM/NIGMS NIH HHS/United States ; },
abstract = {When hybridization or other forms of lateral gene transfer have occurred, evolutionary relationships of species are better represented by phylogenetic networks than by trees. While inference of such networks remains challenging, several recently proposed methods are based on quartet concordance factors - the probabilities that a tree relating a gene sampled from the species displays the possible 4-taxon relationships. Building on earlier results, we investigate what level-1 network features are identifiable from concordance factors under the network multispecies coalescent model. We obtain results on both topological features of the network, and numerical parameters, uncovering a number of failures of identifiability related to 3-cycles in the network.},
}
@article {pmid38257923,
year = {2024},
author = {Monecke, S and Braun, SD and Collatz, M and Diezel, C and Müller, E and Reinicke, M and Cabal Rosel, A and Feßler, AT and Hanke, D and Loncaric, I and Schwarz, S and Cortez de Jäckel, S and Ruppitsch, W and Gavier-Widén, D and Hotzel, H and Ehricht, R},
title = {Molecular Characterization of Chimeric Staphylococcus aureus Strains from Waterfowl.},
journal = {Microorganisms},
volume = {12},
number = {1},
pages = {},
pmid = {38257923},
issn = {2076-2607},
support = {13GW0456//Federal Ministry of Education and Research/ ; },
abstract = {Staphylococcus aureus is a versatile pathogen that does not only occur in humans but also in various wild and domestic animals, including several avian species. When characterizing S. aureus isolates from waterfowl, isolates were identified as atypical CC133 by DNA microarray analysis. They differed from previously sequenced CC133 strains in the presence of the collagen adhesin gene cna; some also showed a different capsule type and a deviant spa type. Thus, they were subjected to whole-genome sequencing. This revealed multiple insertions of large regions of DNA from other S. aureus lineages into a CC133-derived backbone genome. Three distinct strains were identified based on the size and extent of these inserts. One strain comprised two small inserts of foreign DNA up- and downstream of oriC; one of about 7000 nt or 0.25% originated from CC692 and the other, at ca. 38,000 nt or 1.3% slightly larger one was of CC522 provenance. The second strain carried a larger CC692 insert (nearly 257,000 nt or 10% of the strain's genome), and its CC522-derived insert was also larger, at about 53,500 nt or 2% of the genome). The third strain carried an identical CC692-derived region (in which the same mutations were observed as in the second strain), but it had a considerably larger CC522-like insertion of about 167,000 nt or 5.9% of the genome. Both isolates of the first, and two out of four isolates of the second strain also harbored a hemolysin-beta-integrating prophage carrying "bird-specific" virulence factors, ornithine cyclodeaminase D0K6J8 and a putative protease D0K6J9. Furthermore, isolates had two different variants of SCC elements that lacked mecA/mecC genes. These findings highlight the role of horizontal gene transfer in the evolution of S. aureus facilitated by SCC elements, by phages, and by a yet undescribed mechanism for large-scale exchange of core genomic DNA.},
}
@article {pmid38253827,
year = {2024},
author = {Musiyiwa, K and Simbanegavi, TT and Marumure, J and Makuvara, Z and Chaukura, N and Gwenzi, W},
title = {The soil-microbe-plant resistome: A focus on the source-pathway-receptor continuum.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {9},
pages = {12666-12682},
pmid = {38253827},
issn = {1614-7499},
mesh = {Humans ; *Genes, Bacterial ; *Soil/chemistry ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents ; Soil Microbiology ; },
abstract = {The One World, One Health concept implies that antibiotic resistance (AR) in the soil-microbe-plant resistome is intricately linked to the human resistome. However, the literature is mainly confined to sources and types of AR in soils or microbes, but comprehensive reviews tracking AR in the soil-microbe-plant resistome are limited. The present review applies the source-pathway-receptor concept to understand the sources, behaviour, and health hazards of the soil-microbe-plant resistome. The results showed that the soil-microbe-plant system harbours various antibiotic-resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and mobile genetic elements (MGEs). Anthropogenic sources and drivers include soil application of solid waste, wastewater, biosolids, and industrial waste. Water-, wind-, and human-driven processes and horizontal gene transfer circulate AR in the soil-microbe-plant resistome. The AR in bulk soil, soil components that include soil microorganisms, soil meso- and macro-organisms, and possible mechanisms of AR transfer to soil components and ultimately to plants are discussed. The health risks of the soil-microbe-plant resistome are less studied, but potential impacts include (1) the transfer of AR to previously susceptible organisms and other resistomes, including the human resistome. Overall, the study tracks the behaviour and health risks of AR in the soil-plant system. Future research should focus on (1) ecological risks of AR at different levels of biological organization, (2) partitioning of AR among various phases of the soil-plant system, (3) physico-chemical parameters controlling the fate of AR, and (4) increasing research from low-income regions particularly Africa as most of the available literature is from developed countries.},
}
@article {pmid38253607,
year = {2024},
author = {Lehmkuhl, J and Schneider, JS and Werth, KLV and Scherff, N and Mellmann, A and Kampmeier, S},
title = {Role of membrane vesicles in the transmission of vancomycin resistance in Enterococcus faecium.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {1895},
pmid = {38253607},
issn = {2045-2322},
mesh = {*Enterococcus faecium/genetics ; Vancomycin Resistance/genetics ; Vancomycin/pharmacology ; *Vancomycin-Resistant Enterococci/genetics ; Membranes ; },
abstract = {Clonal transmission and horizontal gene transfer (HGT) contribute to the spread of vancomycin-resistant enterococci (VRE) in global healthcare. Our study investigated vesiduction, a HGT mechanism via membrane vesicles (MVs), for vanA and vanB genes that determine vancomycin resistance. We isolated MVs for VRE of different sequence types (STs) and analysed them by nanoparticle tracking analysis. Selected MV samples were subjected to DNA sequence analysis. In resistance transfer experiments, vancomycin-susceptible enterococci were exposed to MVs and bacterial supernatants of VRE. Compared to bacteria grown in lysogeny broth (MVs/LB), cultivation under vancomycin stress (MVs/VAN) resulted in increased particle concentrations of up to 139-fold (ST80). As a key finding, we could show that VRE isolates of ST80 and ST117 produced remarkably more vesicles at subinhibitory antibiotic concentrations (approx. 9.2 × 10[11] particles/ml for ST80 and 2.4 × 10[11] particles/ml for ST117) than enterococci of other STs (range between 1.8 × 10[10] and 5.3 × 10[10] particles/ml). In those MV samples, the respective resistance genes vanA and vanB were completely verifiable using sequence analysis. Nevertheless, no vancomycin resistance transfer via MVs to vancomycin-susceptible Enterococcus faecium was phenotypically detectable. However, our results outline the potential of future research on ST-specific MV properties, promising new insights into VRE mechanisms.},
}
@article {pmid38251876,
year = {2024},
author = {Wang, Y and Unnikrishnan, M and Ramsey, B and El Andlosy, D and Keeley, AT and Murphy, CJ and Gruebele, M},
title = {In-Cell Association of a Bioorthogonal Tubulin.},
journal = {Biomacromolecules},
volume = {25},
number = {2},
pages = {1282-1290},
doi = {10.1021/acs.biomac.3c01253},
pmid = {38251876},
issn = {1526-4602},
mesh = {Humans ; *Tubulin/chemistry ; *Bacterial Proteins/chemistry ; Microtubules/chemistry ; },
abstract = {Studies of proteins from one organism in another organism's cells have shown that such exogenous proteins stick more, pointing toward coevolution of the cytoplasm and protein surface to minimize stickiness. Here we flip this question around by asking whether exogenous proteins can assemble efficiently into their target complexes in a non-native cytoplasm. We use as our model system the assembly of BtubA and BtubB from Prosthecobacter hosted in human U-2 OS cells. BtubA and B evolved from eukaryotic tubulins after horizontal gene transfer, but they have low surface sequence identity with the homologous human tubulins and do not respond to tubulin drugs such as nocodazole. In U-2 OS cells, BtubA and B assemble efficiently into dimers compared to in vitro, and the wild-type BtubA and B proteins subsequently are able to form microtubules as well. We find that generic crowding effects (Ficoll 70 in vitro) contribute significantly to efficient dimer assembly when compared to sticking interactions (U-2 OS cell lysate in vitro), consistent with the notion that a generic mechanism such as crowding can be effective at driving assembly of exogenous proteins, even when protein-cytoplasm quinary structure and sticking have been modified in a non-native cytoplasm. A simple Monte Carlo model of in vitro and in-cell interactions, treating BtubA and B as sticky dipoles in a matrix of sticky or nonsticky crowders, rationalizes all the experimental trends with two adjustable parameters and reveals nucleation as the likely mechanism for the time-scale separation between dimer- and tubule formation in-cell and in vitro.},
}
@article {pmid38251331,
year = {2023},
author = {Vasconcelos, PC and Leite, EL and Saraiva, MMS and Ferrari, RG and Cibulski, SP and Silva, NMV and Freitas Neto, OC and Givisiez, PEN and Vieira, RFC and Oliveira, CJB},
title = {Genomic Analysis of a Community-Acquired Methicillin-Resistant Staphylococcus aureus Sequence Type 1 Associated with Caprine Mastitis.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {1},
pages = {},
pmid = {38251331},
issn = {2076-0817},
support = {Finance code 001//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; CT-INFRA//Financiadora de Estudos e Projetos/ ; 313678/2020-0//Conselho Nacional de Pesquisa e P&#xf3;s-gradua&#xe7;&#xe3;o em Direito/ ; },
mesh = {*Methicillin-Resistant Staphylococcus aureus/genetics/drug effects/isolation &amp; purification ; Animals ; *Goats/microbiology ; *Mastitis/microbiology/epidemiology ; *Staphylococcal Infections/microbiology/epidemiology ; Female ; *Goat Diseases/microbiology/epidemiology/transmission ; *Phylogeny ; *Community-Acquired Infections/microbiology/epidemiology ; Brazil/epidemiology ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Genome, Bacterial/genetics ; Milk/microbiology ; Whole Genome Sequencing ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Genomics ; Polymorphism, Single Nucleotide/genetics ; },
abstract = {This study aimed to investigate the genomic and epidemiological features of a methicillin-resistant Staphylococcus aureus sequence type 1 (MRSA ST1) strain associated with caprine subclinical mastitis. An S. aureus strain was isolated from goat's milk with subclinical mastitis in Paraiba, Northeastern Brazil, by means of aseptic procedures and tested for antimicrobial susceptibility using the disk-diffusion method. Whole genome sequencing was performed using the Illumina MiSeq platform. After genome assembly and annotation, in silico analyses, including multilocus sequence typing (MLST), antimicrobial resistance and stress-response genes, virulence factors, and plasmids detection were performed. A comparative SNP-based phylogenetic analysis was performed using publicly available MRSA genomes. The strain showed phenotypic resistance to cefoxitin, penicillin, and tetracycline and was identified as sequence type 1 (ST1) and spa type 128 (t128). It harbored the SCCmec type IVa (2B), as well as the lukF-PV and lukS-PV genes. The strain was phylogenetically related to six community-acquired MRSA isolates (CA-MRSA) strains associated with human clinical disease in North America, Europe, and Australia. This is the first report of a CA-MRSA strain associated with milk in the Americas. The structural and epidemiologic features reported in the MRSA ST1 carrying a mecA-SCCmec type IVa suggest highly complex mechanisms of horizontal gene transfer in MRSA. The SNP-based phylogenetic analysis suggests a zooanthroponotic transmission, i.e., a strain of human origin.},
}
@article {pmid38240570,
year = {2024},
author = {Kogay, R and Zhaxybayeva, O},
title = {Co-evolution of gene transfer agents and their alphaproteobacterial hosts.},
journal = {Journal of bacteriology},
volume = {206},
number = {2},
pages = {e0039823},
pmid = {38240570},
issn = {1098-5530},
mesh = {Humans ; *Bacteria/genetics ; Archaea/genetics ; DNA ; *Alphaproteobacteria/genetics ; Gene Transfer, Horizontal ; },
abstract = {Gene transfer agents (GTAs) are enigmatic elements that resemble small viruses and are known to be produced during nutritional stress by some bacteria and archaea. The production of GTAs is regulated by quorum sensing, under which a small fraction of the population acts as GTA producers, while the rest becomes GTA recipients. In contrast to canonical viruses, GTAs cannot propagate themselves because they package pieces of the producing cell's genome. In alphaproteobacteria, GTAs are mostly vertically inherited and reside in their hosts' genomes for hundreds of millions of years. While GTAs' ability to transfer genetic material within a population and their long-term preservation suggest an increased fitness of GTA-producing microbes, the associated benefits and type of selection that maintains GTAs are poorly understood. By comparing rates of evolutionary change in GTA genes to the rates in gene families abundantly present across 293 alphaproteobacterial genomes, we detected 59 gene families that likely co-evolve with GTA genes. These gene families are predominantly involved in stress response, DNA repair, and biofilm formation. We hypothesize that biofilm formation enables the physical proximity of GTA-producing cells, limiting GTA-derived benefits only to a group of closely related cells. We further conjecture that the population structure of biofilm-forming sub-populations ensures that the trait of GTA production is maintained despite the inevitable rise of "cheating" genotypes. Because release of GTA particles kills the producing cell, maintenance of GTAs is an exciting example of social evolution in a microbial population.IMPORTANCEGene transfer agents (GTAs) are viruses domesticated by some archaea and bacteria as vehicles for carrying pieces of the host genome. Produced under certain environmental conditions, GTA particles can deliver DNA to neighboring, closely related cells. The function of GTAs remains uncertain. While making GTAs is suicidal for a cell, GTA-encoding genes are widespread in genomes of alphaproteobacteria. Such GTA persistence implies functional benefits but raises questions about how selection maintains this lethal trait. By showing that GTA genes co-evolve with genes involved in stress response, DNA repair, and biofilm formation, we provide support for the hypothesis that GTAs facilitate DNA exchange during the stress conditions and present a model for how GTAs persist in biofilm-forming bacterial populations despite being lethal.},
}
@article {pmid38238664,
year = {2024},
author = {Peng, M and Lin, W and Zhou, A and Jiang, Z and Zhou, F and Wang, Z},
title = {High genetic diversity and different type VI secretion systems in Enterobacter species revealed by comparative genomics analysis.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {26},
pmid = {38238664},
issn = {1471-2180},
support = {32200094//National Natural Science Foundation of China/ ; PT012201//Hubei Key Laboratory of Biological Resources Protection and Utilization (Hubei Minzu University)/ ; 2022CFB674//Natural Science Foundation of Hubei Province/ ; },
mesh = {Humans ; *Type VI Secretion Systems/genetics ; Enterobacter/genetics ; Bacterial Proteins/genetics ; Genomics ; Virulence Factors/genetics ; Genetic Variation ; },
abstract = {The human-pathogenic Enterobacter species are widely distributed in diverse environmental conditions, however, the understanding of the virulence factors and genetic variations within the genus is very limited. In this study, we performed comparative genomics analysis of 49 strains originated from diverse niches and belonged to eight Enterobacter species, in order to further understand the mechanism of adaption to the environment in Enterobacter. The results showed that they had an open pan-genome and high genomic diversity which allowed adaptation to distinctive ecological niches. We found the number of secretion systems was the highest among various virulence factors in these Enterobacter strains. Three types of T6SS gene clusters including T6SS-A, T6SS-B and T6SS-C were detected in most Enterobacter strains. T6SS-A and T6SS-B shared 13 specific core genes, but they had different gene structures, suggesting they probably have different biological functions. Notably, T6SS-C was restricted to E. cancerogenus. We detected a T6SS gene cluster, highly similar to T6SS-C (91.2%), in the remote related Citrobacter rodenitum, suggesting that this unique gene cluster was probably acquired by horizontal gene transfer. The genomes of Enterobacter strains possess high genetic diversity, limited number of conserved core genes, and multiple copies of T6SS gene clusters with differentiated structures, suggesting that the origins of T6SS were not by duplication instead by independent acquisition. These findings provide valuable information for better understanding of the functional features of Enterobacter species and their evolutionary relationships.},
}
@article {pmid38237429,
year = {2024},
author = {Bernabeu, M and Cabello-Yeves, E and Flores, E and Samarra, A and Kimberley Summers, J and Marina, A and Collado, MC},
title = {Role of vertical and horizontal microbial transmission of antimicrobial resistance genes in early life: insights from maternal-infant dyads.},
journal = {Current opinion in microbiology},
volume = {77},
number = {},
pages = {102424},
doi = {10.1016/j.mib.2023.102424},
pmid = {38237429},
issn = {1879-0364},
mesh = {Infant ; Humans ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; Gene Transfer, Horizontal ; },
abstract = {Early life represents a critical window for metabolic, cognitive and immune system development, which is influenced by the maternal microbiome as well as the infant gut microbiome. Antibiotic exposure, mode of delivery and breastfeeding practices modulate the gut microbiome and the reservoir of antibiotic resistance genes (ARGs). Vertical and horizontal microbial gene transfer during early life and the mechanisms behind these transfers are being uncovered. In this review, we aim to provide an overview of the current knowledge on the transfer of antibiotic resistance in the mother-infant dyad through vertical and horizontal transmission and to highlight the main gaps and challenges in this area.},
}
@article {pmid38237397,
year = {2024},
author = {Yu, Z and Wang, Q and Pinilla-Redondo, R and Madsen, JS and Clasen, KAD and Ananbeh, H and Olesen, AK and Gong, Z and Yang, N and Dechesne, A and Smets, B and Nesme, J and Sørensen, SJ},
title = {Horizontal transmission of a multidrug-resistant IncN plasmid isolated from urban wastewater.},
journal = {Ecotoxicology and environmental safety},
volume = {271},
number = {},
pages = {115971},
doi = {10.1016/j.ecoenv.2024.115971},
pmid = {38237397},
issn = {1090-2414},
mesh = {*Wastewater ; *Anti-Bacterial Agents/analysis ; Plasmids/genetics ; Drug Resistance, Microbial/genetics ; Water ; Genes, Bacterial ; },
abstract = {Wastewater treatment plants (WWTPs) are considered reservoirs of antibiotic resistance genes (ARGs). Given that plasmid-mediated horizontal gene transfer plays a critical role in disseminating ARGs in the environment, it is important to inspect the transfer potential of transmissible plasmids to have a better understanding of whether these mobile ARGs can be hosted by opportunistic pathogens and should be included in One Health's considerations. In this study, we used a fluorescent-reporter-gene based exogenous isolation approach to capture extended-spectrum beta-lactamases encoding mobile determinants from sewer microbiome samples that enter an urban water system (UWS) in Denmark. After screening and sequencing, we isolated a ∼73 Kbp IncN plasmid (pDK_DARWIN) that harboured and expressed multiple ARGs. Using a dual fluorescent reporter gene system, we showed that this plasmid can transfer into resident urban water communities. We demonstrated the transfer of pDK_DARWIN to microbiome members of both the sewer (in the upstream UWS compartment) and wastewater treatment (in the downstream UWS compartment) microbiomes. Sequence similarity search across curated plasmid repositories revealed that pDK_DARWIN derives from an IncN backbone harboured by environmental and nosocomial Enterobacterial isolates. Furthermore, we searched for pDK_DARWIN sequence matches in UWS metagenomes from three countries, revealing that this plasmid can be detected in all of them, with a higher relative abundance in hospital sewers compared to residential sewers. Overall, this study demonstrates that this IncN plasmid is prevalent across Europe and an efficient vector capable of disseminating multiple ARGs in the urban water systems.},
}
@article {pmid38234769,
year = {2024},
author = {Coelho, MA and David-Palma, M and Shea, T and Bowers, K and McGinley-Smith, S and Mohammad, AW and Gnirke, A and Yurkov, AM and Nowrousian, M and Sun, S and Cuomo, CA and Heitman, J},
title = {Comparative genomics of Cryptococcus and Kwoniella reveals pathogenesis evolution and contrasting karyotype dynamics via intercentromeric recombination or chromosome fusion.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38234769},
issn = {2692-8205},
support = {R37 AI039115/AI/NIAID NIH HHS/United States ; U54 HG003067/HG/NHGRI NIH HHS/United States ; R01 AI039115/AI/NIAID NIH HHS/United States ; R01 AI050113/AI/NIAID NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; },
abstract = {A large-scale comparative genomic analysis was conducted for the global human fungal pathogens within the Cryptococcus genus, compared to non-pathogenic Cryptococcus species, and related species from the sister genus Kwoniella. Chromosome-level genome assemblies were generated for multiple species of both genera, resulting in a dataset encompassing virtually all of their known diversity. Although Cryptococcus and Kwoniella have comparable genome sizes (about 19.2 and 22.9 Mb) and similar gene content, hinting at pre-adaptive pathogenic potential, our analysis found evidence in pathogenic Cryptococcus species of specific examples of gene gain (via horizontal gene transfer) and gene loss, which might represent evolutionary signatures of pathogenic development. Genome analysis also revealed a significant variation in chromosome number and structure between the two genera. By combining synteny analysis and experimental centromere validation, we found that most Cryptococcus species have 14 chromosomes, whereas most Kwoniella species have fewer (11, 8, 5 or even as few as 3). Reduced chromosome number in Kwoniella is associated with formation of giant chromosomes (up to 18 Mb) through repeated chromosome fusion events, each marked by a pericentric inversion and centromere loss. While similar chromosome inversion-fusion patterns were observed in all Kwoniella species with fewer than 14 chromosomes, no such pattern was detected in Cryptococcus. Instead, Cryptococcus species with less than 14 chromosomes, underwent chromosome reductions primarily through rearrangements associated with the loss of repeat-rich centromeres. Additionally, Cryptococcus genomes exhibited frequent interchromosomal translocations, including intercentromeric recombination facilitated by transposons shared between centromeres. Taken together, our findings advance our understanding of genomic changes possibly associated with pathogenicity in Cryptococcus and provide a foundation to elucidate mechanisms of centromere loss and chromosome fusion driving distinct karyotypes in closely related fungal species, including prominent global human pathogens.},
}
@article {pmid38229742,
year = {2024},
author = {Ward, KT and Williams, APL and Blair, CA and Chatterjee, AM and Karthikeyan, A and Roper, AS and Kellogg, CN and Steed, PR and Wolfe, AL},
title = {Amine Basicity of Quinoline ATP Synthase Inhibitors Drives Antibacterial Activity against Pseudomonas aeruginosa.},
journal = {ACS medicinal chemistry letters},
volume = {15},
number = {1},
pages = {149-155},
pmid = {38229742},
issn = {1948-5875},
support = {R15 AI163474/AI/NIAID NIH HHS/United States ; },
abstract = {Pseudomonas aeruginosa (PA), a Gram-negative pathogen, is a common cause of nosocomial infections, especially in immunocompromised and cystic fibrosis patients. PA is intrinsically resistant to many currently prescribed antibiotics due to its tightly packed, anionic lipopolysaccharide outer membrane, efflux pumps, and ability to form biofilms. PA can acquire additional resistance through mutation and horizontal gene transfer. PA ATP synthase is an attractive target for antibiotic development because it is essential for cell survival even under fermentation conditions. Previously, we developed two lead quinoline compounds that were capable of selectively inhibiting PA ATP synthase and acting as antibacterial agents against multidrug-resistant PA. Herein we conduct a structure-activity relationship analysis of the lead compounds through the synthesis and evaluation of 18 quinoline derivatives. These compounds function as new antibacterial agents while providing insight into the balance of physical properties needed to promote cellular entry while maintaining PA ATP synthase inhibition.},
}
@article {pmid38226780,
year = {2024},
author = {Tokuda, M and Shintani, M},
title = {Microbial evolution through horizontal gene transfer by mobile genetic elements.},
journal = {Microbial biotechnology},
volume = {17},
number = {1},
pages = {e14408},
pmid = {38226780},
issn = {1751-7915},
support = {JP19H02869//Japan Society for the Promotion of Science/ ; JP19H05686//Japan Society for the Promotion of Science/ ; JP22J12723//Japan Society for the Promotion of Science/ ; JP23H02124//Japan Society for the Promotion of Science/ ; L-2023-1-002//Institute for Fermentation, Osaka/ ; //National University Corporation Shizuoka University, Japan/ ; 2023-RIGST-23104//Institute of Green Science and Technology Fund for Research Project Support/ ; //Ohsumi Frontier Science Foundation/ ; JP21wm0225008//Japan Agency for Medical Research and Development/ ; JP21wm0325022//Japan Agency for Medical Research and Development/ ; },
mesh = {*Interspersed Repetitive Sequences ; Gene Transfer, Horizontal ; Plasmids/genetics ; Bacteria/genetics ; *Bacteriophages/genetics ; Anti-Bacterial Agents ; },
abstract = {Mobile genetic elements (MGEs) are crucial for horizontal gene transfer (HGT) in bacteria and facilitate their rapid evolution and adaptation. MGEs include plasmids, integrative and conjugative elements, transposons, insertion sequences and bacteriophages. Notably, the spread of antimicrobial resistance genes (ARGs), which poses a serious threat to public health, is primarily attributable to HGT through MGEs. This mini-review aims to provide an overview of the mechanisms by which MGEs mediate HGT in microbes. Specifically, the behaviour of conjugative plasmids in different environments and conditions was discussed, and recent methodologies for tracing the dynamics of MGEs were summarised. A comprehensive understanding of the mechanisms underlying HGT and the role of MGEs in bacterial evolution and adaptation is important to develop strategies to combat the spread of ARGs.},
}
@article {pmid38220083,
year = {2024},
author = {Ormsby, MJ and Woodford, L and Quilliam, RS},
title = {Can plastic pollution drive the emergence and dissemination of novel zoonotic diseases?.},
journal = {Environmental research},
volume = {246},
number = {},
pages = {118172},
doi = {10.1016/j.envres.2024.118172},
pmid = {38220083},
issn = {1096-0953},
mesh = {Animals ; Humans ; *Plastics ; *Environmental Pollution ; Zoonoses/epidemiology ; Agriculture ; Biofilms ; },
abstract = {As the volume of plastic in the environment increases, so too does human interactions with plastic pollution. Similarly, domestic, feral, and wild animals are increasingly interacting with plastic pollution, highlighting the potential for contamination of plastic wastes with animal faeces, urine, saliva, and blood. Substantial evidence indicates that once in the environment, plastics rapidly become colonised by microbial biofilm (the so-called 'plastisphere), which often includes potentially harmful microbial pathogens (including pathogens that are zoonotic in nature). Climate change, increased urbanisation, and the intensification of agriculture, mean that the three-way interactions between humans, animals, and plastic pollution are becoming more frequent, which is significant as almost 60% of emerging human infectious diseases during the last century have been zoonotic. Here, we critically review the potential for contaminated environmental plastics to facilitate the evolution of novel pathogenic strains of microorganisms, and the subsequent role of plastic pollution in the cyclical dissemination of zoonotic pathogens. As the interactions between humans, animals, and plastic pollution continues to grow, and the volume of plastics entering the environment increases, there is clearly an urgent need to better understand the role of plastic waste in facilitating zoonotic pathogen evolution and dissemination, and the effect this can have on environmental and human health.},
}
@article {pmid38220012,
year = {2024},
author = {Fang, Q and Pan, X},
title = {A systematic review of antibiotic resistance driven by metal-based nanoparticles: Mechanisms and a call for risk mitigation.},
journal = {The Science of the total environment},
volume = {916},
number = {},
pages = {170080},
doi = {10.1016/j.scitotenv.2024.170080},
pmid = {38220012},
issn = {1879-1026},
mesh = {*Metal Nanoparticles ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Risk Assessment ; Gene Transfer, Horizontal ; },
abstract = {Elevations in antibiotic resistance genes (ARGs) are due not only to the antibiotic burden, but also to numerous environmental pressures (e.g., pesticides, metal ions, or psychotropic pharmaceuticals), which have led to an international public health emergency. Metal-based nanoparticles (MNPs) poison bacteria while propelling nanoresistance at ambient or sub-lethal concentrations, acting as a wide spectrum germicidal agent. Awareness of MNPs driven antibiotic resistance has created a surge of investigation into the molecule mechanisms of evolving and spreading environmental antibiotic resistome. Co-occurrence of MNPs resistance and antibiotic resistance emerge in environmental pathogens and benign microbes may entail a crucial outcome for human health. In this review we expound on the systematic mechanism of ARGs proliferation under the stress of MNPs, including reactive oxygen species (ROS) induced mutation, horizontal gene transfer (HGT) relevant genes regulation, nano-property, quorum sensing, and biofilm formation and highlighting on the momentous contribution of nanoparticle released ion. As antibiotic resistance pattern alteration is closely knit with the mediate activation of nanoparticle in water, soil, manure, or sludge habitats, we have proposed a virulence and evolution based antibiotic resistance risk assessment strategy for MNP contaminated areas and discussed practicable approaches that call for risk management in critical environmental compartments.},
}
@article {pmid38218181,
year = {2024},
author = {Peterson, A and Baskett, C and Ratcliff, WC and Burnetti, A},
title = {Transforming yeast into a facultative photoheterotroph via expression of vacuolar rhodopsin.},
journal = {Current biology : CB},
volume = {34},
number = {3},
pages = {648-654.e3},
doi = {10.1016/j.cub.2023.12.044},
pmid = {38218181},
issn = {1879-0445},
mesh = {*Saccharomyces cerevisiae/metabolism ; *Rhodopsin/metabolism ; Phylogeny ; Vacuoles/metabolism ; Chlorophyll ; },
abstract = {Phototrophic metabolism, the capture of light for energy, was a pivotal biological innovation that greatly increased the total energy available to the biosphere. Chlorophyll-based photosynthesis is the most familiar phototrophic metabolism, but retinal-based microbial rhodopsins transduce nearly as much light energy as chlorophyll does,[1] via a simpler mechanism, and are found in far more taxonomic groups. Although this system has apparently spread widely via horizontal gene transfer,[2][,][3][,][4] little is known about how rhodopsin genes (with phylogenetic origins within prokaryotes[5][,][6]) are horizontally acquired by eukaryotic cells with complex internal membrane architectures or the conditions under which they provide a fitness advantage. To address this knowledge gap, we sought to determine whether Saccharomyces cerevisiae, a heterotrophic yeast with no known evolutionary history of phototrophy, can function as a facultative photoheterotroph after acquiring a single rhodopsin gene. We inserted a rhodopsin gene from Ustilago maydis,[7] which encodes a proton pump localized to the vacuole, an organelle normally acidified via a V-type rotary ATPase, allowing the rhodopsin to supplement heterotrophic metabolism. Probes of the physiology of modified cells show that they can deacidify the cytoplasm using light energy, demonstrating the ability of rhodopsins to ameliorate the effects of starvation and quiescence. Further, we show that yeast-bearing rhodopsins gain a selective advantage when illuminated, proliferating more rapidly than their non-phototrophic ancestor or rhodopsin-bearing yeast cultured in the dark. These results underscore the ease with which rhodopsins may be horizontally transferred even in eukaryotes, providing novel biological function without first requiring evolutionary optimization.},
}
@article {pmid38217904,
year = {2024},
author = {Lin, D and Xu, JY and Wang, L and Du, S and Zhu, D},
title = {Long-term application of organic fertilizer prompting the dispersal of antibiotic resistance genes and their health risks in the soil plastisphere.},
journal = {Environment international},
volume = {183},
number = {},
pages = {108431},
doi = {10.1016/j.envint.2024.108431},
pmid = {38217904},
issn = {1873-6750},
mesh = {Humans ; *Soil ; *Anti-Bacterial Agents/pharmacology ; Fertilizers/analysis ; Genes, Bacterial ; Plastics ; Manure/microbiology ; Soil Microbiology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; },
abstract = {Microplastic (MP) pollution is a rapidly growing global environmental concern that has led to the emergence of a new environmental compartment, the plastisphere, which is a hotspot for the accumulation of antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs). However, studies on the effects of long-term organic fertilizer application on the dispersal of ARGs and virulence factor genes (VFGs) in the plastisphere of farmland soil have been limited. Here, we performed a field culture experiment by burying nylon bags filled with MPs in paddy soil that had been treated with different fertilizers for over 30 years to explore the changes of ARGs and VFGs in soil plastisphere. Our results show that the soil plastisphere amplified the ARG and VFG pollution caused by organic fertilization by 1.5 and 1.4 times, respectively. And it also led to a 2.7-fold increase in the risk of horizontal gene transfer. Meanwhile, the plastisphere tended to promote deterministic process in the community assembly of HBPs, with an increase of 1.4 times. Network analysis found a significant correlation between ARGs, VFGs, and bacteria in plastisphere. Correlation analysis highlight the important role of mobile genetic elements (MGEs) and bacterial communities in shaping the abundance of ARGs and VFGs, respectively. Our findings provide new insights into the health risk associated with the soil plastisphere due ARGs and VFGs derived from organic fertilizers.},
}
@article {pmid38216797,
year = {2024},
author = {Iqbal, S and Begum, F},
title = {Identification and characterization of integrated prophages and CRISPR-Cas system in Bacillus subtilis RS10 genome.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {55},
number = {1},
pages = {537-542},
pmid = {38216797},
issn = {1678-4405},
mesh = {Prophages/genetics ; Bacillus subtilis/genetics ; CRISPR-Cas Systems ; *Bacteriophages/genetics ; *Bacillus ; },
abstract = {Bacteriophages have been extensively investigated due to their prominent role in the virulence and resistance of pathogenic bacteria. However, little attention has been given to the non-pathogenic Bacillus phages, and their role in the ecological bacteria genome is overlooked. In the present study, we characterized two Bacillus phages with a linear DNA genome of 33.6 kb with 44.83% GC contents and 129.3 kb with 34.70% GC contents. A total of 46 and 175 putative coding DNA sequences (CDS) were identified in prophage 1 (P1) and prophage 2 (P2), respectively, with no tRNA genes. Comparative genome sequence analysis revealed that P1 shares eight CDS with phage Jimmer 2 (NC-041976), and phage Osiris (NC-028969), and six with phage phi CT9441A (NC-029022). On the other hand, P2 showed high similarity with Bacill_SPbeta_NC_001884 and Bacillus phage phi 105. Further, genome analysis indicates several horizontal gene transfer events in both phages during the evolution process. In addition, we detected two CRISPR-Cas systems for the first time in B. subtilis. The identified CRISPR system consists of 24 and 25 direct repeats and integrase coding genes, while the cas gene which encodes Cas protein involved in the cleavage of a target sequence is missing. These findings will expand the current knowledge of soil phages as well as help to develop a new perspective for investigating more ecological phages to understand their role in bacterial communities and diversity.},
}
@article {pmid38215844,
year = {2024},
author = {Zhuang, X and Fan, H and Li, X and Dong, Y and Wang, S and Zhao, B and Wu, S},
title = {Transfer and accumulation of antibiotic resistance genes and bacterial pathogens in the mice gut due to consumption of organic foods.},
journal = {The Science of the total environment},
volume = {915},
number = {},
pages = {169842},
doi = {10.1016/j.scitotenv.2023.169842},
pmid = {38215844},
issn = {1879-1026},
mesh = {Animals ; Mice ; *Food, Organic ; *Genes, Bacterial ; RNA, Ribosomal, 16S ; Angiotensin Receptor Antagonists/pharmacology ; Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Integrases/genetics/pharmacology ; },
abstract = {Over the last few decades, organic food demand has grown largely because of increasing personal health concerns. Organic farming introduces antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) into foods. However, potential effects of organic foods on the gut microbiome and ARGs have been overlooked. Using high-throughput quantitative PCR and 16S rRNA high-throughput sequencing technology, we examined 132 ARGs from major classes, eight transposase genes, universal class I integron-integrase gene (intI), clinical class I integron-integrase gene (cintI), and the bacterial community in mouse gut after 8 weeks with an either organic or inorganic lettuce and wheat diet. A total of 8 types of major ARGs and 10 mobile genetic elements (MGEs) were detected in mice gut, including tetracycline, multidrug, sulfonamide, aminoglycoside, beta-lactamase, chloramphenicol, MLSB and vancomycin resistance genes. We found that abundance and diversity of ARGs, mobile gene elements, and potential ARB in the gut increased with time after consumption of organic foods, whereas no significant changes were observed in inorganic treated groups. Moreover, MGEs, including IS613, Tp614 and tnpA_03 were found to play an important role in regulating ARG profiles in the gut microbiome following consumption of organic foods. Importantly, feeding organic food increased the relative abundance of the potentially antibiotic-resistant pathogens, Bacteroides and Streptococcus. Our results confirm that there is an increasing risk of ARGs and ARB in the gut microbiome, which highlights the importance of organic food industries taking into account the potential accumulation and transmission of ARGs as a risk factor.},
}
@article {pmid38214578,
year = {2024},
author = {Christinaki, AC and Myridakis, AI and Kouvelis, VN},
title = {Genomic insights into the evolution and adaptation of secondary metabolite gene clusters in fungicolous species Cladobotryum mycophilum ATHUM6906.},
journal = {G3 (Bethesda, Md.)},
volume = {14},
number = {4},
pages = {},
pmid = {38214578},
issn = {2160-1836},
support = {19620//Hellenic Foundation for Research and Innovation/ ; },
mesh = {*Genome, Fungal ; *Hypocreales/genetics ; Genomics ; Multigene Family ; },
abstract = {Mycophilic or fungicolous fungi can be found wherever fungi exist since they are able to colonize other fungi, which occupy a diverse range of habitats. Some fungicolous species cause important diseases on Basidiomycetes, and thus, they are the main reason for the destruction of mushroom cultivations. Nonetheless, despite their ecological significance, their genomic data remain limited. Cladobotryum mycophilum is one of the most aggressive species of the genus, destroying the economically important Agaricus bisporus cultivations. The 40.7 Mb whole genome of the Greek isolate ATHUM6906 is assembled in 16 fragments, including the mitochondrial genome and 2 small circular mitochondrial plasmids, in this study. This genome includes a comprehensive set of 12,282 protein coding, 56 rRNA, and 273 tRNA genes. Transposable elements, CAZymes, and pathogenicity related genes were also examined. The genome of C. mycophilum contained a diverse arsenal of genes involved in secondary metabolism, forming 106 biosynthetic gene clusters, which renders this genome as one of the most BGC abundant among fungicolous species. Comparative analyses were performed for genomes of species of the family Hypocreaceae. Some BGCs identified in C. mycophilum genome exhibited similarities to clusters found in the family Hypocreaceae, suggesting vertical heritage. In contrast, certain BGCs showed a scattered distribution among Hypocreaceae species or were solely found in Cladobotryum genomes. This work provides evidence of extensive BGC losses, horizontal gene transfer events, and formation of novel BGCs during evolution, potentially driven by neutral or even positive selection pressures. These events may increase Cladobotryum fitness under various environmental conditions and potentially during host-fungus interaction.},
}
@article {pmid38214507,
year = {2024},
author = {Charubin, K and Hill, JD and Papoutsakis, ET},
title = {DNA transfer between two different species mediated by heterologous cell fusion in Clostridium coculture.},
journal = {mBio},
volume = {15},
number = {2},
pages = {e0313323},
pmid = {38214507},
issn = {2150-7511},
support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; S10 OD016361/OD/NIH HHS/United States ; },
mesh = {*Clostridium acetobutylicum/genetics/metabolism ; Coculture Techniques ; Cell Fusion ; Clostridium/genetics ; DNA/metabolism ; RNA/metabolism ; },
abstract = {Prokaryotic evolution is driven by random mutations and horizontal gene transfer (HGT). HGT occurs via transformation, transduction, or conjugation. We have previously shown that in syntrophic cocultures of Clostridium acetobutylicum and Clostridium ljungdahlii, heterologous cell fusion leads to a large-scale exchange of proteins and RNA between the two organisms. Here, we present evidence that heterologous cell fusion facilitates the exchange of DNA between the two organisms. Using selective subculturing, we isolated C. acetobutylicum cells which acquired and integrated into their genome portions of plasmid DNA from a plasmid-carrying C. ljungdahlii strain. Limiting-dilution plating and DNA methylation data based on PacBio Single-Molecule Real Time (SMRT) sequencing support the existence of hybrid C. acetobutylicum/C. ljungdahlii cells. These findings expand our understanding of multi-species microbiomes, their survival strategies, and evolution.IMPORTANCEInvestigations of natural multispecies microbiomes and synthetic microbial cocultures are attracting renewed interest for their potential application in biotechnology, ecology, and medical fields. Previously, we have shown the syntrophic coculture of C. acetobutylicum and C. ljungdahlii undergoes heterologous cell-to-cell fusion, which facilitates the exchange of cytoplasmic protein and RNA between the two organisms. We now show that heterologous cell fusion between the two Clostridium organisms can facilitate the exchange of DNA. By applying selective pressures to this coculture system, we isolated clones of wild-type C. acetobutylicum which acquired the erythromycin resistance (erm) gene from the C. ljungdahlii strain carrying a plasmid with the erm gene. Single-molecule real-time sequencing revealed that the erm gene was integrated into the genome in a mosaic fashion. Our data also support the persistence of hybrid C. acetobutylicum/C. ljungdahlii cells displaying hybrid DNA-methylation patterns.},
}
@article {pmid38206425,
year = {2024},
author = {Tartik, M},
title = {The priority of yeast to select among various DNA options to repair genome breaks by homologous recombination.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {99},
pmid = {38206425},
issn = {1573-4978},
support = {BAP FEF.2019.00.0//Bing&#xf6;l &#xdc;niversitesi/ ; },
mesh = {Animals ; *Saccharomyces cerevisiae/genetics ; DNA ; Homologous Recombination/genetics ; *Fractures, Bone ; Gene Regulatory Networks ; },
abstract = {BACKGROUND: Horizontal gene transfer (HGT) is considered an important mechanism to contribute to the evolution of bacteria, plants, and animals by allowing the movement of genetic material between organisms, in difference to vertical inheritance. Thereby it can also play a significant role in spreading traits like antibiotic resistance among bacteria and virulence factors between pathogens. During the HGT, organisms take up free DNA from the environment and incorporate it into their genomes. Although HGT is known to be carried out by many organisms, there is limited information on how organisms select which genetic material for horizontal transfer. Here we have investigated the preference priority of Saccharomyces cerevisiae between different options of gene source presented under certain stress conditions to repair a double-strand break (DSB) in DNA via HR.<br><br>RESULTS: Each genetic module was designed with appropriate sequences being homologous for two sides of the DSB, which is important for yeast to repair the fracture with HR. S. cerevisiae made a random selection between two heterologous T1 (44%) and T2 (56%) modules to repair DSB. Interestingly, yeast corrected the DNA break only with the T3 module (almost 100%) when the homologous T3 module was an option for the selection. It seems that S. cerevisiae tends to prefer T3 over alternatives to fix DSBs when it exists among the options.<br><br>CONCLUSIONS: It seems that S. cerevisiae have a preference for priority to select a particular one under certain conditions when it has various DNA options to repair a DSB in its genome, further studies are required to support our findings.},
}
@article {pmid38193726,
year = {2024},
author = {Li, H and Cai, L and Wang, L and Wang, Y and Xu, J and Zhang, R},
title = {The structure and assembly mechanisms of T4-like cyanophages community in the South China Sea.},
journal = {Microbiology spectrum},
volume = {12},
number = {2},
pages = {e0200223},
pmid = {38193726},
issn = {2165-0497},
support = {41861144018, 42188102//MOST | National Natural Science Foundation of China (NSFC)/ ; 42206133//MOST | National Natural Science Foundation of China (NSFC)/ ; LYG20220003//Lianyungang Postdoctoral Research Funding Program/ ; },
mesh = {Phylogeny ; Ecosystem ; *Bacteriophages/genetics ; Capsid Proteins/genetics ; Capsid ; *Cyanobacteria ; },
abstract = {Marine ecosystems contain an immense diversity of phages, many of which infect cyanobacteria (cyanophage) that are largely responsible for primary productivity. To characterize the genetic diversity and biogeographic distribution of the marine T4-like cyanophage community in the northern South China Sea, the T4-like cyanophage portal protein gene (g20) was amplified. Phylogenetic analysis revealed that marine T4-like cyanophages were highly diverse, with g20 operational taxonomic units being affiliated with five defined clades (Clusters I-V). Cluster II had a wide geographic distribution, Cluster IV was the most abundant in the open sea, and Cluster I was dominant in coastal shelf environments. Our results showed T4-like cyanophages (based on g20) community was generally shaped via heterogeneous selection. Highly variable environmental factors (such as salinity and temperature) can heterogeneously select different cyanophage communities. Nevertheless, the dominant drivers of the T4-like cyanophage community based on the g20 and g23 (T4-like phage major capsid protein gene) were different, probably due to different coverages by the primer sets. Furthermore, the community assembly processes of T4-like cyanophages were affected by host traits (abundance and distribution), viral traits (latent period, burst size, and host range), and environmental properties (temperature and salinity).IMPORTANCECyanophages are abundant and ubiquitous in the oceans, altering population structures and evolution of cyanobacteria, which account for a large portion of global carbon fixation, through host mortality, horizontal gene transfer, and the modulation of host metabolism. However, little is known about the biogeography and ecological drivers that shape the cyanophage community. Here, we use g20 and g23 genes to examine the biogeographic patterns and the assembly mechanisms of T4-like cyanophage community in the northern part of the South China Sea. The different coverages of primer sets might lead to the different dominant drivers of T4-like cyanophage community based on g20 and g23 genes. Our results showed that characteristics of viral traits (latent period, burst size, and host range) and host traits (abundance and distribution) were found to either limit or enhance the biogeographic distribution of T4-like cyanophages. Overall, both virus and host properties are critical to consider when determining rules of community assembly for viruses.},
}
@article {pmid38193706,
year = {2024},
author = {Han, X and Zhou, J and Yu, L and Shao, L and Cai, S and Hu, H and Shi, Q and Wang, Z and Hua, X and Jiang, Y and Yu, Y},
title = {Genome sequencing unveils blaKPC-2-harboring plasmids as drivers of enhanced resistance and virulence in nosocomial Klebsiella pneumoniae.},
journal = {mSystems},
volume = {9},
number = {2},
pages = {e0092423},
pmid = {38193706},
issn = {2379-5077},
support = {32141001//MOST | National Natural Science Foundation of China (NSFC)/ ; 82272373//MOST | National Natural Science Foundation of China (NSFC)/ ; 2018YFE0102100//MOST | National Key Research and Development Program of China (NKPs)/ ; LY22H190001//MOST | NSFC | NSFC-Zhejiang Joint Fund | | Natural Science Foundation of Zhejiang Province (ZJNSF)/ ; 2021C03179//MOST | NSFC | NSFC-Zhejiang Joint Fund | Science and Technology Department of Zhejiang Province ()/ ; 2021C03055//MOST | NSFC | NSFC-Zhejiang Joint Fund | Science and Technology Department of Zhejiang Province ()/ ; },
mesh = {Humans ; Klebsiella pneumoniae/genetics ; Klebsiella/genetics ; *Klebsiella Infections/drug therapy ; *Cross Infection/epidemiology ; Virulence/genetics ; beta-Lactamases/genetics ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; Carbapenems/pharmacology ; },
abstract = {The threat posed by Klebsiella pneumoniae in healthcare settings has worsened due to the evolutionary advantages conferred by blaKPC-2-harboring plasmids (pKPC-2). However, the specific evolutionary pathway of nosocomial K. pneumoniae carrying pKPC-2 and its transmission between patients and healthcare environments are not yet well understood. Between 1 August and 31 December 2019, 237 ST11 KPC-2-producing-carbapenem-resistant K. pneumoniae (CRKP) (KPC-2-CRKP) were collected from patient or ward environments in an intensive care unit and subjected to Illumina sequencing, of which 32 strains were additionally selected for Nanopore sequencing to obtain complete plasmid sequences. Bioinformatics analysis, conjugation experiments, antimicrobial susceptibility tests, and virulence assays were performed to identify the evolutionary characteristics of pKPC-2. The pKPC-2 plasmids were divided into three subgroups with distinct evolutionary events, including Tn3-mediated plasmid homologous recombination, IS26-mediated horizontal gene transfer, and dynamic duplications of antibiotic resistance genes (ARGs). Surprisingly, the incidence rates of multicopy blaKPC-2, blaSHV-12, and blaCTX-M-65 were quite high (ranging from 27.43% to 67.01%), and strains negative for extended-spectrum β-lactamase tended to develop multicopy blaKPC-2. Notably, the presence of multicopy blaSHV-12 reduced sensitivity to ceftazidime/avibactam (CZA), and the relative expression level of blaSHV-12 in the CZA-resistant group was 6.12 times higher than that in the sensitive group. Furthermore, a novel hybrid pKPC-2 was identified, presenting enhanced virulence levels and decreased susceptibility to CZA. This study emphasizes the notable prevalence of multicopy ARGs and provides a comprehensive insight into the intricate and diverse evolutionary pathways of resistant plasmids that disseminate among patients and healthcare environments.IMPORTANCEThis study is based on a CRKP screening program between patients and ward environments in an intensive care unit, describing the pKPC-2 (blaKPC-2-harboring plasmids) population structure and evolutionary characteristics in clinical settings. Long-read sequencing was performed in genetically closely related strains, enabling the high-resolution analysis of evolution pathway between or within pKPC-2 subgroups. We revealed the extremely high rates of multicopy antibiotic resistance genes (ARGs) in clinical settings and its effect on resistance profile toward novel β-lactam/β-lactamase inhibitor combinations, which belongs to the last line treatment choices toward CRKP infection. A novel hybrid pKPC-2 carrying CRKP with enhanced resistance and virulence level was captured during its clonal spread between patients and ward environment. These evidences highlight the threat of pKPC-2 to CRKP treatment and control. Thus, surveillance and timely disinfection in clinical settings should be practiced to prevent transmission of CRKP carrying threatful pKPC-2. And rational use of antibiotics should be called for to prevent inducing of pKPC-2 evolution, especially the multicopy ARGs.},
}
@article {pmid38192262,
year = {2024},
author = {Schuster, CD and Salvatore, F and Moens, L and Martí, MA},
title = {Globin phylogeny, evolution and function, the newest update.},
journal = {Proteins},
volume = {92},
number = {6},
pages = {720-734},
doi = {10.1002/prot.26659},
pmid = {38192262},
issn = {1097-0134},
mesh = {*Globins/genetics/chemistry/metabolism ; *Phylogeny ; *Evolution, Molecular ; Humans ; Bacteria/genetics/metabolism ; Animals ; Archaea/genetics/metabolism ; Protein Domains ; Gene Transfer, Horizontal ; },
abstract = {Our globin census update allows us to refine our vision of globin origin, evolution, and structure to function relationship in the context of the currently accepted tree of life. The modern globin domain originates as a single domain, three-over-three α-helical folded structure before the diversification of the kingdoms of life (Bacteria, Archaea, Eukarya). Together with the diversification of prokaryotes, three monophyletic globin families (M, S, and T) emerged, most likely in Proteobacteria and Actinobacteria, displaying specific sequence and structural features, and spread by vertical and horizontal gene transfer, most probably already present in the last universal common ancestor (LUCA). Non-globin domains were added, and eventually lost again, creating multi-domain structures in key branches of M- (FHb and Adgb) and the vast majority of S globins, which with their coevolved multi-domain architectures, have predominantly "sensor" functions. Single domain T-family globins diverged into four major groups and most likely display functions related to reactive nitrogen and oxygen species (RNOS) chemistry, as well as oxygen storage/transport which drives the evolution of its major branches with their characteristic key distal residues (B10, E11, E7, and G8). M-family evolution also lead to distinctive major types (FHb and Fgb, Ngb, Adgb, GbX vertebrate Gbs), and shows the shift from high oxygen affinity controlled by TyrB10-Gln/AsnE11 likely related to RNOS chemistry in microorganisms, to a moderate oxygen affinity storage/transport function controlled by hydrophobic B10/E11-HisE7 in multicellular animals.},
}
@article {pmid38187688,
year = {2024},
author = {Wolff, R and Garud, NR},
title = {Pervasive selective sweeps across human gut microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38187688},
issn = {2692-8205},
support = {R35 GM151023/GM/NIGMS NIH HHS/United States ; },
abstract = {The human gut microbiome is composed of a highly diverse consortia of species which are continually evolving within and across hosts. The ability to identify adaptations common to many human gut microbiomes would not only reveal shared selection pressures across hosts, but also key drivers of functional differentiation of the microbiome that may affect community structure and host traits. However, to date there has not been a systematic scan for adaptations that have spread across human gut microbiomes. Here, we develop a novel selection scan statistic named the integrated Linkage Disequilibrium Score (iLDS) that can detect the spread of adaptive haplotypes across host microbiomes via migration and horizontal gene transfer. Specifically, iLDS leverages signals of hitchhiking of deleterious variants with the beneficial variant. Application of the statistic to ~30 of the most prevalent commensal gut species from 24 populations around the world revealed more than 300 selective sweeps across species. We find an enrichment for selective sweeps at loci involved in carbohydrate metabolism-potentially indicative of adaptation to features of host diet-and we find that the targets of selection significantly differ between Westernized and non-Westernized populations. Underscoring the potential role of diet in driving selection, we find a selective sweep absent from non-Westernized populations but ubiquitous in Westernized populations at a locus known to be involved in the metabolism of maltodextrin, a synthetic starch that has recently become a widespread component of Western diets. In summary, we demonstrate that selective sweeps across host microbiomes are a common feature of the evolution of the human gut microbiome, and that targets of selection may be strongly impacted by host diet.},
}
@article {pmid38185239,
year = {2024},
author = {Zhu, X and Wang, X and Wang, F and Tian, X and Pang, J},
title = {The integrative and conjugative element ICECiPOL15 mediates horizontal transfer of β-lactam resistance gene in Chryseobacterium indoltheticum POL15.},
journal = {Journal of global antimicrobial resistance},
volume = {36},
number = {},
pages = {223-229},
doi = {10.1016/j.jgar.2023.12.028},
pmid = {38185239},
issn = {2213-7173},
mesh = {*Chryseobacterium ; beta-Lactam Resistance ; Genomics ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {OBJECTIVES: The dissemination of antibiotic resistance genes (ARGs) from the environment, including agricultural sources, is of increasing concern. In this study, we examined the antibiotic resistance profile and genomic sequence of a strain of Chryseobacterium indoltheticum obtained from an agricultural location.<br><br>METHODS: The multidrug-resistant bacterial strain POL15 was isolated from the wastewater of a livestock farm in China. Whole-genome sequencing was performed followed by bioinformatics analyses to identify integrative and conjugative elements (ICEs) and ARGs. Mating assays were performed to analyse ICE transferability.<br><br>RESULTS: Whole-genome sequencing and annotation showed that the genome of POL15 encodes ARGs. Additionally, an ICE named ICECiPOL15, which carries a class C &#x3b2;-lactamase-encoding gene blaAQU, was identified in the POL15 genome. Genes encoding an integrase, an excisionase, a relaxase, a type IV coupling protein and conjugative transposon proteins involved in a type IV secretion system were also identified in ICECiPOL15. Sequence alignment revealed that ICECiPOL15 might have evolved from other Chryseobacterium species. The horizontal transferability of ICECiPOL15 was demonstrated by mating experiments between C. indoltheticum POL15 and Escherichia coli DL21.<br><br>CONCLUSIONS: This study represents the first characterization of a mobilizable antibiotic resistance ICE in a species of C. indoltheticum and provides evidence that C. indoltheticum strains could be important reservoirs and vehicles for ARGs on livestock farms.},
}
@article {pmid38182626,
year = {2024},
author = {Rühlemann, MC and Bang, C and Gogarten, JF and Hermes, BM and Groussin, M and Waschina, S and Poyet, M and Ulrich, M and Akoua-Koffi, C and Deschner, T and Muyembe-Tamfum, JJ and Robbins, MM and Surbeck, M and Wittig, RM and Zuberbühler, K and Baines, JF and Leendertz, FH and Franke, A},
title = {Functional host-specific adaptation of the intestinal microbiome in hominids.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {326},
pmid = {38182626},
issn = {2041-1723},
support = {261376515//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 244372499//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 261376515//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 390884018//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Animals ; *Hominidae ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Pan troglodytes ; Pan paniscus ; },
abstract = {Fine-scale knowledge of the changes in composition and function of the human gut microbiome compared that of our closest relatives is critical for understanding the evolutionary processes underlying its developmental trajectory. To infer taxonomic and functional changes in the gut microbiome across hominids at different timescales, we perform high-resolution metagenomic-based analyzes of the fecal microbiome from over two hundred samples including diverse human populations, as well as wild-living chimpanzees, bonobos, and gorillas. We find human-associated taxa depleted within non-human apes and patterns of host-specific gut microbiota, suggesting the widespread acquisition of novel microbial clades along the evolutionary divergence of hosts. In contrast, we reveal multiple lines of evidence for a pervasive loss of diversity in human populations in correlation with a high Human Development Index, including evolutionarily conserved clades. Similarly, patterns of co-phylogeny between microbes and hosts are found to be disrupted in humans. Together with identifying individual microbial taxa and functional adaptations that correlate to host phylogeny, these findings offer insights into specific candidates playing a role in the diverging trajectories of the gut microbiome of hominids. We find that repeated horizontal gene transfer and gene loss, as well as the adaptation to transient microaerobic conditions appear to have played a role in the evolution of the human gut microbiome.},
}
@article {pmid38181725,
year = {2024},
author = {Jiang, YL and Zhou, CZ},
title = {Multiple masks of a Shigella podophage.},
journal = {Structure (London, England : 1993)},
volume = {32},
number = {1},
pages = {1-2},
doi = {10.1016/j.str.2023.12.002},
pmid = {38181725},
issn = {1878-4186},
support = {2018YFA0903100//Ministry of Science and Technology of China/ ; U19A2020//National Natural Science Foundation of China/ ; 2020452//Youth Innovation Promotion Association of Chinese Academy of Sciences/ ; },
mesh = {*Shigella/virology ; *Bacteriophages/ultrastructure ; },
abstract = {In this issue of Structure, Subramanian et al. present the cryo-EM structure of Shigella podophage HRP29, which possesses a T7-like tail complex surrounded by six P22/Sf6-like tailspikes and two unique decoration proteins. These colorful masks of HRP29 record the frequent events of horizontal gene transfer during evolution.},
}
@article {pmid38181593,
year = {2024},
author = {Zhang, C and Li, S and Sun, H and Li, X and Fu, L and Zhang, C and Sun, S and Zhou, D},
title = {Assessing the impact of low organic loading on effluent safety in wastewater treatment: Insights from an activated sludge reactor study.},
journal = {Journal of hazardous materials},
volume = {465},
number = {},
pages = {133083},
doi = {10.1016/j.jhazmat.2023.133083},
pmid = {38181593},
issn = {1873-3336},
mesh = {Humans ; *Wastewater ; Sewage/microbiology ; Disinfection/methods ; Nitrogen ; *Water Purification/methods ; },
abstract = {In this study, an organic loading (OL) of 300 mg/(L d) was set as the relative normal condition (OL-300), while 150 mg/(L d) was chosen as the condition reflecting excessively low organic loading (OL-150) to thoroughly assess the associated risks in the effluent of the biological wastewater treatment process. Compared with OL-300, OL-150 did not lead to a significant decrease in dissolved organic carbon (DOC) concentration, but it did improve dissolved organic nitrogen (DON) levels by ∼63 %. Interestingly, the dissolved organic matter (DOM) exhibited higher susceptibility to transformation into chlorinated disinfection by-products (Cl-DBPs) in OL-150, resulting in an increase in the compound number of Cl-DBPs by ∼16 %. Additionally, OL-150 induced nutrient stress, which promoted engendered human bacterial pathogens (HBPs) survival by ∼32 % and led to ∼51 % increase in the antibiotic resistance genes (ARGs) abundance through horizontal gene transfer (HGT). These findings highlight the importance of carefully considering the potential risks associated with low organic loading strategies in wastewater treatment processes.},
}
@article {pmid38180978,
year = {2024},
author = {Schilcher, K and Severn, MM and Jenul, C and Avina, YC and Keogh, RA and Horswill, AR},
title = {The Staphylococcus aureus CamS lipoprotein is a repressor of toxin production that shapes host-pathogen interaction.},
journal = {PLoS biology},
volume = {22},
number = {1},
pages = {e3002451},
pmid = {38180978},
issn = {1545-7885},
support = {I01 BX002711/BX/BLRD VA/United States ; P01 AI083211/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Staphylococcus aureus/genetics ; Lipoproteins/genetics ; *Staphylococcal Infections ; Host-Pathogen Interactions ; Cell Adhesion Molecules ; Cytotoxins ; Peptides ; },
abstract = {Lipoproteins of the opportunistic pathogen Staphylococcus aureus play a crucial role in various cellular processes and host interactions. Consisting of a protein and a lipid moiety, they support nutrient acquisition and anchor the protein to the bacterial membrane. Recently, we identified several processed and secreted small linear peptides that derive from the secretion signal sequence of S. aureus lipoproteins. Here, we show, for the first time, that the protein moiety of the S. aureus lipoprotein CamS has a biological role that is distinct from its associated linear peptide staph-cAM373. The small peptide was shown to be involved in interspecies horizontal gene transfer, the primary mechanism for the dissemination of antibiotic resistance among bacteria. We provide evidence that the CamS protein moiety is a potent repressor of cytotoxins, such as α-toxin and leukocidins. The CamS-mediated suppression of toxin transcription was reflected by altered disease severity in in vivo infection models involving skin and soft tissue, as well as bloodstream infections. Collectively, we have uncovered the role of the protein moiety of the staphylococcal lipoprotein CamS as a previously uncharacterized repressor of S. aureus toxin production, which consequently regulates virulence and disease outcomes. Notably, the camS gene is conserved in S. aureus, and we also demonstrated the muted transcriptional response of cytotoxins in 2 different S. aureus lineages. Our findings provide the first evidence of distinct biological functions of the protein moiety and its associated linear peptide for a specific lipoprotein. Therefore, lipoproteins in S. aureus consist of 3 functional components: a lipid moiety, a protein moiety, and a small linear peptide, with putative different biological roles that might not only determine the outcome of host-pathogen interactions but also drive the acquisition of antibiotic resistance determinants.},
}
@article {pmid38178191,
year = {2024},
author = {Mahillon, M and Brodard, J and Dubuis, N and Gugerli, P and Blouin, AG and Schumpp, O},
title = {Mixed infection of ITPase-encoding potyvirid and secovirid in Mercurialis perennis: evidences for a convergent euphorbia-specific viral counterstrike.},
journal = {Virology journal},
volume = {21},
number = {1},
pages = {6},
pmid = {38178191},
issn = {1743-422X},
mesh = {Inosine Triphosphatase ; *Euphorbia ; Phylogeny ; *Coinfection ; *RNA Viruses/genetics ; Nucleotides/genetics ; *Potyviridae/genetics ; *Plant Viruses/genetics ; Plants/genetics ; *Nucleic Acids ; RNA, Viral/genetics ; Genome, Viral ; },
abstract = {BACKGROUND: In cellular organisms, inosine triphosphate pyrophosphatases (ITPases) prevent the incorporation of mutagenic deaminated purines into nucleic acids. These enzymes have also been detected in the genomes of several plant RNA viruses infecting two euphorbia species. In particular, two ipomoviruses produce replicase-associated ITPases to cope with high concentration of non-canonical nucleotides found in cassava tissues.<br><br>METHOD: Using high-throughput RNA sequencing on the wild euphorbia species Mercurialis perennis, two new members of the families Potyviridae and Secoviridae were identified. Both viruses encode for a putative ITPase, and were found in mixed infection with a new partitivirid. Following biological and genomic characterization of these viruses, the origin and function of the phytoviral ITPases were investigated.<br><br>RESULTS: While the potyvirid was shown to be pathogenic, the secovirid and partitivirid could not be transmitted. The secovirid was found belonging to a proposed new Comovirinae genus tentatively named "Mercomovirus", which also accommodates other viruses identified through transcriptome mining, and for which an asymptomatic pollen-associated lifestyle is suspected. Homology and phylogenetic analyses inferred that the ITPases encoded by the potyvirid and secovirid were likely acquired through independent horizontal gene transfer events, forming lineages distinct from the enzymes found in cassava ipomoviruses. Possible origins from cellular organisms are discussed for these proteins. In parallel, the endogenous ITPase of M. perennis was predicted to encode for a C-terminal nuclear localization signal, which appears to be conserved among the ITPases of euphorbias but absent in other plant families. This subcellular localization is in line with the idea that nucleic acids remain protected in the nucleus, while deaminated nucleotides accumulate in the cytoplasm where they act as antiviral molecules.<br><br>CONCLUSION: Three new RNA viruses infecting M. perennis are described, two of which encoding for ITPases. These enzymes have distinct origins, and are likely required by viruses to circumvent high level of cytoplasmic non-canonical nucleotides. This putative plant defense mechanism has emerged early in the evolution of euphorbias, and seems to specifically target certain groups of RNA viruses infecting perennial hosts.},
}
@article {pmid38177692,
year = {2024},
author = {Nguyen, ANT and Gorrell, R and Kwok, T and Connallon, T and McDonald, MJ},
title = {Horizontal gene transfer facilitates the molecular reverse-evolution of antibiotic sensitivity in experimental populations of H. pylori.},
journal = {Nature ecology &amp; evolution},
volume = {8},
number = {2},
pages = {315-324},
pmid = {38177692},
issn = {2397-334X},
mesh = {Humans ; *Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Helicobacter pylori/genetics ; Evolution, Molecular ; Models, Theoretical ; },
abstract = {Reversing the evolution of traits harmful to humans, such as antimicrobial resistance, is a key ambition of applied evolutionary biology. A major impediment to reverse evolution is the relatively low spontaneous mutation rates that revert evolved genotypes back to their ancestral state. However, the repeated re-introduction of ancestral alleles by horizontal gene transfer (HGT) could make reverse evolution likely. Here we evolve populations of an antibiotic-resistant strain of Helicobacter pylori in growth conditions without antibiotics while introducing an ancestral antibiotic-sensitive allele by HGT. We evaluate reverse evolution using DNA sequencing and find that HGT facilitates the molecular reverse evolution of the antibiotic resistance allele, and that selection for high rates of HGT drives the evolution of increased HGT rates in low-HGT treatment populations. Finally, we use a theoretical model and carry out simulations to infer how the fitness costs of antibiotic resistance, rates of HGT and effects of genetic drift interact to determine the probability and predictability of reverse evolution.},
}
@article {pmid38176647,
year = {2024},
author = {Mawla, GD and Kamal, SM and Cao, LY and Purhonen, P and Hebert, H and Sauer, RT and Baker, TA and Römling, U},
title = {The membrane-cytoplasmic linker defines activity of FtsH proteases in Pseudomonas aeruginosa clone C.},
journal = {The Journal of biological chemistry},
volume = {300},
number = {2},
pages = {105622},
pmid = {38176647},
issn = {1083-351X},
support = {R01 AI016892/AI/NIAID NIH HHS/United States ; R35 GM141517/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; *ATP-Dependent Proteases/chemistry/metabolism ; *Bacterial Proteins/metabolism ; Endopeptidases/metabolism ; Membrane Proteins/metabolism ; Peptide Hydrolases/metabolism ; *Pseudomonas aeruginosa/metabolism ; },
abstract = {Pandemic Pseudomonas aeruginosa clone C strains encode two inner-membrane associated ATP-dependent FtsH proteases. PaftsH1 is located on the core genome and supports cell growth and intrinsic antibiotic resistance, whereas PaftsH2, a xenolog acquired through horizontal gene transfer from a distantly related species, is unable to functionally replace PaftsH1. We show that purified PaFtsH2 degrades fewer substrates than PaFtsH1. Replacing the 31-amino acid-extended linker region of PaFtsH2 spanning from the C-terminal end of the transmembrane helix-2 to the first seven highly divergent residues of the cytosolic AAA+ ATPase module with the corresponding region of PaFtsH1 improves hybrid-enzyme substrate processing in vitro and enables PaFtsH2 to substitute for PaFtsH1 in vivo. Electron microscopy indicates that the identity of this linker sequence influences FtsH flexibility. We find membrane-cytoplasmic (MC) linker regions of PaFtsH1 characteristically glycine-rich compared to those from FtsH2. Consequently, introducing three glycines into the membrane-proximal end of PaFtsH2's MC linker is sufficient to elevate its activity in vitro and in vivo. Our findings establish that the efficiency of substrate processing by the two PaFtsH isoforms depends on MC linker identity and suggest that greater linker flexibility and/or length allows FtsH to degrade a wider spectrum of substrates. As PaFtsH2 homologs occur across bacterial phyla, we hypothesize that FtsH2 is a latent enzyme but may recognize specific substrates or is activated in specific contexts or biological niches. The identity of such linkers might thus play a more determinative role in the functionality of and physiological impact by FtsH proteases than previously thought.},
}
@article {pmid38172677,
year = {2024},
author = {Choi, DG and Baek, JH and Han, DM and Khan, SA and Jeon, CO},
title = {Comparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {28},
pmid = {38172677},
issn = {1471-2164},
support = {Graduate Research Scholarship in 2018//Chung-Ang University/ ; PJ01710102//Rural Development Administration/ ; 2018R1A5A1025077//Ministry of Science and ICT, South Korea/ ; },
mesh = {Animals ; Humans ; *Enterococcus faecium ; Phylogeny ; Enterococcus ; Genomics ; Anti-Bacterial Agents ; },
abstract = {BACKGROUND: Enterococcus faecium and E. lactis are phylogenetically closely related lactic acid bacteria that are ubiquitous in nature and are known to be beneficial or pathogenic. Despite their considerable industrial and clinical importance, comprehensive studies on their evolutionary relationships and genomic, metabolic, and pathogenic traits are still lacking. Therefore, we conducted comparative pangenome analyses using all available dereplicated genomes of these species.<br><br>RESULTS: E. faecium was divided into two subclades: subclade I, comprising strains derived from humans, animals, and food, and the more recent phylogenetic subclade II, consisting exclusively of human-derived strains. In contrast, E. lactis strains, isolated from diverse sources including foods, humans, animals, and the environment, did not display distinct clustering based on their isolation sources. Despite having similar metabolic features, noticeable genomic differences were observed between E. faecium subclades I and II, as well as E. lactis. Notably, E. faecium subclade II strains exhibited significantly larger genome sizes and higher gene counts compared to both E. faecium subclade I and E. lactis strains. Furthermore, they carried a higher abundance of antibiotic resistance, virulence, bacteriocin, and mobile element genes. Phylogenetic analysis of antibiotic resistance and virulence genes suggests that E. faecium subclade II strains likely acquired these genes through horizontal gene transfer, facilitating their effective adaptation in response to antibiotic use in humans.<br><br>CONCLUSIONS: Our study offers valuable insights into the adaptive evolution of E. faecium strains, enabling their survival as pathogens in the human environment through horizontal gene acquisitions.},
}
@article {pmid38169326,
year = {2024},
author = {Yarus, M},
title = {Ordering events in a developing genetic code.},
journal = {RNA biology},
volume = {21},
number = {1},
pages = {1-8},
pmid = {38169326},
issn = {1555-8584},
mesh = {Codon ; *Evolution, Molecular ; *Genetic Code ; Anticodon ; Models, Genetic ; },
abstract = {Preexisting partial genetic codes can fuse to evolve towards the complete Standard Genetic Code (SGC). Such code fusion provides a path of 'least selection', readily generating precursor codes that resemble the SGC. Consequently, such least selections produce the SGC via minimal, thus rapid, change. Optimal code evolution therefore requires delayed wobble. Early wobble encoding slows code evolution, very specifically diminishing the most likely SGC precursors: near-complete, accurate codes which are the products of code fusions. In contrast: given delayed wobble, the SGC can emerge from a truncation selection/evolutionary radiation based on proficient fused coding.},
}
@article {pmid38169168,
year = {2024},
author = {Li, S and Duan, G and Xi, Y and Chu, Y and Li, F and Ho, SH},
title = {Insights into the role of extracellular polymeric substances (EPS) in the spread of antibiotic resistance genes.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {343},
number = {},
pages = {123285},
doi = {10.1016/j.envpol.2023.123285},
pmid = {38169168},
issn = {1873-6424},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Wastewater ; Extracellular Polymeric Substance Matrix ; Genes, Bacterial ; Sewage ; Drug Resistance, Microbial/genetics ; },
abstract = {Antibiotic resistance genes (ARG) are prevalent in aquatic environments. Discharge from wastewater treatment plants is an important point source of ARG release into the environment. It has been reported that biological treatment processes may enhance rather than remove ARG because of their presence in sludge. Attenuation of ARG in biotechnological processes has been studied in depth, showing that many microorganisms can secrete complex extracellular polymeric substances (EPS). These EPS can serve as multifunctional elements of microbial communities, involving aspects, such as protection, structure, recognition, adhesion, and physiology. These aspects can influence the interaction between microbial cells and extracellular ARG, as well as the uptake of extracellular ARG by microbial cells, thus changing the transformative capability of extracellular ARG. However, it remains unclear whether EPS can affect horizontal ARG transfer, which is one of the main processes of ARG dissemination. In light of this knowledge gap, this review provides insight into the role of EPS in the transmission of ARGs; furthermore, the mechanism of ARG spread is analyzed, and the molecular compositions and functional properties of EPS are summarized; also, how EPS influence ARG mitigation is addressed, and factors impacting how EPS facilitate ARG during wastewater treatment are summarized. This review provides comprehensive insights into the role of EPS in controlling the transport and fate of ARG during biodegradation processes at the mechanistic level.},
}
@article {pmid38168155,
year = {2023},
author = {Lass, SW and Camphire, S and Smith, BE and Eutsey, RA and Prentice, JA and Yerneni, SS and Arun, A and Bridges, AA and Rosch, JW and Conway, JF and Campbell, P and Hiller, NL},
title = {Pneumococcal Extracellular Vesicles Mediate Horizontal Gene Transfer via the Transformation Machinery.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38168155},
issn = {2692-8205},
support = {S10 OD025009/OD/NIH HHS/United States ; T32 GM133353/GM/NIGMS NIH HHS/United States ; },
abstract = {Bacterial cells secrete extracellular vesicles (EVs), the function of which is a matter of intense investigation. Here, we show that the EVs secreted by the human pathogen Streptococcus pneumoniae (pneumococcus) are associated with bacterial DNA on their surface and can deliver this DNA to the transformation machinery of competent cells. These findings suggest that EVs contribute to gene transfer in Gram-positive bacteria, and in doing so, may promote the spread of drug resistance genes in the population.},
}
@article {pmid38167305,
year = {2024},
author = {Klose, SM and Legione, AR and Monotti, I and Bushell, RN and Sugiyama, T and Browning, GF and Vaz, PK},
title = {Genomic characterization of Mycoplasma edwardii isolated from a dog bite induced cat wound reveals multiple horizontal gene transfer events and loss of the CRISPR/Cas system.},
journal = {Journal of medical microbiology},
volume = {73},
number = {1},
pages = {},
doi = {10.1099/jmm.0.001788},
pmid = {38167305},
issn = {1473-5644},
mesh = {Dogs ; Cats ; Animals ; *Mycoplasma Infections/veterinary/microbiology ; CRISPR-Cas Systems ; Gene Transfer, Horizontal ; *Mycoplasma/genetics ; Genomics ; },
abstract = {A domestic short hair cat (Felis catus) suffering from a purulent wound infection resulting from a dog bite was sampled for bacterial culture and isolation as the wound had been unresponsive to prolonged antimicrobial treatment. A mycoplasma was isolated from the wound. Whole genome sequencing of the isolate was performed using short-read Illumina and long-read Oxford Nanopore chemistry, and the organism was identified as Mycoplasma edwardii. Comparison of the genome sequence of the isolate to a reference M. edwardii genome sequence (canid isolate) identified the loss of several key bacterial factors involved in genome editing, as well the insertion of several novel ORFs most closely related to those found in other canine mycoplasmas, specifically Mycoplasma canis, M. cynos, M. molare and M. maculosa. This is only the second known report of disease caused by M. edwardii in a non-canid species, and the first report of it infecting and causing clinical disease in a cat.},
}
@article {pmid38164507,
year = {2024},
author = {Tuji, A and Ogiso-Tanaka, E and Yamaguchi, H},
title = {Complete Genome Sequence of Annamia dubia, filamentous colony-making Chroococcales with the analysis of FraC gene influencing filament integrity.},
journal = {Journal of genomics},
volume = {12},
number = {},
pages = {1-5},
pmid = {38164507},
issn = {1839-9940},
abstract = {The complete genome of Annamia dubia was sequenced. The genome size is 4.02 Mbp, including 3886286 bp circular chromosome and four circular plasmids (31516, 42453, 38085 and 24903 bp). It included 3718 protein-coding sequences, 45 tRNA genes, three sets of rRNA genes, a microcystin biosynthesis gene cluster and six CRISPR (clustered regularly interspaced short palindromic repeat). Annamia is the only one genus in the Chroococcales that makes filamentous colonies. FraC and FraG were identified in the genome. These genes are required for the integrity of cell junctions and influencing filament integrity and are thought to be related to colony formation. These genes are first reported from Chroococcales, and may play a significant role in the colony formation of this species. In the phylogenetic tree of the FraC gene, A. dubia was located in the basal position of Oscillatoriales. The GC ratio of FraC gene of A. dubia is very low from the genome and the FraC gene of Microcoleaceae. The presence of these genes in the basal region and the low GC ratio suggests that the FraC gene in this species was introduced by horizontal gene transfer. Since the filamentous colony is a fundamental and important taxonomic feature for the classification of cyanobacteria, the possibility of horizontal transmission of genes involved in filamentous cyanobacterial colonies is an important discovery for the classification of cyanobacteria.},
}
@article {pmid38163572,
year = {2024},
author = {Gaviria-Cantin, T and Fernández-Coll, L and Vargas, AF and Jiménez, CJ and Madrid, C and Balsalobre, C},
title = {Expression of accessory genes in Salmonella requires the presence of the Gre factors.},
journal = {Genomics},
volume = {116},
number = {1},
pages = {110777},
doi = {10.1016/j.ygeno.2023.110777},
pmid = {38163572},
issn = {1089-8646},
mesh = {*Salmonella typhimurium/genetics/metabolism ; Plasmids ; Virulence/genetics ; *Bacterial Proteins/genetics/metabolism ; },
abstract = {Genomic studies with Salmonella enterica serovar Typhimurium reveal a crucial role of horizontal gene transfer (HGT) in the acquisition of accessory cellular functions involved in host-interaction. Many virulence genes are located in genomic islands, plasmids and prophages. GreA and GreB proteins, Gre factors, interact transiently with the RNA polymerase alleviating backtracked complexes during transcription elongation. The overall effect of Gre factors depletion in Salmonella expression profile was studied. Both proteins are functionally redundant since only when both Gre factors were depleted a major effect in gene expression was detected. Remarkably, the accessory gene pool is particularly sensitive to the lack of Gre factors, with 18.6% of accessory genes stimulated by the Gre factors versus 4.4% of core genome genes. Gre factors involvement is particularly relevant for the expression of genes located in genomic islands. Our data reveal that Gre factors are required for the expression of accessory genes.},
}
@article {pmid38159121,
year = {2024},
author = {Wang, HM and Hu, GR and Luo, WY and Li, FL},
title = {The horizontal gene transfer of perchlorate reduction genomic island in three bacteria from an ecological niche.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {22},
pmid = {38159121},
issn = {1432-0614},
mesh = {Phylogeny ; Oxidation-Reduction ; *Perchlorates ; *Genomic Islands ; Gene Transfer, Horizontal ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Oxidoreductases/genetics ; Ecosystem ; Transposases/genetics ; },
abstract = {Three new strains of dissimilatory perchlorate-reducing bacteria (DPRB), QD19-16, QD1-5, and P3-1, were isolated from an active sludge. Phylogenetic trees based on 16S rRNA genes indicated that QD19-16, QD1-5, and P3-1 belonged to Brucella, Acidovorax, and Citrobacter, respectively, expanding the distribution of DPRB in the Proteobacteria. The three strains were gram-negative and facultative anaerobes with rod-shaped cells without flagella, which were 1.0-1.6 μm long and 0.5-0.6 μm wide. The three DPRB strains utilized similar broad spectrum of electron donors and acceptors and demonstrated a similar capability to reduce perchlorate within 6 days. The enzyme activity of perchlorate reductase in QD19-16 toward chlorate was higher than that toward perchlorate. The high sequence similarity of the perchlorate reductase operon and chlorite dismutase genes in the perchlorate reduction genomic islands (PRI) of the three strains implied that they were monophyletic origin from a common ancestral PRI. Two transposase genes (tnp1 and tnp2) were found in the PRIs of strain QD19-16 and QD1-5, but were absent in the strain P3-1 PRI. The presence of fragments of IR sequences in the P3-1 PRI suggested that P3-1 PRI had previously contained these two tnp genes. Therefore, it is plausible to suggest that a common ancestral PRI transferred across the strains Brucella sp. QD19-16, Acidovorax sp. QD1-5, and Citrobacter sp. P3-1 through horizontal gene transfer, facilitated by transposases. These results provided a direct evidence of horizontal gene transfer of PRI that could jump across phylogenetically unrelated bacteria through transposase. KEY POINTS: • Three new DPRB strains can effectively remove high concentration of perchlorate. • The PRIs of three DPRB strains are acquired from a single ancestral PRI. • PRIs are incorporated into different bacteria genome through HGT by transposase.},
}
@article {pmid38157363,
year = {2023},
author = {Wedage, WMM and Harischandra, IN and Weerasena, OVDSJ and De Silva, BGDNK},
title = {Genetic diversity and phylogeography of Phlebotomus argentipes (Diptera: Psychodidae, Phlebotominae), using COI and ND4 mitochondrial gene sequences.},
journal = {PloS one},
volume = {18},
number = {12},
pages = {e0296286},
pmid = {38157363},
issn = {1932-6203},
mesh = {Animals ; *Psychodidae/genetics ; *Phlebotomus/genetics ; Phylogeography ; Phylogeny ; Genes, Mitochondrial ; *Leishmaniasis, Cutaneous/genetics ; Sri Lanka ; Genetic Variation ; },
abstract = {BACKGROUND: Phlebotomus argentipes complex is the primary vector for cutaneous leishmaniasis, a burgeoning health concern in contemporary Sri Lanka, where effective vector control is important for proper disease management. Understanding the genetic diversity of the P. argentipes population in Sri Lanka is vital before implementing a successful vector control program. Various studies have indicated that genetic divergence, caused by genetic drift or selection, can significantly influence the vector capacity of arthropod species. To devise innovative control strategies for P. argentipes, exploring genetic diversity and phylogeography can offer valuable insights into vector competence, key genetic trait transfer, and impact on disease epidemiology. The primary objective is to analyze the genetic diversity and phylogeography of the P. argentipes complex in Sri Lanka, based on two mitochondrial genomic regions in modern representatives of P. argentipes populations.<br><br>METHODOLOGY: A total of 159 P. argentipes specimens were collected from five endemic areas of cutaneous leishmaniasis and identified morphologically. Two mitochondrial regions (Cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 4 (ND4) were amplified using the total DNA and subsequently sequenced. Partial sequences of those mitochondrial genes were utilized to analyze genetic diversity indices and to explore phylogenetic and phylogeographic relationships.<br><br>PRINCIPAL FINDINGS: Among five sampling locations, the highest genetic diversity for COI and ND4 was observed in Hambantota (Hd-0.749, &#x3c0;-0.00417) and Medirigiriya (Hd-0.977, &#x3c0;-0.01055), respectively. Phylogeographic analyses conducted using COI sequences and GenBank retrieved sequences demonstrated a significant divergence of P. argentipes haplotypes found in Sri Lanka. Results revealed that they have evolved from the Indian ancestral haplotype due to historical- geographical connections of the Indian subcontinent with Sri Lanka.<br><br>CONCLUSIONS: Utilizing high-mutation-rate mitochondrial genes, such as ND4, can enhance the accuracy of genetic variability analysis in P. argentipes populations in Sri Lanka. The phylogeographical analysis of COI gene markers in this study provides insights into the historical geographical relationship between India and P. argentipes in Sri Lanka. Both COI and ND4 genes exhibited consistent genetic homogeneity in P. argentipes in Sri Lanka, suggesting minimal impact on gene flow. This homogeneity also implies the potential for horizontal gene transfer across populations, facilitating the transmission of genes associated with traits like insecticide resistance. This dynamic undermines disease control efforts reliant on vector control strategies.},
}
@article {pmid38156017,
year = {2023},
author = {Liu, Q and Chen, Y and Xu, XW},
title = {Genomic insight into strategy, interaction and evolution of nitrifiers in metabolizing key labile-dissolved organic nitrogen in different environmental niches.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1273211},
pmid = {38156017},
issn = {1664-302X},
abstract = {Ammonia-oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and complete ammonia oxidizers (comammox) are responsible for nitrification in nature; however, some groups have been reported to utilize labile-dissolved organic nitrogen (LDON) for satisfying nitrogen demands. To understand the universality of their capacity of LDON metabolism, we collected 70 complete genomes of AOA, AOB, NOB, and comammox from typical environments for exploring their potentials in the metabolism of representative LDON (urea, polyamines, cyanate, taurine, glycine betaine, and methylamine). Genomic analyses showed that urea was the most popular LDON used by nitrifiers. Each group harbored unique urea transporter genes (AOA: dur3 and utp, AOB: utp, and NOB and comammox: urtABCDE and utp) accompanied by urease genes ureABC. The differentiation in the substrate affinity of these transporters implied the divergence of urea utilization efficiency in nitrifiers, potentially driving them into different niches. The cyanate transporter (cynABD and focA/nirC) and degradation (cynS) genes were detected mostly in NOB, indicating their preference for a wide range of nitrogen substrates to satisfy high nitrogen demands. The lack of genes involved in the metabolism of polyamines, taurine, glycine betaine, and methylamines in most of nitrifiers suggested that they were not able to serve as a source of ammonium, only if they were degraded or oxidized extracellularly as previously reported. The phylogenetic analyses assisted with comparisons of GC% and the Codon Adaptation Index between target genes and whole genomes of nitrifiers implied that urea metabolic genes dur3 and ureC in AOA evolved independently from bacteria during the transition from Thaumarchaeota to AOA, while utp in terrestrial AOA was acquired from bacteria via lateral gene transfer (LGT). Cyanate transporter genes cynS and focA/nirC detected only in a terrestrial AOA Candidadus Nitrsosphaera gargensis Ga9.2 could be gained synchronously with Nitrospira of NOB by an ancient LGT. Our results indicated that LDON utilization was a common feature in nitrifiers, but metabolic potentials were different among nitrifiers, possibly being intensely interacted with their niches, survival strategies, and evolutions.},
}
@article {pmid38153127,
year = {2024},
author = {Gucwa, K and Wons, E and Wisniewska, A and Jakalski, M and Dubiak, Z and Kozlowski, LP and Mruk, I},
title = {Lethal perturbation of an Escherichia coli regulatory network is triggered by a restriction-modification system's regulator and can be mitigated by excision of the cryptic prophage Rac.},
journal = {Nucleic acids research},
volume = {52},
number = {6},
pages = {2942-2960},
pmid = {38153127},
issn = {1362-4962},
support = {UMO-2019/35/B/NZ2/00701//National Science Center (Poland)/ ; //University of Gdansk, Poland/ ; },
mesh = {*Escherichia coli/genetics/metabolism ; Prophages/genetics/metabolism ; *Escherichia coli Proteins/genetics/metabolism ; Transcription Factors/genetics/metabolism ; DNA Restriction-Modification Enzymes/metabolism ; },
abstract = {Bacterial gene regulatory networks orchestrate responses to environmental challenges. Horizontal gene transfer can bring in genes with regulatory potential, such as new transcription factors (TFs), and this can disrupt existing networks. Serious regulatory perturbations may even result in cell death. Here, we show the impact on Escherichia coli of importing a promiscuous TF that has adventitious transcriptional effects within the cryptic Rac prophage. A cascade of regulatory network perturbations occurred on a global level. The TF, a C regulatory protein, normally controls a Type II restriction-modification system, but in E. coli K-12 interferes with expression of the RacR repressor gene, resulting in de-repression of the normally-silent Rac ydaT gene. YdaT is a prophage-encoded TF with pleiotropic effects on E. coli physiology. In turn, YdaT alters expression of a variety of bacterial regulons normally controlled by the RcsA TF, resulting in deficient lipopolysaccharide biosynthesis and cell division. At the same time, insufficient RacR repressor results in Rac DNA excision, halting Rac gene expression due to loss of the replication-defective Rac prophage. Overall, Rac induction appears to counteract the lethal toxicity of YdaT. We show here that E. coli rewires its regulatory network, so as to minimize the adverse regulatory effects of the imported C TF. This complex set of interactions may reflect the ability of bacteria to protect themselves by having robust mechanisms to maintain their regulatory networks, and/or suggest that regulatory C proteins from mobile operons are under selection to manipulate their host's regulatory networks for their own benefit.},
}
@article {pmid38148908,
year = {2023},
author = {Valenzuela, X and Hedman, H and Villagomez, A and Cardenas, P and Eisenberg, JNS and Levy, K and Zhang, L and Trueba, G},
title = {Distribution of blaCTX-M-gene variants in E. coli from different origins in Ecuador.},
journal = {Medicine in microecology},
volume = {18},
number = {},
pages = {},
pmid = {38148908},
issn = {2590-0978},
support = {K01 AI103544/AI/NIAID NIH HHS/United States ; R01 AI050038/AI/NIAID NIH HHS/United States ; R01 AI137679/AI/NIAID NIH HHS/United States ; R01 AI167989/AI/NIAID NIH HHS/United States ; },
abstract = {The increasing abundance of extended spectrum (β-lactamase (ESBL) genes in E. coli, and other commensal and pathogenic bacteria, endangers the utility of third or more recent generation cephalosporins, which are major tools for fighting deadly infections. The role of domestic animals in the transmission of ESBL carrying bacteria has been recognized, especially in low- and middle-income countries, however the horizontal gene transfer of these genes is difficult to assess. Here we investigate blaCTX-M gene diversity (and flanking nucleotide sequences) in E. coli from chicken and humans, in an Ecuadorian rural community and from chickens in another location in Ecuador. The blaCTX-M associated sequences in isolates from humans and chickens in the same remote community showed greater similarity than those found in E. coli in a chicken industrial operation 200 km away. Our study may provide evidence of blaCTX-M transfer between chickens and humans in the community.},
}
@article {pmid38147751,
year = {2024},
author = {Xu, JY and Ding, J and Du, S and Zhu, D},
title = {Tire particles and its leachates: Impact on antibiotic resistance genes in coastal sediments.},
journal = {Journal of hazardous materials},
volume = {465},
number = {},
pages = {133333},
doi = {10.1016/j.jhazmat.2023.133333},
pmid = {38147751},
issn = {1873-3336},
mesh = {*Plastics ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Genes, Bacterial ; },
abstract = {Tire particles (TPs), a significant group of microplastics, can be discharged into the coastal environments in various ways. However, our understanding of how TPs impact the antibiotic resistance and pathogenic risks of microorganisms in coastal sediments remains limited. In this study, we used metagenomics to investigate how TPs and their leachates could affect the prevalence of antibiotic resistance genes (ARGs), virulence factor genes (VFGs), and their potential risks to the living creatures such as soil invertebrates and microorganisms in the coastal sediments. We discovered that TP addition significantly increased the abundance and diversity of ARGs and VFGs in coastal sediments, with raw TPs displayed higher impacts than TP leachates and TPs after leaching on ARGs and VFGs. With increasing TP exposure concentrations, the co-occurrence frequency of ARGs and mobile genetic elements (MGEs) in the same contig also increased, suggesting that TPs could enhance the dispersal risk of ARGs. Our metagenome-based binning analysis further revealed that exposure to TPs increased the abundance of potentially pathogenic antibiotic-resistant bacteria (PARB). In addition, chemical additives of TP leachates (e.g., Zn and N-cyclohexylformamide) significantly affected the changes of ARGs in the pore water. In summary, our study provides novel insights into the adverse effects of TP pollutions on aggravating the dissemination and pathogenic risks of ARGs and PARB in the coastal environment.},
}
@article {pmid38147560,
year = {2024},
author = {Beavan, AJS and Domingo-Sananes, MR and McInerney, JO},
title = {Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {1},
pages = {e2304934120},
pmid = {38147560},
issn = {1091-6490},
support = {BB/Y513374/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {Bacteria/genetics ; *Escherichia coli/genetics ; Evolution, Molecular ; *Genome, Bacterial/genetics ; Phylogeny ; Prokaryotic Cells ; },
abstract = {Pangenomes exhibit remarkable variability in many prokaryotic species, much of which is maintained through the processes of horizontal gene transfer and gene loss. Repeated acquisitions of near-identical homologs can easily be observed across pangenomes, leading to the question of whether these parallel events potentiate similar evolutionary trajectories, or whether the remarkably different genetic backgrounds of the recipients mean that postacquisition evolutionary trajectories end up being quite different. In this study, we present a machine learning method that predicts the presence or absence of genes in the Escherichia coli pangenome based on complex patterns of the presence or absence of other accessory genes within a genome. Our analysis leverages the repeated transfer of genes through the E. coli pangenome to observe patterns of repeated evolution following similar events. We find that the presence or absence of a substantial set of genes is highly predictable from other genes alone, indicating that selection potentiates and maintains gene-gene co-occurrence and avoidance relationships deterministically over long-term bacterial evolution and is robust to differences in host evolutionary history. We propose that at least part of the pangenome can be understood as a set of genes with relationships that govern their likely cohabitants, analogous to an ecosystem's set of interacting organisms. Our findings indicate that intragenomic gene fitness effects may be key drivers of prokaryotic evolution, influencing the repeated emergence of complex gene-gene relationships across the pangenome.},
}
@article {pmid38145799,
year = {2024},
author = {Souguir, M and Châtre, P and Drapeau, A and Azaiez, S and Hmidi, I and Ncir, S and Lupo, A and Madec, JY and Haenni, M and Mansour, W},
title = {CTX-M-15/27-positive Escherichia coli and VIM-2-producing Pseudomonas putida in free-living pigeons (Columba livia) in Tunisia.},
journal = {Journal of global antimicrobial resistance},
volume = {36},
number = {},
pages = {70-75},
doi = {10.1016/j.jgar.2023.12.013},
pmid = {38145799},
issn = {2213-7173},
mesh = {Animals ; Humans ; Columbidae/genetics ; Escherichia coli ; *Pseudomonas putida/genetics ; Multilocus Sequence Typing ; Tunisia/epidemiology ; Phylogeny ; beta-Lactamases/genetics ; *Anti-Infective Agents ; },
abstract = {OBJECTIVES: Wild birds are vectors of antimicrobial resistance. Birds living in close contact with humans or other animals, like feral pigeons (Columba livia), might be especially prone to acquire resistance genes such as those encoding extended-spectrum beta-lactamases (ESBLs) and carbapenemases.<br><br>METHODS: Cloacal samples (n = 206) of free-living feral pigeons (C. livia) were collected in Sousse and Monastir, Tunisia. Antimicrobial susceptibility profiles were determined by disc-diffusion, and resistant isolates were short- and long-read whole-genome sequenced. Sequence analysis was performed using tools of the Centre for Genomic Epidemiology, and Phylogenetic analysis was performed based on the core-genome MLST.<br><br>RESULTS: Fourteen (14/206, 6.8%) pigeons harboured Enterobacterales resistant to last-generations cephalosporins, of which 10 were CTX-M-15- or CTX-M-27-producers, while two (1.0%) carried a VIM-2-producing Pseudomonas putida. Positive pigeons lived on four different livestock farms. Three STs (ST206, ST5584, ST8149) were identified among E. coli, of which ST5584 and ST8149 were found in two different farms. Genetic diversity was also observed in Enterobacter cloacae and P. putida isolates. The blaCTX-M-27 genes were chromosomally encoded, while the blaCTX-M-15 genes were carried on highly similar IncF/F-:A-:B53 plasmids. The blaVIM-2 gene was located on a class 1 integron co-harbouring several resistance genes.<br><br>CONCLUSION: Pigeons living on livestock farms carried clinically important resistance genes encoding ESBLs and carbapenemases. Our results evidenced that both clonal (ST8149 and ST5584) and plasmidic (IncF/F-:A-:B53) transfers played a role in the spread of resistance genes among pigeons. Further studies are needed to identify factors favouring the transfer and persistence of resistance genes within the pigeon communities.},
}
@article {pmid38145364,
year = {2024},
author = {Gong, C and Guo, Z and Hu, Y and Yang, Z and Xia, J and Yang, X and Xie, W and Wang, S and Wu, Q and Ye, W and Zhou, X and Turlings, TCJ and Zhang, Y},
title = {A Horizontally Transferred Plant Fatty Acid Desaturase Gene Steers Whitefly Reproduction.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {11},
number = {10},
pages = {e2306653},
pmid = {38145364},
issn = {2198-3844},
support = {CAAS-ASTIP-IVFCAAS//Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences/ ; 788949//European Research Council Advanced/ ; 32221004//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 2021YFD1400600//Key Technologies Research and Development Program/ ; CARS-23//Earmarked Fund for China Agriculture Research System/ ; //Beijing Key Laboratory for Pest Control and Sustainable Cultivation of Vegetables/ ; },
mesh = {Animals ; *Fatty Acid Desaturases/genetics ; *Hemiptera/genetics ; Drosophila melanogaster ; Fatty Acids, Unsaturated ; Stearoyl-CoA Desaturase ; Reproduction ; },
abstract = {Polyunsaturated fatty acids (PUFAs) are essential nutrients for all living organisms. PUFA synthesis is mediated by Δ12 desaturases in plants and microorganisms, whereas animals usually obtain PUFAs through their diet. The whitefly Bemisia tabaci is an extremely polyphagous agricultural pest that feeds on phloem sap of many plants that do not always provide them with sufficient PUFAs. Here, a plant-derived Δ12 desaturase gene family BtFAD2 is characterized in B. tabaci and it shows that the BtFAD2-9 gene enables the pest to synthesize PUFAs, thereby significantly enhancing its fecundity. The role of BtFAD2-9 in reproduction is further confirmed by transferring the gene to Drosophila melanogaster, which also increases the fruit fly's reproduction. These findings reveal an extraordinary evolutionary scenario whereby a phytophagous insect acquired a family of plant genes that enables it to synthesize essential nutrients, thereby lessening its nutritional dependency and allowing it to feed and reproduce on many host plants.},
}
@article {pmid38145107,
year = {2023},
author = {Dabbaghie, F and Srikakulam, SK and Marschall, T and Kalinina, OV},
title = {PanPA: generation and alignment of panproteome graphs.},
journal = {Bioinformatics advances},
volume = {3},
number = {1},
pages = {vbad167},
pmid = {38145107},
issn = {2635-0041},
abstract = {MOTIVATION: Compared to eukaryotes, prokaryote genomes are more diverse through different mechanisms, including a higher mutation rate and horizontal gene transfer. Therefore, using a linear representative reference can cause a reference bias. Graph-based pangenome methods have been developed to tackle this problem. However, comparisons in DNA space are still challenging due to this high diversity. In contrast, amino acid sequences have higher similarity due to evolutionary constraints, whereby a single amino acid may be encoded by several synonymous codons. Coding regions cover the majority of the genome in prokaryotes. Thus, panproteomes present an attractive alternative leveraging the higher sequence similarity while not losing much of the genome in non-coding regions.<br><br>RESULTS: We present PanPA, a method that takes a set of multiple sequence alignments of protein sequences, indexes them, and builds a graph for each multiple sequence alignment. In the querying step, it can align DNA or amino acid sequences back to these graphs. We first showcase that PanPA generates correct alignments on a panproteome from 1350 Escherichia coli. To demonstrate that panproteomes allow comparisons at longer phylogenetic distances, we compare DNA and protein alignments from 1073 Salmonella enterica assemblies against E.coli reference genome, pangenome, and panproteome using BWA, GraphAligner, and PanPA, respectively; with PanPA aligning around 22% more sequences. We also aligned a DNA short-reads whole genome sequencing (WGS) sample from S.enterica against the E.coli reference with BWA and the panproteome with PanPA, where PanPA was able to find alignment for 68% of the reads compared to 5% with BWA.<br><br>PanPA is available at https://github.com/fawaz-dabbaghieh/PanPA.},
}
@article {pmid38143074,
year = {2023},
author = {Kurushima, J},
title = {[Mechanism of high-frequent horizontal gene transfer in Gram positive bacterial pathogens].},
journal = {Nihon saikingaku zasshi. Japanese journal of bacteriology},
volume = {78},
number = {4},
pages = {179-187},
doi = {10.3412/jsb.78.179},
pmid = {38143074},
issn = {1882-4110},
mesh = {*Gene Transfer, Horizontal ; Plasmids/genetics ; Gram-Positive Bacteria/genetics ; Enterococcus faecalis/genetics ; *Anti-Infective Agents ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; },
abstract = {Horizontal gene transfer through transconjugation and natural transformation plays a major role in the spread of antimicrobial resistance. Although the phenomenon of genetic element transmission has long been known, the rapid increase in the number of antimicrobial resistant bacteria in recent years and the accompanying accumulation of genomic information have revealed that horizontal gene transfer contributes to genome plasticity in various ways. The author reported the molecular mechanism of the antimicrobial activity of the accessory factor bacteriocin encoded by the junctional transfer plasmid of Enterococcus faecalis, a representative Gram-positive opportunistic pathogen that is concerned as highly antimicrobial resistant, and found diversity in the selfimmune system based on epidemiological studies. In addition, the author established a technique to visualize and quantify genomic recombination by natural transformation in Streptococcus pneumoniae which is also one of the most concerns for antimicrobial resistance and vaccine escape, at single cells level resolution in real time. Focuses on outcome from these research, this paper introduces the molecular mechanisms that promote horizontal gene transmission and the prospects for their technological application.},
}
@article {pmid38142651,
year = {2024},
author = {Ni, B and Zhang, TL and Cai, TG and Xiang, Q and Zhu, D},
title = {Effects of heavy metal and disinfectant on antibiotic resistance genes and virulence factor genes in the plastisphere from diverse soil ecosystems.},
journal = {Journal of hazardous materials},
volume = {465},
number = {},
pages = {133335},
doi = {10.1016/j.jhazmat.2023.133335},
pmid = {38142651},
issn = {1873-3336},
mesh = {Soil ; Anti-Bacterial Agents/pharmacology ; Ecosystem ; *Disinfectants/pharmacology ; *Metals, Heavy ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Environmental Pollutants ; Soil Microbiology ; },
abstract = {Antibiotic-resistance genes (ARGs) are world-wide contaminants posing potential health risks. Quaternary ammonium compounds (QACs) and heavy metals can apply selective pressure on antibiotic resistance. However, there is a lack of evidence regarding their coupled effect on changes in ARGs and virulence factor genes (VFGs) in various soil types and their plastispheres. Herein, we conducted a microcosm experiment to explore the abundances and profiles of ARGs and VFGs in soil plastispheres from three distinct types of soils amended with Cu and disinfectants. The plastispheres enriched the ARGs' abundance compared to soils and stimulated the coupling effect of combined pollutants on promoting the abundances of ARGs and VFGs. Horizontal gene transfer inevitably accelerates the propagation of ARGs and VFGs in plastispheres under pollutant stress. In plastispheres, combined exposure to disinfectants and Cu increased some potential pathogens' relative abundances. Moreover, the combined effect of disinfectants and Cu on ARGs and VFGs changed with soil type in plastispheres, emphasising the necessity to incorporate soil type considerations into health risk assessments for ARGs and VFGs. Overall, this study highlights the high health risks of ARGs under the selective pressure of combined pollutants in plastispheres and provides valuable insights for future risk assessments related to antibiotic resistance.},
}
@article {pmid38141819,
year = {2024},
author = {Veloo, ACM and Boiten, KE and Hendrickx, APA and van Prehn, J and Rossen, JWA},
title = {Horizontal gene transfer of a cfiA element between two different Bacteroides species within a clinical specimen.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {30},
number = {4},
pages = {554-555},
doi = {10.1016/j.cmi.2023.12.022},
pmid = {38141819},
issn = {1469-0691},
mesh = {Humans ; *Bacteroides/genetics ; *Gene Transfer, Horizontal ; Anti-Bacterial Agents ; Meropenem ; Bacterial Proteins/genetics ; beta-Lactamases/genetics ; Microbial Sensitivity Tests ; },
}
@article {pmid38136990,
year = {2023},
author = {Skoog, EJ and Fournier, GP and Bosak, T},
title = {Assessing the Influence of HGT on the Evolution of Stress Responses in Microbial Communities from Shark Bay, Western Australia.},
journal = {Genes},
volume = {14},
number = {12},
pages = {},
pmid = {38136990},
issn = {2073-4425},
support = {327126//Simons Foundation/ ; 344707//Simons Foundation/ ; },
mesh = {Western Australia ; *Bays ; Gene Transfer, Horizontal ; *Microbiota ; Metagenome ; },
abstract = {Pustular microbial mats in Shark Bay, Western Australia, are modern analogs of microbial systems that colonized peritidal environments before the evolution of complex life. To understand how these microbial communities evolved to grow and metabolize in the presence of various environmental stresses, the horizontal gene transfer (HGT) detection tool, MetaCHIP, was used to identify the horizontal transfer of genes related to stress response in 83 metagenome-assembled genomes from a Shark Bay pustular mat. Subsequently, maximum-likelihood phylogenies were constructed using these genes and their most closely related homologs from other environments in order to determine the likelihood of these HGT events occurring within the pustular mat. Phylogenies of several stress-related genes-including those involved in response to osmotic stress, oxidative stress and arsenic toxicity-indicate a potentially long history of HGT events and are consistent with these transfers occurring outside of modern pustular mats. The phylogeny of a particular osmoprotectant transport gene reveals relatively recent adaptations and suggests interactions between Planctomycetota and Myxococcota within these pustular mats. Overall, HGT phylogenies support a potentially broad distribution in the relative timing of the HGT events of stress-related genes and demonstrate ongoing microbial adaptations and evolution in these pustular mat communities.},
}
@article {pmid38136957,
year = {2023},
author = {Qin, Y and Qu, B and Lee, B},
title = {Propidium Monoazide-Treated, Cell-Direct, Quantitative PCR for Detecting Viable Chloramphenicol-Resistant Escherichia coli and Corynebacterium glutamicum Cells.},
journal = {Genes},
volume = {14},
number = {12},
pages = {},
pmid = {38136957},
issn = {2073-4425},
support = {20014752//Ministry of Trade, Industry and Energy/ ; },
mesh = {*Escherichia coli/genetics ; *Corynebacterium glutamicum/genetics ; Real-Time Polymerase Chain Reaction/methods ; Ecosystem ; DNA ; },
abstract = {With the rapid development and commercialization of industrial genetically modified microorganisms (GMMs), public concerns regarding their potential effects are on the rise. It is imperative to promptly monitor the unintended release of viable GMMs into wastewater, the air, and the surrounding ecosystems to prevent the risk of horizontal gene transfer to native microorganisms. In this study, we have developed a method that combines propidium monoazide (PMA) with a dual-plex quantitative PCR (qPCR) approach based on TaqMan probes. This method targets the chloramphenicol-resistant gene (CmR) along with the endogenous genes D-1-deoxyxylulose 5-phosphate synthase (dxs) and chromosomal replication initiator protein (dnaA). It allows for the direct quantitative detection of viable genetically modified Escherichia coli and Corynebacterium glutamicum cells, eliminating the requirement for DNA isolation. The dual-plex qPCR targeting CmR/dxs and CmR/dnaA demonstrated excellent performance across various templates, including DNA, cultured cells, and PMA-treated cells. Repeatability and precision, defined as RSDr% and bias%, respectively, were calculated and found to fall within the acceptable limits specified by the European Network of GMO Laboratories (ENGL). Through PMA-qPCR assays, we determined the detection limits for viable chloramphenicol-resistant E. coli and C. glutamicum strains to be 20 and 51 cells, respectively, at a 95% confidence level. Notably, this method demonstrated superior sensitivity compared to Enzyme-Linked Immunosorbent Assay (ELISA), which has a detection limit exceeding 1000 viable cells for both GM bacterial strains. This approach offers the potential to accurately and efficiently detect viable cells of GMMs, providing a time-saving and cost-effective solution.},
}
@article {pmid38136751,
year = {2023},
author = {Golikova, MV and Alieva, KN and Strukova, EN and Kondratieva, DA and Petrova, NF and Petrova, MA and Zinner, SH},
title = {Comparative Meropenem Pharmacodynamics and Emergence of Resistance against Carbapenem-Susceptible Non-Carbapenemase-Producing and Carbapenemase-Producing Enterobacterales: A Pharmacodynamic Study in a Hollow-Fiber Infection Model.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {12},
pages = {},
pmid = {38136751},
issn = {2079-6382},
support = {23-25-00525//Russian Science Foundation/ ; },
abstract = {Resistance to carbapenems has become a problem due to Klebsiella pneumoniae (K. pneumoniae), harboring carbapenemases. Among them, there are isolates that are recognized as carbapenem-susceptible; however, these carbapenemase-producing strains with low meropenem minimal inhibitory concentrations (MICs) may pose a threat to public health. We aimed to investigate the impact of the ability to produce carbapenemases by a bacterial isolate on the effectiveness of meropenem in the hollow-fiber infection model. K. pneumoniae and Escherichia coli (E. coli) strains with equal meropenem MICs but differing in their ability to produce carbapenemases were used in pharmacodynamic simulations with meropenem. In addition to standard MIC determination, we assessed the MICs against tested strains at high inoculum density to test if the inoculum effect occurs. According to pharmacodynamic data, the carbapenemase-producing strains were characterized with a relatively decreased meropenem effectiveness compared to non-producers. Meanwhile, the effect of meropenem perfectly correlated with the meropenem exposure expressed as the DOSE/MIC ratio when high-inoculum (HI) MICs but not standard-inoculum (SI) MICs were used for regression analysis. It could be concluded that meropenem-susceptible carbapenemase-producing strains may not respond to meropenem therapy; the antibiotic inoculum effect (IE) may have a prognostic value to reveal the meropenem-susceptible Enterobacterales that harbor carbapenemase genes.},
}
@article {pmid38135742,
year = {2023},
author = {Fang, Z and Xu, M and Shen, S and Sun, W and Yu, Q and Wu, Q and Xiang, L and Weng, Q},
title = {Prediction and characterization of prophages of Stenotrophomonas maltophilia reveals a remarkable phylogenetic diversity of prophages.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {22941},
pmid = {38135742},
issn = {2045-2322},
support = {U1812401//Joint Fund of the National Natural Science Foundation of China and the Karst Science Research Center of Guizhou Province/ ; },
mesh = {*Prophages/genetics ; Phylogeny ; *Stenotrophomonas maltophilia/genetics ; Genomics ; Gene Transfer, Horizontal ; },
abstract = {Prophages, which enables bacterial hosts to acquire novel traits, and increase genetic variation and evolutionary innovation, are considered to be one of the greatest drivers of bacterial diversity and evolution. Stenotrophomonas maltophilia is widely distributed and one of the most important multidrug resistant bacteria in hospitals. However, the distribution and genetic diversity of S. maltophilia prophages have not been elucidated. In this study, putative prophages were predicted in S. maltophilia genomes by using virus prediction tools, and the genetic diversity and phylogeny of S. maltophilia and the prophages they harbor were further analyzed. A total of 356 prophage regions were predicted from 88 S. maltophilia genomes. Among them, 144 were intact prophages, but 77.09% of the intact prophages did not match any known phage sequences in the public database. The number of prophage carried by S. maltophilia is related to its host habitat and is an important factor affecting the size of the host genome, but it is not related to the genetic diversity of the prophage. The prediction of auxiliary genes encoded by prophage showed that antibiotic resistance genes was not predicted for any of the prophages except for one questionable prophage, while 53 virulence genes and 169 carbohydrate active enzymes were predicted from 11.24 and 44.1% prophages, respectively. Most of the prophages (72.29%) mediated horizontal gene transfer of S. maltophilia genome, but only involved in 6.25% of the horizontal gene transfer events. In addition, CRISPR prediction indicated 97.75% S. maltophilia strains contained the CRISPR-Cas system containing 818 spacer sequences. However, these spacer sequences did not match any known S. maltophilia phages, and only a few S. maltophilia prophages. Comparative genomic analysis revealed a highly conserved and syntenic organization with genomic rearrangement between the prophages and the known related S. maltophilia phages. Our results indicate a high prevalence and genetic diversity of prophages in the genome of S. maltophilia, as well as the presence of a large number of uncharacterized phages. It provides an important complement to understanding the diversity and biological characteristics of phages, as well as the interactions and evolution between bacteria and phages.},
}
@article {pmid38135225,
year = {2024},
author = {Wang, M and Wang, C and Yang, J and Liu, X and Xie, B and Ren, P and Kong, X and Fu, Y},
title = {Biochar induces different responses of intracellular and extracellular antibiotic resistance genes and suppresses horizontal transfer during lincomycin fermentation dregs composting.},
journal = {Bioresource technology},
volume = {394},
number = {},
pages = {130227},
doi = {10.1016/j.biortech.2023.130227},
pmid = {38135225},
issn = {1873-2976},
mesh = {*Anti-Bacterial Agents/pharmacology ; Lincomycin/pharmacology ; *Composting ; Fermentation ; Escherichia coli/genetics ; Genes, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; *Charcoal ; },
abstract = {This study aims to indicate the influence of biochar on extracellular and intracellular ARGs (e/iARGs) variation and proliferation during lincomycin fermentation dregs (LFDs) compost. Biochar addition made iARGs keep reducing but eARGs increase to the maximum at the middle thermophilic phase and reduce at the end of the compost. Compared to control 3.15-log and 5.42-log reduction of iARGs and eARGs were observed, respectively. Biochar addition, bacterial community, and MGEs were the major contributors to iARGs and eARGs removal, with the contribution percentages of 38.4%, 31.0%, 23.7%, and 27.2%, 29.1%, and 34.9%, respectively. Moreover, biochar significantly inhibited eARGs transformation and RP4 plasmid conjugative transfer among E. coli DH5α and Pseudomonas aeruginosa HLS-6. The underlying mechanism involved in broken cell membranes of bacteria, and altered expression of oxidative stress genes and save our souls (SOS) response-related genes. The results indicated that biochar addition in composting could limit the dissemination of ARGs.},
}
@article {pmid38135177,
year = {2024},
author = {Mukherjee, A and Kizziah, JL and Hawkins, NC and Nasef, MO and Parker, LK and Dokland, T},
title = {Structure of the Portal Complex from Staphylococcus aureus Pathogenicity Island 1 Transducing Particles In Situ and In Isolation.},
journal = {Journal of molecular biology},
volume = {436},
number = {4},
pages = {168415},
pmid = {38135177},
issn = {1089-8638},
support = {P30 CA013148/CA/NCI NIH HHS/United States ; R01 AI083255/AI/NIAID NIH HHS/United States ; S10 OD024978/OD/NIH HHS/United States ; U24 GM116789/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Capsid Proteins/chemistry ; Cryoelectron Microscopy ; *Genomic Islands ; *Staphylococcus aureus/genetics/pathogenicity/virology ; *Staphylococcus Phages/genetics ; Virulence Factors/genetics ; Transduction, Genetic ; DNA Packaging ; Nucleic Acid Conformation ; },
abstract = {Staphylococcus aureus is an important human pathogen, and the prevalence of antibiotic resistance is a major public health concern. The evolution of pathogenicity and resistance in S. aureus often involves acquisition of mobile genetic elements (MGEs). Bacteriophages play an especially important role, since transduction represents the main mechanism for horizontal gene transfer. S. aureus pathogenicity islands (SaPIs), including SaPI1, are MGEs that carry genes encoding virulence factors, and are mobilized at high frequency through interactions with specific "helper" bacteriophages, such as 80α, leading to packaging of the SaPI genomes into virions made from structural proteins supplied by the helper. Among these structural proteins is the portal protein, which forms a ring-like portal at a fivefold vertex of the capsid, through which the DNA is packaged during virion assembly and ejected upon infection of the host. We have used high-resolution cryo-electron microscopy to determine structures of the S. aureus bacteriophage 80α portal itself, produced by overexpression, and in situ in the empty and full SaPI1 virions, and show how the portal interacts with the capsid. These structures provide a basis for understanding portal and capsid assembly and the conformational changes that occur upon DNA packaging and ejection.},
}
@article {pmid38134694,
year = {2024},
author = {Fang, Y and Chen, C and Cui, B and Zhou, D},
title = {Nanoscale zero-valent iron alleviate antibiotic resistance risk during managed aquifer recharge (MAR) by regulating denitrifying bacterial network.},
journal = {Journal of hazardous materials},
volume = {465},
number = {},
pages = {133238},
doi = {10.1016/j.jhazmat.2023.133238},
pmid = {38134694},
issn = {1873-3336},
mesh = {Iron ; Bacteria ; Anti-Bacterial Agents ; *Groundwater ; Drug Resistance, Microbial ; *Water Pollutants, Chemical ; },
abstract = {The frequent occurrence of antibiotics in reclaimed water is concerning, in the case of managed aquifer recharge (MAR), it inevitably hinders further water purification and accelerates the evolutionary resistance in indigenous bacteria. In this study, we constructed two column reactors and nanoscale zero-valent iron (nZVI) amendment was applied for its effects on water quality variation, microbial community succession, and antibiotic resistance genes (ARGs) dissemination, deciphered the underlying mechanism of resistance risk reduction. Results showed that nZVI was oxidized to iron oxides in the sediment column, and total effluent iron concentration was within permissible limits. nZVI enhanced NO3[-]-N removal by 15.5% through enriching denitrifying bacteria and genes, whereas made no effects on oxacillin (OXA) removal. In addition, nZVI exhibited a pivotal impact on ARGs and plasmids decreasing. Network analysis elucidated that the diversity and richness of ARG host declined with nZVI amendment. Denitrifying bacteria play a key role in suppressing horizontal gene transfer (HGT). The underlying mechanisms of inhibited HGT included the downregulated SOS response, the inhibited Type-Ⅳ secretion system and the weakened driving force. This study afforded vital insights into ARG spread control, providing a reference for future applications of nZVI in MAR.},
}
@article {pmid38134686,
year = {2024},
author = {Zhang, J and Lu, K and Zhu, L and Li, N and Lin, D and Cheng, Y and Wang, M},
title = {Inhibition of quorum sensing serves as an effective strategy to mitigate the risks of human bacterial pathogens in soil.},
journal = {Journal of hazardous materials},
volume = {465},
number = {},
pages = {133272},
doi = {10.1016/j.jhazmat.2023.133272},
pmid = {38134686},
issn = {1873-3336},
mesh = {Humans ; *Quorum Sensing ; *Biofilms ; Soil ; Bacteria ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The coexistence of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factor genes (VFGs) in human bacterial pathogens (HBPs) increases their risks to ecological security and human health and no effective strategy is available. Herein, we demonstrated two typical quorum sensing (QS) interfering agents, 4-nitropyridine-N-oxide (4-NPO, a QS inhibitor) and Acylase Ⅰ (a quorum quenching (QQ) enzyme), effectively decreased the abundance of HBPs by 48.30% and 72.54%, respectively, which was accompanied by the reduction of VFGs, ARGs, and MGEs. The decrease in QS signals mediated by QS interfering agents disturbed bacterial communication and inhibited biofilm formation. More importantly, QS interfering agents reduced the intra-species and inter-species conjugation frequencies among bacteria, considerably inhibiting the dissemination of ARGs and VFGs via horizontal gene transfer. Furthermore, the QS interfering agents did not significantly affect the metabolic function of other nonpathogenic microorganisms in the soil. Collectively, our study provides an effective and eco-friendly strategy to mitigate the risks of HBPs in soil.},
}
@article {pmid38133813,
year = {2023},
author = {Seethalakshmi, PS and Prabhakaran, A and Kiran, GS and Selvin, J},
title = {Genomic insights into plasmid-mediated antimicrobial resistance in the bacterium Bhargavaea beijingensis strain PS04.},
journal = {Archives of microbiology},
volume = {206},
number = {1},
pages = {33},
pmid = {38133813},
issn = {1432-072X},
support = {BT/IN/Indo-UK/AMR-Env/02/JS/2020-21//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {Plasmids/genetics ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; Genomics ; *Anti-Bacterial Agents/pharmacology ; Humans ; Planococcaceae ; Soil ; },
abstract = {The dissemination of antimicrobial-resistant bacteria through environment is a major health concern for public health. Pathogenic bacteria in natural environment can mediate the transfer of antimicrobial-resistant genes via horizontal gene transfer to naturally occurring bacteria in the soil. Bhargavaea beijingensis is a Gram-negative bacterium that is commonly found in soil and water. In recent years, there has been an emergence of antibiotic-resistant strains of environmental bacteria, which pose a significant threat to human health. One mechanism of antibiotic resistance in bacteria is through the acquisition of plasmids, which can carry genes that confer resistance to various antibiotics. In this study, a novel plasmid of repUS12 replicon type was identified in the strain PS04 of B. beijingensis, which carried the ermT and tet(L) genes, encoding resistance to macrolides, lincosamides, and tetracycline. The plasmid was found to be the first of its kind in B. beijingensis and was thought to have been acquired through horizontal gene transfer. The emergence of plasmid-mediated resistance in B. beijingensis highlights the need for continued surveillance and monitoring of antibiotic resistance in environmental bacteria.},
}
@article {pmid38133341,
year = {2023},
author = {Zell, R and Groth, M and Selinka, L and Selinka, HC},
title = {Exploring the Diversity of Plant-Associated Viruses and Related Viruses in Riverine Freshwater Samples Collected in Berlin, Germany.},
journal = {Pathogens (Basel, Switzerland)},
volume = {12},
number = {12},
pages = {},
pmid = {38133341},
issn = {2076-0817},
abstract = {Plant-infecting RNA viruses from 30 families and floating genera, as well as a great number of uncultured as yet-unclassified plant-associated viruses have been described. Even so, the plant RNA virosphere is still underexplored. RNA extracted from enriched virus particles of 50 L water samples from the Teltow Canal and the Havel River in Berlin, Germany, was sequenced using Illumina next-generation sequencing. Sequences were searched for plant viruses with BLAST and DIAMOND. Phylogenetic analyses were conducted with IQ-TREE 2. Altogether, 647 virus sequences greater than 1 kb were detected and further analyzed. These data revealed the presence of accepted and novel viruses related to Albetovirus, Alphaflexiviridae, Aspiviridae, Bromoviridae, Endornaviridae, Partitiviridae, Potyviridae, Solemoviridae, Tombusviridae and Virgaviridae. The vast majority of the sequences were novel and could not be taxonomically assigned. Several tombus- and endorna-like viruses make use of alternative translation tables that suggest unicellular green algae, ciliates, or diplomonades as their hosts. The identification of 27 albeto-like satellite viruses increases available sequence data five-fold. Sixteen new poty-like viruses align with other poty-like viruses in a link that combines the Astroviridae and Potyviridae families. Further, the identification of viruses with peptidase A6-like and peptidase A21-like capsid proteins suggests horizontal gene transfer in the evolution of these viruses.},
}
@article {pmid38132959,
year = {2023},
author = {Entfellner, E and Baumann, KBL and Edwards, C and Kurmayer, R},
title = {High Structural Diversity of Aeruginosins in Bloom-Forming Cyanobacteria of the Genus Planktothrix as a Consequence of Multiple Recombination Events.},
journal = {Marine drugs},
volume = {21},
number = {12},
pages = {},
pmid = {38132959},
issn = {1660-3397},
support = {P 32193/FWF_/Austrian Science Fund FWF/Austria ; P32193//FWF Austrian Science Fund/ ; DOC [Doktorand/inn/enprogramm]//Austrian Academy of Sciences/ ; P24070//FWF Austrian Science Fund/ ; },
mesh = {Planktothrix ; *Cyanobacteria/genetics ; Microcystins/genetics ; *Microcystis ; Fresh Water ; Recombination, Genetic ; },
abstract = {Many compounds produced by cyanobacteria act as serine protease inhibitors, such as the tetrapeptides aeruginosins (Aer), which are found widely distributed. The structural diversity of Aer is intriguingly high. However, the genetic basis of this remains elusive. In this study, we explored the genetic basis of Aer synthesis among the filamentous cyanobacteria Planktothrix spp. In total, 124 strains, isolated from diverse freshwater waterbodies, have been compared regarding variability within Aer biosynthesis genes and the consequences for structural diversity. The high structural variability could be explained by various recombination processes affecting Aer synthesis, above all, the acquisition of accessory enzymes involved in post synthesis modification of the Aer peptide (e.g., halogenases, glycosyltransferases, sulfotransferases) as well as a large-range recombination of Aer biosynthesis genes, probably transferred from the bloom-forming cyanobacterium Microcystis. The Aer structural composition differed between evolutionary Planktothrix lineages, adapted to either shallow or deep waterbodies of the temperate climatic zone. Thus, for the first time among bloom-forming cyanobacteria, chemical diversification of a peptide family related to eco-evolutionary diversification has been described. It is concluded that various Aer peptides resulting from the recombination event act in chemical defense, possibly as a replacement for microcystins.},
}
@article {pmid38131669,
year = {2024},
author = {Hofstaedter, CE and Chandler, CE and Met, CM and Gillespie, JJ and Harro, JM and Goodlett, DR and Rasko, DA and Ernst, RK},
title = {Divergent Pseudomonas aeruginosa LpxO enzymes perform site-specific lipid A 2-hydroxylation.},
journal = {mBio},
volume = {15},
number = {2},
pages = {e0282323},
pmid = {38131669},
issn = {2150-7511},
support = {R01 AI104895/AI/NIAID NIH HHS/United States ; U19 AI110820/AI/NIAID NIH HHS/United States ; R21 AI146773/AI/NIAID NIH HHS/United States ; T32 AI162579/AI/NIAID NIH HHS/United States ; R21 AI156762/AI/NIAID NIH HHS/United States ; R01 AI147314/AI/NIAID NIH HHS/United States ; R21 AI166832/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; Animals ; Mice ; Pseudomonas aeruginosa/metabolism ; Lipid A/metabolism ; Persistent Infection ; Laurates/metabolism ; Hydroxylation ; *Cystic Fibrosis/microbiology ; *Pseudomonas Infections/microbiology ; *Dioxygenases/metabolism ; },
abstract = {Pseudomonas aeruginosa can survive in a myriad of environments, partially due to modifications of its lipid A, the membrane anchor of lipopolysaccharide. We previously demonstrated that divergent late acyltransferase paralogs, HtrB1 and HtrB2, add acyloxyacyl laurate to lipid A 2- and 2'-acyl chains, respectively. The genome of P. aeruginosa also has genes which encode two dioxygenase enzymes, LpxO1 and LpxO2, that individually hydroxylate a specific secondary laurate. LpxO1 acts on the 2'-acyloxyacyl laurate (added by HtrB2), whereas LpxO2 acts on the 2-acyloxyacyl laurate (added by HtrB1) in a site-specific manner. Furthermore, while both enzyme pairs are evolutionarily linked, phylogenomic analysis suggests the LpxO1/HtrB2 enzyme pair as being of ancestral origin, present throughout the Pseudomonas lineage, whereas the LpxO2/HtrB1 enzyme pair likely arose via horizontal gene transfer and has been retained in P. aeruginosa over time. Using a murine pulmonary infection model, we showed that both LpxO1 and LpxO2 enzymes are functional in vivo, as direct analysis of in vivo lipid A structure from bronchoalveolar lavage fluid revealed 2-hydroxylated lipid A. Gene expression analysis reveals increased lpxO2 but unchanged lpxO1 expression in vivo, suggesting differential regulation of these enzymes during infection. We also demonstrate that loss-of-function mutations arise in lpxO1 and lpxO2 during chronic lung infection in people with cystic fibrosis (CF), indicating a potential role for pathogenesis and airway adaptation. Collectively, our study characterizes lipid A 2-hydroxylation during P. aeruginosa airway infection that is regulated by two distinct lipid A dioxygenase enzymes.IMPORTANCEPseudomonas aeruginosa is an opportunistic pathogen that causes severe infection in hospitalized and chronically ill individuals. During infection, P. aeruginosa undergoes adaptive changes to evade host defenses and therapeutic interventions, increasing mortality and morbidity. Lipid A structural alteration is one such change that P. aeruginosa isolates undergo during chronic lung infection in CF. Investigating genetic drivers of this lipid A structural variation is crucial in understanding P. aeruginosa adaptation during infection. Here, we describe two lipid A dioxygenases with acyl-chain site specificity, each with different evolutionary origins. Further, we show that loss of function in these enzymes occurs in CF clinical isolates, suggesting a potential pathoadaptive phenotype. Studying these bacterial adaptations provides insight into selection pressures of the CF airway on P. aeruginosa phenotypes that persist during chronic infection. Understanding these adaptive changes may ultimately provide clinicians better control over bacterial populations during chronic infection.},
}
@article {pmid38128981,
year = {2024},
author = {Carusi, J and Kabuki, DY and de Seixas Pereira, PM and Cabral, L},
title = {Aeromonas spp. in drinking water and food: Occurrence, virulence potential and antimicrobial resistance.},
journal = {Food research international (Ottawa, Ont.)},
volume = {175},
number = {},
pages = {113710},
doi = {10.1016/j.foodres.2023.113710},
pmid = {38128981},
issn = {1873-7145},
mesh = {Animals ; Humans ; *Aeromonas ; Virulence/genetics ; Anti-Bacterial Agents/pharmacology ; *Drinking Water ; Base Composition ; Drug Resistance, Bacterial ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; *Anti-Infective Agents ; },
abstract = {Aeromonas sp. is a Gram-negative, non-spore-forming, rod-shaped, oxidase-positive, facultative anaerobic bacterium and a natural contaminant found in aquatic environments. Some species can invade, colonize, and damage host cells due to the presence of virulence factors, such as flagella, elastase, hemolysins, aerolysins, adhesins, enterotoxins, phospholipases and lipases, that lead to pathogenic activities. Consequently, can cause many health disorders that range from gastrointestinal problems, enteric infections, and ulcers to hemorrhagic septicemia. Aeromonas has been isolated and identified from a variety of sources, including drinking water and ready-to-eat foods (fish, meat, fresh vegetables, dairy products, and others). Some species of this opportunistic pathogen are resistant to several commercial antibiotics, including some used as a last resort for treatment, which represents a major challenge in the clinical segment. Antimicrobial resistance can be attributed to the indiscriminate use of antibiotics by society in aquaculture and horticulture. In addition, antibiotic resistance is attributed to plasmid transfer between microorganisms and horizontal gene transfer. This review aimed to (i) verify the occurrence of Aeromonas species in water and food intended for human consumption; (ii) identify the methods used to detect Aeromonas species; (iii) report on the virulence genes carried by different species; and (iv) report on the antimicrobial resistance of this genus in the last 5 years of research. Additionally, we present the existence of Aeromonas spp. resistant to antimicrobials in food and drinking water represents a potential threat to public health.},
}
@article {pmid38124028,
year = {2023},
author = {Naidoo, N and Zishiri, OT},
title = {Comparative genomics analysis and characterization of Shiga toxin-producing Escherichia coli O157:H7 strains reveal virulence genes, resistance genes, prophages and plasmids.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {791},
pmid = {38124028},
issn = {1471-2164},
mesh = {Virulence/genetics ; *Prophages/genetics ; Plasmids/genetics ; *Escherichia coli O157/genetics ; Genomics ; },
abstract = {Escherichia coli O157:H7 is a foodborne pathogen that has been linked to global disease outbreaks. These diseases include hemorrhagic colitis and hemolytic uremic syndrome. It is vital to know the features that make this strain pathogenic to understand the development of disease outbreaks. In the current study, a comparative genomic analysis was carried out to determine the presence of structural and functional features of O157:H7 strains obtained from 115 National Center for Biotechnology Information database. These strains of interest were analysed in the following programs: BLAST Ring Image Generator, PlasmidFinder, ResFinder, VirulenceFinder, IslandViewer 4 and PHASTER. Five strains (ECP19-198, ECP19-798, F7508, F8952, H2495) demonstrated a great homology with Sakai because of a few regions missing. Five resistant genes were identified, however, Macrolide-associated resistance gene mdf(A) was commonly found in all genomes. Majority of the strains (97%) were positive for 15 of the virulent genes (espA, espB, espF, espJ, gad, chuA, eae, iss, nleA, nleB, nleC, ompT, tccP, terC and tir). The plasmid analysis demonstrated that the IncF group was the most prevalent in the strains analysed. The prophage and genomic island analysis showed a distribution of bacteriophages and genomic islands respectively. The results indicated that structural and functional features of the many O157:H7 strains differ and may be a result of obtaining mobile genetic elements via horizontal gene transfer. Understanding the evolution of O157:H7 strains pathogenicity in terms of their structural and functional features will enable the development of detection and control of transmission strategies.},
}
@article {pmid38114770,
year = {2023},
author = {Toh, SI and Elaine Keisha, J and Wang, YL and Pan, YC and Jhu, YH and Hsiao, PY and Liao, WT and Chen, PY and Ko, TM and Chang, CY},
title = {Discovery and characterization of genes conferring natural resistance to the antituberculosis antibiotic capreomycin.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {1282},
pmid = {38114770},
issn = {2399-3642},
support = {111-2113-M-002-025//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; },
mesh = {*Capreomycin/pharmacology ; *Anti-Bacterial Agents/pharmacology/metabolism ; Bacteria/genetics ; Genes, Bacterial ; Immunity, Innate ; },
abstract = {Metagenomic-based studies have predicted an extraordinary number of potential antibiotic-resistance genes (ARGs). These ARGs are hidden in various environmental bacteria and may become a latent crisis for antibiotic therapy via horizontal gene transfer. In this study, we focus on a resistance gene cph, which encodes a phosphotransferase (Cph) that confers resistance to the antituberculosis drug capreomycin (CMN). Sequence Similarity Network (SSN) analysis classified 353 Cph homologues into five major clusters, where the proteins in cluster I were found in a broad range of actinobacteria. We examine the function and antibiotics targeted by three putative resistance proteins in cluster I via biochemical and protein structural analysis. Our findings reveal that these three proteins in cluster I confer resistance to CMN, highlighting an important aspect of CMN resistance within this gene family. This study contributes towards understanding the sequence-structure-function relationships of the phosphorylation resistance genes that confer resistance to CMN.},
}
@article {pmid38113741,
year = {2024},
author = {Zhang, B and Zhang, J and Wang, Y and Qu, J and Jiang, Z and Zhang, X and Tao, Y and Wang, Y and Kang, Z and Han, S and Zhang, J and Zhang, Y},
title = {Biodegradation of atrazine with biochar-mediated functional bacterial biofilm: Construction, characterization and mechanisms.},
journal = {Journal of hazardous materials},
volume = {465},
number = {},
pages = {133237},
doi = {10.1016/j.jhazmat.2023.133237},
pmid = {38113741},
issn = {1873-3336},
mesh = {*Atrazine/chemistry ; Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Herbicides/metabolism ; Soil/chemistry ; Bacteria/metabolism ; Biofilms ; Soil Microbiology ; *Charcoal ; },
abstract = {The abuse and residue of herbicides in the black soil area had seriously affected the soil structure, function and crop growth, posing severe threats to agricultural soil environment and public health. Given the limitation of routine microbial remediation, innovative and eco-friendly functional bacterial biofilm which could adapt under adverse conditions was developed on the biochar to investigate its enhanced bioremediation and metabolic characteristics of typical herbicide atrazine. Results revealed that the atrazine degrading strain Acinetobacter lwoffii had competitive advantage in soil indigenous microorganisms and formed dense biofilms on the biochar which was beneficial to cell viability maintenance and aggregations. Metatranscriptomics and RT-qPCR analysis demonstrated that the biochar-mediated biofilm improved the frequency of intercellular communications through quorum sensing and two-component signal regulation systems, and enhanced the atrazine biodegradation efficiency through horizontal gene transfer in co-metabolism mode, providing important scientific basis for the biological remediation of farmland soil non-point source pollution.},
}
@article {pmid38112751,
year = {2023},
author = {Gould, AL and Henderson, JB},
title = {Comparative genomics of symbiotic Photobacterium using highly contiguous genome assemblies from long read sequences.},
journal = {Microbial genomics},
volume = {9},
number = {12},
pages = {},
pmid = {38112751},
issn = {2057-5858},
support = {DP5 OD026405/OD/NIH HHS/United States ; },
mesh = {Animals ; *Photobacterium/genetics ; *Symbiosis ; DNA, Bacterial/genetics ; Genomics ; Genome, Bacterial ; },
abstract = {This study presents the assembly and comparative genomic analysis of luminous Photobacterium strains isolated from the light organs of 12 fish species using Oxford Nanopore Technologies (ONT) sequencing. The majority of assemblies achieved chromosome-level continuity, consisting of one large (>3 Mbp) and one small (~1.5 Mbp) contig, with near complete BUSCO scores along with varying plasmid sequences. Leveraging this dataset, this study significantly expanded the available genomes for P. leiognathi and its subspecies P. 'mandapamensis', enabling a comparative genomic analysis between the two lineages. An analysis of the large and small chromosomes unveiled distinct patterns of core and accessory genes, with a larger fraction of the core genes residing on the large chromosome, supporting the hypothesis of secondary chromosome evolution from megaplasmids in Vibrionaceae. In addition, we discovered a proposed new species, Photobacterium acropomis sp. nov., isolated from an acropomatid host, with an average nucleotide identify (ANI) of 93 % compared to the P. leiognathi and P. 'mandapamensis' strains. A comparison of the P. leiognathi and P. 'mandapamensis' lineages revealed minimal differences in gene content, yet highlighted the former's larger genome size and potential for horizontal gene transfer. An investigation of the lux-rib operon, responsible for light production, indicated congruence between the presence of luxF and host family, challenging its role in differentiating P. 'mandapamensis' from P. leiognathi. Further insights were derived from the identification of metabolic differences, such as the presence of the NADH:quinone oxidoreductase respiratory complex I in P. leiognathi as well as variations in the type II secretion system (T2S) genes between the lineages, potentially impacting protein secretion and symbiosis. In summary, this study advances our understanding of Photobacterium genome evolution, highlighting subtle differences between closely related lineages, specifically P. leiognathi and P. 'mandapamensis'. These findings highlight the benefit of long read sequencing for bacterial genome assembly and pangenome analysis and provide a foundation for exploring early bacterial speciation processes of these facultative light organ symbionts.},
}
@article {pmid38112433,
year = {2024},
author = {Ding, Y and Jiang, X and Wu, J and Wang, Y and Zhao, L and Pan, Y and Xi, Y and Zhao, G and Li, Z and Zhang, L},
title = {Synergistic horizontal transfer of antibiotic resistance genes and transposons in the infant gut microbial genome.},
journal = {mSphere},
volume = {9},
number = {1},
pages = {e0060823},
pmid = {38112433},
issn = {2379-5042},
support = {Grant No. 82172320//MOST | National Natural Science Foundation of China (NSFC)/ ; Grant No. 2022M711915//China Postdoctoral Science Foundation (China Postdoctoral Foundation Project)/ ; Grant No. ZR2022QC169//Shandong Provincial Natural Science Foundation/ ; //TaiShan Industrial Experts Program tscy20190612/ ; //Shandong University Outstanding Young Scholars Program/ ; },
mesh = {Infant ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Genome, Microbial ; },
abstract = {Transposons, plasmids, bacteriophages, and other mobile genetic elements facilitate horizontal gene transfer in the gut microbiota, allowing some pathogenic bacteria to acquire antibiotic resistance genes (ARGs). Currently, the relationship between specific ARGs and specific transposons in the comprehensive infant gut microbiome has not been elucidated. In this study, ARGs and transposons were annotated from the Unified Human Gastrointestinal Genome (UHGG) and the Early-Life Gut Genomes (ELGG). Association rules mining was used to explore the association between specific ARGs and specific transposons in UHGG, and the robustness of the association rules was validated using the external database in ELGG. Our results suggested that ARGs and transposons were more likely to be relevant in infant gut microbiota compared to adult gut microbiota, and nine robust association rules were identified, among which Klebsiella pneumoniae, Enterobacter hormaechei_A, and Escherichia coli_D played important roles in this association phenomenon. The emphasis of this study is to investigate the synergistic transfer of specific ARGs and specific transposons in the infant gut microbiota, which can contribute to the study of microbial pathogenesis and the ARG dissemination dynamics.IMPORTANCEThe transfer of transposons carrying antibiotic resistance genes (ARGs) among microorganisms accelerates antibiotic resistance dissemination among infant gut microbiota. Nonetheless, it is unclear what the relationship between specific ARGs and specific transposons within the infant gut microbiota. K. pneumoniae, E. hormaechei_A, and E. coli_D were identified as key players in the nine robust association rules we discovered. Meanwhile, we found that infant gut microorganisms were more susceptible to horizontal gene transfer events about specific ARGs and specific transposons than adult gut microorganisms. These discoveries could enhance the understanding of microbial pathogenesis and the ARG dissemination dynamics within the infant gut microbiota.},
}
@article {pmid38105949,
year = {2024},
author = {Shropshire, JD and Conner, WR and Vanderpool, D and Hoffmann, AA and Turelli, M and Cooper, BS},
title = {Rapid host switching of Wolbachia and even more rapid turnover of their phages and incompatibility-causing loci.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38105949},
issn = {2692-8205},
support = {R35 GM124701/GM/NIGMS NIH HHS/United States ; },
abstract = {About half of all insect species carry maternally inherited Wolbachia alphaproteobacteria, making Wolbachia the most common endosymbionts known in nature. Often Wolbachia spread to high frequencies within populations due to cytoplasmic incompatibility (CI), a Wolbachia-induced sperm modification caused by prophage-associated genes (cifs) that kill embryos without Wolbachia. Several Wolbachia variants also block viruses, including wMel from Drosophila melanogaster when transinfected into the mosquito Aedes aegypti. CI enables the establishment and stable maintenance of pathogen-blocking wMel in natural Ae. aegypti populations. These transinfections are reducing dengue disease incidence on multiple continents. While it has long been known that closely related Wolbachia occupy distantly related hosts, the timing of Wolbachia host switching and molecular evolution has not been widely quantified. We provide a new, conservative calibration for Wolbachia chronograms based on examples of co-divergence of Wolbachia and their insect hosts. Synthesizing publicly available and new genomic data, we use our calibration to demonstrate that wMel-like variants separated by only about 370,000 years have naturally colonized holometabolous dipteran and hymenopteran insects that diverged approximately 350 million years ago. Data from Wolbachia variants closely related to those currently dominant in D. melanogaster and D. simulans illustrate that cifs are rapidly acquired and lost among Wolbachia genomes, on a time scale of 10[4]-10[5] years. This turnover occurs with and without the Wovirus prophages that contain them, with closely related cifs found in distantly related phages and distantly related cifs found in closely related phages. We present evidence for purifying selection on CI rescue function and on particular Cif protein domains. Our results quantify the tempo and mode of rapid host switching and horizontal gene transfer that underlie the spread and diversity of Wolbachia sampled from diverse host species. The wMel variants we highlight from hosts in different climates may offer new options for broadening Wolbachia-based biocontrol of diseases and pests.},
}
@article {pmid38101014,
year = {2024},
author = {Zhang, S and Cui, L and Zhao, Y and Xie, H and Song, M and Wu, H and Hu, Z and Liang, S and Zhang, J},
title = {The critical role of microplastics in the fate and transformation of sulfamethoxazole and antibiotic resistance genes within vertical subsurface-flow constructed wetlands.},
journal = {Journal of hazardous materials},
volume = {465},
number = {},
pages = {133222},
doi = {10.1016/j.jhazmat.2023.133222},
pmid = {38101014},
issn = {1873-3336},
mesh = {*Anti-Bacterial Agents ; *Sulfamethoxazole ; Microplastics ; Plastics ; Wastewater ; Waste Disposal, Fluid/methods ; Wetlands ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; },
abstract = {Constructed wetlands (CWs) are reservoirs of microplastics (MPs) in the environment. However, knowledge about the impact of MPs on antibiotic removal and the fate of antibiotic resistance genes (ARGs) is limited. We focused on sulfamethoxazole (SMX) as a representative compound to examine the effects of MPs on SMX removal and the proliferation and dissemination of two SMX-related ARGs (sul1 and sul2) in vertical subsurface-flow CW (VFCW) microcosm. The presence of MPs in the substrate was found to enhance the proliferation of microorganisms owing to the large specific surface area of the MPs and the release of dissolved organic carbon (DOC) on MP surfaces, which resulted in a high SMX removal ranging from 97.80 % to 99.80 %. However, the presence of MPs promoted microbial interactions and the horizontal gene transfer (HGT) of ARGs, which led to a significant increase in the abundances of sul1 and sul2 of 68.47 % and 17.20 %, respectively. It is thus imperative to implement rigorous monitoring strategies for MPs to mitigate their potential ecological hazards.},
}
@article {pmid38099617,
year = {2024},
author = {Schwarzerova, J and Zeman, M and Babak, V and Jureckova, K and Nykrynova, M and Varga, M and Weckwerth, W and Dolejska, M and Provaznik, V and Rychlik, I and Cejkova, D},
title = {Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis.},
journal = {Microbiology spectrum},
volume = {12},
number = {1},
pages = {e0196423},
pmid = {38099617},
issn = {2165-0497},
support = {GA22-16786S//Czech Science Foundation/ ; 206/2023/FVHE//Internal Grant Agency of the University of Veterinary Sciences Brno/ ; },
mesh = {Animals ; Swine ; *Gene Transfer, Horizontal ; *Microbiota ; Genome, Bacterial ; Anti-Bacterial Agents ; Bacteria/genetics ; Genes, Bacterial ; },
abstract = {Horizontal gene transfer (HGT) is a key driver in the evolution of bacterial genomes. The acquisition of genes mediated by HGT may enable bacteria to adapt to ever-changing environmental conditions. Long-term application of antibiotics in intensive agriculture is associated with the dissemination of antibiotic resistance genes among bacteria with the consequences causing public health concern. Commensal farm-animal-associated gut microbiota are considered the reservoir of the resistance genes. Therefore, in this study, we identified known and not-yet characterized mobilized genes originating from chicken and porcine fecal samples using our innovative pipeline followed by network analysis to provide appropriate visualization to support proper interpretation.},
}
@article {pmid38098417,
year = {2023},
author = {Chen, R and Cheng, JH and Tang, XY},
title = {[Characteristics of Antibiotic Resistance Genes Distribution in Different Types of Agricultural Land Soils in Highly Cultivated Hilly Areas].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {44},
number = {12},
pages = {6947-6954},
doi = {10.13227/j.hjkx.202210109},
pmid = {38098417},
issn = {0250-3301},
mesh = {*Soil ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Drug Resistance, Microbial/genetics ; Vegetables ; Manure ; },
abstract = {To characterize the distribution of antibiotic resistance genes(ARGs) in different types of agricultural soil in highly cultivated hilly areas, the abundance and diversity of ARGs in vegetable, orchard, and arable soils were analyzed in this study. The results showed that 70 ARGs and four mobile genetic elements(MGEs) were detected in all soil samples, with β-lactam cphA-01 being the most abundant genes in the agricultural soils. In vegetable and orchard soils, the main ARG subtypes were cphA-01 and cmx(A) genes, whereas the mexF and aacC genes were predominant in cropland soils. The relative abundance and diversity of soil ARGs showed that cropland<vegetable land<orchard, which was related to the nutrient conditions of different agricultural soils. Similarly, the relative abundance and diversity of MGEs were lowest in cropland, whereas their highest values were detected in vegetable and orchard soils, respectively. The significant positive correlation(P<0.05) between the abundance of soil MGEs and ARGs suggests that horizontal gene transfer may facilitate the spread of antibiotic resistance in the agricultural soils in highly cultivated hilly areas.},
}
@article {pmid38098126,
year = {2023},
author = {Elsayed, SW and Elghaish, RA and Badr, E and Mouftah, SF and Saif, NA and Naga, IS and Shata, AH and Pascoe, B and Sheppard, SK and Elhadidy, M},
title = {Recombination-mediated dissemination of Methicillin-resistant S. aureus clonal complex 1 in the Egyptian health care settings.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {22},
number = {1},
pages = {109},
pmid = {38098126},
issn = {1476-0711},
mesh = {Humans ; *Methicillin-Resistant Staphylococcus aureus ; Methicillin Resistance/genetics ; Egypt/epidemiology ; Linezolid/pharmacology ; Pilot Projects ; *Staphylococcal Infections/epidemiology/drug therapy ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Clone Cells ; Recombination, Genetic ; Delivery of Health Care ; Microbial Sensitivity Tests ; },
abstract = {BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is a rapidly evolving pathogen that is frequently associated with outbreaks and sustained epidemics. This study investigated the population structure, resistome, virulome, and the correlation between antimicrobial resistance determinants with phenotypic resistance profiles of 36 representative hospital-acquired MRSA isolates recovered from hospital settings in Egypt.<br><br>RESULTS: The community-acquired MRSA lineage, clonal complex 1 (CC1) was the most frequently detected clone, followed by three other globally disseminated clones, CC121, CC8, and CC22. Most isolates carried SCCmec type V and more than half of isolates demonstrated multi-drug resistant phenotypes. Resistance to linezolid, a last resort antibiotic for treating multidrug resistant MRSA, was observed in 11.11% of the isolates belonging to different genetic backgrounds. Virulome analysis indicated that most isolates harboured a large pool of virulence factors and toxins. Genes encoding aureolysin, gamma hemolysins, and serine proteases were the most frequently detected virulence encoding genes. CC1 was observed to have a high pool of AMR resistance determinants including cfr, qacA, and qacB genes, which are involved in linezolid and quaternary ammonium compounds resistance, as well as high content of virulence-related genes, including both of the PVL toxin genes. Molecular clock analysis revealed that CC1 had the greatest frequency of recombination (compared to mutation) among the four major clones, supporting the role of horizontal gene transfer in modulating AMR and hypervirulence in this clone.<br><br>CONCLUSIONS: This pilot study provided evidence on the dissemination success of CA-MRSA clone CC1 among Egyptian hospitals. Co-detection of multiple AMR and virulence genes in this lineage pose a broad public health risk, with implications for successful treatment. The results of this study, together with other surveillance studies in Egypt, should be used to develop strategies for controlling MRSA infections in Egyptian health-care settings.},
}
@article {pmid38095456,
year = {2024},
author = {Røder, HL and Christidi, E and Amador, CI and Music, S and Olesen, AK and Svensson, B and Madsen, JS and Herschend, J and Kreft, J-U and Burmølle, M},
title = {Flagellar interference with plasmid uptake in biofilms: a joint experimental and modeling study.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {1},
pages = {e0151023},
pmid = {38095456},
issn = {1098-5336},
support = {11-106246//Independent Research Fund Denmark/ ; 10098, 35906//Villum Fonden (Villum Foundation)/ ; N62909-18-2179//DOD | USN | ONR | Office of Naval Research Global (ONRG)/ ; 34434//Villum Fonden (Villum Foundation)/ ; //Darwin Trust of Edinburgh (Darwin Trust)/ ; NC/R001707/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; //Velux Fonden (Velux Foundations)/ ; NC/K000683/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; },
mesh = {Plasmids ; *Xanthomonas/genetics ; Biofilms ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; Conjugation, Genetic ; *Pseudomonas putida/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Plasmid conjugation is a key facilitator of horizontal gene transfer (HGT), and plasmids encoding antibiotic resistance drive the increasing prevalence of antibiotic resistance. In natural, engineered, and clinical environments, bacteria often grow in protective biofilms. Therefore, a better understanding of plasmid transfer in biofilms is needed. Our aim was to investigate plasmid transfer in a biofilm-adapted wrinkly colony mutant of Xanthomonas retroflexus (XRw) with enhanced matrix production and reduced motility. We found that XRw biofilms had an increased uptake of the broad host-range IncP-1ϵ plasmid pKJK5 compared to the wild type (WT). Proteomics revealed fewer flagellar-associated proteins in XRw, suggesting that flagella were responsible for reducing plasmid uptake. This was confirmed by the higher plasmid uptake of non-flagellated fliM mutants of the X. retroflexus wrinkly mutant as well as the wild type. Moreover, testing several flagellar mutants of Pseudomonas putida suggested that the flagellar effect was more general. We identified seven mechanisms with the potential to explain the flagellar effect and simulated them in an individual-based model. Two mechanisms could thus be eliminated (increased distances between cells and increased lag times due to flagella). Another mechanism identified as viable in the modeling was eliminated by further experiments. The possibility of steric hindrance of pilus movement and binding by flagella, reducing the frequency of contact and thus plasmid uptake, proved viable, and the three other viable mechanisms had a reduced probability of plasmid transfer in common. Our findings highlight the important yet complex effects of flagella during bacterial conjugation in biofilms.IMPORTANCEBiofilms are the dominant form of microbial life and bacteria living in biofilms are markedly different from their planktonic counterparts, yet the impact of the biofilm lifestyle on horizontal gene transfer (HGT) is still poorly understood. Horizontal gene transfer by conjugative plasmids is a major driver in bacterial evolution and adaptation, as exemplified by the troubling spread of antibiotic resistance. To either limit or promote plasmid prevalence and dissemination, we need a better understanding of plasmid transfer between bacterial cells, especially in biofilms. Here, we identified a new factor impacting the transfer of plasmids, flagella, which are required for many types of bacterial motility. We show that their absence or altered activity can lead to enhanced plasmid uptake in two bacterial species, Xanthomonas retroflexus and Pseudomonas putida. Moreover, we demonstrate the utility of mathematical modeling to eliminate hypothetical mechanisms.},
}
@article {pmid38088550,
year = {2024},
author = {Salinas, L and Cárdenas, P and Graham, JP and Trueba, G},
title = {IS26 drives the dissemination of bla CTX-M genes in an Ecuadorian community.},
journal = {Microbiology spectrum},
volume = {12},
number = {1},
pages = {e0250423},
pmid = {38088550},
issn = {2165-0497},
support = {R01 AI135118/AI/NIAID NIH HHS/United States ; R01 AI167989/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Child ; Humans ; *Escherichia coli Infections/epidemiology ; Plasmids/genetics ; Ecuador ; Escherichia coli/genetics ; *Anti-Infective Agents ; Animals, Domestic/genetics ; beta-Lactamases/genetics ; Microbial Sensitivity Tests ; },
abstract = {The horizontal gene transfer events are the major contributors to the current spread of CTX-M-encoding genes, the most common extended-spectrum β-lactamase (ESBL), and many clinically crucial antimicrobial resistance (AMR) genes. This study presents evidence of the critical role of IS26 transposable element for the mobility of bla CTX-M gene among Escherichia coli isolates from children and domestic animals in the community. We suggest that the nucleotide sequences of IS26-bla CTX-M could be used to study bla CTX-M transmission between humans, domestic animals, and the environment, because understanding of the dissemination patterns of AMR genes is critical to implement effective measures to slow down the dissemination of these clinically important genes.},
}
@article {pmid38086386,
year = {2023},
author = {Amrofell, MB and Rengarajan, S and Vo, ST and Ramirez Tovar, ES and LoBello, L and Dantas, G and Moon, TS},
title = {Engineering E. coli strains using antibiotic-resistance-gene-free plasmids.},
journal = {Cell reports methods},
volume = {3},
number = {12},
pages = {100669},
pmid = {38086386},
issn = {2667-2375},
support = {R01 AT009741/AT/NCCIH NIH HHS/United States ; },
mesh = {Animals ; Mice ; *Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics ; Plasmids/genetics ; Drug Resistance, Microbial/genetics ; Cloning, Molecular ; },
abstract = {We created a generalizable pipeline for antibiotic-resistance-gene-free plasmid (ARGFP)-based cloning using a dual auxotrophic- and essential-gene-based selection strategy. We use auxotrophic selection to construct plasmids in engineered E. coli DH10B cloning strains and both auxotrophic- and essential-gene-based selection to (1) select for recombinant strains and (2) maintain a plasmid in E. coli Nissle 1917, a common chassis for engineered probiotic applications, and E. coli MG1655, the laboratory "wild-type" E. coli strain. We show that our approach has comparable efficiency to that of antibiotic-resistance-gene-based cloning. We also show that the double-knockout Nissle and MG1655 strains are simple to transform with plasmids of interest. Notably, we show that the engineered Nissle strains are amenable to long-term plasmid maintenance in repeated culturing as well as in the mouse gut, demonstrating the potential for broad applications while minimizing the risk of antibiotic resistance spread via horizontal gene transfer.},
}
@article {pmid38085089,
year = {2024},
author = {Zhang, T and Mu, Y and Gao, Y and Tang, Y and Mao, S and Liu, J},
title = {Fecal microbial gene transfer contributes to the high-grain diet-induced augmentation of aminoglycoside resistance in dairy cattle.},
journal = {mSystems},
volume = {9},
number = {1},
pages = {e0081023},
pmid = {38085089},
issn = {2379-5077},
support = {32372904//MOST | National Natural Science Foundation of China (NSFC)/ ; RENCAI2023008//MOST | NSFC | National Science Fund for Distinguished Young Scholars (National Science Foundation for Distinguished Young Scholars)/ ; BK20210402//JST | Natural Science Foundation of Jiangsu Province (Jiangsu Natural Science Foundation)/ ; },
mesh = {Animals ; Cattle ; Female ; *Aminoglycosides/pharmacology ; Anti-Bacterial Agents/pharmacology ; Diet/veterinary ; Genes, Microbial ; *Lactation ; },
abstract = {A high-grain (HG) diet can rapidly lower the rumen pH and thus modify the gastrointestinal microbiome in dairy cattle. Although the prevalence of antibiotic resistance is strongly linked with the gut microbiome, the influences of HG diet on animals' gut resistome remain largely unexplored. Here, we examined the impact and mechanism of an HG diet on the fecal resistome in dairy cattle by metagenomically characterizing the gut microbiome. Eight lactating Holstein cattle were randomly allocated into two groups and fed either a conventional (CON) or HG diet for 3 weeks. The fecal microbiome and resistome were significantly altered in dairy cattle from HG, demonstrating an adaptive response that peaks at day 14 after the dietary transition. Importantly, we determined that feeding an HG diet specifically elevated the prevalence of resistance to aminoglycosides (0.11 vs 0.24 RPKG, P < 0.05). This diet-induced resistance increase is interrelated with the disproportional propagation of microbes in Lachnospiraceae, indicating a potential reservoir of aminoglycosides resistance. We further showed that the prevalence of acquired resistance genes was also modified by introducing a different diet, likely due to the augmented frequency of lateral gene transfer (LGT) in microbes (CON vs HG: 254 vs 287 taxa) such as Lachnospiraceae. Consequently, we present that diet transition is associated with fecal resistome modification in dairy cattle and an HG diet specifically enriched aminoglycosides resistance that is likely by stimulating microbial LGT.IMPORTANCEThe increasing prevalence of antimicrobial resistance is one of the most severe threats to public health, and developing novel mitigation strategies deserves our top priority. High-grain (HG) diet is commonly applied in dairy cattle to enhance animals' performance to produce more high-quality milk. We present that despite such benefits, the application of an HG diet is correlated with an elevated prevalence of resistance to aminoglycosides, and this is a combined effect of the expansion of antibiotic-resistant bacteria and increased frequency of lateral gene transfer in the fecal microbiome of dairy cattle. Our results provided new knowledge in a typically ignored area by showing an unexpected enrichment of antibiotic resistance under an HG diet. Importantly, our findings laid the foundation for designing potential dietary intervention strategies to lower the prevalence of antibiotic resistance in dairy production.},
}
@article {pmid38081548,
year = {2024},
author = {Wan, S and Zhou, A and Chen, R and Fang, S and Lu, J and Lv, N and Wang, C and Gao, J and Li, J and Wu, W},
title = {Metagenomics next-generation sequencing (mNGS) reveals emerging infection induced by Klebsiella pneumoniaeniae.},
journal = {International journal of antimicrobial agents},
volume = {63},
number = {2},
pages = {107056},
doi = {10.1016/j.ijantimicag.2023.107056},
pmid = {38081548},
issn = {1872-7913},
mesh = {Humans ; Male ; Aged ; *Klebsiella ; *Klebsiella Infections/drug therapy ; Carbapenems/pharmacology/therapeutic use ; Klebsiella pneumoniae ; Anti-Bacterial Agents/pharmacology/therapeutic use ; High-Throughput Nucleotide Sequencing ; },
abstract = {OBJECTIVES: The increasing emergence of hypervirulent Klebsiella pneumoniae (hv-Kp) and carbapenem-resistant K. pneumoniae (CR-Kp) is a serious and substantial public health problem. The use of the last resort antimicrobials, tigecycline and polymyxin to combat infections is complicated by the expanding repertoire of newly-identified CR-hvKp. The transmission and co-occurrence of the corresponding antimicrobial resistance and virulence determinants are largely unknown. The aim of this study was to investigate the dissemination and dynamics of CR-Kp and its antibiotic resistance in a hospitalised patient.<br><br>METHODS: Metagenomic next-generation sequencing (mNGS) was conducted for different specimens collected from an elderly male hospitalised patient. CR-Kp strains were examined using antibiotic susceptibility and string testing. Antimicrobial and virulence genes were annotated using whole-genome sequencing (WGS).<br><br>RESULTS: A clinical case of a patient infected with a variety of CR-Kp isolates was reported. The co-occurrence of KPC-2 and NDM-1 in the patient was revealed. The CR-Kp isolates, such as BALF2, and Sputum T1 and T3, were classified into ST11 and ST147, respectively. The genetic signature (iuc operon) of hypervirulence was identified in strain T1, although string testing indicated its intermediate virulence.<br><br>CONCLUSIONS: In this study, multiple infections of CR-Kp isolates were revealed by mNGS, and their dissemination was attributed to plasmid variations, mgrB inactivation and integrative conjugative elements (ICEs). Furthermore, the finding indicated one likely convergence to form CR-hvKp, different from acquisition of carbapenem-resistance determinants in hvKp. A combination of mNGS and WGS is beneficial for clinical diagnosis and anti-infection therapy, and facilitates a better understanding of genetic variants conferring antimicrobial and virulence properties.},
}
@article {pmid38079200,
year = {2023},
author = {Piña-Iturbe, A and Hoppe-Elsholz, G and Suazo, ID and Kalergis, AM and Bueno, SM},
title = {Subinhibitory antibiotic concentrations promote the excision of a genomic island carried by the globally spread carbapenem-resistant Klebsiella pneumoniae sequence type 258.},
journal = {Microbial genomics},
volume = {9},
number = {12},
pages = {},
pmid = {38079200},
issn = {2057-5858},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Klebsiella pneumoniae ; Phylogeny ; Genomic Islands/genetics ; Carbapenems/pharmacology ; },
abstract = {The ICEKp258.2 genomic island (GI) has been proposed as an important factor for the emergence and success of the globally spread carbapenem-resistant Klebsiella pneumoniae sequence type (ST) 258. However, a characterization of this horizontally acquired element is lacking. Using bioinformatic and experimental approaches, we found that ICEKp258.2 is not confined to ST258 and ST512, but also carried by ST3795 strains and emergent invasive multidrug-resistant pathogens from ST1519. We also identified several ICEKp258.2-like GIs spread among different K. pneumoniae STs, other Klebsiella species and even other pathogen genera, uncovering horizontal gene transfer events between different STs and bacterial genera. Also, the comparative and phylogenetic analyses of the ICEKp258.2-like GIs revealed that the most closely related ICEKp258.2-like GIs were harboured by ST11 strains. Importantly, we found that subinhibitory concentrations of antibiotics used in treating K. pneumoniae infections can induce the excision of this GI and modulate its gene expression. Our findings provide the basis for the study of ICEKp258.2 and its role in the success of K. pneumoniae ST258. They also highlight the potential role of antibiotics in the spread of ICEKp258.2-like GIs among bacterial pathogens.},
}
@article {pmid38078984,
year = {2023},
author = {Yang, X and Sui, X and Liu, Q and Wang, H and Sun, H and Bai, X and Xiong, Y},
title = {Characterization of the novel temperate Escherichia coli phage phiStx2k.},
journal = {Archives of virology},
volume = {169},
number = {1},
pages = {5},
pmid = {38078984},
issn = {1432-8798},
support = {82072254//National Nature Science Foundation of China/ ; },
mesh = {*Escherichia coli/genetics ; Coliphages/genetics ; *Bacteriophages/genetics ; },
abstract = {A novel temperate phage, phiStx2k, was induced from a clinical Escherichia coli isolate producing Shiga toxin (Stx) 2k. The phage particles have an icosahedral head (50 nm in diameter) and a long non-contractile tail (149 nm long). The phage genome consists of 46,647 bp of double-stranded DNA with an average G + C content of 51%. Genome sequence comparisons suggested that phiStx2k represents a new genus in the class Caudoviricetes. phiStx2k was capable of converting non-Stx-producing E. coli strains to Stx producers. These results expand our knowledge on the characteristics of Stx phages and highlight the potential risks of the emergence of Stx-producing strains or novel pathogens via horizontal gene transfer.},
}
@article {pmid38078732,
year = {2024},
author = {Lages, MA and do Vale, A and Lemos, ML and Balado, M},
title = {Remodulation of bacterial transcriptome after acquisition of foreign DNA: the case of irp-HPI high-pathogenicity island in Vibrio anguillarum.},
journal = {mSphere},
volume = {9},
number = {1},
pages = {e0059623},
pmid = {38078732},
issn = {2379-5042},
support = {PID2019-103891RJ-100//Ministerio de Ciencia e Innovaci&#xf3;n (MCIN)/ ; PID2019-103891RJ-100//Agencia Estatal de Investigaci&#xf3;n (AEI)/ ; PID2021-122732OB-C21//Ministerio de Ciencia e Innovaci&#xf3;n (MCIN)/ ; PID2021-122732OB-C21//Agencia Estatal de Investigaci&#xf3;n (AEI)/ ; FEMS-GO-2019-600//Federation of European Microbiological Societies (FEMS)/ ; 2021.02251.CEECIND/CP1663/CT0016//COMPETE 2020 FEDER/ ; },
mesh = {Humans ; *Genomic Islands/genetics ; Transcriptome ; Lipopolysaccharides ; *Vibrio/genetics ; DNA ; *Organophosphorus Compounds ; },
abstract = {The high-pathogenicity island irp-HPI is widespread in Vibrionaceae and encodes the siderophore piscibactin, as well as the regulator PbtA that is essential for its expression. In this work, we aim to study whether PbtA directly interacts with irp-HPI promoters. Furthermore, we hypothesize that PbtA, and thereby the acquisition of irp-HPI island, may also influence the expression of other genes elsewhere in the bacterial genome. To address this question, an RNAseq analysis was conducted to identify differentially expressed genes after pbtA deletion in Vibrio anguillarum RV22 genetic background. The results showed that PbtA not only modulates the irp-HPI genes but also modulates the expression of a plethora of V. anguillarum core genome genes, inducing nitrate, arginine, and sulfate metabolism, T6SS1, and quorum sensing, while repressing lipopolysaccharide (LPS) production, MARTX toxin, and major porins such as OmpV and ChiP. The direct binding of the C-terminal domain of PbtA to piscibactin promoters (PfrpA and PfrpC), quorum sensing (vanT), LPS transporter wza, and T6SS structure- and effector-encoding genes was demonstrated by electrophoretic mobility shift assay (EMSA). The results provide valuable insights into the regulatory mechanisms underlying the expression of irp-HPI island and its impact on Vibrios transcriptome, with implications in pathogenesis.IMPORTANCEHorizontal gene transfer enables bacteria to acquire traits, such as virulence factors, thereby increasing the risk of the emergence of new pathogens. irp-HPI genomic island has a broad dissemination in Vibrionaceae and is present in numerous potentially pathogenic marine bacteria, some of which can infect humans. Previous works showed that certain V. anguillarum strains exhibit an expanded host range plasticity and heightened virulence, a phenomenon linked to the acquisition of the irp-HPI genomic island. The present work shows that this adaptive capability is likely achieved through comprehensive changes in the transcriptome of the bacteria and that these changes are mediated by the master regulator PbtA encoded within the irp-HPI element. Our results shed light on the broad implications of horizontal gene transfer in bacterial evolution, showing that the acquired DNA can directly mediate changes in the expression of the core genome, with profounds implications in pathogenesis.},
}
@article {pmid38077655,
year = {2023},
author = {Mbewana Ntshanka, NG and Msagati, TAM},
title = {Trends and Progress on Antibiotic-Resistant Mycobacterium tuberculosis and Genes in relation to Human Immunodeficiency Virus.},
journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale},
volume = {2023},
number = {},
pages = {6659212},
pmid = {38077655},
issn = {1712-9532},
abstract = {Human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) and tuberculosis (TB) are among the infectious diseases that cause high rates of mortality worldwide. The epidemiology of antibiotic resistance in correlation to people that live with TB and HIV has not been thoroughly investigated particularly in South Africa. Numerous cases of multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB) have been announced immensely worldwide. The spread and control of the MDR-TB pandemic due to unsuccessful treatment is one of the most serious public issues of concern, and this challenge is of international interest. Despite all measures that have been executed to overcome the challenge of MDR-TB in recent decades, the global MDR-TB trends have kept on accelerating with more and more people becoming victims. This is attributed to the abuse, misuse, and overuse of different antibacterial agents in human medicine, animal farms, and agricultural activities which serve as a wellspring for the evolution of antimicrobial resistance within the population. Over and above, the impetuous evolution, mutation, and the transfer of resistant genes via horizontal gene transfer are well-known contributive factors towards the antimicrobial resistance problem. Among the public health concerns in the world currently is the ever-increasing problem of antibiotic resistance which outpaces the progress of newly developed antimicrobials. The propagation of antimicrobial resistance (AMR) is even more amplified in areas where the pressure of antimicrobial resistant pathogens is elevated, and hence the population with ubiquitous HIV and AIDS is considered the hotspot. This review therefore aims to give in-depth coverage on the trends and the progress on the development of TB and HIV-resistant strains, highlight strategies to solve the problem, and accentuate the repercussions of the COVID-19 epidemic on the AMR.},
}
@article {pmid38075892,
year = {2023},
author = {Wolters, JF and LaBella, AL and Opulente, DA and Rokas, A and Hittinger, CT},
title = {Mitochondrial genome diversity across the subphylum Saccharomycotina.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1268944},
pmid = {38075892},
issn = {1664-302X},
support = {R01 AI153356/AI/NIAID NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; },
abstract = {INTRODUCTION: Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available.<br><br>METHODS: By extracting mitochondrial assemblies from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades.<br><br>RESULTS: Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera Metschnikowia and Saccharomyces trended larger, while several species in the order Saccharomycetales, which includes S. cerevisiae, exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but they were highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements.<br><br>DISCUSSION: As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.},
}
@article {pmid38075610,
year = {2023},
author = {Alexyuk, P and Alexyuk, M and Moldakhanov, Y and Berezin, V and Bogoyavlenskiy, A},
title = {Draft genome sequences data of Mammaliicoccus lentus isolated from horse farm soil.},
journal = {Data in brief},
volume = {51},
number = {},
pages = {109752},
pmid = {38075610},
issn = {2352-3409},
abstract = {Mammallicoccus lentus is a member of the commensal microflora of the Staphylococcaceae family, which colonizes the skin of several species of farm animals, including poultry and dairy animals (Huber et al., 2011; Zhang et al., 2009). The study of the members of the Staphylococcaceae family, such as the Mammaliicoccus genus, isolated from various sources is of great importance for agriculture and public health as contributes to the accumulation of knowledge and understanding of the mechanisms of antibiotic resistance gene transmission among bacterial pathogens. This thesis is supported by recent studies showing that some members of the Mammallicoccus genus serve as a reservoir of virulence and antibiotic resistance genes and may also be a source of horizontal gene transfer (Saraiva et al., 2021). Here, we present a draft genome sequence of Mammallicoccus lentus strain PVZ.22 from a horse farm soil sample. The sequencing was performed on the Illumina MiSeq platform. The genome was assembled using the Geneious software package. The genome contains 2,802,282 bp with a total of 2805 genes, 8 perfect and 12 strict AMR genes and 58 tRNAs genes.},
}
@article {pmid38071466,
year = {2024},
author = {Chowdhury, AR and Mukherjee, D and Chatterjee, R and Chakravortty, D},
title = {Defying the odds: Determinants of the antimicrobial response of Salmonella Typhi and their interplay.},
journal = {Molecular microbiology},
volume = {121},
number = {2},
pages = {213-229},
doi = {10.1111/mmi.15209},
pmid = {38071466},
issn = {1365-2958},
support = {//ASTRA Chair Professorship and TATA Innovation fellowship funds/ ; //CSIR-SRF fellowship/ ; //DBT-IISc Partnership Program/ ; DAE0195//Department of Atomic Energy, Government of India/ ; //Department of Biotechnology (DBT)/ ; //IISc fellowship/ ; //Ministry of Science and Technology; Department of Science and Technology (DST)/ ; },
mesh = {Humans ; Salmonella typhi/genetics ; *Typhoid Fever/drug therapy/microbiology ; Anti-Bacterial Agents/pharmacology ; *Salmonella Infections/drug therapy ; DNA ; Microbial Sensitivity Tests ; },
abstract = {Salmonella Typhi, the invasive serovar of S. enterica subspecies enterica, causes typhoid fever in healthy human hosts. The emergence of antibiotic-resistant strains has consistently challenged the successful treatment of typhoid fever with conventional antibiotics. Antimicrobial resistance (AMR) in Salmonella is acquired either by mutations in the genomic DNA or by acquiring extrachromosomal DNA via horizontal gene transfer. In addition, Salmonella can form a subpopulation of antibiotic persistent (AP) cells that can survive at high concentrations of antibiotics. These have reduced the effectiveness of the first and second lines of antibiotics used to treat Salmonella infection. The recurrent and chronic carriage of S. Typhi in human hosts further complicates the treatment process, as a remarkable shift in the immune response from pro-inflammatory Th1 to anti-inflammatory Th2 is observed. Recent studies have also highlighted the overlap between AP, persistent infection (PI) and AMR. These incidents have revealed several areas of research. In this review, we have put forward a timeline for the evolution of antibiotic resistance in Salmonella and discussed the different mechanisms of the same availed by the pathogen at the genotypic and phenotypic levels. Further, we have presented a detailed discussion on Salmonella antibiotic persistence (AP), PI, the host and bacterial virulence factors that can influence PI, and how both AP and PI can lead to AMR.},
}
@article {pmid38070340,
year = {2024},
author = {La Manna, P and De Carluccio, M and Oliva, G and Vigliotta, G and Rizzo, L},
title = {Urban wastewater disinfection by iron chelates mediated solar photo-Fenton: Effects on seven pathogens and antibiotic resistance transfer potential.},
journal = {Water research},
volume = {249},
number = {},
pages = {120966},
doi = {10.1016/j.watres.2023.120966},
pmid = {38070340},
issn = {1879-2448},
mesh = {*Wastewater ; *Escherichia coli ; Iron/pharmacology ; Disinfection/methods ; Hydrogen Peroxide/pharmacology ; Sunlight ; Drug Resistance, Microbial ; Iron Chelating Agents/pharmacology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The effects of solar photo-Fenton (SPF) process mediated by the iron chelate Fe[3+] imminodisuccinic acid (Fe:IDS) on both the inactivation of seven relevant pathogens and the potential for antibiotic resistance transfer (degradation of antibiotic resistance genes (ARGs) and after treatment regrowth), in real secondary treated urban wastewater, were investigated for the first time. A comparison with results obtained by sunlight/H2O2 process and Fe[3+] ethylenediaminedisuccinic acid (Fe:EDDS) SPF was also carried out. ARGs were quantified by polymerase chain reaction (PCR) in samples before and after (3 h) the treatment. The persistence of the selected pathogens and ARGs was also evaluated in regrowth tests (72 h) under environmentally mimicking conditions. Fe:IDS SPF resulted to be more effective (from 1.4 log removal for Staphylococcus spp. to 4.3 log removal for Escherichia coli) than Fe:EDDS SPF (from 0.8 log removal for Pseudomonas aeruginosa to 2.0 log removal for Total coliphages) and sunlight/H2O2 (from 1.2 log removal for Clostridium perfringens to 3.3 log removal for E. coli) processes for the seven pathogens investigated. Potential pathogens regrowth was also severely affected, as no substantial regrowth was observed, both in presence and absence of catalase. A similar trend was observed for ARGs removal too (until 0.001 fold change expression for qnrS after 3 h). However, a poor effect and a slight increase in fold change was observed after treatment especially for gyrA, mefA and intl1. Overall, the effect of the investigated processes on ARGs was found to be ARG dependent. Noteworthy, coliphages can regrow after sunlight/H2O2 treatment unlike SPF processes, increasing the risk of antibiotic resistance transfer by transduction mechanism. In conclusion, Fe:IDS SPF is an attractive solution for tertiary treatment of urban wastewater in small wastewater treatment plants as it can provide effective disinfection and a higher protection against antibiotic resistance transfer than the other investigated processes.},
}
@article {pmid38069672,
year = {2023},
author = {Li, Z and Xue, AZ and Maeda, GP and Li, Y and Nabity, PD and Moran, NA},
title = {Phylloxera and Aphids Show Distinct Features of Genome Evolution Despite Similar Reproductive Modes.},
journal = {Molecular biology and evolution},
volume = {40},
number = {12},
pages = {},
pmid = {38069672},
issn = {1537-1719},
support = {R35 GM131738/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Male ; *Aphids/genetics ; X Chromosome/genetics ; Parthenogenesis/genetics ; Reproduction ; Evolution, Molecular ; },
abstract = {Genomes of aphids (family Aphididae) show several unusual evolutionary patterns. In particular, within the XO sex determination system of aphids, the X chromosome exhibits a lower rate of interchromosomal rearrangements, fewer highly expressed genes, and faster evolution at nonsynonymous sites compared with the autosomes. In contrast, other hemipteran lineages have similar rates of interchromosomal rearrangement for autosomes and X chromosomes. One possible explanation for these differences is the aphid's life cycle of cyclical parthenogenesis, where multiple asexual generations alternate with 1 sexual generation. If true, we should see similar features in the genomes of Phylloxeridae, an outgroup of aphids which also undergoes cyclical parthenogenesis. To investigate this, we generated a chromosome-level assembly for the grape phylloxera, an agriculturally important species of Phylloxeridae, and identified its single X chromosome. We then performed synteny analysis using the phylloxerid genome and 30 high-quality genomes of aphids and other hemipteran species. Unexpectedly, we found that the phylloxera does not share aphids' patterns of chromosome evolution. By estimating interchromosomal rearrangement rates on an absolute time scale, we found that rates are elevated for aphid autosomes compared with their X chromosomes, but this pattern does not extend to the phylloxera branch. Potentially, the conservation of X chromosome gene content is due to selection on XO males that appear in the sexual generation. We also examined gene duplication patterns across Hemiptera and uncovered horizontal gene transfer events contributing to phylloxera evolution.},
}
@article {pmid38069639,
year = {2023},
author = {Jeong, DE and Sundrani, S and Hall, RN and Krupovic, M and Koonin, EV and Fire, AZ},
title = {DNA Polymerase Diversity Reveals Multiple Incursions of Polintons During Nematode Evolution.},
journal = {Molecular biology and evolution},
volume = {40},
number = {12},
pages = {},
pmid = {38069639},
issn = {1537-1719},
support = {R35 GM130366/GM/NIGMS NIH HHS/United States ; R35GM130366/GM/NIGMS NIH HHS/United States ; /NH/NIH HHS/United States ; /LM/NLM NIH HHS/United States ; },
mesh = {Humans ; Animals ; Phylogeny ; DNA Transposable Elements ; DNA-Directed DNA Polymerase/genetics ; *Viruses/genetics ; *Nematoda/genetics ; },
abstract = {Polintons are double-stranded DNA, virus-like self-synthesizing transposons widely found in eukaryotic genomes. Recent metagenomic discoveries of Polinton-like viruses are consistent with the hypothesis that Polintons invade eukaryotic host genomes through infectious viral particles. Nematode genomes contain multiple copies of Polintons and provide an opportunity to explore the natural distribution and evolution of Polintons during this process. We performed an extensive search of Polintons across nematode genomes, identifying multiple full-length Polinton copies in several species. We provide evidence of both ancient Polinton integrations and recent mobility in strains of the same nematode species. In addition to the major nematode Polinton family, we identified a group of Polintons that are overall closely related to the major family but encode a distinct protein-primed DNA polymerase B (pPolB) that is related to homologs from a different group of Polintons present outside of the Nematoda. Phylogenetic analyses on the pPolBs support the evolutionary scenarios in which these extrinsic pPolBs that seem to derive from Polinton families present in oomycetes and molluscs replaced the canonical pPolB in subsets of Polintons found in terrestrial and marine nematodes, respectively, suggesting interphylum horizontal gene transfers. The pPolBs of the terrestrial nematode and oomycete Polintons share a unique feature, an insertion of an HNH nuclease domain, whereas the pPolBs in the marine nematode Polintons share an insertion of a VSR nuclease domain with marine mollusc pPolBs. We hypothesize that horizontal gene transfer occurs among Polintons from widely different but cohabiting hosts.},
}
@article {pmid38064674,
year = {2023},
author = {Liang, H and Mower, JP and Chia, CP},
title = {Functional Prokaryotic-Like Deoxycytidine Triphosphate Deaminases and Thymidylate Synthase in Eukaryotic Social Amoebae: Vertical, Endosymbiotic, or Horizontal Gene Transfer?.},
journal = {Molecular biology and evolution},
volume = {40},
number = {12},
pages = {},
pmid = {38064674},
issn = {1537-1719},
mesh = {DCMP Deaminase/genetics/metabolism ; Gene Transfer, Horizontal ; Escherichia coli/genetics/metabolism ; *Amoeba/metabolism ; Thymidylate Synthase/genetics ; *Dictyostelium ; Deoxycytidine Monophosphate ; },
abstract = {The de novo synthesis of deoxythymidine triphosphate uses several pathways: gram-negative bacteria use deoxycytidine triphosphate deaminase to convert deoxycytidine triphosphate into deoxyuridine triphosphate, whereas eukaryotes and gram-positive bacteria instead use deoxycytidine monophosphate deaminase to transform deoxycytidine monophosphate to deoxyuridine monophosphate. It is then unusual that in addition to deoxycytidine monophosphate deaminases, the eukaryote Dictyostelium discoideum has 2 deoxycytidine triphosphate deaminases (Dcd1Dicty and Dcd2Dicty). Expression of either DcdDicty can fully rescue the slow growth of an Escherichia coli dcd knockout. Both DcdDicty mitigate the hydroxyurea sensitivity of a Schizosaccharomyces pombe deoxycytidine monophosphate deaminase knockout. Phylogenies show that Dcd1Dicty homologs may have entered the common ancestor of the eukaryotic groups of Amoebozoa, Obazoa, Metamonada, and Discoba through an ancient horizontal gene transfer from a prokaryote or an ancient endosymbiotic gene transfer from a mitochondrion, followed by horizontal gene transfer from Amoebozoa to several other unrelated groups of eukaryotes. In contrast, the Dcd2Dicty homologs were a separate horizontal gene transfer from a prokaryote or a virus into either Amoebozoa or Rhizaria, followed by a horizontal gene transfer between them. ThyXDicty, the D. discoideum thymidylate synthase, another enzyme of the deoxythymidine triphosphate biosynthesis pathway, was suggested previously to be acquired from the ancestral mitochondria or by horizontal gene transfer from alpha-proteobacteria. ThyXDicty can fully rescue the E. coli thymidylate synthase knockout, and we establish that it was obtained by the common ancestor of social amoebae not from mitochondria but from a bacterium. We propose horizontal gene transfer and endosymbiotic gene transfer contributed to the enzyme diversity of the deoxythymidine triphosphate synthesis pathway in most social amoebae, many Amoebozoa, and other eukaryotes.},
}
@article {pmid38064485,
year = {2023},
author = {Culbertson, EM and Levin, TC},
title = {Eukaryotic CD-NTase, STING, and viperin proteins evolved via domain shuffling, horizontal transfer, and ancient inheritance from prokaryotes.},
journal = {PLoS biology},
volume = {21},
number = {12},
pages = {e3002436},
pmid = {38064485},
issn = {1545-7885},
support = {R00 AI139344/AI/NIAID NIH HHS/United States ; R35 GM150681/GM/NIGMS NIH HHS/United States ; S10 OD028483/OD/NIH HHS/United States ; },
mesh = {Humans ; Animals ; *Bacteria/genetics/metabolism ; *Bacterial Proteins/metabolism ; Biological Evolution ; Nucleotidyltransferases/genetics/metabolism ; Antiviral Agents ; Mammals/metabolism ; },
abstract = {Animals use a variety of cell-autonomous innate immune proteins to detect viral infections and prevent replication. Recent studies have discovered that a subset of mammalian antiviral proteins have homology to antiphage defense proteins in bacteria, implying that there are aspects of innate immunity that are shared across the Tree of Life. While the majority of these studies have focused on characterizing the diversity and biochemical functions of the bacterial proteins, the evolutionary relationships between animal and bacterial proteins are less clear. This ambiguity is partly due to the long evolutionary distances separating animal and bacterial proteins, which obscures their relationships. Here, we tackle this problem for 3 innate immune families (CD-NTases [including cGAS], STINGs, and viperins) by deeply sampling protein diversity across eukaryotes. We find that viperins and OAS family CD-NTases are ancient immune proteins, likely inherited since the earliest eukaryotes first arose. In contrast, we find other immune proteins that were acquired via at least 4 independent events of horizontal gene transfer (HGT) from bacteria. Two of these events allowed algae to acquire new bacterial viperins, while 2 more HGT events gave rise to distinct superfamilies of eukaryotic CD-NTases: the cGLR superfamily (containing cGAS) that has since diversified via a series of animal-specific duplications and a previously undefined eSMODS superfamily, which more closely resembles bacterial CD-NTases. Finally, we found that cGAS and STING proteins have substantially different histories, with STING protein domains undergoing convergent domain shuffling in bacteria and eukaryotes. Overall, our findings paint a picture of eukaryotic innate immunity as highly dynamic, where eukaryotes build upon their ancient antiviral repertoires through the reuse of protein domains and by repeatedly sampling a rich reservoir of bacterial antiphage genes.},
}
@article {pmid38063386,
year = {2024},
author = {Parra, B and Cockx, B and Lutz, VT and Brøndsted, L and Smets, BF and Dechesne, A},
title = {Isolation and characterization of novel plasmid-dependent phages infecting bacteria carrying diverse conjugative plasmids.},
journal = {Microbiology spectrum},
volume = {12},
number = {1},
pages = {e0253723},
pmid = {38063386},
issn = {2165-0497},
support = {101026675//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; 230416//Villum Fonden (Villum Foundation)/ ; },
mesh = {Humans ; *Bacteriophages ; Anti-Bacterial Agents ; Plasmids/genetics ; Escherichia coli/genetics ; *Salmonella enterica/genetics ; Conjugation, Genetic ; },
abstract = {This work was undertaken because plasmid-dependent phages can reduce the prevalence of conjugative plasmids and can be leveraged to prevent the acquisition and dissemination of ARGs by bacteria. The two novel phages described in this study, Lu221 and Hi226, can infect Escherichia coli, Salmonella enterica, Kluyvera sp. and Enterobacter sp. carrying conjugative plasmids. This was verified with plasmids carrying resistance determinants and belonging to the most common plasmid families among Gram-negative pathogens. Therefore, the newly isolated phages could have the potential to help control the spread of ARGs and thus help combat the antimicrobial resistance crisis.},
}
@article {pmid38062354,
year = {2023},
author = {Hochstedler-Kramer, BR and Ene, A and Putonti, C and Wolfe, AJ},
title = {Comparative genomic analysis of clinical Enterococcus faecalis distinguishes strains isolated from the bladder.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {752},
pmid = {38062354},
issn = {1471-2164},
support = {TL1 DK132769/DK/NIDDK NIH HHS/United States ; U2C DK129917/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Enterococcus faecalis/genetics ; *Genome, Bacterial ; DNA Transposable Elements/genetics ; Urinary Bladder ; Genomics ; Anti-Bacterial Agents ; Prophages/genetics ; },
abstract = {BACKGROUND: Enterococcus faecalis is the most commonly isolated enterococcal species in clinical infection. This bacterium is notorious for its ability to share genetic content within and outside of its species. With this increased proficiency for horizontal gene transfer, tremendous genomic diversity within this species has been identified. Many researchers have hypothesized E. faecalis exhibits niche adaptation to establish infections or colonize various parts of the human body. Here, we hypothesize that E. faecalis strains isolated from the human bladder will carry unique genomic content compared to clinical strains isolated from other sources.<br><br>RESULTS: This analysis includes comparison of 111 E. faecalis genomes isolated from bladder, urogenital, blood, and fecal samples. Phylogenomic comparison shows no association between isolation source and lineage; however, accessory genome comparison differentiates blood and bladder genomes. Further gene enrichment analysis identifies gene functions, virulence factors, antibiotic resistance genes, and plasmid-associated genes that are enriched or rare in bladder genomes compared to urogenital, blood, and fecal genomes. Using these findings as training data and 682 publicly available genomes as test data, machine learning classifiers successfully distinguished between bladder and non-bladder strains with high accuracy. Genes identified as important for this differentiation were often related to transposable elements and phage, including 3 prophage species found almost exclusively in bladder and urogenital genomes.<br><br>CONCLUSIONS: E. faecalis strains isolated from the bladder contain unique genomic content when compared to strains isolated from other body sites. This genomic diversity is most likely due to horizontal gene transfer, as evidenced by lack of phylogenomic clustering and enrichment of transposable elements and prophages. Investigation into how these enriched genes influence host-microbe interactions may elucidate gene functions required for successful bladder colonization and disease establishment.},
}
@article {pmid38059467,
year = {2023},
author = {Ren, CY and Zhao, HP},
title = {Synthetic Nuclease-Producing Microbiome Achieves Efficient Removal of Extracellular Antibiotic Resistance Genes from Wastewater Effluent.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {50},
pages = {21224-21234},
doi = {10.1021/acs.est.3c07974},
pmid = {38059467},
issn = {1520-5851},
mesh = {Humans ; *Anti-Bacterial Agents ; Wastewater ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; *Microbiota ; },
abstract = {Antibiotic resistance gene (ARG) transmission poses significant threats to human health. The effluent of wastewater treatment plants is demonstrated as a hotspot source of ARGs released into the environment. In this study, a synthetic microbiome containing nuclease-producing Deinococcus radiodurans was constructed to remove extracellular ARGs. Results of quantitative polymerase chain reaction (qPCR) showed significant reduction in plasmid RP4-associated ARGs (by more than 3 orders of magnitude) and reduction of indigenous ARG sul1 and mobile genetic element (MGE) intl1 (by more than 1 order of magnitude) in the synthetic microbiome compared to the control without D. radiodurans. Metagenomic analysis revealed a decrease in ARG and MGE diversity in extracellular DNA (eDNA) of the treated group. Notably, whereas eight antibiotic-resistant plasmids with mobility risk were detected in the control, only one was detected in the synthetic microbiome. The abundance of the nuclease encoding gene exeM, quantified by qPCR, indicated its enrichment in the synthetic microbiome, which ensures stable eDNA degradation even when D. radiodurans decreased. Moreover, intracellular ARGs and MGEs and pathogenic ARG hosts in the river receiving treated effluent were lower than those in the river receiving untreated effluent. Overall, this study presents a new approach for removing extracellular ARGs and further reducing the risk of ARG transmission in receiving rivers.},
}
@article {pmid38056093,
year = {2024},
author = {Wang, M and Masoudi, A and Wang, C and Wu, C and Zhang, Z and Zhao, X and Liu, Y and Yu, Z and Liu, J},
title = {Impacts of net cages on pollutant accumulation and its consequence on antibiotic resistance genes (ARGs) dissemination in freshwater ecosystems: Insights for sustainable urban water management.},
journal = {Environment international},
volume = {183},
number = {},
pages = {108357},
doi = {10.1016/j.envint.2023.108357},
pmid = {38056093},
issn = {1873-6750},
mesh = {Humans ; *Genes, Bacterial ; Water ; *Environmental Pollutants ; Ecosystem ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Fresh Water ; Water Supply ; },
abstract = {There has been increasing interest in the role of human activities in disseminating antibiotic-resistance genes (ARGs) in aquatic ecosystems. However, the influence of pollutant accumulation on anthropogenic pollutant-ARG synergistic actions is limited. This study explored the association of net cages with the propagation of anthropogenic pollutants and their consequences for influencing the enrichment of ARGs using high-throughput metagenomic sequencing. We showed that net cages could substantially impact the ecology of freshwater systems by enhancing i) ARG diversity and the tendency for ARG-horizontal gene transfer and ii) the overlap of mobile genetic elements (MGEs) with biocide-metal resistance genes (BMRGs) and ARGs. These findings suggested that the cotransfer of these three genetic determinants would be favored in net cage plots and that nonantibiotic factors such as metal(loid)s, particularly iron (Fe), displayed robust selective pressures on ARGs exerted by the net cage. The resistome risk scores of net cage sediments and biofilms were higher than those from off-net cage plots, indicating that the net cage-origin antibiotic resistome should be of great concern. The combination of deterministic and stochastic processes acting on bacterial communities could explain the higher ARG variations in cage plots (8.2%) than in off-cage plots (3.4%). Moreover, MGEs and pollutants together explained 43.3% of the total variation in ARG communities, which was higher than that of off-cage plots (8.8%), considering pollutants, environmental variables, MGEs, and assembly processes. These findings will inform the development of policies and guidelines to more effectively limit the spread of antimicrobial resistance and achieve the goal of sustainability in freshwater systems in urban areas.},
}
@article {pmid38053766,
year = {2023},
author = {Gisriel, CJ and Bryant, DA and Brudvig, GW and Cardona, T},
title = {Molecular diversity and evolution of far-red light-acclimated photosystem I.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1289199},
pmid = {38053766},
issn = {1664-462X},
support = {K99 GM140174/GM/NIGMS NIH HHS/United States ; MR/T017546/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {The need to acclimate to different environmental conditions is central to the evolution of cyanobacteria. Far-red light (FRL) photoacclimation, or FaRLiP, is an acclimation mechanism that enables certain cyanobacteria to use FRL to drive photosynthesis. During this process, a well-defined gene cluster is upregulated, resulting in changes to the photosystems that allow them to absorb FRL to perform photochemistry. Because FaRLiP is widespread, and because it exemplifies cyanobacterial adaptation mechanisms in nature, it is of interest to understand its molecular evolution. Here, we performed a phylogenetic analysis of the photosystem I subunits encoded in the FaRLiP gene cluster and analyzed the available structural data to predict ancestral characteristics of FRL-absorbing photosystem I. The analysis suggests that FRL-specific photosystem I subunits arose relatively late during the evolution of cyanobacteria when compared with some of the FRL-specific subunits of photosystem II, and that the order Nodosilineales, which include strains like Halomicronema hongdechloris and Synechococcus sp. PCC 7335, could have obtained FaRLiP via horizontal gene transfer. We show that the ancestral form of FRL-absorbing photosystem I contained three chlorophyll f-binding sites in the PsaB2 subunit, and a rotated chlorophyll a molecule in the A0B site of the electron transfer chain. Along with our previous study of photosystem II expressed during FaRLiP, these studies describe the molecular evolution of the photosystem complexes encoded by the FaRLiP gene cluster.},
}
@article {pmid38051116,
year = {2024},
author = {Beltrán, L and Torsilieri, H and Patkowski, JB and Yang, JE and Casanova, J and Costa, TRD and Wright, ER and Egelman, EH},
title = {The mating pilus of E. coli pED208 acts as a conduit for ssDNA during horizontal gene transfer.},
journal = {mBio},
volume = {15},
number = {1},
pages = {e0285723},
pmid = {38051116},
issn = {2150-7511},
support = {P30 CA044579/CA/NCI NIH HHS/United States ; R35 GM122510/GM/NIGMS NIH HHS/United States ; U24 GM139168/GM/NIGMS NIH HHS/United States ; },
mesh = {*Escherichia coli/genetics/metabolism ; DNA, Bacterial/genetics/metabolism ; *Gene Transfer, Horizontal ; Conjugation, Genetic ; Fimbriae, Bacterial/genetics/metabolism ; Plasmids ; },
abstract = {Bacteria are constantly exchanging DNA, which constitutes horizontal gene transfer. While some of these occurs by a non-specific process called natural transformation, some occurs by a specific mating between a donor and a recipient cell. In specific conjugation, the mating pilus is extended from the donor cell to make contact with the recipient cell, but whether DNA is actually transferred through this pilus or by another mechanism involving the type IV secretion system complex without the pilus has been an open question. Using Escherichia coli, we show that DNA can be transferred through this pilus between a donor and a recipient cell that has not established a tight mating junction, providing a new picture for the role of this pilus.},
}
@article {pmid38047929,
year = {2023},
author = {Kocsis, B},
title = {Hypervirulent Klebsiella pneumoniae: An update on epidemiology, detection and antibiotic resistance.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {70},
number = {4},
pages = {278-287},
doi = {10.1556/030.2023.02186},
pmid = {38047929},
issn = {1588-2640},
mesh = {Humans ; *Klebsiella pneumoniae ; Abscess/drug therapy ; *Klebsiella Infections/epidemiology/drug therapy ; Virulence/genetics ; Virulence Factors/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Microbial ; },
abstract = {Klebsiella pneumoniae is a major human pathogen as it is responsible for various infections. In the past years hypervirulent K. pneumoniae (hvKP) emerged and disseminated worldwide. In this review a summary will be given about epidemiology, detection and antibiotic resistance of hypervirulent K. pneumoniae. A common feature of hypervirulent K. pneumoniae is a combined expression of several virulence factors. A mucoviscosus phenotype, certain capsulare serotypes (e.g.: K1, K2, K28, K47, K63) together with additional genetic markers namely, magA, rmpA or iucABCD, are needed in combinations to achieve the hypervirulent pathotype. Plasmid coded virulence determinants are also detected, that indicates horizontal gene transfer of hypervirulence factors in K. pneumoniae.Interestingly, infections caused by hypervirulent K. pneumoniae occur usually in the community in otherwise healthy people, and during these infections multiple infection sites are detected. Clinical pictures include both invasive infections and local abscess formation. Pyogenic liver abscess is the most frequently reported clinical manifestation and abscess formation in brain, spleen and lung are also diagnosed. Additionally, meningitis, endophthalmitis, trombophlebitis, pneumonia can also develop.In the early reports, hypervirulent K. pneumoniae strains exhibited enhanced virulence but these were susceptible to commonly used antibiotics. However, recently KPC, VIM, NDM and OXA-48 carbapenemase producing hypervirulent K. pneumoniae strains are increasingly reported, furthermore, well-known high-risk K. pneumoniae clones (e.g.: ST11, ST147, ST307) can develop hypervirulent pathotype, that poses an even more alarming challenge.},
}
@article {pmid38047691,
year = {2024},
author = {Nakabachi, A and Suzaki, T},
title = {Ultrastructure of the bacteriome and bacterial symbionts in the Asian citrus psyllid, Diaphorina citri.},
journal = {Microbiology spectrum},
volume = {12},
number = {1},
pages = {e0224923},
pmid = {38047691},
issn = {2165-0497},
support = {21687020, 26292174, 20H02998//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
mesh = {Animals ; *Hemiptera ; Bacteria/genetics ; Symbiosis ; },
abstract = {Omics analyses suggested a mutually indispensable tripartite association among the host D. citri and organelle-like bacteriome associates, Carsonella and Profftella, which are vertically transmitted through host generations. This relationship is based on the metabolic complementarity among these organisms, which is partly enabled by horizontal gene transfer between partners. However, little was known about the fine morphology of the symbionts and the bacteriome, the interface among these organisms. As a first step to address this issue, the present study performed transmission electron microscopy, which revealed previously unrecognized ultrastructures, including aggregations of ribosomes in Carsonella, numerous tubes and occasional protrusions of Profftella, apparently degrading Profftella, and host organelles with different abundance and morphology in distinct cell types. These findings provide insights into the behaviors of the symbionts and host cells to maintain the symbiotic relationship in D. citri.},
}
@article {pmid38045412,
year = {2025},
author = {Lind, AL and McDonald, NA and Gerrick, ER and Bhatt, AS and Pollard, KS},
title = {Contiguous and complete assemblies of Blastocystis gut microbiome-associated protists reveal evolutionary diversification to host ecology.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38045412},
issn = {2692-8205},
support = {K22 AI173181/AI/NIAID NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; R01 AI148623/AI/NIAID NIH HHS/United States ; R01 HL160862/HL/NHLBI NIH HHS/United States ; },
abstract = {Blastocystis, an obligate host-associated protist, is the most common microbial eukaryote in the human gut and is widely distributed across vertebrate hosts. The evolutionary transition of Blastocystis from its free-living stramenopile ancestors to a radiation of host-associated organisms is poorly understood. To explore this, we cultured and sequenced eight strains representing the significant phylogenetic diversity of the genus using long-read, short-read, and Hi-C DNA sequencing, alongside gene annotation and RNA sequencing. Comparative genomic analyses revealed significant variation in gene content and genome structure across Blastocystis. Notably, three strains from herbivorous tortoises, phylogenetically distant from human subtypes, have markedly larger genomes with longer introns and intergenic regions, and retain canonical stop codons absent in the human-associated strains. Despite these genetic differences, all eight isolates exhibit gene losses linked to the reduced cellular complexity of Blastocystis, including losses of cilia and flagella genes, microtubule motor genes, and signal transduction genes. Isolates from herbivorous tortoises contained higher numbers of plant carbohydrate-metabolizing enzymes, suggesting that like gut bacteria, these protists ferment plant material in the host gut. We find evidence that some of these carbohydrate-metabolizing enzymes were horizontally acquired from bacteria, indicating that horizontal gene transfer is an ongoing process in Blastocystis that has contributed to host-related adaptation. Together, these results highlight substantial genetic and metabolic diversity within the Blastocystis genus, indicating different lineages of Blastocystis have varied ecological roles in the host gut.},
}
@article {pmid38045280,
year = {2023},
author = {Sun, L and David, KT and Wolters, JF and Karlen, SD and Gonçalves, C and Opulente, DA and Leavitt LaBella, A and Groenewald, M and Zhou, X and Shen, XX and Rokas, A and Todd Hittinger, C},
title = {Functional and evolutionary integration of a fungal gene with a bacterial operon.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38045280},
issn = {2692-8205},
support = {R01 AI153356/AI/NIAID NIH HHS/United States ; },
abstract = {Siderophores are crucial for iron-scavenging in microorganisms. While many yeasts can uptake siderophores produced by other organisms, they are typically unable to synthesize siderophores themselves. In contrast, Wickerhamiella/Starmerella (W/S) clade yeasts gained the capacity to make the siderophore enterobactin following the remarkable horizontal acquisition of a bacterial operon enabling enterobactin synthesis. Yet, how these yeasts absorb the iron bound by enterobactin remains unresolved. Here, we demonstrate that Enb1 is the key enterobactin importer in the W/S-clade species Starmerella bombicola. Through phylogenomic analyses, we show that ENB1 is present in all W/S clade yeast species that retained the enterobactin biosynthetic genes. Conversely, it is absent in species that lost the ent genes, except for Starmerella stellata, making this species the only cheater in the W/S clade that can utilize enterobactin without producing it. Through phylogenetic analyses, we infer that ENB1 is a fungal gene that likely existed in the W/S clade prior to the acquisition of the ent genes and subsequently experienced multiple gene losses and duplications. Through phylogenetic topology tests, we show that ENB1 likely underwent horizontal gene transfer from an ancient W/S clade yeast to the order Saccharomycetales, which includes the model yeast Saccharomyces cerevisiae, followed by extensive secondary losses. Taken together, these results suggest that the fungal ENB1 and bacterial ent genes were cooperatively integrated into a functional unit within the W/S clade that enabled adaptation to iron-limited environments. This integrated fungal-bacterial circuit and its dynamic evolution determines the extant distribution of yeast enterobactin producers and cheaters.},
}
@article {pmid38044873,
year = {2024},
author = {Shen, Z and Qin, J and Xiang, G and Chen, T and Nurxat, N and Gao, Q and Wang, C and Zhang, H and Liu, Y and Li, M},
title = {Outer membrane vesicles mediating horizontal transfer of the epidemic blaOXA-232 carbapenemase gene among Enterobacterales.},
journal = {Emerging microbes &amp; infections},
volume = {13},
number = {1},
pages = {2290840},
pmid = {38044873},
issn = {2222-1751},
mesh = {*beta-Lactamases/genetics/metabolism ; *Gene Transfer, Horizontal ; *Bacterial Proteins/genetics/metabolism ; Humans ; *Plasmids/genetics ; Klebsiella pneumoniae/genetics ; Enterobacteriaceae/genetics/enzymology ; Enterobacteriaceae Infections/microbiology/epidemiology ; Cross Infection/microbiology/epidemiology ; },
abstract = {OXA-232 is one of the most common OXA-48-like carbapenemase derivatives and is widely disseminated in nosocomial settings across countries. The blaOXA-232 gene is located on a 6-kb non-conjugative ColKP3-type plasmid, while the dissemination of blaOXA-232 into different Enterobacterales species and the polyclonal dissemination of OXA-232-producing K. pneumoniae revealed the horizontal transfer of blaOXA-232. However, it's still unclear how this non-conjugative ColKP3 plasmid could facilitate the mobilization of blaOXA-232. Here, we observed the in vivo intraspecies transfer of blaOXA-232 during a nosocomial outbreak of OXA-232-producing K. pneumoniae. We demonstrated the presence of ColKP3 OXA-232 plasmid in the outer membrane vesicles (OMVs) derived from clinical isolates, and OMVs could facilitate the horizontal transfer of blaOXA-232 among Enterobacterales. In contrast, for the most prevalent carbapenemase genes, including blaKPC-2 and blaNDM-1, though the presence of carbapenemase genes and plasmid backbones in the vesicular lumen was observed, OMVs couldn't promote effective transformation, probably due to the low copy number of plasmids in clinical isolates and the low number of plasmids loaded into vesicles. Conjugation assay revealed that the epidemic IncX3 NDM-1 and IncFII(pHN7A8)/IncR KPC-2 plasmids were conjugative and could be horizontally transferred via independent conjugation or with the help of a co-existent conjugative plasmid. For the large-size and low-copy number conjugative plasmids carrying carbapenemase genes, OMVs-mediated gene exchange may only serve as an alternative pathway for horizontal transfer. In conclusion, diverse mobilization strategies were employed by plasmids harbouring carbapenemase genes, and plasmids display a proper choice of mobility pathway due to their individual properties.},
}
@article {pmid38043355,
year = {2024},
author = {Chen, Y and Yan, Z and Zhou, Y and Zhang, Y and Jiang, R and Wang, M and Yuan, S and Lu, G},
title = {Dynamic evolution of antibiotic resistance genes in plastisphere in the vertical profile of urban rivers.},
journal = {Water research},
volume = {249},
number = {},
pages = {120946},
doi = {10.1016/j.watres.2023.120946},
pmid = {38043355},
issn = {1879-2448},
mesh = {*Genes, Bacterial ; *Plastics ; Anti-Bacterial Agents/pharmacology ; Rivers ; Drug Resistance, Microbial/genetics ; Microplastics ; Polyesters ; Water ; },
abstract = {Microplastics (MPs) can vertically transport in the aquatic environment due to their aging and biofouling, forming distinct plastisphere in different water layers. However, even though MPs have been regarded as hotspots for antibiotic resistance genes (ARGs), little is known about the propagation and transfer of ARGs in plastisphere in waters, especially in the vertical profile. Therefore, this study investigated the dynamic responses and evolution of ARGs in different plastisphere distributed vertically in an urbanized river. The biofilm biomass in the polylactic acid (PLA) plastisphere was relatively higher than that in the polyethylene terephthalate (PET), showing depth-decay variations. The ARGs abundance in plastisphere were much higher than that in the surrounding waters, especially for the PLA. In the vertical profiles, the ARGs abundance in the PET plastisphere increased with water depths, while the highest abundance of ARGs in the PLA mostly appeared at intermediate waters. In the temporal dynamic, the ARGs abundance in plastisphere increased and then decreased, which may be dominated by the MP types at the initial periods. After long-term exposure, the influences of water depths seemed to be strengthened, especially in the PET plastisphere. Compared with surface waters, the microbiota attached in plastisphere in deep waters showed high species richness, strong diversity, and complex interactions, which was basically consistent with the changes of nutrient contents in different water layers. These vertical variations in microbiota and nutrients (e.g., nitrogen) may be responsible for the propagation of ARGs in plastisphere in deep waters. The host bacteria for ARGs in plastisphere was also developed as water depth increased, leading to an enrichment of ARGs in deep waters. In addition, the abundance of ARGs in plastisphere in bottom waters was positively correlated with the mobile genetic elements (MGEs) of intI1 and tnpA05, indicative of a frequent horizontal gene transfer of ARGs. Overall, water depth played a critical role in the propagation of ARGs in plastisphere, which should not be ignored in a long time series. This study provides new insights into the dynamic evolution of ARGs propagation in plastisphere under increasing global MPs pollution, especially in the vertical profile.},
}
@article {pmid38041553,
year = {2024},
author = {Schmitz, M and Querques, I},
title = {DNA on the move: mechanisms, functions and applications of transposable elements.},
journal = {FEBS open bio},
volume = {14},
number = {1},
pages = {13-22},
pmid = {38041553},
issn = {2211-5463},
support = {//Branco Weiss Fellowship - Society in Science/ ; ALTF 296-2020//European Molecular Biology Organization/ ; //Federation of European Biochemical Societies/ ; //UZH Postdoc Grant/ ; },
mesh = {*DNA Transposable Elements/genetics ; Mutagenesis, Insertional ; *Bacteria/genetics ; CRISPR-Cas Systems/genetics ; Gene Transfer Techniques ; },
abstract = {Transposons are mobile genetic elements that have invaded all domains of life by moving between and within their host genomes. Due to their mobility (or transposition), transposons facilitate horizontal gene transfer in bacteria and foster the evolution of new molecular functions in prokaryotes and eukaryotes. As transposition can lead to detrimental genomic rearrangements, organisms have evolved a multitude of molecular strategies to control transposons, including genome defense mechanisms provided by CRISPR-Cas systems. Apart from their biological impacts on genomes, DNA transposons have been leveraged as efficient gene insertion vectors in basic research, transgenesis and gene therapy. However, the close to random insertion profile of transposon-based tools limits their programmability and safety. Despite recent advances brought by the development of CRISPR-associated genome editing nucleases, a strategy for efficient insertion of large, multi-kilobase transgenes at user-defined genomic sites is currently challenging. The discovery and experimental characterization of bacterial CRISPR-associated transposons (CASTs) led to the attractive hypothesis that these systems could be repurposed as programmable, site-specific gene integration technologies. Here, we provide a broad overview of the molecular mechanisms underpinning DNA transposition and of its biological and technological impact. The second focus of the article is to describe recent mechanistic and functional analyses of CAST transposition. Finally, current challenges and desired future advances of CAST-based genome engineering applications are briefly discussed.},
}
@article {pmid38039844,
year = {2023},
author = {Harada, R and Inagaki, Y},
title = {Gleaning Euglenozoa-specific DNA polymerases in public single-cell transcriptome data.},
journal = {Protist},
volume = {174},
number = {6},
pages = {125997},
doi = {10.1016/j.protis.2023.125997},
pmid = {38039844},
issn = {1618-0941},
mesh = {*Euglenozoa ; Transcriptome ; DNA-Directed DNA Polymerase/genetics/metabolism ; *Euglenida ; },
abstract = {Multiple genes encoding family A DNA polymerases (famA DNAPs), which are evolutionary relatives of DNA polymerase I (PolI) in bacteria and phages, have been found in eukaryotic genomes, and many of these proteins are used mainly in organelles. Among members of the phylum Euglenozoa, distinct types of famA DNAP, PolIA, PolIBCD+, POP, and eugPolA, have been found. It is intriguing how the suite of famA DNAPs had been established during the evolution of Euglenozoa, but the DNAP data have not been sampled from the taxa that sufficiently represent the diversity of this phylum. In particular, little sequence data were available for basal branching species in Euglenozoa until recently. Thanks to the single-cell transcriptome data from symbiontids and phagotrophic euglenids, we have an opportunity to cover the "hole" in the repertory of famA DNAPs in the deep branches in Euglenozoa. The current study identified 16 new famA DNAP sequences in the transcriptome data from 33 phagotrophic euglenids and two symbiontids, respectively. Based on the new famA DNAP sequences, the updated diversity and evolution of famA DNAPs in Euglenozoa are discussed.},
}
@article {pmid38032214,
year = {2023},
author = {Kubori, T},
title = {A two-component system serves as a central hub for connecting energy metabolism and plasmid dissemination in bacteria.},
journal = {mBio},
volume = {14},
number = {6},
pages = {e0247423},
pmid = {38032214},
issn = {2150-7511},
support = {//Takeda Science Foundation (TSF)/ ; },
mesh = {*Plasmids/genetics ; *Acinetobacter baumannii/genetics/metabolism ; *Energy Metabolism/genetics ; *Conjugation, Genetic ; Bacterial Proteins/genetics/metabolism ; Type IV Secretion Systems/genetics/metabolism ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Gene Expression Regulation, Bacterial ; },
abstract = {Mobile genetic elements such as conjugative plasmids play a key role in the acquisition of antibiotic resistance by pathogenic bacteria. Resistance genes on plasmids can be transferred between bacteria using specialized conjugation machinery. Acinetobacter baumannii, the most common bacterium associated with nosocomial infections, harbors a large conjugative plasmid that encodes a type IV secretion system (T4SS). Feng et al. recently found that the A. baumannii T4SS is specialized for plasmid transfer, suggesting that it may be involved in multidrug resistance (Z. Feng, L. Wang, Q. Guan, X. Chu, and Z.-Q. Luo, mBio e02276-23, 2023, https://doi.org/10.1128/mbio.02276-23), T4SS-encoding genes are shown to be controlled by a versatile GacA/S two-component regulatory system. GacA/S is also found to regulate genes involved in central metabolism. The coordinated regulation of metabolism and plasmid conjugation may be a bacterial strategy for adapting to selective pressure from antibiotics.},
}
@article {pmid38032189,
year = {2023},
author = {Zheng, Q and Li, L and Yin, X and Che, Y and Zhang, T},
title = {Is ICE hot? A genomic comparative study reveals integrative and conjugative elements as "hot" vectors for the dissemination of antibiotic resistance genes.},
journal = {mSystems},
volume = {8},
number = {6},
pages = {e0017823},
pmid = {38032189},
issn = {2379-5077},
support = {T21-705/20-N//Research Grants Council, University Grants Committee ()/ ; T21-705/20-N//Research Grants Council, University Grants Committee ()/ ; T21-705/20-N//Research Grants Council, University Grants Committee ()/ ; T21-705/20-N//Research Grants Council, University Grants Committee ()/ ; T21-705/20-N//Research Grants Council, University Grants Committee ()/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology ; *Conjugation, Genetic ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal/genetics ; Genomics ; Phylogeny ; },
abstract = {Different from other extensively studied mobile genetic elements (MGEs) whose discoveries were initiated decades ago (1950s-1980s), integrative and conjugative elements (ICEs), a diverse array of more recently identified elements that were formally termed in 2002, have aroused increasing concern for their crucial contribution to the dissemination of antibiotic resistance genes (ARGs). However, the comprehensive understanding on ICEs' ARG profile across the bacterial tree of life is still blurred. Through a genomic study by comparison with two key MGEs, we, for the first time, systematically investigated the ARG profile as well as the host range of ICEs and also explored the MGE-specific potential to facilitate ARG propagation across phylogenetic barriers. These findings could serve as a theoretical foundation for risk assessment of ARGs mediated by distinct MGEs and further to optimize therapeutic strategies aimed at restraining antibiotic resistance crises.},
}
@article {pmid38031909,
year = {2023},
author = {Kröger, C and Lerminiaux, NA and Ershova, AS and MacKenzie, KD and Kirzinger, MW and Märtlbauer, E and Perry, BJ and Cameron, ADS and Schauer, K},
title = {Plasmid-encoded lactose metabolism and mobilized colistin resistance (mcr-9) genes in Salmonella enterica serovars isolated from dairy facilities in the 1980s.},
journal = {Microbial genomics},
volume = {9},
number = {11},
pages = {},
pmid = {38031909},
issn = {2057-5858},
mesh = {*Colistin/pharmacology ; *Salmonella enterica/genetics ; Lactose ; Serogroup ; Drug Resistance, Bacterial/genetics ; Plasmids/genetics ; },
abstract = {Horizontal gene transfer by plasmids can confer metabolic capabilities that expand a host cell's niche. Yet, it is less understood whether the coalescence of specialized catabolic functions, antibiotic resistances and metal resistances on plasmids provides synergistic benefits. In this study, we report whole-genome assembly and phenotypic analysis of five Salmonella enterica strains isolated in the 1980s from milk powder in Munich, Germany. All strains exhibited the unusual phenotype of lactose-fermentation and encoded either of two variants of the lac operon. Surprisingly, all strains encoded the mobilized colistin resistance gene 9 (mcr-9), long before the first report of this gene in the literature. In two cases, the mcr-9 gene and the lac locus were linked within a large gene island that formed an IncHI2A-type plasmid in one strain but was chromosomally integrated in the other strain. In two other strains, the mcr-9 gene was found on a large IncHI1B/IncP-type plasmid, whereas the lac locus was encoded on a separate chromosomally integrated plasmidic island. The mcr-9 sequences were identical and genomic contexts could not explain the wide range of colistin resistances exhibited by the Salmonella strains. Nucleotide variants did explain phenotypic differences in motility and exopolysaccharide production. The observed linkage of mcr-9 to lactose metabolism, an array of heavy-metal detoxification systems, and other antibiotic resistance genes may reflect a coalescence of specialized phenotypes that improve the spread of colistin resistance in dairy facilities, much earlier than previously suspected.},
}
@article {pmid38013098,
year = {2024},
author = {Fang, GY and Liu, XQ and Jiang, YJ and Mu, XJ and Huang, BW},
title = {Horizontal gene transfer in activated sludge enhances microbial antimicrobial resistance and virulence.},
journal = {The Science of the total environment},
volume = {912},
number = {},
pages = {168908},
doi = {10.1016/j.scitotenv.2023.168908},
pmid = {38013098},
issn = {1879-1026},
mesh = {*Sewage/microbiology ; Virulence/genetics ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; Virulence Factors/genetics ; },
abstract = {Activated sludge (AS) plays a vital role in removing organic pollutants and nutrients from wastewater. However, the risks posed by horizontal gene transfer (HGT) between bacteria in AS are still unclear. Here, a total of 478 high-quality non-redundant metagenome-assembled genomes (MAGs) were obtained. >50 % and 5 % of MAGs were involved in at least one HGT and recent HGT, respectively. Most of the transfers (82.4 %) of antimicrobial resistance genes (ARGs) occurred among the classes of Alphaproteobacteria and Gammaproteobacteria. The bacteria involved in the transfers of virulence factor genes (VFGs) mainly include Alphaproteobacteria (42.3 %), Bacteroidia (19.2 %), and Gammaproteobacteria (11.5 %). Moreover, the number of ARGs and VFGs in the classes of Alphaproteobacteria and Gammaproteobacteria was higher than that in other bacteria (P < 0.001). Mobile genetic elements were important contributors to ARGs and VFGs in AS bacteria. These results have implications for the management of antimicrobial resistance and virulence in activated sludge microorganisms.},
}
@article {pmid38012331,
year = {2023},
author = {Zhu, H and Yu, J and Fu, Y and Mao, X and Yang, H},
title = {Two-Omics Probe on the Potential of Pseudomonas sp. GDMCC 1.1703 Under Phenol Stress.},
journal = {Current microbiology},
volume = {81},
number = {1},
pages = {21},
pmid = {38012331},
issn = {1432-0991},
support = {2019YFC1803801//Key Technologies Research and Development Program/ ; 2019YFC1803800//Key Technology Research and Development Program of Shandong/ ; },
mesh = {*Pseudomonas/metabolism ; *Phenol/metabolism ; RNA, Ribosomal, 16S/metabolism ; Base Sequence ; Bacteria/genetics ; Biodegradation, Environmental ; },
abstract = {Pseudomonas sp. harbors genetic diversity and readily adapts to environmental challenges, conferring upon it the ability to remediate. It is important to genetically determine the effects of bacterial application. The two-omics integration approach may shed more light on Pseudomonas isolates, filling the knowledge gap between genetic potential and dynamic function. In the present study, a strain from the Xi River was isolated using benzene-selective enrichment medium and phylogenetically identified as Pseudomonas sp. GDMCC 1.1703 by 16S rRNA gene sequencing. Its phenol degradability was optimally assessed at a rate of 45.7% (by statistics P < 0.05) in 12 h with a 200 mg/L concentration. Genomics and transcriptomics analyses were successively used to identify the genes and pathways responsible for phenol degradation. At least 42 genes were genomically identified to be involved in xenobiotic biodegradation. The degradative genes clustered into operons were hypothesized to have evolved through horizontal gene transfer. On the basis of genomic authentication, transcriptome analysis dynamically revealed that phenol degradation and responsive mechanisms were both upregulated as defense between the Ctrl (control) and PS (phenol-stressed) groups. Quantitative reverse transcription-PCR not only validated the key genes identified via RNA sequencing but also consistently confirmed the realistic intracellular expression. The approach of omics integration, which is effective in exploring the potential of isolates, will hopefully become an established method for determining the remediation potential of a candidate for development.},
}
@article {pmid38007474,
year = {2023},
author = {Liu, Y and Brinkhoff, T and Berger, M and Poehlein, A and Voget, S and Paoli, L and Sunagawa, S and Amann, R and Simon, M},
title = {Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {265},
pmid = {38007474},
issn = {2049-2618},
support = {TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; 205321_184955//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 205321_184955//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 51NF40_180575//National Center of Competence in Research Quantum Science and Technology/ ; },
mesh = {*Roseobacter/genetics ; Seawater/microbiology ; Metagenome ; Phylogeny ; Oceans and Seas ; Metagenomics ; },
abstract = {BACKGROUND: The RCA (Roseobacter clade affiliated) cluster belongs to the family Roseobacteracea and represents a major Roseobacter lineage in temperate to polar oceans. Despite its prevalence and abundance, only a few genomes and one described species, Planktomarina temperata, exist. To gain more insights into our limited understanding of this cluster and its taxonomic and functional diversity and biogeography, we screened metagenomic datasets from the global oceans and reconstructed metagenome-assembled genomes (MAG) affiliated to this cluster.<br><br>RESULTS: The total of 82 MAGs, plus five genomes of isolates, reveal an unexpected diversity and novel insights into the genomic features, the functional diversity, and greatly refined biogeographic patterns of the RCA cluster. This cluster is subdivided into three genera: Planktomarina, Pseudoplanktomarina, and the most deeply branching Candidatus Paraplanktomarina. Six of the eight Planktomarina species have larger genome sizes (2.44-3.12 Mbp) and higher G&#x2009;+&#x2009;C contents (46.36-53.70%) than the four Pseudoplanktomarina species (2.26-2.72 Mbp, 42.22-43.72 G&#x2009;+&#x2009;C%). Cand. Paraplanktomarina is represented only by one species with a genome size of 2.40 Mbp and a G&#x2009;+&#x2009;C content of 45.85%. Three novel species of the genera Planktomarina and Pseudoplanktomarina are validly described according to the SeqCode nomenclature for prokaryotic genomes. Aerobic anoxygenic photosynthesis (AAP) is encoded in three Planktomarina species. Unexpectedly, proteorhodopsin (PR) is encoded in the other Planktomarina and all Pseudoplanktomarina species, suggesting that this light-driven proton pump is the most important mode of acquiring complementary energy of the RCA cluster. The Pseudoplanktomarina species exhibit differences in functional traits compared to Planktomarina species and adaptations to more resource-limited conditions. An assessment of the global biogeography of the different species greatly expands the range of occurrence and shows that the different species exhibit distinct biogeographic patterns. They partially reflect the genomic features of the species.<br><br>CONCLUSIONS: Our detailed MAG-based analyses shed new light on the diversification, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. The taxonomic delineation and validation by the SeqCode nomenclature of prominent genera and species of the RCA cluster may be a promising way for a refined taxonomic identification of major prokaryotic lineages and sublineages in marine and other prokaryotic communities assessed by metagenomics approaches. Video Abstract.},
}
@article {pmid38007076,
year = {2024},
author = {Zhang, Z and Bo, L and Wang, S and Li, C and Zhang, X and Xue, B and Yang, X and He, X and Shen, Z and Qiu, Z and Zhao, C and Wang, J},
title = {Multidrug-resistant plasmid RP4 inhibits the nitrogen removal capacity of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, and comammox in activated sludge.},
journal = {Environmental research},
volume = {242},
number = {},
pages = {117739},
doi = {10.1016/j.envres.2023.117739},
pmid = {38007076},
issn = {1096-0953},
mesh = {*Archaea/genetics/metabolism ; Sewage/microbiology ; Ammonia ; Nitrogen/metabolism ; Denitrification ; In Situ Hybridization, Fluorescence ; Oxidation-Reduction ; Bacteria/genetics/metabolism ; Plasmids/genetics ; *Betaproteobacteria/genetics/metabolism ; Anti-Bacterial Agents ; Phylogeny ; Soil Microbiology ; },
abstract = {In wastewater treatment plants (WWTPs), ammonia oxidation is primarily carried out by three types of ammonia oxidation microorganisms (AOMs): ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and comammox (CMX). Antibiotic resistance genes (ARGs), which pose an important public health concern, have been identified at every stage of wastewater treatment. However, few studies have focused on the impact of ARGs on ammonia removal performance. Therefore, our study sought to investigate the effect of the representative multidrug-resistant plasmid RP4 on the functional microorganisms involved in ammonia oxidation. Using an inhibitor-based method, we first evaluated the contributions of AOA, AOB, and CMX to ammonia oxidation in activated sludge, which were determined to be 13.7%, 41.1%, and 39.1%, respectively. The inhibitory effects of C2H2, C8H14, and 3,4-dimethylpyrazole phosphate (DMPP) were then validated by qPCR. After adding donor strains to the sludge, fluorescence in situ hybridization (FISH) imaging analysis demonstrated the co-localization of RP4 plasmids and all three AOMs, thus confirming the horizontal gene transfer (HGT) of the RP4 plasmid among these microorganisms. Significant inhibitory effects of the RP4 plasmid on the ammonia nitrogen consumption of AOA, AOB, and CMX were also observed, with inhibition rates of 39.7%, 36.2%, and 49.7%, respectively. Moreover, amoA expression in AOB and CMX was variably inhibited by the RP4 plasmid, whereas AOA amoA expression was not inhibited. These results demonstrate the adverse environmental effects of the RP4 plasmid and provide indirect evidence supporting plasmid-mediated conjugation transfer from bacteria to archaea.},
}
@article {pmid38006896,
year = {2024},
author = {Yang, QE and Ma, X and Zeng, L and Wang, Q and Li, M and Teng, L and He, M and Liu, C and Zhao, M and Wang, M and Hui, D and Madsen, JS and Liao, H and Walsh, TR and Zhou, S},
title = {Interphylum dissemination of NDM-5-positive plasmids in hospital wastewater from Fuzhou, China: a single-centre, culture-independent, plasmid transmission study.},
journal = {The Lancet. Microbe},
volume = {5},
number = {1},
pages = {e13-e23},
doi = {10.1016/S2666-5247(23)00227-6},
pmid = {38006896},
issn = {2666-5247},
mesh = {Female ; Pregnancy ; Child ; Humans ; *Escherichia coli/genetics ; Wastewater ; RNA, Ribosomal, 16S/genetics ; Plasmids/genetics ; Bacteria/genetics ; Hospitals ; *Anti-Infective Agents ; },
abstract = {BACKGROUND: The global spread of plasmid-borne carbapenem resistance is an ongoing public health challenge; however, the nature of such horizontal gene transfer events among complex bacterial communities remains poorly understood. We examined the in-situ transfer of the globally dominant New Delhi metallo-β-lactamase (NDM)-5-positive IncX3 plasmid (denoted pX3_NDM-5) in hospital wastewater to simulate a real-world, One Health antimicrobial resistance context.<br><br>METHODS: For this transmission study, we tagged pX3_NDM-5 with the green fluorescent protein gene, gfp, using a CRISPR-based method and transferred the plasmid to a donor Escherichia coli strain. Bacteria were extracted from a hospital wastewater treatment plant (Fujian Provincial Maternity and Children's Hospital, Fuzhou, China) as the bacterial recipient community. We mixed this recipient community with the E coli donor strain carrying the gfp-tagged plasmid, both with and without sodium hypochlorite (NaClO) as an environmental stressor, and conducted several culture-based and culture-independent conjugation assays. The conjugation events were observed microscopically and quantified by fluorescence-activated cell sorting. We analysed the taxonomic composition of the sorted transconjugal pool by 16S rRNA gene amplicon sequencing and assessed the stability of the plasmid in the isolated transconjugants and its ability to transfer back to E coli.<br><br>FINDINGS: We show that the plasmid pX3_NDM-5 has a broad host range and can transfer across various bacterial phyla, including between Gram-negative and Gram-positive bacteria. Although environmental stress with NaClO did not affect the overall plasmid transfer frequency, it reduced the breadth of the transconjugant pool. The taxonomic composition of the transconjugal pool was distinct from that of the recipient communities, and environmental stress modulated the permissiveness of some operational taxonomic units towards the acquisition of pX3_NDM-5. Notably, pX3_NDM-5 transconjugants included the Gram-positive pathogen Enterococcus faecalis, and the plasmid could subsequently be reconjugated back to E coli. These findings suggest that E faecalis could act as a natural shuttle vector for the wide dissemination of pX3_NDM-5 plasmids.<br><br>INTERPRETATION: Our culture-independent conjugation model simulates natural environmental conditions and challenges the established theory that Gram-negative and Gram-positive bacteria rarely exchange clinically important plasmids. The data show that plasmids disseminate more widely across genera and phyla than previously thought. These findings have substantial implications when considering the spread of antimicrobial resistance across One Health sectors.<br><br>FUNDING: The Laboratory of Lingnan Modern Agriculture Project, the National Natural Science Foundation of China, the Natural Science Foundation of Fujian Province of China, and the Outstanding Young Research Talents Program of Fujian Agriculture and Forestry University.},
}
@article {pmid38006562,
year = {2024},
author = {Serbus, LR},
title = {A Light in the Dark: Uncovering Wolbachia-Host Interactions Using Fluorescence Imaging.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2739},
number = {},
pages = {349-373},
pmid = {38006562},
issn = {1940-6029},
mesh = {Animals ; *Wolbachia/genetics ; *Arthropods/microbiology ; *Nematoda ; Symbiosis ; Optical Imaging ; },
abstract = {The success of microbial endosymbionts, which reside naturally within a eukaryotic "host" organism, requires effective microbial interaction with, and manipulation of, the host cells. Fluorescence microscopy has played a key role in elucidating the molecular mechanisms of endosymbiosis. For 30 years, fluorescence analyses have been a cornerstone in studies of endosymbiotic Wolbachia bacteria, focused on host colonization, maternal transmission, reproductive parasitism, horizontal gene transfer, viral suppression, and metabolic interactions in arthropods and nematodes. Fluorescence-based studies stand to continue informing Wolbachia-host interactions in increasingly detailed and innovative ways.},
}
@article {pmid38006561,
year = {2024},
author = {Bordenstein, SR},
title = {Isolation of Phage WO Particles from Wolbachia-Infected Arthropods.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2739},
number = {},
pages = {337-348},
pmid = {38006561},
issn = {1940-6029},
mesh = {Animals ; *Arthropods ; *Wolbachia/genetics ; *Bacteriophages/genetics ; Prophages ; Myoviridae ; },
abstract = {Nearly all arthropod-associated Wolbachia contain intact and/or genomic remnants of phage WO, temperate bacteriophages that facilitate horizontal gene transfer, genomic rearrangement of the bacterial chromosome, and symbiotic interactions between Wolbachia and their arthropod hosts. Integrated prophage WO genomes produce active, lytic particles; but the lack of a cell-free culturing system for Wolbachia render them difficult to purify and study. This chapter describes polyethylene glycol (PEG) precipitation of phage particles from Wolbachia-infected arthropods, followed by confirmation of phage WO isolation and purification using electron microscopy and PCR.},
}
@article {pmid38005943,
year = {2023},
author = {Loney, RE and Delesalle, VA and Chaudry, BE and Czerpak, M and Guffey, AA and Goubet-McCall, L and McCarty, M and Strine, MS and Tanke, NT and Vill, AC and Krukonis, GP},
title = {A Novel Subcluster of Closely Related Bacillus Phages with Distinct Tail Fiber/Lysin Gene Combinations.},
journal = {Viruses},
volume = {15},
number = {11},
pages = {},
pmid = {38005943},
issn = {1999-4915},
support = {52007540/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {*Bacillus Phages/genetics ; Genome, Viral ; *Bacteriophages/genetics ; Base Sequence ; Soil ; },
abstract = {Bacteriophages (phages) are the most numerous entities on Earth, but we have only scratched the surface of describing phage diversity. We isolated seven Bacillus subtilis phages from desert soil in the southwest United States and then sequenced and characterized their genomes. Comparative analyses revealed high nucleotide and amino acid similarity between these seven phages, which constitute a novel subcluster. Interestingly, the tail fiber and lysin genes of these phages seem to come from different origins and carry out slightly different functions. These genes were likely acquired by this subcluster of phages via horizontal gene transfer. In conjunction with host range assays, our data suggest that these phages are adapting to hosts with different cell walls.},
}
@article {pmid38005684,
year = {2023},
author = {Khafizova, GV and Sierro, N and Ivanov, NV and Sokornova, SV and Polev, DE and Matveeva, TV},
title = {Nicotiana noctiflora Hook. Genome Contains Two Cellular T-DNAs with Functional Genes.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {22},
pages = {},
pmid = {38005684},
issn = {2223-7747},
support = {21-14-00050//Russian Science Foundation/ ; },
abstract = {Agrobacterium (Rhizobium)-mediated transformation leads to the formation of crown galls or hairy roots on infected plants. These effects develop due to the activity of T-DNA genes, gathered on a big plasmid, acquired from agrobacteria during horizontal gene transfer. However, a lot of plant species are known to contain such sequences, called cellular T-DNAs (cT-DNAs), and maintain normal phenotypes. Some of the genes remain intact, which leads to the conclusion of their functional role in plants. In this study, we present a comprehensive analysis of the cT-DNAs in the Nicotiana noctiflora Hook. genome, including gene expression and opine identification. Deep sequencing of the Nicotiana noctiflora genome revealed the presence of two different cT-DNAs, NnT-DNA1 and NnT-DNA2, which contain the intact genes iaaM, iaaH, acs, orf13, orf13a, and orf14. According to the expression analysis results, all these genes are most active in roots in comparison with other organs, which is consistent with data on cT-DNA gene expression in other plant species. We also used genetic engineering approaches and HPTLC and HPLC-MS methods to investigate the product of the acs gene (agrocinopine synthase), which turned out to be similar to agrocinopine A. Overall, this study expands our knowledge of cT-DNAs in plants and brings us closer to understanding their possible functions. Further research of cT-DNAs in different species and their functional implications could contribute to advancements in plant genetics and potentially unveil novel traits with practical applications in agriculture and other fields.},
}
@article {pmid38004737,
year = {2023},
author = {Cai, T and Tang, H and Du, X and Wang, W and Tang, K and Wang, X and Liu, D and Wang, P},
title = {Genomic Island-Encoded Diguanylate Cyclase from Vibrio alginolyticus Regulates Biofilm Formation and Motility in Pseudoalteromonas.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004737},
issn = {2076-2607},
support = {42188102, 91951203 and 32070175//the National Science Foundation of China/ ; 2022YFC3103600//the National Key R&amp;D Program of China/ ; 2021345//the Youth Innovation Promotion Association CAS/ ; 2019BT02Y262//the Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program/ ; GJTD-2020-12//the K. C. Wong Education Foundation/ ; 2021B1212050023//the Science and Technology Planning Project of Guangdong Province of China/ ; },
abstract = {Many bacteria use the second messenger c-di-GMP to regulate exopolysaccharide production, biofilm formation, motility, virulence, and other phenotypes. The c-di-GMP level is controlled by the complex network of diguanylate cyclases (DGCs) and phosphodiesterases (PDEs) that synthesize and degrade c-di-GMP. In addition to chromosomally encoded DGCs, increasing numbers of DGCs were found to be located on mobile genetic elements. Whether these mobile genetic element-encoded DGCs can modulate the physiological phenotypes in recipient bacteria after horizontal gene transfer should be investigated. In our previous study, a genomic island encoding three DGC proteins (Dgc137, Dgc139, and Dgc140) was characterized in Vibrio alginolyticus isolated from the gastric cavity of the coral Galaxea fascicularis. Here, the effect of the three DGCs in four Pseudoalteromonas strains isolated from coral Galaxea fascicularis and other marine environments was explored. The results showed that when dgc137 is present rather than the three DGC genes, it obviously modulates biofilm formation and bacterial motility in these Pseudoalteromonas strains. Our findings implied that mobile genetic element-encoded DGC could regulate the physiological status of neighboring bacteria in a microbial community by modulating the c-di-GMP level after horizontal gene transfer.},
}
@article {pmid38004480,
year = {2023},
author = {Muteeb, G and Rehman, MT and Shahwan, M and Aatif, M},
title = {Origin of Antibiotics and Antibiotic Resistance, and Their Impacts on Drug Development: A Narrative Review.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {16},
number = {11},
pages = {},
pmid = {38004480},
issn = {1424-8247},
support = {xxx//King Faisal University/ ; },
abstract = {Antibiotics have revolutionized medicine, saving countless lives since their discovery in the early 20th century. However, the origin of antibiotics is now overshadowed by the alarming rise in antibiotic resistance. This global crisis stems from the relentless adaptability of microorganisms, driven by misuse and overuse of antibiotics. This article explores the origin of antibiotics and the subsequent emergence of antibiotic resistance. It delves into the mechanisms employed by bacteria to develop resistance, highlighting the dire consequences of drug resistance, including compromised patient care, increased mortality rates, and escalating healthcare costs. The article elucidates the latest strategies against drug-resistant microorganisms, encompassing innovative approaches such as phage therapy, CRISPR-Cas9 technology, and the exploration of natural compounds. Moreover, it examines the profound impact of antibiotic resistance on drug development, rendering the pursuit of new antibiotics economically challenging. The limitations and challenges in developing novel antibiotics are discussed, along with hurdles in the regulatory process that hinder progress in this critical field. Proposals for modifying the regulatory process to facilitate antibiotic development are presented. The withdrawal of major pharmaceutical firms from antibiotic research is examined, along with potential strategies to re-engage their interest. The article also outlines initiatives to overcome economic challenges and incentivize antibiotic development, emphasizing international collaborations and partnerships. Finally, the article sheds light on government-led initiatives against antibiotic resistance, with a specific focus on the Middle East. It discusses the proactive measures taken by governments in the region, such as Saudi Arabia and the United Arab Emirates, to combat this global threat. In the face of antibiotic resistance, a multifaceted approach is imperative. This article provides valuable insights into the complex landscape of antibiotic development, regulatory challenges, and collaborative efforts required to ensure a future where antibiotics remain effective tools in safeguarding public health.},
}
@article {pmid38002987,
year = {2023},
author = {Wang, B and Finazzo, M and Artsimovitch, I},
title = {Machine Learning Suggests That Small Size Helps Broaden Plasmid Host Range.},
journal = {Genes},
volume = {14},
number = {11},
pages = {},
pmid = {38002987},
issn = {2073-4425},
support = {R01 GM067153/GM/NIGMS NIH HHS/United States ; },
mesh = {*Host Specificity ; Plasmids/genetics ; *Bacteria/genetics ; beta-Lactamases/genetics ; Machine Learning ; },
abstract = {Plasmids mediate gene exchange across taxonomic barriers through conjugation, shaping bacterial evolution for billions of years. While plasmid mobility can be harnessed for genetic engineering and drug-delivery applications, rapid plasmid-mediated spread of resistance genes has rendered most clinical antibiotics useless. To solve this urgent and growing problem, we must understand how plasmids spread across bacterial communities. Here, we applied machine-learning models to identify features that are important for extending the plasmid host range. We assembled an up-to-date dataset of more than thirty thousand bacterial plasmids, separated them into 1125 clusters, and assigned each cluster a distribution possibility score, taking into account the host distribution of each taxonomic rank and the sampling bias of the existing sequencing data. Using this score and an optimized plasmid feature pool, we built a model stack consisting of DecisionTreeRegressor, EvoTreeRegressor, and LGBMRegressor as base models and LinearRegressor as a meta-learner. Our mathematical modeling revealed that sequence brevity is the most important determinant for plasmid spread, followed by P-loop NTPases, mobility factors, and β-lactamases. Ours and other recent results suggest that small plasmids may broaden their range by evading host defenses and using alternative modes of transfer instead of autonomous conjugation.},
}
@article {pmid38000736,
year = {2024},
author = {Yao, N and Li, W and Hu, L and Fang, N},
title = {Do mould inhibitors alter the microbial community structure and antibiotic resistance gene profiles on textiles?.},
journal = {The Science of the total environment},
volume = {911},
number = {},
pages = {168808},
doi = {10.1016/j.scitotenv.2023.168808},
pmid = {38000736},
issn = {1879-1026},
mesh = {Humans ; *Genes, Bacterial ; Camphor ; Bacteria/genetics ; *Microbiota ; Drug Resistance, Microbial/genetics ; Fungi ; Textiles ; Naphthalenes/pharmacology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Mould inhibitors are closely associated with human health and have been extensively applied to textiles to prevent mould and insect infestations. However, the impact of these mould inhibitors on the microbial community structure on textiles and antibiotic resistance gene (ARG) profiles remains largely unexplored. In this study, testing techniques, including high-throughput quantitative PCR and Illumina sequencing, were employed to analyse the effects of three types of mould inhibitors -para-dichlorobenzene (PDCB), naphthalene, and natural camphor balls-on the composition of microbial communities and ARG profiles. The microbial mechanisms underlying these effects were also investigated. The experiments revealed that PDCB reduced the diversity of bacterial communities on textiles, whereas naphthalene and natural camphor balls exerted relatively minor effects. In contrast with bacterial diversity, PDCB enhanced the diversity of fungal communities on textiles, but significantly reduced their abundance. Naphthalene had the least impact on fungal communities; however, it notably increased the relative abundance of Basidiomycota. All three types of mould inhibitors substantially altered ARG profiles. Potential mechanisms responsible for the alterations in ARG profiles include microbial community succession and horizontal gene transfer mediated by mobile genetic elements. PDCB prominently increased the abundance of ARGs, mainly attributable to the relative enrichment of potential hosts (including certain γ-Proteobacteria and Bacillales) for specific ARGs. Thus, this study has important implications for the selection of mould inhibitors, as well as the assessment of microbial safety in textiles.},
}
@article {pmid37999346,
year = {2023},
author = {Marinacci, B and Krzyżek, P and Pellegrini, B and Turacchio, G and Grande, R},
title = {Latest Update on Outer Membrane Vesicles and Their Role in Horizontal Gene Transfer: A Mini-Review.},
journal = {Membranes},
volume = {13},
number = {11},
pages = {},
pmid = {37999346},
issn = {2077-0375},
abstract = {Outer membrane vesicles (OMVs) are spherical, lipid-based nano-structures, which are released by Gram-negative bacteria in both in vitro and in vivo conditions. The size and composition of OMVs depend on not only the producer bacterial species but also cells belonging to the same strain. The mechanism of vesicles' biogenesis has a key role in determining their cargo and the pattern of macromolecules exposed on their surface. Thus, the content of proteins, lipids, nucleic acids, and other biomolecules defines the properties of OMVs and their beneficial or harmful effects on human health. Many studies have provided evidence that OMVs can be involved in a plethora of biological processes, including cell-to-cell communication and bacteria-host interactions. Moreover, there is a growing body of literature supporting their role in horizontal gene transfer (HGT). During this process, OMVs can facilitate the spreading of genes involved in metabolic pathways, virulence, and antibiotic resistance, guaranteeing bacterial proliferation and survival. For this reason, a deeper understanding of this new mechanism of genetic transfer could improve the development of more efficient strategies to counteract infections sustained by Gram-negative bacteria. In line with this, the main aim of this mini-review is to summarize the latest evidence concerning the involvement of OMVs in HGT.},
}
@article {pmid37995998,
year = {2024},
author = {Huang, B and Lv, X and Zheng, H and Yu, H and Zhang, Y and Zhang, C and Wang, J},
title = {Microbial organic fertilizer prepared by co-composting of Trichoderma dregs mitigates dissemination of resistance, virulence genes, and bacterial pathogens in soil and rhizosphere.},
journal = {Environmental research},
volume = {241},
number = {},
pages = {117718},
doi = {10.1016/j.envres.2023.117718},
pmid = {37995998},
issn = {1096-0953},
mesh = {*Composting ; Soil ; Fertilizers/analysis ; *Trichoderma/genetics ; Genes, Bacterial ; Rhizosphere ; Virulence ; Bacteria ; Anti-Bacterial Agents/pharmacology ; Manure/analysis/microbiology ; Soil Microbiology ; },
abstract = {The use of manure, mycelium dregs and other waste as organic fertilizer is the main source of antibiotic resistance genes (ARGs) and pathogens in farmland. Composting of waste may effectively remove ARGs and pathogens. However, the profiles and drivers of changes in metal resistance genes (MRGs), biocide resistance genes (BRGs), and virulence genes (VGs) in soil-crop rhizosphere systems after compost application remain largely unknown. Here, we prepared two kinds of microbial organic fertilizers (MOF) by using Trichoderma dregs (TDs) and organic fertilizer mixing method (MOF1) and TDs co-composting method (MOF2). The effects of different types and doses of MOF on resistance genes, VGs and pathogens in soil-rhizosphere system and their potential mechanisms were studied. The results showed that co-composting of TDs promoted the decomposition of organic carbon and decreased the absolute abundance of ARGs and mobile genetic elements (MGEs) by 53.4-65.0%. MOF1 application significantly increased the abundance and diversity of soil ARGs, BRGs, and VGs, while low and medium doses of MOF2 significantly decreased their abundance and diversity in soil and rhizosphere. Patterns of positive co-occurrence between MGEs and VGs/MRGs/BRGs/ARGs were observed through statistical analysis and gene arrangements. ARGs/MRGs reductions in MOF2 soil were directly driven by weakened horizontal gene transfer triggered by MGEs. Furthermore, MOF2 reduced soil BRGs/VGs levels by shifting bacterial communities (e.g., reduced bacterial host) or improving soil property. Our study provided new insights into the rational use of waste to minimize the spread of resistomes and VGs in soil.},
}
@article {pmid37988660,
year = {2024},
author = {Zhang, M and Tong, X and Wang, W and Wang, J and Qu, W},
title = {Agarose biodegradation by deep-sea bacterium Vibrio natriegens WPAGA4 with the agarases through horizontal gene transfer.},
journal = {Journal of basic microbiology},
volume = {64},
number = {4},
pages = {e2300521},
doi = {10.1002/jobm.202300521},
pmid = {37988660},
issn = {1521-4028},
support = {2022C02040//"Pioneer" and "Leading Goose" R&amp;D Program of Zhejiang/ ; },
mesh = {Sepharose/metabolism ; *Bacterial Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Glycoside Hydrolases/metabolism ; *Vibrio/genetics ; },
abstract = {This study aimed to reveal the importance of horizontal gene transfer (HGT) for the agarose-degrading ability and the related degradation pathway of a deep-sea bacterium Vibrio natriegens WPAGA4, which was rarely reported in former works. A total of four agarases belonged to the GH50 family, including Aga3418, Aga3419, Aga3420, and Aga3472, were annotated and expressed in Escherichia coli cells. The agarose degradation products of Aga3418, Aga3420, and Aga3472 were neoagarobiose, while those of Aga3419 were neoagarobiose and neoagarotetraose. The RT-qPCR analysis showed that the expression level ratio of Aga3418, Aga3419, Aga3420, and Aga3472 was stable at about 1:1:1.5:2.5 during the degradation, which indicated the optimal expression level ratio of the agarases for agarose degradation by V. natriegens WPAGA4. Based on the genomic information, three of four agarases and other agarose-degrading related genes were in a genome island with a G + C content that was obviously lower than that of the whole genome of V. natriegens WPAGA4, indicating that these agarose-degrading genes were required through HGT. Our results demonstrated that the expression level ratio instead of the expression level itself of agarase genes was crucial for agarose degradation by V. natriegens WPAGA4, and HGT occurred in the deep-sea environment, thereby promoting the deep-sea carbon cycle and providing a reference for studying the evolution and transfer pathways of agar-related genes.},
}
@article {pmid37987191,
year = {2023},
author = {Garbisu, C and Alkorta, I},
title = {A case for the importance of following antibiotic resistant bacteria throughout the soil food web.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {45},
number = {12},
pages = {e2300153},
doi = {10.1002/bies.202300153},
pmid = {37987191},
issn = {1521-1878},
support = {PID2020-116495RB-I00//MCIN/AEI/10.13039/501100011033/ ; IT1578-22//Basque Government/ ; //JRL Environmental Antibiotic Resistance/ ; },
mesh = {Animals ; *Soil ; *Bacteria/genetics ; Manure/microbiology ; Food Chain ; Ecosystem ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Genes, Bacterial ; },
abstract = {It is necessary to complement next-generation sequencing data on the soil resistome with theoretical knowledge provided by ecological studies regarding the spread of antibiotic resistant bacteria (ARB) in the abiotic and, especially, biotic fraction of the soil ecosystem. Particularly, when ARB enter agricultural soils as a consequence of the application of animal manure as fertilizer, from a microbial ecology perspective, it is important to know their fate along the soil food web, that is, throughout that complex network of feeding interactions among members of the soil biota that has crucial effects on species richness and ecosystem productivity and stability. It is critical to study how the ARB that enter the soil through the application of manure can reach other taxonomical groups (e.g., fungi, protists, nematodes, arthropods, earthworms), paying special attention to their presence in the gut microbiomes of mesofauna-macrofauna and to the possibilities for horizontal gene transfer of antibiotic resistant genes.},
}
@article {pmid37983489,
year = {2023},
author = {Simmons, M and Horbelt, N and Sverko, T and Scoppola, E and Jackson, DJ and Harrington, MJ},
title = {Invasive mussels fashion silk-like byssus via mechanical processing of massive horizontally acquired coiled coils.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {48},
pages = {e2311901120},
pmid = {37983489},
issn = {1091-6490},
support = {RGPIN-2018-05243//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; CRC Tier 2 950-231953//Canada Research Chairs (Chaires de recherche du Canada)/ ; 528314512//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {Animals ; Silk/chemistry ; Proteomics ; *Bivalvia/chemistry ; *Dreissena ; Protein Precursors/metabolism ; },
abstract = {Zebra and quagga mussels (Dreissena spp.) are invasive freshwater biofoulers that perpetrate devastating economic and ecological impact. Their success depends on their ability to anchor onto substrates with protein-based fibers known as byssal threads. Yet, compared to other mussel lineages, little is understood about the proteins comprising their fibers or their evolutionary history. Here, we investigated the hierarchical protein structure of Dreissenid byssal threads and the process by which they are fabricated. Unique among bivalves, we found that threads possess a predominantly β-sheet crystalline structure reminiscent of spider silk. Further analysis revealed unexpectedly that the Dreissenid thread protein precursors are mechanoresponsive α-helical proteins that are mechanically processed into β-crystallites during thread formation. Proteomic analysis of the byssus secretory organ and byssus fibers revealed a family of ultrahigh molecular weight (354 to 467 kDa) asparagine-rich (19 to 20%) protein precursors predicted to form α-helical coiled coils. Moreover, several independent lines of evidence indicate that the ancestral predecessor of these proteins was likely acquired via horizontal gene transfer. This chance evolutionary event that transpired at least 12 Mya has endowed Dreissenids with a distinctive and effective fiber formation mechanism, contributing significantly to their success as invasive species and possibly, inspiring new materials design.},
}
@article {pmid37982820,
year = {2023},
author = {Cheatle Jarvela, AM and Wexler, JR},
title = {Advances in genome sequencing reveal changes in gene content that contribute to arthropod macroevolution.},
journal = {Development genes and evolution},
volume = {233},
number = {2},
pages = {59-76},
pmid = {37982820},
issn = {1432-041X},
mesh = {Animals ; *Arthropods/genetics ; Genome ; Genomics ; Base Sequence ; Evolution, Molecular ; Phylogeny ; },
abstract = {Current sequencing technology allows for the relatively affordable generation of highly contiguous genomes. Technological advances have made it possible for researchers to investigate the consequences of diverse sorts of genomic variants, such as gene gain and loss. With the extraordinary number of high-quality genomes now available, we take stock of how these genomic variants impact phenotypic evolution. We take care to point out that the identification of genomic variants of interest is only the first step in understanding their impact. Painstaking lab or fieldwork is still required to establish causal relationships between genomic variants and phenotypic evolution. We focus mostly on arthropod research, as this phylum has an impressive degree of phenotypic diversity and is also the subject of much evolutionary genetics research. This article is intended to both highlight recent advances in the field and also to be a primer for learning about evolutionary genetics and genomics.},
}
@article {pmid37982629,
year = {2023},
author = {Tian, D and Zhao, M and Zheng, S and Jiang, X and Zhang, B},
title = {Involvement of Tn3 transposon in formation and transmission of hypervirulent and carbapenem-resistant Klebsiella pneumoniae.},
journal = {Microbiology spectrum},
volume = {11},
number = {6},
pages = {e0303823},
pmid = {37982629},
issn = {2165-0497},
support = {2022M721338//China Postdoctoral Science Foundation (China Postdoctoral Foundation Project)/ ; SDBX2022052//Shandong Postdoctoral Innovation Talents Support Program/ ; ZR2023QH215//Shandong Provincial Natural Science Foundation/ ; 2022KJ106//Project of Shandong Province Higher Educational Youth Innovation Science and Technology Program/ ; tsqn202306400//Tai Shan Young Scholar Foundation of Shandong Province/ ; },
mesh = {Humans ; Klebsiella pneumoniae ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Virulence/genetics ; Plasmids/genetics ; *Carbapenem-Resistant Enterobacteriaceae/genetics ; *Klebsiella Infections/microbiology ; },
abstract = {Carbapenem-resistant Klebsiella pneumoniae (CRKP) is resistant to most common antibiotics, becoming the most important and prevalent nosocomial opportunity pathogen. Besides, K. pneumoniae can also cause severe community-acquired infections, such as primary liver abscess and endophthalmitis. These pathogens are commonly referred to as hvKp. CRKP and hvKp have evolved separately, each occupying its own clonal lineage and exhibiting a variety of properties. Our study provides important insights into the evolutionary events related to the arousal of virulence and drug resistance in K. pneumoniae through plasmid transmission, mediated by Tn3 transposon. Our study also provides evidence that multiple mechanisms contribute to the successful transfer of non-conjugative virulence plasmid, and the involvement of transposons enhances the efficiency. A good knowledge of its transmission mechanisms is fundamental to finding effective strategies to combat these threatening pathogens. Transposons are widely present in bacteria, spreading resistance and virulence genes between the environment and humans. Therefore, emerging transposon-mediated hypervirulent and carbapenem-resistant pathogens should be highly valued.},
}
@article {pmid37981687,
year = {2023},
author = {Chen, X and Wang, Z and Zhang, C and Hu, J and Lu, Y and Zhou, H and Mei, Y and Cong, Y and Guo, F and Wang, Y and He, K and Liu, Y and Li, F},
title = {Unraveling the complex evolutionary history of lepidopteran chromosomes through ancestral chromosome reconstruction and novel chromosome nomenclature.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {265},
pmid = {37981687},
issn = {1741-7007},
support = {2019FY100400//National Science &amp; Technology Fundamental Resources Investigation Program of China/ ; 2022YFD1401600//Key Technologies Research and Development Program/ ; LZ23C140002//Natural Science Foundation of Zhejiang Province/ ; LY22C140005//Natural Science Foundation of Zhejiang Province/ ; 32202366//National science foundation of China/ ; 32102271//National science foundation of China/ ; },
mesh = {Animals ; Female ; Male ; Geminin/genetics ; *Biological Evolution ; Genome ; Sex Chromosomes/genetics ; *Lepidoptera/genetics ; Evolution, Molecular ; },
abstract = {BACKGROUND: Lepidoptera is one of the most species-rich animal groups, with substantial karyotype variations among species due to chromosomal rearrangements. Knowledge of the evolutionary patterns of lepidopteran chromosomes still needs to be improved.<br><br>RESULTS: Here, we used chromosome-level genome assemblies of 185 lepidopteran insects to reconstruct an ancestral reference genome and proposed a new chromosome nomenclature. Thus, we renamed over 5000 extant chromosomes with this system, revealing the historical events of chromosomal rearrangements and their features. Additionally, our findings indicate that, compared with autosomes, the Z chromosome in Lepidoptera underwent a fast loss of conserved genes, rapid acquisition of lineage-specific genes, and a low rate of gene duplication. Moreover, we presented evidence that all available 67 W chromosomes originated from a common ancestor chromosome, with four neo-W chromosomes identified, including one generated by fusion with an autosome and three derived through horizontal gene transfer. We also detected nearly 4000 inter-chromosomal gene movement events. Notably, Geminin is transferred from the autosome to the Z chromosome. When located on the autosome, Geminin shows female-biased expression, but on the Z chromosome, it exhibits male-biased expression. This contributes to the sexual dimorphism of body size in silkworms.<br><br>CONCLUSIONS: Our study sheds light on the complex evolutionary history of lepidopteran chromosomes based on ancestral chromosome reconstruction and novel chromosome nomenclature.},
}
@article {pmid37980566,
year = {2023},
author = {Lee, IPA and Eldakar, OT and Gogarten, JP and Andam, CP},
title = {Protocol for an agent-based model of recombination in bacteria playing a public goods game.},
journal = {STAR protocols},
volume = {4},
number = {4},
pages = {102733},
pmid = {37980566},
issn = {2666-1667},
mesh = {*Game Theory ; *Bacteria ; },
abstract = {Agent-based models are composed of individual agents coded for traits, such as cooperation and cheating, that interact in a virtual world based on defined rules. Here, we describe the use of an agent-based model of homologous recombination in bacteria playing a public goods game. We describe steps for software installation, setting model parameters, running and testing models, and visualization and statistical analysis. This protocol is useful in analyses of horizontal gene transfer, bacterial sociobiology, and game theory. For complete details on the use and execution of this protocol, please refer to Lee et al.[1].},
}
@article {pmid37980337,
year = {2023},
author = {Yenew, B and Ghodousi, A and Diriba, G and Tesfaye, E and Cabibbe, AM and Amare, M and Moga, S and Alemu, A and Dagne, B and Sinshaw, W and Mollalign, H and Meaza, A and Tadesse, M and Gamtesa, DF and Abebaw, Y and Seid, G and Zerihun, B and Getu, M and Chiacchiaretta, M and Gaudin, C and Marceau, M and Didelot, X and Tolera, G and Abdella, S and Kebede, A and Getahun, M and Mehammed, Z and Supply, P and Cirillo, DM},
title = {A smooth tubercle bacillus from Ethiopia phylogenetically close to the Mycobacterium tuberculosis complex.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {7519},
pmid = {37980337},
issn = {2041-1723},
support = {D43 TW009127/TW/FIC NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Mycobacterium tuberculosis ; Phylogeny ; Ethiopia ; *Tuberculosis/microbiology ; Africa, Eastern ; },
abstract = {The Mycobacterium tuberculosis complex (MTBC) includes several human- and animal-adapted pathogens. It is thought to have originated in East Africa from a recombinogenic Mycobacterium canettii-like ancestral pool. Here, we describe the discovery of a clinical tuberculosis strain isolated in Ethiopia that shares archetypal phenotypic and genomic features of M. canettii strains, but represents a phylogenetic branch much closer to the MTBC clade than to the M. canettii strains. Analysis of genomic traces of horizontal gene transfer in this isolate and previously identified M. canettii strains indicates a persistent albeit decreased recombinogenic lifestyle near the emergence of the MTBC. Our findings support that the MTBC emergence from its putative free-living M. canettii-like progenitor is evolutionarily very recent, and suggest the existence of a continuum of further extant derivatives from ancestral stages, close to the root of the MTBC, along the Great Rift Valley.},
}
@article {pmid37976849,
year = {2024},
author = {Li, YJ and Yuan, Y and Tan, WB and Xi, BD and Wang, H and Hui, KL and Chen, JB and Zhang, YF and Wang, LF and Li, RF},
title = {Antibiotic resistance genes and heavy metals in landfill: A review.},
journal = {Journal of hazardous materials},
volume = {464},
number = {},
pages = {132395},
doi = {10.1016/j.jhazmat.2023.132395},
pmid = {37976849},
issn = {1873-3336},
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Metals, Heavy ; Drug Resistance, Microbial/genetics ; Waste Disposal Facilities ; },
abstract = {Landfill is reservoir containing antibiotic resistance genes (ARGs) that pose a threat to human life and health. Heavy metals impose lasting effects on ARGs. This review investigated and analyzed the distribution, composition, and abundance of heavy metals and ARGs in landfill. The abundance ranges of ARGs detected in refuse and leachate were similar. The composition of ARG varied with sampling depth in refuse. ARG in leachate varies with the distribution of ARG in the refuse. The ARG of sulI was associated with 11 metals (Co, Pb, Mn, Zn, Cu, Cr, Ni, Sb, As, Cd, and Al). The effects of the total metal concentration on ARG abundance were masked by many factors. Low heavy metal concentrations showed positive effects on ARG diffusion; conversely, high heavy metal concentrations showed negative effects. Organic matter had a selective pressure effect on microorganisms and could provide energy for the diffusion of ARGs. Complexes of heavy metals and organic matter were common in landfill. Therefore, the hypothesis was proposed that organic matter and heavy metals have combined effects on the horizontal gene transfer (HGT) of ARGs during landfill stabilization. This work provides a new basis to better understand the HGT of ARGs in landfill.},
}
@article {pmid37976735,
year = {2024},
author = {Gao, Y and Liu, J and Fang, Y and Xu, X and Wang, F and Tang, Y and Yin, D and Cookson, AL and Zhu, W and Mao, S and Zhong, R},
title = {Straw-based compost cultivation disproportionally contributes to the environmental persistence of antibiotic resistance from raw cattle manure to organic vegetables.},
journal = {Microbiological research},
volume = {278},
number = {},
pages = {127540},
doi = {10.1016/j.micres.2023.127540},
pmid = {37976735},
issn = {1618-0623},
mesh = {*Manure ; Drug Resistance, Microbial/genetics ; Metagenome ; Anti-Bacterial Agents/pharmacology ; *Composting ; Cattle ; Soil/chemistry ; Agaricus ; Animals ; Vegetables ; },
abstract = {Cattle manure, is a reservoir of antimicrobial resistance genes, but the mechanisms by which they migrate from farm to table remain obscure. Here, we chose Agaricus bisporus as a model vegetable to examine such migration and characterized the resistome in 112 metagenomes covering samples from raw manure, composting substrates, rhizosphere, and surfaces of mushrooms. A total of 1864 resistance genes, representing 113 unique mechanisms of resistance, were identified. Monensin treatment on beef specifically enriched fecal resistance genes within Moraxellaceae, but this effect did not persist in downstream mushrooms. Interestingly, we found that resistance genes were significantly more enriched on mushroom surfaces when cultivated with corn-based compost compared to rice and wheat, likely a result of the disproportional propagation of Pseudomonadaceae and varied ability of lateral gene transfer. Importantly, our sequence alignment together with genome-centric analysis observed that 89 resistance genes, mainly conferring resistance to drug and biocide (20.22%) and mercury (19.10%), were shared across all types of samples, indicating an efficient transmission of resistance in food production. Moreover, co-occurrence of genes conferring resistance to different compounds frequently occurred in parallel with microbial migration. Together, we present the influences of antibiotic treatment and straw-based composting on resistome along the mushroom production chain (from manure to straw-based compost, rhizosphere of compost cultivated mushroom and surface of mushroom) and highlighted the risks of resistance genes migration.},
}
@article {pmid37975503,
year = {2023},
author = {Irby, I and Brown, SP},
title = {The social lives of viruses and other mobile genetic elements: a commentary on Leeks et al. 2023.},
journal = {Journal of evolutionary biology},
volume = {36},
number = {11},
pages = {1582-1586},
pmid = {37975503},
issn = {1420-9101},
support = {R21 AI156817/AI/NIAID NIH HHS/United States ; 5R21AI156817-02/NH/NIH HHS/United States ; },
mesh = {*Onions/genetics ; Gene Transfer, Horizontal ; Plasmids ; *Viruses/genetics ; Interspersed Repetitive Sequences ; },
abstract = {Illustration of life-histories of phages and plasmids through horizontal and vertical transmission (see Figure 1 for more information).},
}
@article {pmid37974331,
year = {2024},
author = {Zhang, Y and Ding, N and Li, Y and Ouyang, M and Fu, P and Peng, Y and Tan, Y},
title = {Transcription factor FOXM1 specifies chromatin DNA to extracellular vesicles.},
journal = {Autophagy},
volume = {20},
number = {5},
pages = {1054-1071},
pmid = {37974331},
issn = {1554-8635},
mesh = {*Extracellular Vesicles/metabolism ; *Forkhead Box Protein M1/metabolism/genetics ; Humans ; *Chromatin/metabolism ; *DNA/metabolism ; *Autophagy/genetics ; Lysosomes/metabolism ; Microtubule-Associated Proteins/metabolism ; Protein Binding ; Cell Nucleus/metabolism ; Homeodomain Proteins/metabolism/genetics ; },
abstract = {Extracellular vesicle DNAs (evDNAs) hold significant diagnostic value for various diseases and facilitate transcellular transfer of genetic material. Our study identifies transcription factor FOXM1 as a mediator for directing chromatin genes or DNA fragments (termed FOXM1-chDNAs) to extracellular vesicles (EVs). FOXM1 binds to MAP1LC3/LC3 in the nucleus, and FOXM1-chDNAs, such as the DUX4 gene and telomere DNA, are designated by FOXM1 binding and translocated to the cytoplasm before being released to EVs through the secretory autophagy during lysosome inhibition (SALI) process involving LC3. Disrupting FOXM1 expression or the SALI process impairs FOXM1-chDNAs incorporation into EVs. FOXM1-chDNAs can be transmitted to recipient cells via EVs and expressed in recipient cells when they carry functional genes. This finding provides an example of how chromatin DNA fragments are specified to EVs by transcription factor FOXM1, revealing its contribution to the formation of evDNAs from nuclear chromatin. It provides a basis for further exploration of the roles of evDNAs in biological processes, such as horizontal gene transfer.Abbreviation: ATG5: autophagy related 5; CCFs: cytoplasmic chromatin fragments; ChIP: chromatin immunoprecipitation; cytoDNA: cytoplasmic DNA; CQ: chloroquine; FOXM1-DBD: FOXM1 DNA binding domain; DUX4:double homeobox 4; EVs: extracellular vesicles; evDNAs: extracellular vesicle DNAs; FOXM1: forkhead box M1; FOXM1-chDNAs: chromatin DNA fragments directed by FOXM1 to EVs; HGT: horizontal gene transfer; LC3-II: lipid modified LC3; LMNB1: lamin B1; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MVBs: multivesicular bodies; M1-binding DNA: a linear DNA containing 72× FOXM1 binding sites; SALI: secretory autophagy during lysosome inhibition; siRNA: small interfering RNA; TetO-DUX4: TetO array-containing DUX4 DNA; TetO: tet operator; TetR: tet repressor.},
}
@article {pmid37974017,
year = {2023},
author = {Thepmanee, O and Munkongwongsiri, N and Prachumwat, A and Saksmerprome, V and Jitrakorn, S and Sritunyalucksana, K and Vanichviriyakit, R and Chanarat, S and Jaroenlak, P and Itsathitphaisarn, O},
title = {Molecular and cellular characterization of four putative nucleotide transporters from the shrimp microsporidian Enterocytozoon hepatopenaei (EHP).},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {20008},
pmid = {37974017},
issn = {2045-2322},
mesh = {Animals ; *Microsporidia ; Nucleotides ; Phylogeny ; *Enterocytozoon/genetics ; *Penaeidae/parasitology ; },
abstract = {Microsporidia are obligate intracellular parasites that lost several enzymes required in energy production. The expansion of transporter families in these organisms enables them to hijack ATP from hosts. In this study, nucleotide transporters of the microsporidian Enterocytozoon hepatopenaei (EHP), which causes slow growth in economically valuable Penaeus shrimp, were characterized. Analysis of the EHP genome suggested the presence of four putative nucleotide transporter genes, namely EhNTT1, EhNTT2, EhNTT3, and EhNTT4. Sequence alignment revealed four charged amino acids that are conserved in previously characterized nucleotide transporters. Phylogenetic analysis suggested that EhNTT1, 3, and 4 were derived from one horizontal gene transfer event, which was independent from that of EhNTT2. Localization of EhNTT1 and EhNTT2 using immunofluorescence analysis revealed positive signals within the envelope of developing plasmodia and on mature spores. Knockdown of EhNTT2 by double administration of sequence specific double-stranded RNA resulted in a significant reduction in EHP copy numbers, suggesting that EhNTT2 is crucial for EHP replication in shrimp. Taken together, the insight into the roles of NTTs in microsporidian proliferation can provide the biological basis for the development of alternative control strategies for microsporidian infection in shrimp.},
}
@article {pmid37973843,
year = {2023},
author = {Allard, N and Collette, A and Paquette, J and Rodrigue, S and Côté, JP},
title = {Systematic investigation of recipient cell genetic requirements reveals important surface receptors for conjugative transfer of IncI2 plasmids.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {1172},
pmid = {37973843},
issn = {2399-3642},
support = {5014521//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en G&#xe9;nie du Canada)/ ; 571440//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en G&#xe9;nie du Canada)/ ; 314063//Fonds de Recherche du Qu&#xe9;bec - Nature et Technologies (Quebec Fund for Research in Nature and Technology)/ ; },
mesh = {Plasmids/genetics ; *Escherichia coli/metabolism ; *Conjugation, Genetic ; Adhesins, Bacterial/genetics ; Gene Transfer, Horizontal ; },
abstract = {Bacterial conjugation is a major horizontal gene transfer mechanism. While the functions encoded by many conjugative plasmids have been intensively studied, the contribution of recipient chromosome-encoded genes remains largely unknown. Here, we analyzed the genetic requirement of recipient cells for conjugation of IncI2 plasmid TP114, which was recently shown to transfer at high rates in the gut microbiota. We performed transfer assays with ~4,000 single-gene deletion mutants of Escherichia coli. When conjugation occurs on a solid medium, we observed that recipient genes impairing transfer rates were not associated with a specific cellular function. Conversely, transfer assays performed in broth were largely dependent on the lipopolysaccharide biosynthesis pathway. We further identified specific structures in lipopolysaccharides used as recipient cell surface receptors by PilV adhesins associated with the type IVb accessory pilus of TP114. Our strategy is applicable to study other mobile genetic elements and understand important host cell factors for their dissemination.},
}
@article {pmid37972772,
year = {2024},
author = {Xin, R and Zhang, Y and Zhang, K and Yang, Y and Ma, Y and Niu, Z},
title = {Investigation of the antimicrobial susceptibility patterns of marine cyanobacteria in Bohai Bay: Cyanobacteria may be important hosts of antibiotic resistance genes in marine environment.},
journal = {The Science of the total environment},
volume = {909},
number = {},
pages = {168516},
doi = {10.1016/j.scitotenv.2023.168516},
pmid = {37972772},
issn = {1879-1026},
mesh = {*Anti-Bacterial Agents/pharmacology/analysis ; Genes, Bacterial ; Bays ; Drug Resistance, Microbial/genetics ; *Cyanobacteria/genetics ; },
abstract = {Marine cyanobacteria, as widely distributed and photosynthetically autotrophic bacteria in the ocean, may contribute to the global dissemination of antibiotic resistance genes (ARGs) and develop a different antimicrobial susceptibility pattern from heterotrophic bacteria and cyanobacteria from freshwater environments. However, studies on antimicrobial susceptibility and the carriage of ARGs in marine cyanobacteria are still very limited. In this study, the antibiotic resistance characteristics of cyanobacteria in nearshore waters were examined through field monitoring and laboratory investigations, which included PCR detection and ARG transformation. The results showed a positive correlation between marine cyanobacteria and some ARGs in the nearshore waters of Bohai Bay. Moreover, most screened cyanobacteria showed high minimum inhibitory concentration (MIC) values for polymyxins, tetracyclines, kanamycin, and sulfonamides, moderate MIC values for streptomycin, chloramphenicol, rifampicin, and norfloxacin, and low MIC values for roxithromycin and cephalosporins. The blaTEM, blaKPC, sul1, sul2, strA, tetA, tetB, tetC, tetM, mdfA, and intI1 genes were detected in the screened marine cyanobacteria. The highest detection rates were observed for blaTEM (93.3 %), sul1 (56.6 %), sul2 (90 %), and strA (73.3 %). The detection rate of tetA (33.3 %) was the highest among the tetracycline resistance genes, and mdfA, a multidrug-resistant pump gene with resistance to tetracycline, also showed a high detection level (23.3 %). Overall, most of the screened marine cyanobacteria were found to tolerate multiple antibiotics in seawater, and the condition of the ARGs carriage was serious. Furthermore, the screened marine Synechocystis sp. C12-2 demonstrated the ability to accept ARGs on the RP4 plasmid through natural transformation and showed reduced sensitivity to ampicillin, suggesting the possibility that some marine cyanobacteria could acquire ARGs from the environment through horizontal gene transfer. Thus, marine cyanobacteria may play an important role in the propagation of marine ARGs.},
}
@article {pmid37971327,
year = {2023},
author = {Förster, M and Rathmann, I and Yüksel, M and Power, JJ and Maier, B},
title = {Genome-wide transformation reveals extensive exchange across closely related Bacillus species.},
journal = {Nucleic acids research},
volume = {51},
number = {22},
pages = {12352-12366},
pmid = {37971327},
issn = {1362-4962},
support = {CRC 1310//Deutsche Forschungsgemeinschaft/ ; //University of Cologne/ ; },
mesh = {*Bacillus/classification/genetics ; Bacillus subtilis/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial/genetics ; Phylogeny ; *Transformation, Genetic ; },
abstract = {Bacterial transformation is an important mode of horizontal gene transfer that helps spread genetic material across species boundaries. Yet, the factors that pose barriers to genome-wide cross-species gene transfer are poorly characterized. Here, we develop a replacement accumulation assay to study the effects of genomic distance on transfer dynamics. Using Bacillus subtilis as recipient and various species of the genus Bacillus as donors, we find that the rate of orthologous replacement decreases exponentially with the divergence of their core genomes. We reveal that at least 96% of the B. subtilis core genes are accessible to replacement by alleles from Bacillus spizizenii. For the more distantly related Bacillus atrophaeus, gene replacement events cluster at genomic locations with high sequence identity and preferentially replace ribosomal genes. Orthologous replacement also creates mosaic patterns between donor and recipient genomes, rearranges the genome architecture, and governs gain and loss of accessory genes. We conclude that cross-species gene transfer is dominated by orthologous replacement of core genes which occurs nearly unrestricted between closely related species. At a lower rate, the exchange of accessory genes gives rise to more complex genome dynamics.},
}
@article {pmid37971255,
year = {2023},
author = {Martínez-Alvarez, L and Ramond, J-B and Vikram, S and León-Sobrino, C and Maggs-Kölling, G and Cowan, DA},
title = {With a pinch of salt: metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {12},
pages = {e0062923},
pmid = {37971255},
issn = {1098-5336},
support = {113308//National Research Foundation (NRF)/ ; },
mesh = {*Bacteria/genetics ; Desert Climate ; Soil Microbiology ; Sodium Chloride ; *Microbiota ; },
abstract = {The hyperarid Namib Desert is one of the oldest deserts on Earth. It contains multiple clusters of playas which are saline-rich springs surrounded by halite evaporites. Playas are of great ecological importance, and their indigenous (poly)extremophilic microorganisms are potentially involved in the precipitation of minerals such as carbonates and sulfates and have been of great biotechnological importance. While there has been a considerable amount of microbial ecology research performed on various Namib Desert edaphic microbiomes, little is known about the microbial communities inhabiting its multiple playas. In this work, we provide a comprehensive taxonomic and functional potential characterization of the microbial, including viral, communities of sediment mats and halites from two distant salt pans of the Namib Desert, contributing toward a better understanding of the ecology of this biome.},
}
@article {pmid37971242,
year = {2023},
author = {Lerminiaux, N and Mitchell, R and Bartoszko, J and Davis, I and Ellis, C and Fakharuddin, K and Hota, SS and Katz, K and Kibsey, P and Leis, JA and Longtin, Y and McGeer, A and Minion, J and Mulvey, M and Musto, S and Rajda, E and Smith, SW and Srigley, JA and Suh, KN and Thampi, N and Tomlinson, J and Wong, T and Mataseje, L and , },
title = {Plasmid genomic epidemiology of blaKPC carbapenemase-producing Enterobacterales in Canada, 2010-2021.},
journal = {Antimicrobial agents and chemotherapy},
volume = {67},
number = {12},
pages = {e0086023},
pmid = {37971242},
issn = {1098-6596},
support = {//Public Health Agency of Canada (PHAC)/ ; },
mesh = {Humans ; Canada/epidemiology ; *beta-Lactamases/genetics/metabolism ; Plasmids/genetics ; Bacterial Proteins/genetics ; Klebsiella pneumoniae ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Genomics ; *Klebsiella Infections/epidemiology ; Microbial Sensitivity Tests ; },
abstract = {Carbapenems are considered last-resort antibiotics for the treatment of infections caused by multidrug-resistant Enterobacterales, but carbapenem resistance due to acquisition of carbapenemase genes is a growing threat that has been reported worldwide. Klebsiella pneumoniae carbapenemase (blaKPC) is the most common type of carbapenemase in Canada and elsewhere; it can hydrolyze penicillins, cephalosporins, aztreonam, and carbapenems and is frequently found on mobile plasmids in the Tn4401 transposon. This means that alongside clonal expansion, blaKPC can disseminate through plasmid- and transposon-mediated horizontal gene transfer. We applied whole genome sequencing to characterize the molecular epidemiology of 829 blaKPC carbapenemase-producing isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short-read and long-read sequencing, we obtained 202 complete and circular blaKPC-encoding plasmids. Using MOB-suite, 10 major plasmid clusters were identified from this data set which represented 87% (175/202) of the Canadian blaKPC-encoding plasmids. We further estimated the genomic location of incomplete blaKPC-encoding contigs and predicted a plasmid cluster for 95% (603/635) of these. We identified different patterns of carbapenemase mobilization across Canada related to different plasmid clusters, including clonal transmission of IncF-type plasmids (108/829, 13%) in K. pneumoniae clonal complex 258 and novel repE(pEh60-7) plasmids (44/829, 5%) in Enterobacter hormaechei ST316, and horizontal transmission of IncL/M (142/829, 17%) and IncN-type plasmids (149/829, 18%) across multiple genera. Our findings highlight the diversity of blaKPC genomic loci and indicate that multiple, distinct plasmid clusters have contributed to blaKPC spread and persistence in Canada.},
}
@article {pmid37968548,
year = {2024},
author = {Naidoo, Y and Pierneef, RE and Cowan, DA and Valverde, A},
title = {Characterization of the soil resistome and mobilome in Namib Desert soils.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {27},
number = {4},
pages = {967-975},
pmid = {37968548},
issn = {1618-1905},
mesh = {*Soil Microbiology ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Desert Climate ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; Gene Transfer, Horizontal ; Soil/chemistry ; Genes, Bacterial ; Interspersed Repetitive Sequences ; },
abstract = {The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics. We detected a variety of antibiotic resistance genes (ARGs) that conferred resistance to antibiotics such as elfamycin, rifampicin, and fluoroquinolones, metal/biocide resistance genes (MRGs/BRGs) conferring resistance to metals such as arsenic and copper, and mobile genetic elements (MGEs) such as the ColE1-like plasmid. The presence of metal/biocide resistance genes in close proximity to ARGs indicated a potential for co-selection of resistance to antibiotics and metals/biocides. The co-existence of MGEs and horizontally acquired ARGs most likely contributed to a decoupling between bacterial community composition and ARG profiles. Overall, this study indicates that soil bacterial communities in Namib Desert soils host a diversity of resistance elements and that horizontal gene transfer, rather than host phylogeny, plays an essential role in their dynamics.},
}
@article {pmid37966605,
year = {2024},
author = {Chu Yuan Kee, MJ and Chen, J},
title = {Phage Transduction of Staphylococcus aureus.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2738},
number = {},
pages = {263-275},
pmid = {37966605},
issn = {1940-6029},
mesh = {Humans ; *Lysogeny ; Transduction, Genetic ; Staphylococcus aureus/genetics ; Staphylococcus Phages/genetics ; Anti-Bacterial Agents ; *Staphylococcal Infections/microbiology ; Gene Transfer, Horizontal ; },
abstract = {Bacteriophage transduction is the major mechanism of horizontal gene transfer (HGT) among many bacteria. In Staphylococcus aureus, the phage-mediated acquisition of mobile genetic elements (MGEs) that encode virulence and antibiotic resistance genes largely contribute to its evolutionary adaptation and genetic plasticity. In molecular biology, generalized transduction is routinely used as a technique to manipulate and construct bacterial strains. Here, we describe optimized protocols for generalized transduction, applicable for the transfer of plasmid or chromosomal deoxyribonucleic acid (DNA) from donor to recipient S. aureus strains.},
}
@article {pmid37966239,
year = {2023},
author = {Maccario, L and Silva, AF and Nesme, J and Amador, CI and Sørensen, SJ and Cooper, VS and Røder, HL},
title = {Draft genomes of seven isolates from Danish wastewater facilities belonging to Pseudomonas, Bacillus, Pseudochrobactrum, Brevundimonas, and Pandoraea.},
journal = {Microbiology resource announcements},
volume = {12},
number = {12},
pages = {e0052923},
pmid = {37966239},
issn = {2576-098X},
support = {794315//Horizon 2020 Framework Programme (H2020)/ ; 34434//Villum Fonden (Villum Foundation)/ ; 874735//EC | Horizon 2020 Framework Programme (H2020)/ ; },
abstract = {We report here seven draft genomes of bacterial strains from two Danish wastewater facilities, two of which might be characterized as a new group within the Pseudomonas and Pseudochrobactrum genera, respectively. These genomes will provide useful references for understanding bacterial interactions and horizontal gene transfer within bacterial communities.},
}
@article {pmid37965050,
year = {2023},
author = {Kormos, A and Dimopoulos, G and Bier, E and Lanzaro, GC and Marshall, JM and James, AA},
title = {Conceptual risk assessment of mosquito population modification gene-drive systems to control malaria transmission: preliminary hazards list workshops.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {11},
number = {},
pages = {1261123},
pmid = {37965050},
issn = {2296-4185},
support = {R01 AI158615/AI/NIAID NIH HHS/United States ; R01 GM117321/GM/NIGMS NIH HHS/United States ; R21 AI168873/AI/NIAID NIH HHS/United States ; R01 AI170692/AI/NIAID NIH HHS/United States ; R01 AI162911/AI/NIAID NIH HHS/United States ; },
abstract = {The field-testing and eventual adoption of genetically-engineered mosquitoes (GEMs) to control vector-borne pathogen transmission will require them meeting safety criteria specified by regulatory authorities in regions where the technology is being considered for use and other locales that might be impacted. Preliminary risk considerations by researchers and developers may be useful for planning the baseline data collection and field research used to address the anticipated safety concerns. Part of this process is to identify potential hazards (defined as the inherent ability of an entity to cause harm) and their harms, and then chart the pathways to harm and evaluate their probability as part of a risk assessment. The University of California Malaria Initiative (UCMI) participated in a series of workshops held to identify potential hazards specific to mosquito population modification strains carrying gene-drive systems coupled to anti-parasite effector genes and their use in a hypothetical island field trial. The hazards identified were placed within the broader context of previous efforts discussed in the scientific literature. Five risk areas were considered i) pathogens, infections and diseases, and the impacts of GEMs on human and animal health, ii) invasiveness and persistence of GEMs, and interactions of GEMs with target organisms, iii) interactions of GEMs with non-target organisms including horizontal gene transfer, iv) impacts of techniques used for the management of GEMs and v) evolutionary and stability considerations. A preliminary hazards list (PHL) was developed and is made available here. This PHL is useful for internal project risk evaluation and is available to regulators at prospective field sites. UCMI project scientists affirm that the subsequent processes associated with the comprehensive risk assessment for the application of this technology should be driven by the stakeholders at the proposed field site and areas that could be affected by this intervention strategy.},
}
@article {pmid37963249,
year = {2023},
author = {Goldlust, K and Ducret, A and Halte, M and Dedieu-Berne, A and Erhardt, M and Lesterlin, C},
title = {The F pilus serves as a conduit for the DNA during conjugation between physically distant bacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {47},
pages = {e2310842120},
pmid = {37963249},
issn = {1091-6490},
support = {FRM-EQU202103012587//Fondation pour la Recherche M&#xe9;dicale (FRM)/ ; ANR-18-CE35-0008//Agence Nationale de la Recherche (ANR)/ ; ANR-22-CE12-0032//Agence Nationale de la Recherche (ANR)/ ; no. 113_MC_GH_MEL-BER_Erhardt_HU//Berlin University Alliance (BUA)/ ; },
mesh = {*Escherichia coli/genetics ; *Genes, Bacterial ; Plasmids/genetics ; Fimbriae, Bacterial/genetics ; DNA, Bacterial/genetics ; Conjugation, Genetic ; DNA ; Gene Transfer, Horizontal ; },
abstract = {Horizontal transfer of F-like plasmids by bacterial conjugation is responsible for disseminating antibiotic resistance and virulence determinants among pathogenic Enterobacteriaceae species, a growing health concern worldwide. Central to this process is the conjugative F pilus, a long extracellular filamentous polymer that extends from the surface of plasmid donor cells, allowing it to probe the environment and make contact with the recipient cell. It is well established that the F pilus can retract to bring mating pair cells in tight contact before DNA transfer. However, whether DNA transfer can occur through the extended pilus has been a subject of active debate. In this study, we use live-cell microscopy to show that while most transfer events occur between cells in direct contact, the F pilus can indeed serve as a conduit for the DNA during transfer between physically distant cells. Our findings enable us to propose a unique model for conjugation that revises our understanding of the DNA transfer mechanism and the dissemination of drug resistance and virulence genes within complex bacterial communities.},
}
@article {pmid37959048,
year = {2023},
author = {Qin, Y and Huang, W and Yang, J and Zhao, Y and Zhao, M and Xu, H and Zhang, M},
title = {The Antibiotic Resistome and Its Association with Bacterial Communities in Raw Camel Milk from Altay Xinjiang.},
journal = {Foods (Basel, Switzerland)},
volume = {12},
number = {21},
pages = {},
pmid = {37959048},
issn = {2304-8158},
support = {2022D01C404//Natural Science Foundation of Xinjiang/ ; 2019Q002//Natural Science Foundation of Xinjiang/ ; 2022D01D42//Natural Science Foundation of Xinjiang/ ; },
abstract = {Raw camel milk is generally contaminated with varied microbiota, including antibiotic-resistant bacteria (ARB), that can act as a potential pathway for the spread of antibiotic resistance genes (ARGs). In this study, high-throughput quantitative PCR and 16S rRNA gene-based Illumine sequencing data were used to establish a comprehensive understanding of the antibiotic resistome and its relationship with the bacterial community in Bactrian camel milk from Xinjiang. A total of 136 ARGs and up to 1.33 × 10[8] total ARG copies per gram were identified, which predominantly encode resistance to β-lactamas and multidrugs. The ARGs' profiles were mainly explained by interactions between the bacteria community and physicochemical indicators (77.9%). Network analysis suggested that most ARGs exhibited co-occurrence with Corynebacterium, Leuconostoc and MGEs. Overall, raw camel milk serves as a reservoir for ARGs, which may aggravate the spread of ARGs through vertical and horizontal gene transfer in the food chain.},
}
@article {pmid37955258,
year = {2024},
author = {Gong, P and Liu, H and Yu, T and Jiang, C and Gou, E and Guan, J and Chen, H and Kang, H},
title = {Evaluation of resistance risk in soil due to antibiotics during application of penicillin V fermentation residue.},
journal = {Environmental technology},
volume = {45},
number = {24},
pages = {5173-5181},
doi = {10.1080/09593330.2023.2283807},
pmid = {37955258},
issn = {1479-487X},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Soil Microbiology ; *Penicillin V ; Soil Pollutants/analysis ; Fermentation ; Drug Resistance, Microbial/genetics ; Soil/chemistry ; Genes, Bacterial ; Gene Transfer, Horizontal ; },
abstract = {The soil application of hydrothermally treated penicillin V fermentation residue (PFR) is attractive but challenged, due to the concern of the resistance risk in soil related to residual antibiotics. In this study, a lab-scale incubation experiment was conducted to investigate the influence of penicillin V on antibiotic resistance genes (ARGs) in PFR-amended soil via qPCR. The introduced penicillin V in soil could not be persistent, and its degradation occurred mainly within 2 days. The higher number of soil ARGs was detected under 108 mg/kg of penicillin V than lower contents (≤54 mg/kg). Additionally, the relative abundance of ARGs was higher in soil spiked with penicillin V than that in blank soil, and the great increase in the relative abundance of soil ARGs occurred earlier under 108 mg/kg of penicillin V than lower contents. The horizontal gene transfer might contribute to the shift of ARGs in PFR-amended soil. The results indicated that the residual penicillin V could cause the proliferation of soil ARGs and should be completely removed by hydrothermal treatment before soil application. The results of this study provide a comprehensive understanding of the resistance risk posed by penicillin V during the application of hydrothermally pretreated PFR.},
}
@article {pmid37953666,
year = {2023},
author = {Pandey, T and Kalluraya, CA and Wang, B and Xu, T and Huang, X and Guang, S and Daugherty, MD and Ma, DK},
title = {Acquired stress resilience through bacteria-to-nematode interdomain horizontal gene transfer.},
journal = {The EMBO journal},
volume = {42},
number = {24},
pages = {e114835},
pmid = {37953666},
issn = {1460-2075},
support = {P40 OD010440/OD/NIH HHS/United States ; R35 GM133633/GM/NIGMS NIH HHS/United States ; R35 GM139618/GM/NIGMS NIH HHS/United States ; P40 OD010440/CD/ODCDC CDC HHS/United States ; },
mesh = {Animals ; Caenorhabditis elegans/metabolism ; Phylogeny ; Gene Transfer, Horizontal ; Rhamnose/metabolism ; *Resilience, Psychological ; *Nematoda ; Bacteria/genetics ; },
abstract = {Natural selection drives the acquisition of organismal resilience traits to protect against adverse environments. Horizontal gene transfer (HGT) is an important evolutionary mechanism for the acquisition of novel traits, including metazoan acquisitions in immunity, metabolic, and reproduction function via interdomain HGT (iHGT) from bacteria. Here, we report that the nematode gene rml-3 has been acquired by iHGT from bacteria and that it enables exoskeleton resilience and protection against environmental toxins in Caenorhabditis elegans. Phylogenetic analysis reveals that diverse nematode RML-3 proteins form a single monophyletic clade most similar to bacterial enzymes that biosynthesize L-rhamnose, a cell-wall polysaccharide component. C. elegans rml-3 is highly expressed during larval development and upregulated in developing seam cells upon heat stress and during the stress-resistant dauer stage. rml-3 deficiency impairs cuticle integrity, barrier functions, and nematode stress resilience, phenotypes that can be rescued by exogenous L-rhamnose. We propose that interdomain HGT of an ancient bacterial rml-3 homolog has enabled L-rhamnose biosynthesis in nematodes, facilitating cuticle integrity and organismal resilience to environmental stressors during evolution. These findings highlight a remarkable contribution of iHGT on metazoan evolution conferred by the domestication of a bacterial gene.},
}
@article {pmid37952399,
year = {2023},
author = {Salter, C and Westrick, JA and Chaganti, SR and Birbeck, JA and Peraino, NJ and Weisener, CG},
title = {Elucidating microbial mechanisms of microcystin-LR degradation in Lake Erie beach sand through metabolomics and metatranscriptomics.},
journal = {Water research},
volume = {247},
number = {},
pages = {120816},
doi = {10.1016/j.watres.2023.120816},
pmid = {37952399},
issn = {1879-2448},
mesh = {Lakes/microbiology ; Microcystins/metabolism ; Sand ; *Cyanobacteria/metabolism ; *Microbiota ; Nitrogen/metabolism ; Ontario ; },
abstract = {As one of five Laurentian Great Lakes, Lake Erie ranks among the top freshwater drinking sources and ecosystems globally. Historical and current agriculture mismanagement and climate change sustains the environmental landscape for late summer cyanobacterial harmful algal blooms, and consequently, cyanotoxins such as microcystin (MC). Microcystin microbial degradation is a promising mitigation strategy, however the mechanisms controlling the breakdown of MCs in Lake Erie are not well understood. Pelee Island, Ontario, Canada is located in the western basin of Lake Erie and the bacterial community in the sand has demonstrated the capacity of metabolizing the toxin. Through a multi-omic approach, the metabolic, functional and taxonomical signatures of the Pelee Island microbial community during MC-LR degradation was investigated over a 48-hour period to comprehensively study the degradation mechanism. Cleavage of bonds surrounding nitrogen atoms and the upregulation of nitrogen deamination (dadA, alanine dehydrogenase, leucine dehydrogenase) and assimilation genes (glnA, gltB) suggests a targeted isolation of nitrogen by the microbial community for energy production. Methylotrophic pathways RuMP and H4MPT control assimilation and dissimilation of carbon, respectively and differential abundance of Methylophilales indicates an interconnected role through electron exchange of denitrification and methylotrophic pathways. The detected metabolites did not resolve a clear breakdown pathway, but rather the diversity of products in combination with taxonomic and functional results supports that a variety of strategies are applied, such as epoxidation, hydroxylation, and aromatic degradation. Annual repeated exposure to the toxin may have allowed the community to adaptatively establish a novel pathway through functional plasticity and horizontal gene transfer. The culmination of these results reveals the complexity of the Pelee Island sand community and supports a dynamic and cooperative metabolism between microbial species to achieve MC degradation.},
}
@article {pmid37951253,
year = {2024},
author = {Kang, Y and Zhao, S and Cheng, H and Xu, W and You, R and Hu, J},
title = {The distribution profiles of tetracycline resistance genes in rice: Comparisons using four genotypes.},
journal = {The Science of the total environment},
volume = {908},
number = {},
pages = {168359},
doi = {10.1016/j.scitotenv.2023.168359},
pmid = {37951253},
issn = {1879-1026},
mesh = {Humans ; *Oryza/genetics ; Tetracycline Resistance/genetics ; Genes, Bacterial ; Tetracycline ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Genotype ; },
abstract = {The potential transmission of antibiotic resistance genes (ARGs) from the rhizosphere to plants and humans poses a significant concern. This study aims to investigate the distribution of tetracycline resistance genes (TRGs) in rice using four genotypes and identify the primary source of TRGs in grains. Quantitative polymerase chain reaction (qPCR) was employed to determine the abundance of seven TRGs and intI1 in four rice varieties and three partitions during the jointing and heading stages, respectively. The analysis of the bacterial community was conducted to elucidate the underlying mechanism of the profiles of TRGs. It was observed that tetZ was predominantly present in the rhizosphere and endoroot, whereas tetX became dominant in grains. The relative abundances of TRGs and intI1 exhibited significant variations across both the variety and partition. However, no significant differences were observed in grains, where the abundances of TRGs were several orders of magnitude lower compared to those in the rhizosphere. Nevertheless, the potential risk of the dissemination of TRGs to humans, particularly those carried by potential pathogens in grains, warrants attention. The increased likelihood of TRGs accumulation in the rhizosphere and endoroot of hybrid rice varieties, as opposed to japonica varieties, may be attributed to the heightened metabolic activities of their roots. The significant associations observed between intI1 and TRGs, coupled with the substantial alterations in potential hosts for intI1 across various treatments, indicate that intI1-mediated horizontal gene transfer plays a role in the diverse range of bacterial hosts for TRGs. The study also revealed that rhizosphere bacteria during the jointing stage serve as the primary contributors of TRGs in grains through the endoroot junction. The findings indicate that Japonica rice varieties exhibit superior control over TRGs compared to hybrid varieties, emphasizing the need for early interventions throughout the entire growth period of rice.},
}
@article {pmid37944236,
year = {2024},
author = {Xiao, T and Chen, R and Cai, C and Yuan, S and Dai, X and Dong, B and Xu, Z},
title = {Abatement of antibiotics and resistance genes during catalytic ozonation enhanced sludge dewatering process: Synchronized in volume and hazardousness reduction.},
journal = {Journal of hazardous materials},
volume = {463},
number = {},
pages = {132912},
doi = {10.1016/j.jhazmat.2023.132912},
pmid = {37944236},
issn = {1873-3336},
mesh = {Sewage/microbiology ; Anti-Bacterial Agents/pharmacology ; Tetracycline ; Bacteria/genetics ; Genes, Bacterial ; Norfloxacin ; Ofloxacin ; *Oxytetracycline ; *Ozone ; },
abstract = {Based on the efficiency of the catalytic ozonation techniques (HDWS+O3 and MnFe2O4 @SBC+O3) in enhancing the sludge dewaterability, the effectiveness in synchronized abatement antibiotics and antibiotic resistance genes (ARGs) was conducted to determine. The results revealed that catalytic ozonation conditioning altered the distribution of target antibiotics (tetracycline (TC), oxytetracycline (OTC), norfloxacin (NOR), ofloxacin (OFL)) in the dewatered filtrate, the dewatered sludge cake and the extra-microcolony/cellular polymers (EMPS/ECPS) layers, achieving the redistribution from solid-phase adsorption to liquid-phase dissolution. The total degradation rate was over 90% for TC and OTC, 72-78% for NOR and OFL; the abatement efficiency of eleven ARGs reached 1.47-3.01 log and 1.64-3.59 log, respectively, and more than four eARGs were eliminated. The effective abatement of the absolute abundance of Mobile genetic elements (MGEs) (0.91-1.89 log) demonstrated that catalytic ozonation conditioning could also significantly inhibit horizontal gene transfer (HGT). The abundance of resistant bacteria was greatly reduced and the signal transduction of the typical ARGs host bacteria was inhibited. The highly reactive oxidation species (ROS) generated were responsible for the abatement of antibiotics and ARGs. These findings provided new insights into the sludge conditioning for ideal and synchronized reduction in volume and hazardousness by catalytic ozonation processes in sludge treatment.},
}
@article {pmid37940998,
year = {2023},
author = {Schaller, D and Hartmann, T and Lafond, M and Stadler, PF and Wieseke, N and Hellmuth, M},
title = {Relative timing information and orthology in evolutionary scenarios.},
journal = {Algorithms for molecular biology : AMB},
volume = {18},
number = {1},
pages = {16},
pmid = {37940998},
issn = {1748-7188},
support = {RGPIN-2019-05817//Natural Sciences and Engineering Research Council of Canada/ ; 214087123//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree T to vertices and edges of a species tree S. The relative timing of the last common ancestors of two extant genes (leaves of T) and the last common ancestors of the two species (leaves of S) in which they reside is indicative of horizontal gene transfers (HGT) and ancient duplications. Orthologous gene pairs, on the other hand, require that their last common ancestors coincides with a corresponding speciation event. The relative timing information of gene and species divergences is captured by three colored graphs that have the extant genes as vertices and the species in which the genes are found as vertex colors: the equal-divergence-time (EDT) graph, the later-divergence-time (LDT) graph and the prior-divergence-time (PDT) graph, which together form an edge partition of the complete graph.<br><br>RESULTS: Here we give a complete characterization in terms of informative and forbidden triples that can be read off the three graphs and provide a polynomial time algorithm for constructing an evolutionary scenario that explains the graphs, provided such a scenario exists. While both LDT and PDT graphs are cographs, this is not true for the EDT graph in general. We show that every EDT graph is perfect. While the information about LDT and PDT graphs is necessary to recognize EDT graphs in polynomial-time for general scenarios, this extra information can be dropped in the HGT-free case. However, recognition of EDT graphs without knowledge of putative LDT and PDT graphs is NP-complete for general scenarios. In contrast, PDT graphs can be recognized in polynomial-time. We finally connect the EDT graph to the alternative definitions of orthology that have been proposed for scenarios with horizontal gene transfer. With one exception, the corresponding graphs are shown to be colored cographs.},
}
@article {pmid37938748,
year = {2023},
author = {Zeldes, B and Poehlein, A and Jain, S and Baum, C and Daniel, R and Müller, V and Basen, M},
title = {DNA uptake from a laboratory environment drives unexpected adaptation of a thermophile to a minor medium component.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {2},
pmid = {37938748},
issn = {2730-6151},
support = {BA 5757/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 031B0857A//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0857C//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0857B//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; },
abstract = {DNA uptake is widespread among microorganisms and considered a strategy for rapid adaptation to new conditions. While both DNA uptake and adaptation are referred to in the context of natural environments, they are often studied in laboratories under defined conditions. For example, a strain of the thermophile Thermoanaerobacter kivui had been adapted to growth on high concentrations of carbon monoxide (CO). Unusual phenotypes of the CO-adapted strain prompted us to examine it more closely, revealing a horizontal gene transfer (HGT) event from another thermophile, Thermoanaerobacter sp. strain X514, being cultured in the same laboratory. The transferred genes conferred on T. kivui the ability to utilize trehalose, a trace component of the yeast-extract added to the media during CO-adaptation. This same HGT event simultaneously deleted a native operon for thiamine biosynthesis, which likely explains why the CO-adapted strain grows poorly without added vitamins. Attempts to replicate this HGT by providing T. kivui with genomic DNA from Thermoanaerobacter sp. strain X514 revealed that it is easily reproducible in the lab. This subtle form of "genome contamination" is difficult to detect, since the genome remains predominantly T. kivui, and no living cells from the original contamination remain. Unexpected HGT between two microorganisms as well as simultaneous adaptation to several conditions may occur often and unrecognized in laboratory environments, requiring caution and careful monitoring of phenotype and genotype of microorganisms that are naturally-competent for DNA uptake.},
}
@article {pmid37935916,
year = {2023},
author = {An, T and Cai, Y and Li, G and Li, S and Wong, PK and Guo, J and Zhao, H},
title = {Prevalence and transmission risk of colistin and multidrug resistance in long-distance coastal aquaculture.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {115},
pmid = {37935916},
issn = {2730-6151},
support = {U1901210//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41425015//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42122056//&#xc9;cole Nationale d'Ing&#xe9;nieurs de Saint-Etienne (National Engineering School of Saint-&#xc9;tienne)/ ; },
abstract = {Due to the wide use of antibiotics, intensive aquaculture farms have been recognized as a significant reservoir of antibiotic resistomes. Although the prevalence of colistin resistance genes and multidrug-resistant bacteria (MDRB) has been documented, empirical evidence for the transmission of colistin and multidrug resistance between bacterial communities in aquaculture farms through horizontal gene transfer (HGT) is lacking. Here, we report the prevalence and transmission risk of colistin and multidrug resistance in 27 aquaculture water samples from 9 aquaculture zones from over 5000 km of subtropical coastlines in southern China. The colistin resistance gene mcr-1, mobile genetic element (MGE) intl1 and 13 typical antibiotic resistance genes (ARGs) were prevalent in all the aquaculture water samples. Most types of antibiotic (especially colistin) resistance are transmissible in bacterial communities based on evidence from laboratory conjugation and transformation experiments. Diverse MDRB were detected in most of the aquaculture water samples, and a strain with high-level colistin resistance, named Ralstonia pickettii MCR, was isolated. The risk of horizontal transfer of the colistin resistance of R. pickettii MCR through conjugation and transformation was low, but the colistin resistance could be steadily transmitted to offspring through vertical transfer. The findings have important implications for the future regulation of antibiotic use in aquaculture farms globally to address the growing threat posed by antibiotic resistance to human health.},
}
@article {pmid37934408,
year = {2023},
author = {Martinez-Varela, A and Casas, G and Berrojalbiz, N and Lundin, D and Piña, B and Dachs, J and Vila-Costa, M},
title = {Metatranscriptomic responses and microbial degradation of background polycyclic aromatic hydrocarbons in the coastal Mediterranean and Antarctica.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {57},
pages = {119988-119999},
pmid = {37934408},
issn = {1614-7499},
support = {CTM2015-70535-P//Ministerio de Ciencia e Innovaci&#xf3;n/ ; CTM2015-65691-R//Ministerio de Ciencia e Innovaci&#xf3;n/ ; CEX2018-000794-S//Ministerio de Ciencia e Innovaci&#xf3;n/ ; 2017SGR800//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; },
mesh = {*Polycyclic Aromatic Hydrocarbons/analysis ; Antarctic Regions ; Seawater ; *Microbiota ; *Alphaproteobacteria/metabolism ; Biodegradation, Environmental ; },
abstract = {Although microbial degradation is a key sink of polycyclic aromatic hydrocarbons (PAH) in surface seawaters, there is a dearth of field-based evidences of regional divergences in biodegradation and the effects of PAHs on site-specific microbial communities. We compared the magnitude of PAH degradation and its impacts in short-term incubations of coastal Mediterranean and the Maritime Antarctica microbiomes with environmentally relevant concentrations of PAHs. Mediterranean bacteria readily degraded the less hydrophobic PAHs, with rates averaging 4.72 ± 0.5 ng L h[-1]. Metatranscriptomic responses showed significant enrichments of genes associated to horizontal gene transfer, stress response, and PAH degradation, mainly harbored by Alphaproteobacteria. Community composition changed and increased relative abundances of Bacteroidota and Flavobacteriales. In Antarctic waters, there was no degradation of PAH, and minimal metatranscriptome responses were observed. These results provide evidence for factors such as geographic region, community composition, and pre-exposure history to predict PAH biodegradation in seawater.},
}
@article {pmid37931146,
year = {2023},
author = {Kosterlitz, O and Grassi, N and Werner, B and McGee, RS and Top, EM and Kerr, B},
title = {Evolutionary "Crowdsourcing": Alignment of Fitness Landscapes Allows for Cross-species Adaptation of a Horizontally Transferred Gene.},
journal = {Molecular biology and evolution},
volume = {40},
number = {11},
pages = {},
pmid = {37931146},
issn = {1537-1719},
support = {R01 AI084918/AI/NIAID NIH HHS/United States ; },
mesh = {Genotype ; *Anti-Bacterial Agents ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genomics ; },
abstract = {Genes that undergo horizontal gene transfer (HGT) evolve in different genomic backgrounds. Despite the ubiquity of cross-species HGT, the effects of switching hosts on gene evolution remains understudied. Here, we present a framework to examine the evolutionary consequences of host-switching and apply this framework to an antibiotic resistance gene commonly found on conjugative plasmids. Specifically, we determined the adaptive landscape of this gene for a small set of mutationally connected genotypes in 3 enteric species. We uncovered that the landscape topographies were largely aligned with minimal host-dependent mutational effects. By simulating gene evolution over the experimentally gauged landscapes, we found that the adaptive evolution of the mobile gene in one species translated to adaptation in another. By simulating gene evolution over artificial landscapes, we found that sufficient alignment between landscapes ensures such "adaptive equivalency" across species. Thus, given adequate landscape alignment within a bacterial community, vehicles of HGT such as plasmids may enable a distributed form of genetic evolution across community members, where species can "crowdsource" adaptation.},
}
@article {pmid37930866,
year = {2024},
author = {Camargo, AP and Call, L and Roux, S and Nayfach, S and Huntemann, M and Palaniappan, K and Ratner, A and Chu, K and Mukherjeep, S and Reddy, TBK and Chen, IA and Ivanova, NN and Eloe-Fadrosh, EA and Woyke, T and Baltrus, DA and Castañeda-Barba, S and de la Cruz, F and Funnell, BE and Hall, JPJ and Mukhopadhyay, A and Rocha, EPC and Stalder, T and Top, E and Kyrpides, NC},
title = {IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata.},
journal = {Nucleic acids research},
volume = {52},
number = {D1},
pages = {D164-D173},
pmid = {37930866},
issn = {1362-4962},
support = {MR/W02666X/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; *Metagenome ; Metadata ; Software ; Databases, Genetic ; Plasmids/genetics ; *Microbiota ; },
abstract = {Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.},
}
@article {pmid37928655,
year = {2023},
author = {Wang, Z and Zhang, N and Li, C and Shao, L},
title = {Diversity of antibiotic resistance genes in soils with four different fertilization treatments.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1291599},
pmid = {37928655},
issn = {1664-302X},
abstract = {Although the enrichment of resistance genes in soil has been explored in recent years, there are still some key questions to be addressed regarding the variation of ARG composition in soil with different fertilization treatments, such as the core ARGs in soil after different fertilization treatments, the correlation between ARGs and bacterial taxa, etc. For soils after different fertilization treatments, the distribution and combination of ARG in three typical fertilization methods (organic fertilizer alone, chemical fertilizer alone, and conventional fertilizer) and non-fertilized soils were investigated in this study using high-throughput fluorescence quantitative PCR (HT-qPCR) technique. The application of organic fertilizers significantly increased the abundance and quantity of ARGs and their subtypes in the soil compared to the non-fertilized soil, where sul1 was the ARGs specific to organic fertilizers alone and in higher abundance. The conventional fertilizer application also showed significant enrichment of ARGs, which indicated that manure addition often had a more decisive effect on ARGs in soil than chemical fertilizers, and three bacteria, Pseudonocardia, Irregularibacter, and Castllaniella, were the key bacteria affecting ARG changes in soil after fertilization. In addition, nutrient factors and heavy metals also affect the distribution of ARGs in soil and are positively correlated. This paper reveals the possible reasons for the increase in the number of total soil ARGs and their relative abundance under different fertilization treatments, which has positive implications for controlling the transmission of ARGs through the soil-human pathway.},
}
@article {pmid37923145,
year = {2023},
author = {Geoffroy, F and Uecker, H},
title = {Limits to evolutionary rescue by conjugative plasmids.},
journal = {Theoretical population biology},
volume = {154},
number = {},
pages = {102-117},
doi = {10.1016/j.tpb.2023.10.001},
pmid = {37923145},
issn = {1096-0325},
mesh = {*Conjugation, Genetic ; Plasmids/genetics ; *Biological Evolution ; Gene Transfer, Horizontal ; Bacteria/genetics ; },
abstract = {Plasmids may carry genes coding for beneficial traits and thus contribute to adaptation of bacterial populations to environmental stress. Conjugative plasmids can horizontally transfer between cells, which a priori facilitates the spread of adaptive alleles. However, if the potential recipient cell is already colonized by another incompatible plasmid, successful transfer may be prevented. Competition between plasmids can thus limit horizontal transfer. Previous modeling has indeed shown that evolutionary rescue by a conjugative plasmid is hampered by incompatible resident plasmids in the population. If the rescue plasmid is a mutant variant of the resident plasmid, both plasmids transfer at the same rates. A high conjugation rate then has two, potentially opposing, effects - a direct positive effect on spread of the rescue plasmid and an increase in the fraction of resident plasmid cells. This raises the question whether a high conjugation rate always benefits evolutionary rescue. In this article, we systematically analyze three models of increasing complexity to disentangle the benefits and limits of increasing horizontal gene transfer in the presence of plasmid competition and plasmid costs. We find that the net effect can be positive or negative and that the optimal transfer rate is thus not always the highest one. These results can contribute to our understanding of the many facets of plasmid-driven adaptation and the wide range of transfer rates observed in nature.},
}
@article {pmid37923139,
year = {2023},
author = {Arriaza, RH and Abiskaroon, B and Patel, M and Daneshian, L and Kluza, A and Snoeck, S and Watkins, MB and Hopkins, JB and Van Leeuwen, T and Grbic, M and Grbic, V and Borowski, T and Chruszcz, M},
title = {Structural and functional studies reveal the molecular basis of substrate promiscuity of a glycosyltransferase originating from a major agricultural pest.},
journal = {The Journal of biological chemistry},
volume = {299},
number = {12},
pages = {105421},
pmid = {37923139},
issn = {1083-351X},
support = {P30 GM138395/GM/NIGMS NIH HHS/United States ; },
mesh = {Genome ; *Glycosyltransferases/chemistry/genetics/metabolism ; Plants/parasitology ; Uridine Diphosphate ; Substrate Specificity ; *Tetranychidae/enzymology/genetics ; },
abstract = {The two-spotted spider mite, Tetranychus urticae, is a major cosmopolitan pest that feeds on more than 1100 plant species. Its genome contains an unprecedentedly large number of genes involved in detoxifying and transporting xenobiotics, including 80 genes that code for UDP glycosyltransferases (UGTs). These enzymes were acquired via horizontal gene transfer from bacteria after loss in the Chelicerata lineage. UGTs are well-known for their role in phase II metabolism; however, their contribution to host adaptation and acaricide resistance in arthropods, such as T. urticae, is not yet resolved. TuUGT202A2 (Tetur22g00270) has been linked to the ability of this pest to adapt to tomato plants. Moreover, it was shown that this enzyme can glycosylate a wide range of flavonoids. To understand this relationship at the molecular level, structural, functional, and computational studies were performed. Structural studies provided specific snapshots of the enzyme in different catalytically relevant stages. The crystal structure of TuUGT202A2 in complex with UDP-glucose was obtained and site-directed mutagenesis paired with molecular dynamic simulations revealed a novel lid-like mechanism involved in the binding of the activated sugar donor. Two additional TuUGT202A2 crystal complexes, UDP-(S)-naringenin and UDP-naringin, demonstrated that this enzyme has a highly plastic and open-ended acceptor-binding site. Overall, this work reveals the molecular basis of substrate promiscuity of TuUGT202A2 and provides novel insights into the structural mechanism of UGTs catalysis.},
}
@article {pmid37924893,
year = {2024},
author = {Stevenson, EM and Buckling, A and Cole, M and Lindeque, PK and Murray, AK},
title = {Selection for antimicrobial resistance in the plastisphere.},
journal = {The Science of the total environment},
volume = {908},
number = {},
pages = {168234},
doi = {10.1016/j.scitotenv.2023.168234},
pmid = {37924893},
issn = {1879-1026},
mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Microplastics ; Plastics ; Commerce ; },
abstract = {Microplastics and antimicrobials are widespread contaminants that threaten global systems and frequently co-exist in the presence of human or animal pathogens. Whilst the impact of each of these contaminants has been studied in isolation, the influence of this co-occurrence in driving antimicrobial resistance (AMR)[1] in microplastic-adhered microbial communities, known as 'the Plastisphere', is not well understood. This review proposes the mechanisms by which interactions between antimicrobials and microplastics may drive selection for AMR in the Plastisphere. These include: 1) increased rates of horizontal gene transfer in the Plastisphere compared with free-living counterparts and natural substrate controls due to the proximity of cells, co-occurrence of environmental microplastics with AMR selective compounds and the sequestering of extracellular antibiotic resistance genes in the biofilm matrix. 2) An elevated AMR selection pressure in the Plastisphere due to the adsorbing of AMR selective or co-selective compounds to microplastics at concentrations greater than those found in surrounding mediums and potentially those adsorbed to comparator particles. 3) AMR selection pressure may be further elevated in the Plastisphere due to the incorporation of antimicrobial or AMR co-selective chemicals in the plastic matrix during manufacture. Implications for both ecological functioning and environmental risk assessments are discussed, alongside recommendations for further research.},
}
@article {pmid37917352,
year = {2023},
author = {Rekadwad, BN and Shouche, YS and Jangid, K},
title = {Investigation of tRNA-based relatedness within the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum: a comparative analysis.},
journal = {Archives of microbiology},
volume = {205},
number = {12},
pages = {366},
pmid = {37917352},
issn = {1432-072X},
support = {PDFSS-2013-14-ST-MAH-4350//University Grants Commission/ ; },
mesh = {*Escherichia coli/genetics ; *RNA, Transfer/genetics/metabolism ; Verrucomicrobia/genetics ; Amino Acids/metabolism ; Planctomycetes ; Evolution, Molecular ; },
abstract = {The PVC superphylum is a diverse group of prokaryotes that require stringent growth conditions. RNA is a fascinating molecule to find evolutionary relatedness according to the RNA World Hypothesis. We conducted tRNA gene analysis to find evolutionary relationships in the PVC phyla. The analysis of genomic data (P = 9, V = 4, C = 8) revealed that the number of tRNA genes varied from 28 to 90 in Planctomycetes and Chlamydia, respectively. Verrucomicrobia has whole genomes and the longest scaffold (3 + 1), with tRNA genes ranging from 49 to 53 in whole genomes and 4 in the longest scaffold. Most tRNAs in the E. coli genome clustered with homologs, but approximately 43% clustered with tRNAs encoding different amino acids. Planctomyces, Akkermansia, Isosphaera, and Chlamydia were similar to E. coli tRNAs. In a phylum, tRNAs coding for different amino acids clustered at a range of 8 to 10%. Further analysis of these tRNAs showed sequence similarity with Cyanobacteria, Proteobacteria, Viridiplantae, Ascomycota and Basidiomycota (Eukaryota). This indicates the possibility of horizontal gene transfer or, otherwise, a different origin of tRNA in PVC bacteria. Hence, this work proves its importance for determining evolutionary relatedness and potentially identifying bacteria using tRNA. Thus, the analysis of these tRNAs indicates that primitive RNA may have served as the genetic material of LUCA before being replaced by DNA. A quantitative analysis is required to test these possibilities that relate the evolutionary significance of tRNA to the origin of life.},
}
@article {pmid37909761,
year = {2023},
author = {Xedzro, C and Shimamoto, T and Yu, L and Zuo, H and Sugawara, Y and Sugai, M and Shimamoto, T},
title = {Emergence of colistin-resistant Enterobacter cloacae and Raoultella ornithinolytica carrying the phosphoethanolamine transferase gene, mcr-9, derived from vegetables in Japan.},
journal = {Microbiology spectrum},
volume = {11},
number = {6},
pages = {e0106323},
pmid = {37909761},
issn = {2165-0497},
support = {20202002//Cabinet Office, Government of Japan/ ; 22fk0108604j0002//Japan Agency for Medical Research and Development (AMED)/ ; 21HA2009//Japan Agency for Medical Research and Development (AMED)/ ; JP23fk0108664j0001//Japan Agency for Medical Research and Development (AMED)/ ; },
mesh = {Plasmids/genetics ; *Colistin/pharmacology ; Transferases/genetics ; Japan ; Drug Resistance, Bacterial/genetics ; *Enterobacter cloacae/genetics ; Vegetables/microbiology ; Anti-Bacterial Agents/pharmacology ; Enterobacteriaceae ; Microbial Sensitivity Tests ; },
abstract = {Plasmid-mediated mobile colistin-resistance genes have been recognized as a global threat because they jeopardize the efficacy of colistin in therapeutic practice. Here, we described the genetic features of two mcr-9.1-carrying Gram-negative bacteria with a colistin-resistant phenotype derived from vegetables in Japan. The colistin-resistant mcr-9.1, which has never been detected in vegetables, was located on a large plasmid in Enterobacter cloacae CST17-2 and Raoultella ornithinolytica CST129-1, suggesting a high chance of horizontal gene transfer. To the best of our knowledge, this is the first report of mcr-9 in R. ornithinolytica. This study indicates that fresh vegetables might be a potential source for the transmission of mcr-9 genes encoding resistance to frontline (colistin) and clinically relevant antimicrobials. The study also provides additional consideration for colistin use and the relevance of routine surveillance in epidemiological perspective to curb the continuous spread of mcr alleles.},
}
@article {pmid37909043,
year = {2024},
author = {Subramanian, S and Bergland Drarvik, SM and Tinney, KR and Parent, KN},
title = {Cryo-EM structure of a Shigella podophage reveals a hybrid tail and novel decoration proteins.},
journal = {Structure (London, England : 1993)},
volume = {32},
number = {1},
pages = {24-34.e4},
pmid = {37909043},
issn = {1878-4186},
support = {R01 GM110185/GM/NIGMS NIH HHS/United States ; R35 GM140803/GM/NIGMS NIH HHS/United States ; U24 GM116789/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Cryoelectron Microscopy ; *Bacteriophages/chemistry ; *Shigella/metabolism ; Capsid Proteins/metabolism ; Capsid/chemistry ; Viral Tail Proteins/chemistry ; },
abstract = {There is a paucity of high-resolution structures of phages infecting Shigella, a human pathogen and a serious threat to global health. HRP29 is a Shigella podophage belonging to the Autographivirinae family, and has very low sequence identity to other known phages. Here, we resolved the structure of the entire HRP29 virion by cryo-EM. Phage HRP29 has a highly unusual tail that is a fusion of a T7-like tail tube and P22-like tailspikes mediated by interactions from a novel tailspike adaptor protein. Understanding phage tail structures is critical as they mediate hosts interactions. Furthermore, we show that the HRP29 capsid is stabilized by two novel, and essential decoration proteins, gp47 and gp48. Only one high resolution structure is currently available for Shigella podophages. The presence of a hybrid tail and an adapter protein suggests that it may be a product of horizontal gene transfer, and may be prevalent in other phages.},
}
@article {pmid37907163,
year = {2024},
author = {Su, X and Qian, F and Bao, Y},
title = {The effect of bulk-biochar and nano-biochar amendment on the removal of antibiotic resistance genes in microplastic contaminated soil.},
journal = {Environmental research},
volume = {240},
number = {Pt 2},
pages = {117488},
doi = {10.1016/j.envres.2023.117488},
pmid = {37907163},
issn = {1096-0953},
mesh = {*Microplastics ; *Plastics ; Anti-Bacterial Agents ; Drug Resistance, Microbial ; Soil ; },
abstract = {Biochar amendment has significant benefits in removing antibiotic resistance genes (ARGs) in the soil. Nevertheless, there is little information on ARGs removal in microplastic contaminated soil. Herein, a 42-day soil microcosm experiment were carried out to study how two coconut shell biochars (bulk- and nano-size) eliminate soil ARGs with/without microplastic presence. The results showed that microplastic increased significantly the numbers and abundances of ARGs in soil at 14d of cultivation. And, two biochars amendment effectively inhibited soil ARGs spread whether or not microplastic was present, especially for nano-biochar which had more effective removal compared to bulk-biochar. However, microplastic weakened soil ARGs removal after applying same biochar. Two biochars removed ARGs through decreasing horizontal gene transfer (HGT) of ARGs, potential host-bacteria abundances, some bacteria crowding the eco-niche of hosts and promoting soil properties. The adverse effect of microplastic on ARGs removal was mainly caused by weakening mobile genetic elements (MGEs) removal, and by changing soil properties. Structural equation modeling (SEM) analysis indicated that biochar's effect on ARGs profile was changed by its size and microplastic presence through altering MGEs abundances. These results highlight that biochar amendment is still an effective method for ARGs removal in microplastic contaminated soil.},
}
@article {pmid37902330,
year = {2023},
author = {Benigno, V and Carraro, N and Sarton-Lohéac, G and Romano-Bertrand, S and Blanc, DS and van der Meer, JR},
title = {Diversity and evolution of an abundant ICEclc family of integrative and conjugative elements in Pseudomonas aeruginosa.},
journal = {mSphere},
volume = {8},
number = {6},
pages = {e0051723},
pmid = {37902330},
issn = {2379-5042},
support = {310030_204897//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; },
mesh = {*Pseudomonas aeruginosa/genetics ; *Gene Transfer, Horizontal ; },
abstract = {Microbial populations swiftly adapt to changing environments through horizontal gene transfer. While the mechanisms of gene transfer are well known, the impact of environmental conditions on the selection of transferred gene functions remains less clear. We investigated ICEs, specifically the ICEclc-type, in Pseudomonas aeruginosa clinical isolates. Our findings revealed co-evolution between ICEs and their hosts, with ICE transfers occurring within strains. Gene functions carried by ICEs are positively selected, including potential virulence factors and heavy metal resistance. Comparison to publicly available P. aeruginosa genomes unveiled widespread antibiotic-resistance determinants within ICEclc clades. Thus, the ubiquitous ICEclc family significantly contributes to P. aeruginosa's adaptation and fitness in diverse environments.},
}
@article {pmid37901845,
year = {2023},
author = {Li, L and Zhang, H and Meng, D and Yin, H},
title = {Transcriptomics of Lactobacillus paracasei: metabolism patterns and cellular responses under high-density culture conditions.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {11},
number = {},
pages = {1274020},
pmid = {37901845},
issn = {2296-4185},
abstract = {Lactobacillus paracasei has significant potential for development and application in the environmental field, particularly in addressing malodor pollution. This study aims to investigate the cellular response of L. paracasei B1 under high-density culture conditions. The selected strain has previously shown effective deodorizing and bacteriostatic abilities. Transcriptomics techniques are employed to dissect the nutrient metabolism pattern of L. paracasei B1 and its response mechanism under environmental stress. The study characterizes the functions of key differentially expressed genes during growth before and after optimizing the culture conditions. The optimization of fermentation culture conditions provides a suitable growth environment for L. paracasei B1, inducing an enhancement of its phosphotransferase system for sugar source uptake and maintaining high levels of glycolysis and pyruvate metabolism. Consequently, the strain is able to grow and multiply rapidly. Under acid stress conditions, glycolysis and pyruvate metabolism are inhibited, and L. paracasei B1 generates additional energy through aerobic respiration to meet the energy demand. The two-component system and quorum sensing play roles in the response and regulation of L. paracasei B1 to adverse environments. The strain mitigates oxygen stress damage through glutathione metabolism, cysteine and methionine metabolism, base excision repair, and purine and pyrimidine metabolism. Additionally, the strain enhances lysine synthesis, the alanine, aspartate, and glutamate metabolic pathways, and relies on the ABC transport system to accumulate amino acid-compatible solutes to counteract acid stress and osmotic stress during pH regulation. These findings establish a theoretical basis for the further development and application of L. paracasei B1 for its productive properties.},
}
@article {pmid37900760,
year = {2023},
author = {Yan, XM and Zhou, SS and Liu, H and Zhao, SW and Tian, XC and Shi, TL and Bao, YT and Li, ZC and Jia, KH and Nie, S and Guo, JF and Kong, L and Porth, IM and Mao, JF},
title = {Unraveling the evolutionary dynamics of the TPS gene family in land plants.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1273648},
pmid = {37900760},
issn = {1664-462X},
abstract = {Terpenes and terpenoids are key natural compounds for plant defense, development, and composition of plant oil. The synthesis and accumulation of a myriad of volatile terpenoid compounds in these plants may dramatically alter the quality and flavor of the oils, which provide great commercial utilization value for oil-producing plants. Terpene synthases (TPSs) are important enzymes responsible for terpenic diversity. Investigating the differentiation of the TPS gene family could provide valuable theoretical support for the genetic improvement of oil-producing plants. While the origin and function of TPS genes have been extensively studied, the exact origin of the initial gene fusion event - it occurred in plants or microbes - remains uncertain. Furthermore, a comprehensive exploration of the TPS gene differentiation is still pending. Here, phylogenetic analysis revealed that the fusion of the TPS gene likely occurred in the ancestor of land plants, following the acquisition of individual C- and N- terminal domains. Potential mutual transfer of TPS genes was observed among microbes and plants. Gene synteny analysis disclosed a differential divergence pattern between TPS-c and TPS-e/f subfamilies involved in primary metabolism and those (TPS-a/b/d/g/h subfamilies) crucial for secondary metabolites. Biosynthetic gene clusters (BGCs) analysis suggested a correlation between lineage divergence and potential natural selection in structuring terpene diversities. This study provides fresh perspectives on the origin and evolution of the TPS gene family.},
}
@article {pmid37898203,
year = {2024},
author = {Jian, J and Wu, Z and Silva-Núñez, A and Li, X and Zheng, X and Luo, B and Liu, Y and Fang, X and Workman, CT and Larsen, TO and Hansen, PJ and Sonnenschein, EC},
title = {Long-read genome sequencing provides novel insights into the harmful algal bloom species Prymnesium parvum.},
journal = {The Science of the total environment},
volume = {908},
number = {},
pages = {168042},
doi = {10.1016/j.scitotenv.2023.168042},
pmid = {37898203},
issn = {1879-1026},
mesh = {Animals ; *Harmful Algal Bloom ; *Haptophyta/genetics/metabolism ; Fishes ; },
abstract = {Prymnesium parvum is a toxin-producing haptophyte that causes harmful algal blooms worldwide, which are often associated with massive fish-kills and subsequent economic losses. In here, we present nuclear and plastid genome assemblies using PacBio HiFi long reads and DNBseq short reads for the two P. parvum strains UTEX 2797 and CCMP 3037, representing producers of type A prymnesins. Our results show that the P. parvum strains have a moderate haptophyte genome size of 97.56 and 107.32 Mb. The genome assemblies present one of highest contiguous assembled contig sequences to date consisting of 463 and 362 contigs with a contig N50 of 596.99 kb and 968.39 kb for strain UTEX 2797 and CCMP 3037, respectively. The assembled contigs of UTEX 2797 and CCMP 3037 were anchored to 34 scaffolds, with a scaffold N50 of 5.35 Mb and 3.61 Mb, respectively, accounting for 93.2 % and 97.9 % of the total length. Each plastid genome comprises a circular contig. A total of 20,578 and 19,426 protein-coding genes were annotated for UTEX 2797 and CCMP 3037. The expanded gene family analysis showed that starch and sucrose metabolism, sulfur metabolism, energy metabolism and ABC transporters are involved in the evolution of P. parvum. Polyketide synthase (PKS) genes responsible for the production of secondary metabolites such as prymnesins displayed different expression patterns under nutrient limitation. Overlap with repeats and horizontal gene transfer may be two contributing factors to the high number of PKS genes found in this species. The two high quality P. parvum genomes will serve as valuable resources for ecological, genetic, and toxicological studies of haptophytes that can be used to monitor and potentially manage harmful blooms of ichthyotoxic P. parvum in the future.},
}
@article {pmid37894729,
year = {2023},
author = {Bravo, A and Moreno-Blanco, A and Espinosa, M},
title = {One Earth: The Equilibrium between the Human and the Bacterial Worlds.},
journal = {International journal of molecular sciences},
volume = {24},
number = {20},
pages = {},
pmid = {37894729},
issn = {1422-0067},
support = {PID2019-104553RB-C21//Spanish Ministry of Science and Innovation (MCIN/AEI/10.13039/501100011033)/ ; },
mesh = {Humans ; Animals ; Cattle ; *Bacteria/genetics ; Genes, Bacterial ; *Bacterial Infections/microbiology ; Drug Resistance, Microbial ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; },
abstract = {Misuse and abuse of antibiotics on humans, cattle, and crops have led to the selection of multi-resistant pathogenic bacteria, the most feared 'superbugs'. Infections caused by superbugs are progressively difficult to treat, with a subsequent increase in lethality: the toll on human lives is predicted to reach 10 million by 2050. Here we review three concepts linked to the growing resistance to antibiotics, namely (i) the Resistome, which refers to the collection of bacterial genes that confer resistance to antibiotics, (ii) the Mobilome, which includes all the mobile genetic elements that participate in the spreading of antibiotic resistance among bacteria by horizontal gene transfer processes, and (iii) the Nichome, which refers to the set of genes that are expressed when bacteria try to colonize new niches. We also discuss the strategies that can be used to tackle bacterial infections and propose an entente cordiale with the bacterial world so that instead of war and destruction of the 'fierce enemy' we can achieve a peaceful coexistence (the One Earth concept) between the human and the bacterial worlds. This, in turn, will contribute to microbial biodiversity, which is crucial in a globally changing climate due to anthropogenic activities.},
}
@article {pmid37894082,
year = {2023},
author = {Anton, BP and Roberts, RJ},
title = {A Survey of Archaeal Restriction-Modification Systems.},
journal = {Microorganisms},
volume = {11},
number = {10},
pages = {},
pmid = {37894082},
issn = {2076-2607},
abstract = {When compared with bacteria, relatively little is known about the restriction-modification (RM) systems of archaea, particularly those in taxa outside of the haloarchaea. To improve our understanding of archaeal RM systems, we surveyed REBASE, the restriction enzyme database, to catalog what is known about the genes and activities present in the 519 completely sequenced archaeal genomes currently deposited there. For 49 (9.4%) of these genomes, we also have methylome data from Single-Molecule Real-Time (SMRT) sequencing that reveal the target recognition sites of the active m[6]A and m[4]C DNA methyltransferases (MTases). The gene-finding pipeline employed by REBASE is trained primarily on bacterial examples and so will look for similar genes in archaea. Nonetheless, the organizational structure and protein sequence of RM systems from archaea are highly similar to those of bacteria, with both groups acquiring systems from a shared genetic pool through horizontal gene transfer. As in bacteria, we observe numerous examples of "persistent" DNA MTases conserved within archaeal taxa at different levels. We experimentally validated two homologous members of one of the largest "persistent" MTase groups, revealing that methylation of C(m[5]C)WGG sites may play a key epigenetic role in Crenarchaea. Throughout the archaea, genes encoding m[6]A, m[4]C, and m[5]C DNA MTases, respectively, occur in approximately the ratio 4:2:1.},
}
@article {pmid37888586,
year = {2023},
author = {Ortega-Balleza, JL and Guerrero, A and Castro-Escarpulli, G and Martínez-Vázquez, AV and Cruz-Hernández, MA and Luna-Santillana, EJ and Acosta-Cruz, E and Rodríguez-Sánchez, IP and Rivera, G and Bocanegra-García, V},
title = {Genomic Analysis of Multidrug-Resistant Escherichia coli Strains Isolated in Tamaulipas, Mexico.},
journal = {Tropical medicine and infectious disease},
volume = {8},
number = {10},
pages = {},
pmid = {37888586},
issn = {2414-6366},
abstract = {The global spread of antimicrobial resistance genes (ARGs) is a major public health concern. Mobile genetic elements (MGEs) are the main drivers of this spread by horizontal gene transfer (HGT). Escherichia coli is widespread in various environments and serves as an indicator for monitoring antimicrobial resistance (AMR). Therefore, the objective of this work was to evaluate the whole genome of multidrug-resistant E. coli strains isolated from human clinical, animal, and environmental sources. Four E. coli strains previously isolated from human urine (n = 2), retail meat (n = 1), and water from the Rio Grande River (n = 1) collected in northern Tamaulipas, Mexico, were analyzed. E. coli strains were evaluated for antimicrobial susceptibility, followed by whole genome sequencing and bioinformatic analysis. Several ARGs were detected, including blaCTX-M-15, blaOXA-1, blaTEM-1B, blaCMY-2, qnrB, catB3, sul2, and sul3. Additionally, plasmid replicons (IncFIA, IncFIB, IncFII, IncY, IncR, and Col) and intact prophages were also found. Insertion sequences (ISs) were structurally linked with resistance and virulence genes. Finally, these findings indicate that E. coli strains have a large repertoire of resistance determinants, highlighting a high pathogenic potential and the need to monitor them.},
}
@article {pmid37887056,
year = {2023},
author = {Sandmann, G},
title = {Genes and Pathway Reactions Related to Carotenoid Biosynthesis in Purple Bacteria.},
journal = {Biology},
volume = {12},
number = {10},
pages = {},
pmid = {37887056},
issn = {2079-7737},
abstract = {In purple bacteria, the genes of the carotenoid pathways are part of photosynthesis gene clusters which were distributed among different species by horizontal gene transfer. Their close organisation facilitated the first-time cloning of carotenogenic genes and promoted the molecular investigation of spheroidene and spirilloxanthin biosynthesis. This review highlights the cloning of the spheroidene and spirilloxanthin pathway genes and presents the current knowledge on the enzymes involved in the carotenoid biosynthesis of purple sulphur and non-sulphur bacteria. Mostly, spheroidene or spirilloxanthin biosynthesis exists in purple non-sulphur bacteria but both pathways operate simultaneously in Rubrivivax gelatinosus. In the following years, genes from other bacteria including purple sulphur bacteria with an okenone pathway were cloned. The individual steps were investigated by kinetic studies with heterologously expressed pathway genes which supported the establishment of the reaction mechanisms. In particular, the substrate and product specificities revealed the sequential order of the speroidene and spiriloxanthin pathways as well as their interactions. Information on the enzymes involved revealed that the phytoene desaturase determines the type of pathway by the formation of different products. By selection of mutants with amino acid exchanges in the putative substrate-binding site, the neurosporene-forming phytoene desaturase could be changed into a lycopene-producing enzyme and vice versa. Concerning the oxygen groups in neurosporene and lycopene, the tertiary alcohol group at C1 is formed from water and not by oxygenation, and the C2 or C4 keto groups are inserted differently by an oxygen-dependent or oxygen-independent ketolation reaction, respectively.},
}
@article {pmid37886666,
year = {2023},
author = {Arbé-Carton, K and Rey-Sogo, A and Santos-Fernández, N and Altube, O and Garbisu, C and Arana, L and Alkorta, I},
title = {Development of a high-throughput platform to measure plasmid transfer frequency.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1269732},
pmid = {37886666},
issn = {2235-2988},
mesh = {Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; },
abstract = {Antibiotic resistance represents one of the greatest threats to global health. The spread of antibiotic resistance genes among bacteria occurs mostly through horizontal gene transfer via conjugation mediated by plasmids. This process implies a direct contact between a donor and a recipient bacterium which acquires the antibiotic resistance genes encoded by the plasmid and, concomitantly, the capacity to transfer the acquired plasmid to a new recipient. Classical assays for the measurement of plasmid transfer frequency (i.e., conjugation frequency) are often characterized by a high variability and, hence, they require many biological and technical replicates to reduce such variability and the accompanying uncertainty. In addition, classical conjugation assays are commonly tedious and time-consuming because they typically involve counting colonies on a large number of plates for the quantification of donors, recipients, and transconjugants (i.e., the bacteria that have received the genetic material by conjugation). Due to the magnitude of the antibiotic resistance problem, it is critical to develop reliable and rapid methods for the quantification of plasmid transfer frequency that allow the simultaneous analysis of many samples. Here, we present the development of a high-throughput, reliable, quick, easy, and cost-effective method to simultaneously accomplish and measure multiple conjugation events in 96-well plates, in which the quantification of donors, recipients, and transconjugants is estimated from the time required to reach a specific threshold value (OD600 value) in the bacterial growth curves. Our method successfully discriminates different plasmid transfer frequencies, yielding results that are equivalent to those obtained by a classical conjugation assay.},
}
@article {pmid37884245,
year = {2023},
author = {Zhang, Z and Li, B and Chai, Z and Yang, Z and Zhang, F and Kang, F and Ren, H and Jin, Y and Yue, J},
title = {Evolution of the ability to evade host innate immune defense by Talaromyces marneffei.},
journal = {International journal of biological macromolecules},
volume = {253},
number = {Pt 8},
pages = {127597},
doi = {10.1016/j.ijbiomac.2023.127597},
pmid = {37884245},
issn = {1879-0003},
mesh = {Humans ; *Talaromyces/genetics ; Phylogeny ; *Mycoses/genetics/microbiology ; Immunity, Innate/genetics ; },
abstract = {Talaromyces (Penicillium) marneffei is an intracellular pathogenic fungus. Some strains of this fungus have been misidentified due to the similarity between Talaromyces and Penicillium. T. marneffei has mainly been found to afflict immunocompromised individuals, causing respiratory, skin, and systemic mycosis. Mp1p is a key virulence factor that can help T. marneffei evade clearance by the normally functioning immune system. Understanding how novel functions arise is an intriguing question in many fields of biology. Mp1p has two homologous domains (Mp1p-LBD1 and Mp1p-LBD2). Sequence similarity searches with Mp1p-LBD sequences revealed Mp1p homologs in many other pathogenic fungi. Integrated information on the taxonomic distribution, phylogenetic relationships, and sequence similarity of Mp1p domains revealed that the ancestor of Mp1p-LBDs was acquired through horizontal gene transfer (HGT). Additional evidence revealed that Mp1p homologs have undergone extensive gene duplications in T. marneffei. Mp1p might be a result of gene fusion following gene duplication. Furthermore, we propose a new method for identifying Talaromyces and identify 4 strains with misclassification errors. Our results characterize the evolutionary mechanism of T. marneffei evasion of host innate immune defense and clearly demonstrate the role of gene duplication and HGT in the evolution of host immune escape by T. marneffei.},
}
@article {pmid37883987,
year = {2024},
author = {Parthasarathy, R and Wakefield, D and Santiago, FS and Kaakoush, NO and Tedla, N},
title = {Horizontal gene transfer and endogenous retroviruses as mechanisms for molecular mimicry.},
journal = {The Lancet. Microbe},
volume = {5},
number = {1},
pages = {e4-e5},
doi = {10.1016/S2666-5247(23)00316-6},
pmid = {37883987},
issn = {2666-5247},
mesh = {*Endogenous Retroviruses/genetics ; Molecular Mimicry ; Gene Transfer, Horizontal ; Amino Acid Sequence ; Gene Products, env/genetics ; },
}
@article {pmid37882558,
year = {2023},
author = {Marti, H and Biggel, M and Shima, K and Onorini, D and Rupp, J and Charette, SJ and Borel, N},
title = {Chlamydia suis displays high transformation capacity with complete cloning vector integration into the chromosomal rrn-nqrF plasticity zone.},
journal = {Microbiology spectrum},
volume = {11},
number = {6},
pages = {e0237823},
pmid = {37882558},
issn = {2165-0497},
support = {323530_177579/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Animals ; Humans ; Swine ; *Chlamydia/genetics ; Chlamydia trachomatis ; *Chlamydia Infections/microbiology ; Anti-Bacterial Agents ; Genetic Vectors ; },
abstract = {The obligate intracellular Chlamydia genus contains many pathogens with a negative impact on global health and economy. Despite recent progress, there is still a lack of genetic tools limiting our understanding of these complex bacteria. This study provides new insights into genetic manipulation of Chlamydia with the opportunistic porcine pathogen Chlamydia suis, the only chlamydial species naturally harboring an antibiotic resistance gene, originally obtained by horizontal gene transfer. C. suis is transmissible to humans, posing a potential public health concern. We report that C. suis can take up vectors that lack the native plasmid, a requirement for most chlamydial transformation systems described to date. Additionally, we show that C. trachomatis, the most common cause for bacterial sexually transmitted infections and infectious blindness worldwide, can be transformed with C. suis vectors. Finally, the chromosomal region that harbors the resistance gene of C. suis is highly susceptible to complete vector integration.},
}
@article {pmid37880110,
year = {2024},
author = {Tanaka, E and Wajima, T and Ota, R and Uchiya, KI},
title = {The Association between Transformation Ability and Antimicrobial Resistant Potential in Haemophilus influenzae.},
journal = {Biological &amp; pharmaceutical bulletin},
volume = {47},
number = {1},
pages = {154-158},
doi = {10.1248/bpb.b23-00583},
pmid = {37880110},
issn = {1347-5215},
mesh = {Humans ; Haemophilus influenzae/genetics ; Anti-Bacterial Agents/pharmacology ; *Haemophilus Infections/drug therapy ; *Anti-Infective Agents ; *Quinolones ; Microbial Sensitivity Tests ; },
abstract = {The prevalence of quinolone low-susceptible Haemophilus influenzae has increased in Japan. Low quinolone susceptibility is caused by point mutations in target genes; however, it can also be caused by horizontal gene transfer via natural transformation. In this study, we examined whether this horizontal gene transfer could be associated with resistance to not only quinolones but also other antimicrobial agents. Horizontal transfer ability was quantified using the experimental transfer assay method for low quinolone susceptibility. Further, the association between horizontal transfer ability and resistance to β-lactams, the first-choice drugs for H. influenzae infection, was investigated. The transformation efficiency of 50 clinical isolates varied widely, ranging from 10[2] to 10[6] colony forming unit (CFU) of the colonies obtained by horizontal transfer assay. Efficiency was associated with β-lactam resistance caused by ftsI mutations, indicating that strains with high horizontal transfer ability acquired quinolone low-susceptibility as well as β-lactam resistance more easily. Strains with high transformation efficiency increased the transcript level of comA, suggesting that enhanced com operon was associated with a high DNA uptake ability. Overall, this study revealed that the transformation ability of H. influenzae was associated with multiple antimicrobial resistance. Increase in the number of strains with high horizontal transformation ability has raised concerns regarding the rapid spread of antimicrobial-resistant H. influenzae.},
}
@article {pmid37875161,
year = {2023},
author = {Ribes-Navarro, A and Kabeya, N and Castro, LFC and Gomes-Dos-Santos, A and Fonseca, MM and Alberts-Hubatsch, H and Hontoria, F and Navarro, JC and Monroig, &#xd3;},
title = {Examination of gammarid transcriptomes reveals a widespread occurrence of key metabolic genes from epibiont bdelloid rotifers in freshwater species.},
journal = {Open biology},
volume = {13},
number = {10},
pages = {230196},
pmid = {37875161},
issn = {2046-2441},
mesh = {Fatty Acid Elongases/genetics/metabolism ; Phylogeny ; *Transcriptome ; *Fatty Acid Desaturases/genetics/metabolism ; Fatty Acids, Unsaturated ; Fresh Water ; },
abstract = {Previous data revealed the unexpected presence of genes encoding for long-chain polyunsaturated fatty acid (LC-PUFA) biosynthetic enzymes in transcriptomes from freshwater gammarids but not in marine species, even though closely related species were compared. This study aimed to clarify the origin and occurrence of selected LC-PUFA biosynthesis gene markers across all published gammarid transcriptomes. Through systematic searches, we confirmed the widespread occurrence of sequences from seven elongases and desaturases involved in LC-PUFA biosynthesis, in transcriptomes from freshwater gammarids but not marine species, and clarified that such occurrence is independent from the gammarid species and geographical origin. The phylogenetic analysis established that the retrieved elongase and desaturase sequences were closely related to bdelloid rotifers, confirming that multiple transcriptomes from freshwater gammarids contain contaminating rotifers' genetic material. Using the Adineta steineri genome, we investigated the genomic location and exon-intron organization of the elongase and desaturase genes, establishing they are all genome-anchored and, importantly, identifying instances of horizontal gene transfer. Finally, we provide compelling evidence demonstrating Bdelloidea desaturases and elongases enable these organisms to perform all the reactions for de novo biosynthesis of PUFA and, from them, LC-PUFA, an advantageous trait when considering the low abundance of these essential nutrients in freshwater environments.},
}
@article {pmid37875024,
year = {2023},
author = {Wang, X and Qin, J and Xiang, G and Wang, C and Wang, Q and Qin, J and Wang, H and Shen, Z},
title = {Nosocomial dissemination of blaIMP-4 among Klebsiella pneumoniae by horizontal gene transfer and clonal spread: the epidemic IncN plasmids and the emerging high-risk IMP-4-producing ST101 clone.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {78},
number = {12},
pages = {2890-2894},
doi = {10.1093/jac/dkad326},
pmid = {37875024},
issn = {1460-2091},
support = {82272374//National Natural Science Foundation of China/ ; 22PJ1409600//Shanghai Pujiang Program/ ; RJTJ22-MS-018//Renji Hospital/ ; },
mesh = {Humans ; Child ; Klebsiella pneumoniae/genetics ; *Enterobacteriaceae Infections/microbiology ; Gene Transfer, Horizontal ; *Cross Infection/epidemiology/microbiology ; Prospective Studies ; China/epidemiology ; beta-Lactamases/genetics ; Plasmids/genetics ; Bacterial Proteins/genetics ; *Klebsiella Infections/epidemiology ; Microbial Sensitivity Tests ; Anti-Bacterial Agents ; },
abstract = {OBJECTIVES: To determine the genomic features of IMP-4-producing Klebsiella pneumoniae isolates recovered from paediatric patients and the transmission dynamics of blaIMP-4.<br><br>METHODS: IMP-producing K. pneumoniae isolates were collected from paediatric patients in Shanghai Children's Medical Center from 2013 to 2020. WGS was performed for all isolates, and the complete genomes of three IMP-4-producing isolates were generated. The distribution of blaIMP-4-harbouring plasmids was determined, and a conjugation assay was employed to investigate the horizontal transfer of blaIMP-4-harbouring plasmids.<br><br>RESULTS: We collected 21 blaIMP-carrying K. pneumoniae isolates, with IMP-4 (16/21, 76.2%) as the predominant subtype, followed by IMP-8 (n&#x200a;=&#x200a;3) and IMP-26 (n&#x200a;=&#x200a;2). IMP-4-producing isolates displayed a diverse population structure and all blaIMP-4 genes were located on plasmids, including IncN (n&#x200a;=&#x200a;9), IncHI5 (n&#x200a;=&#x200a;5), IncFII(K) (n&#x200a;=&#x200a;1) and IncFII(pKP91) (n&#x200a;=&#x200a;1), although only IncN plasmids were conjugative. Clonal transmission of ST101 strains carrying IncHI5 blaIMP-4-harbouring plasmids was observed, and the acquisition of blaIMP-4 by the international high-risk ST101 clone constituted a novel combination of ST101 clone and carbapenemase genes. Plasmid analysis demonstrated that the conjugal transfer of the IncHI5 blaIMP-4-harbouring plasmid might be blocked by the ST101 bacterial host.<br><br>CONCLUSIONS: The horizontal transfer of IncN plasmids and clonal spread of the international high-risk ST101 clone facilitated the nosocomial dissemination of blaIMP-4 among K. pneumoniae. The emerging IMP-4-producing ST101 clone displays diverse combinations of carbapenemase genes, and this clone could be a continually evolving threat and warrants prospective monitoring.},
}
@article {pmid37873201,
year = {2023},
author = {Attah, V and Milner, DS and Fang, Y and Yan, X and Leonard, G and Heitman, J and Talbot, NJ and Richards, TA},
title = {Duplication and neofunctionalization of a horizontally-transferred xyloglucanase as a facet of the red queen co-evolutionary dynamic.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37873201},
issn = {2692-8205},
support = {R01 AI039115/AI/NIAID NIH HHS/United States ; },
abstract = {UNLABELLED: Oomycetes are heterotrophic protists that share phenotypic similarities with fungi, including the ability to cause plant diseases, but branch in a separate and distant region of the eukaryotic tree of life. It has been suggested that multiple horizontal gene transfers (HGTs) from fungi-to-oomycetes contributed to the evolution of plant-pathogenic traits. These HGTs are predicted to include secreted proteins that degrade plant cell walls. This is a key trait in the pathology of many oomycetes, as the plant cell wall represents a primary barrier to pathogen invasion and a rich source of carbohydrates. Many of the HGT gene families identified have undergone multiple rounds of duplication. Using a combination of phylogenomic analysis and functional assays, we investigate the diversification of a horizontally-transferred xyloglucanase gene family in the model oomycete species Phytophthora sojae. Our analyses detect 11 genes retained in P. sojae among a complex pattern of gene duplications and losses. Using a phenotype assay, based on heterologous expression in yeast, we show that eight of these paralogs have xyloglucanase function, including variants with distinct protein characteristics, such as a long-disordered C-terminal extension that can increase xyloglucanase activity. The functional xyloglucanase variants analysed subtend an ancestral node close to the fungi-oomycetes gene transfer, suggesting the horizontally-transferred gene was a bona fide xyloglucanase. Expression of xyloglucanase paralogs in Nicotiana benthamiana triggers distinct patterns of reactive oxygen species (ROS) generation, demonstrating that enzyme variants differentially stimulate pattern-triggered immunity in plants. Mass spectrometry of detectable enzymatic products demonstrates that some paralogs catalyze production of variant breakdown profiles, suggesting that secretion of multiple xyloglucanase variants increases efficiency of xyloglucan breakdown, as well as potentially diversifying the range of Damage-Associated Molecular Patterns (DAMPs) released during pathogen attack. We suggest that such patterns of protein neofunctionalization, and variant host responses, represent an aspect of the Red Queen host-pathogen co-evolutionary dynamic.<br><br>SIGNIFICANCE STATEMENT: The oomycetes are a diverse group of eukaryotic microbes that include some of the most devastating pathogens of plants. Oomycetes perceive, invade, and colonize plants in similar ways to fungi, in part because they acquired the genes to attack and feed on plants from fungi. These genes are predicted to be useful to oomycete plant pathogens because they have undergone multiple rounds of gene duplication. One key enzyme for attacking plant cell wall structures is called xyloglucanase. Xyloglucanase in the oomycetes has undergone multiple rounds of gene duplication, leading to variants including an enzyme with a C-terminal extension that increases activity. Some xyloglucanase variants trigger unique patterns of reactive oxygen species (ROS) in planta, and generate different profiles of cell wall breakdown products - such outcomes could act to mystify and increase the workload of the plant immune system, allowing successful pathogens to proliferate.},
}
@article {pmid37873187,
year = {2023},
author = {Hamrick, GS and Maddamsetti, R and Son, HI and Wilson, ML and Davis, HM and You, L},
title = {Programming dynamic division of labor using horizontal gene transfer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.10.03.560696},
pmid = {37873187},
issn = {2692-8205},
abstract = {The metabolic engineering of microbes has broad applications, including in biomanufacturing, bioprocessing, and environmental remediation. The introduction of a complex, multi-step pathway often imposes a substantial metabolic burden on the host cell, restraining the accumulation of productive biomass and limiting pathway efficiency. One strategy to alleviate metabolic burden is division of labor (DOL), in which different subpopulations carry out different parts of the pathway and work together to convert a substrate into a final product. However, the maintenance of different engineered subpopulations is challenging due to competition and convoluted inter-strain population dynamics. Through modeling, we show that dynamic division of labor (DDOL) mediated by horizontal gene transfer (HGT) can overcome these limitations and enable the robust maintenance of burdensome, multi-step pathways. We also use plasmid genomics to uncover evidence that DDOL is a strategy utilized by natural microbial communities. Our work suggests that bioengineers can harness HGT to stabilize synthetic metabolic pathways in microbial communities, enabling the development of robust engineered systems for deployment in a variety of contexts.},
}
@article {pmid37871361,
year = {2023},
author = {Moussa, J and Nassour, E and Tahan, E and El Chaar, M and Jisr, T and Tokajian, S},
title = {Carbapenem resistance determinants and their transmissibility among clinically isolated Enterobacterales in Lebanon.},
journal = {Journal of infection and public health},
volume = {16},
number = {12},
pages = {1947-1953},
doi = {10.1016/j.jiph.2023.10.003},
pmid = {37871361},
issn = {1876-035X},
mesh = {Humans ; Lebanon/epidemiology ; *Carbapenems/pharmacology ; Imipenem ; Meropenem ; *Anti-Infective Agents ; },
abstract = {BACKGROUND: The occurrence of carbapenem-resistant bacterial infections has increased significantly over the years with Gram-negative bacteria exhibiting the broadest resistance range. In this study we aimed to investigate the genomic characteristics of clinical carbapenem-resistant Enterobacterales (CRE).<br><br>METHODS: Seventeen representative multi-drug resistant (MDR) isolates from a hospital setting showing high level of resistance to carbapenems (ertapenem, meropenem and imipenem) were chosen for further characterization through whole-genome sequencing. Resistance mechanisms and transferability of plasmids carrying carbapenemase-encoding genes were also determined in silico and through conjugative mating assays.<br><br>RESULTS: We detected 18 different &#x3b2;-lactamases, including four carbapenemases (blaNDM-1, blaNDM-5, blaNDM-7, blaOXA-48) on plasmids with different Inc groups. The combined results from PBRT and in silico replicon typing revealed 20 different replicons linked to plasmids ranging in size between 80 and 200&#xa0;kb. The most prevalent Inc groups were IncFIB(K) and IncM. OXA-48, detected on 76-kb IncM1 conjugable plasmid, was the most common carbapenemase. We also detected other conjugative plasmids with different carbapenemases confirming the role of horizontal gene transfer in the dissemination of antimicrobial resistance genes.<br><br>CONCLUSION: Our findings verified the continuing spread of carbapenemases in Enterobacterales and revealed the types of mobile elements circulating in a hospital setting and contributing to the spread of resistance determinants. The occurrence and transmission of plasmids carrying carbapenemase-encoding genes call for strengthening active surveillance and prevention efforts to control antimicrobial resistance dissemination in healthcare settings.},
}
@article {pmid37870180,
year = {2023},
author = {Zhang, Q and Xu, N and Lei, C and Chen, B and Wang, T and Ma, Y and Lu, T and Penuelas, J and Gillings, M and Zhu, YG and Fu, Z and Qian, H},
title = {Metagenomic Insight into The Global Dissemination of The Antibiotic Resistome.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {10},
number = {33},
pages = {e2303925},
pmid = {37870180},
issn = {2198-3844},
support = {2022YFD1700400//National Key Research and Development Program of China/ ; 21976161//National Natural Science Foundation of China/ ; 22376187//National Natural Science Foundation of China/ ; 42307158//National Natural Science Foundation of China/ ; LZ23B070001//Natural Science Foundation of Zhejiang Province/ ; TED2021-132627B-I00//Department of Local Government, Sport and cultural industries/ ; },
mesh = {Animals ; Humans ; *Genes, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Metagenome/genetics ; Feces ; },
abstract = {The global crisis in antimicrobial resistance continues to grow. Estimating the risks of antibiotic resistance transmission across habitats is hindered by the lack of data on mobility and habitat-specificity. Metagenomic samples of 6092 are analyzed to delineate the unique core resistomes from human feces and seven other habitats. This is found that most resistance genes (≈85%) are transmitted between external habitats and human feces. This suggests that human feces are broadly representative of the global resistome and are potentially a hub for accumulating and disseminating resistance genes. The analysis found that resistance genes with ancient horizontal gene transfer (HGT) events have a higher efficiency of transfer across habitats, suggesting that HGT may be the main driver for forming unique but partly shared resistomes in all habitats. Importantly, the human fecal resistome is historically different and influenced by HGT and age. The most important routes of cross-transmission of resistance are from the atmosphere, buildings, and animals to humans. These habitats should receive more attention for future prevention of antimicrobial resistance. The study will disentangle transmission routes of resistance genes between humans and other habitats in a One Health framework and can identify strategies for controlling the ongoing dissemination and antibiotic resistance.},
}
@article {pmid37865329,
year = {2024},
author = {Ye, C and Chen, C and Zhang, K and Feng, M and Yu, X},
title = {Solar/periodate inhibits ARGs transformation by degradation of DNA without damaging cell membrane.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {340},
number = {Pt 1},
pages = {122766},
doi = {10.1016/j.envpol.2023.122766},
pmid = {37865329},
issn = {1873-6424},
mesh = {*Genes, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Wastewater ; Bacteria ; Disinfection/methods ; Cell Membrane ; Water ; },
abstract = {Antibiotic-resistant bacterial infections are a growing global threat to public health. Chlorine-based water disinfection and some advanced oxidation processes significantly increase the risk of ARGs release and transmission in the aquatic environment. Therefore, it is critical to develop or optimize disinfection methods to reduce the conversion and transmission of ARGs in natural water. This study investigated whether the solar/periodate (PI) system inhibited the natural transmission of ARGs and its mechanism. The results showed that solar/PI systems could effectively inhibit the propagation of ARGs in two simulated natural transformation systems, up to more than 100 times. By characterizing the cellular process of bacteria treated by the solar/PI system, we found that the solar/PI system could directly cause damage to DNA bases and its dual effect with almost no damage to the bacterial cell membrane, which was the main reason why this technology could inhibit natural transformation processes. Specifically, the inhibition effect of solar/PI on bacteria did not result in enhanced membrane permeability under appropriate PI dosage (<200 μM), which greatly reduced the risk of secondary contamination of eARGs released by traditional disinfection. Our findings could help improve existing disinfection strategies to ensure that antibiotic resistance is not spread in the natural water environment.},
}
@article {pmid37864197,
year = {2023},
author = {Abante, J and Wang, PL and Salzman, J},
title = {DIVE: a reference-free statistical approach to diversity-generating and mobile genetic element discovery.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {240},
pmid = {37864197},
issn = {1474-760X},
support = {R35 GM139517/GM/NIGMS NIH HHS/United States ; },
mesh = {*Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; DNA Transposable Elements ; },
abstract = {Diversity-generating and mobile genetic elements are key to microbial and viral evolution and can result in evolutionary leaps. State-of-the-art algorithms to detect these elements have limitations. Here, we introduce DIVE, a new reference-free approach to overcome these limitations using information contained in sequencing reads alone. We show that DIVE has improved detection power compared to existing reference-based methods using simulations and real data. We use DIVE to rediscover and characterize the activity of known and novel elements and generate new biological hypotheses about the mobilome. Building on DIVE, we develop a reference-free framework capable of de novo discovery of mobile genetic elements.},
}
@article {pmid37863223,
year = {2024},
author = {Jiménez-Volkerink, SN and Jordán, M and Smidt, H and Minguillón, C and Vila, J and Grifoll, M},
title = {Metagenomic insights into the microbial cooperative networks of a benz(a)anthracene-7,12-dione degrading community from a creosote-contaminated soil.},
journal = {The Science of the total environment},
volume = {907},
number = {},
pages = {167832},
doi = {10.1016/j.scitotenv.2023.167832},
pmid = {37863223},
issn = {1879-1026},
mesh = {Microbial Consortia ; Creosote ; Sand ; *Polycyclic Aromatic Hydrocarbons/metabolism ; Biodegradation, Environmental ; Carbon ; *Soil Pollutants/metabolism ; Soil Microbiology ; Soil ; },
abstract = {Genotoxicity of PAH-contaminated soils can eventually increase after bioremediation due to the formation and accumulation of polar transformation products, mainly oxygenated PAHs (oxy-PAHs). Biodegradation of oxy-PAHs has been described in soils, but information on the microorganisms and mechanisms involved is still scarce. Benz(a)anthracene-7,12-dione (BaAQ), a transformation product from benz(a)anthracene frequently detected in soils, presents higher genotoxic potential than its parent PAH. Here, using sand-in-liquid microcosms we identified a specialized BaAQ-degrading subpopulation in a PAH-contaminated soil. A BaAQ-degrading microbial consortium was obtained by enrichment in sand-in-liquid cultures with BaAQ as sole carbon source, and its metagenomic analysis identified members of Sphingobium, Stenotrophomonas, Pusillimonas, Olivibacter, Pseudomonas, Achromobacter, and Hyphomicrobiales as major components. The integration of data from metabolomic and metagenomic functional gene analyses of the consortium revealed that the BaAQ metabolic pathway was initiated by Baeyer-Villiger monooxygenases (BVMOs). The presence of plasmid pANTQ-1 in the metagenomic sequences, identified in a previous multi-omic characterization of a 9,10-anthraquinone-degrading isolate recovered from the same soil, suggested the occurrence of a horizontal gene transfer event. Further metagenomic analysis of the BaAQ-degrading consortium also provided insights into the potential roles and interactions within the consortium members. Several potential auxotrophies were detected, indicating that relevant nutritional interdependencies and syntrophic associations were taking place within the community members, not only to provide suitable carbon and energy sources, but also to supply essential nutrients and cofactors. Our work confirms the essential role that BVMO may play as a detoxification mechanism to mitigate the risk posed by oxy-PAH formation during bioremediation of contaminated soils.},
}
@article {pmid37863060,
year = {2023},
author = {Mishina, T and Chiu, MC and Hashiguchi, Y and Oishi, S and Sasaki, A and Okada, R and Uchiyama, H and Sasaki, T and Sakura, M and Takeshima, H and Sato, T},
title = {Massive horizontal gene transfer and the evolution of nematomorph-driven behavioral manipulation of mantids.},
journal = {Current biology : CB},
volume = {33},
number = {22},
pages = {4988-4994.e5},
doi = {10.1016/j.cub.2023.09.052},
pmid = {37863060},
issn = {1879-0445},
mesh = {Animals ; *Mantodea ; Host-Parasite Interactions/genetics ; Behavior Control ; Gene Transfer, Horizontal ; *Parasites ; },
abstract = {To complete their life cycle, a wide range of parasites must manipulate the behavior of their hosts.[1] This manipulation is a well-known example of the "extended phenotype,[2]" where genes in one organism have phenotypic effects on another organism. Recent studies have explored the parasite genes responsible for such manipulation of host behavior, including the potential molecular mechanisms.[3][,][4] However, little is known about how parasites have acquired the genes involved in manipulating phylogenetically distinct hosts.[4] In a fascinating example of the extended phenotype, nematomorph parasites have evolved the ability to induce their terrestrial insect hosts to enter bodies of water, where the parasite then reproduces. Here, we comprehensively analyzed nematomorphs and their mantid hosts, focusing on the transcriptomic changes associated with host manipulations and sequence similarity between host and parasite genes to test molecular mimicry. The nematomorph's transcriptome changed during host manipulation, whereas no distinct changes were found in mantids. We then discovered numerous possible host-derived genes in nematomorphs, and these genes were frequently up-regulated during host manipulation. Our findings suggest a possible general role of horizontal gene transfer (HGT) in the molecular mechanisms of host manipulation, as well as in the genome evolution of manipulative parasites. The evidence of HGT between multicellular eukaryotes remains scarce but is increasing and, therefore, elucidating its mechanisms will advance our understanding of the enduring influence of HGT on the evolution of the web of life.},
}
@article {pmid37858689,
year = {2023},
author = {Sajjad, W and Ali, B and Niu, H and Ilahi, N and Rafiq, M and Bahadur, A and Banerjee, A and Kang, S},
title = {High prevalence of antibiotic-resistant and metal-tolerant cultivable bacteria in remote glacier environment.},
journal = {Environmental research},
volume = {239},
number = {Pt 2},
pages = {117444},
doi = {10.1016/j.envres.2023.117444},
pmid = {37858689},
issn = {1096-0953},
mesh = {*Genes, Bacterial ; *Ice Cover/microbiology ; Prevalence ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria ; Anti-Bacterial Agents/pharmacology/analysis ; Metals/analysis ; Gram-Negative Bacteria/genetics ; Drug Resistance, Bacterial/genetics ; },
abstract = {Studies of antibiotic-resistant bacteria (ARB) have mainly originated from anthropic-influenced environments, with limited information from pristine environments. Remote cold environments are major reservoirs of ARB and have been determined in polar regions; however, their abundance in non-polar cold habitats is underexplored. This study evaluated antibiotics and metals resistance profiles, prevalence of antibiotic resistance genes (ARGs) and metals tolerance genes (MTGs) in 38 ARB isolated from the glacier debris and meltwater from Baishui Glacier No 1, China. Molecular identification displayed Proteobacteria (39.3%) predominant in debris, while meltwater was dominated by Actinobacteria (30%) and Proteobacteria (30%). Bacterial isolates exhibited multiple antibiotic resistance index values > 0.2. Gram-negative bacteria displayed higher resistance to antibiotics and metals than Gram-positive. PCR amplification exhibited distinct ARGs in bacteria dominated by β-lactam genes blaCTX-M (21.1-71.1%), blaACC (21.1-60.5%), tetracycline-resistant gene tetA (21.1-60.5%), and sulfonamide-resistant gene sulI (18.4-52.6%). Moreover, different MTGs were reported in bacterial isolates, including mercury-resistant merA (21.1-63.2%), copper-resistant copB (18.4-57.9%), chromium-resistant chrA (15.8-44.7%) and arsenic-resistant arsB (10.5-44.7%). This highlights the co-selection and co-occurrence of MTGs and ARGs in remote glacier environments. Different bacteria shared same ARGs, signifying horizontal gene transfer between species. Strong positive correlation among ARGs and MTGs was reported. Metals tolerance range exhibited that Gram-negative and Gram-positive bacteria clustered distinctly. Gram-negative bacteria were significantly tolerant to metals. Amino acid sequences of blaACC,blaCTX-M,blaSHV,blaampC,qnrA, sulI, tetA and blaTEM revealed variations. This study presents promising ARB, harboring ARGs with variations in amino acid sequences, highlighting the need to assess the transcriptome study of glacier bacteria conferring ARGs and MTGs.},
}
@article {pmid37856515,
year = {2023},
author = {Johansson, MHK and Aarestrup, FM and Petersen, TN},
title = {Importance of mobile genetic elements for dissemination of antimicrobial resistance in metagenomic sewage samples across the world.},
journal = {PloS one},
volume = {18},
number = {10},
pages = {e0293169},
pmid = {37856515},
issn = {1932-6203},
mesh = {*Sewage/microbiology ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; Interspersed Repetitive Sequences/genetics ; },
abstract = {We are facing an ever-growing threat from increasing antimicrobial resistance (AMR) in bacteria. To mitigate this, we need a better understanding of the global spread of antimicrobial resistance genes (ARGs). ARGs are often spread among bacteria by horizontal gene transfer facilitated by mobile genetic elements (MGE). Here we use a dataset consisting of 677 metagenomic sequenced sewage samples from 97 countries or regions to study how MGEs are geographically distributed and how they disseminate ARGs worldwide. The ARGs, MGEs, and bacterial abundance were calculated by reference-based read mapping. We found systematic differences in the abundance of MGEs and ARGs, where some elements were prevalent on all continents while others had higher abundance in separate geographic areas. Different MGEs tended to be localized to temperate or tropical climate zones, while different ARGs tended to separate according to continents. This suggests that the climate is an important factor influencing the local flora of MGEs. MGEs were also found to be more geographically confined than ARGs. We identified several integrated MGEs whose abundance correlated with the abundance of ARGs and bacterial genera, indicating the ability to mobilize and disseminate these genes. Some MGEs seemed to be more able to mobilize ARGs and spread to more bacterial species. The host ranges of MGEs seemed to differ between elements, where most were associated with bacteria of the same family. We believe that our method could be used to investigate the population dynamics of MGEs in complex bacterial populations.},
}
@article {pmid37856455,
year = {2023},
author = {Aubin, E and Llauro, C and Garrigue, J and Mirouze, M and Panaud, O and El Baidouri, M},
title = {Genome-wide analysis of horizontal transfer in non-model wild species from a natural ecosystem reveals new insights into genetic exchange in plants.},
journal = {PLoS genetics},
volume = {19},
number = {10},
pages = {e1010964},
pmid = {37856455},
issn = {1553-7404},
mesh = {*Ecosystem ; Pilot Projects ; *Genome, Plant/genetics ; Genomics ; Retroelements ; Phylogeny ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; },
abstract = {Horizontal transfer (HT) refers to the exchange of genetic material between divergent species by mechanisms other than reproduction. In recent years, several studies have demonstrated HTs in eukaryotes, particularly in the context of parasitic relationships and in model species. However, very little is known about HT in natural ecosystems, especially those involving non-parasitic wild species, and the nature of the ecological relationships that promote these HTs. In this work, we conducted a pilot study investigating HTs by sequencing the genomes of 17 wild non-model species from a natural ecosystem, the Massane forest, located in southern France. To this end, we developed a new computational pipeline called INTERCHANGE that is able to characterize HTs at the whole genome level without prior annotation and directly in the raw sequencing reads. Using this pipeline, we identified 12 HT events, half of which occurred between lianas and trees. We found that mainly low copy number LTR-retrotransposons from the Copia superfamily were transferred between these wild plant species, especially those of the Ivana and Ale lineages. This study revealed a possible new route for HTs between non-parasitic plants and provides new insights into the genomic characteristics of horizontally transferred DNA in plant genomes.},
}
@article {pmid37855620,
year = {2023},
author = {Jia, C and Wang, Z and Huang, C and Teng, L and Zhou, H and An, H and Liao, S and Liu, Y and Huang, L and Tang, B and Yue, M},
title = {Mobilome-driven partitions of the resistome in Salmonella.},
journal = {mSystems},
volume = {8},
number = {6},
pages = {e0088323},
pmid = {37855620},
issn = {2379-5077},
mesh = {*Salmonella/drug effects/genetics ; *Drug Resistance, Bacterial ; },
abstract = {Antimicrobial resistance (AMR) has become a significant global challenge, with an estimated 10 million deaths annually by 2050. The emergence of AMR is mainly attributed to mobile genetic elements (MGEs or mobilomes), which accelerate wide dissemination among pathogens. The interaction between mobilomes and AMR genes (or resistomes) in Salmonella, a primary cause of diarrheal diseases that results in over 90 million cases annually, remains poorly understood. The available fragmented or incomplete genomes remain a significant limitation in investigating the relationship between AMR and MGEs. Here, we collected the most extensive closed Salmonella genomes (n = 1,817) from various sources across 58 countries. Notably, our results demonstrate that resistome transmission between Salmonella lineages follows a specific pattern of MGEs and is influenced by external drivers, including certain socioeconomic factors. Therefore, targeted interventions are urgently needed to mitigate the catastrophic consequences of Salmonella AMR.},
}
@article {pmid37855599,
year = {2023},
author = {Feng, Z and Wang, L and Guan, Q and Chu, X and Luo, Z-Q},
title = {Acinetobacter baumannii coordinates central metabolism, plasmid dissemination, and virulence by sensing nutrient availability.},
journal = {mBio},
volume = {14},
number = {6},
pages = {e0227623},
pmid = {37855599},
issn = {2150-7511},
support = {YDZJ202201ZYTS025//Department of Science and Technology of Jilin Province ()/ ; },
mesh = {*Acinetobacter baumannii/genetics/metabolism/pathogenicity ; *Plasmids/genetics ; Virulence ; *Nutrients/metabolism ; *Gene Transfer, Horizontal ; Bacterial Proteins/genetics/metabolism ; Metabolic Networks and Pathways/genetics ; Conjugation, Genetic ; Gene Expression Regulation, Bacterial ; Humans ; },
abstract = {Plasmid conjugation is known to be an energy-expensive process, but our understanding of the molecular linkage between conjugation and metabolism is limited. Our finding reveals that Acinetobacter baumannii utilizes a two-component system to co-regulate metabolism, plasmid transfer, and virulence by sensing reaction intermediates of key metabolic pathways, which suggests that nutrient availability dictates not only bacterial proliferation but also horizontal gene transfer. The identification of Dot/Icm-like proteins as components of a conjugation system involved in the dissemination of antibiotic-resistance genes by A. baumannii has provided important targets for the development of agents capable of inhibiting virulence and the spread of anti-microbial-resistance genes in bacterial communities.},
}
@article {pmid37850911,
year = {2023},
author = {Yee, W-X and Elsener, T and Cehovin, A and Maiden, MCJ and Tang, CM},
title = {Evolution and exchange of plasmids in pathogenic Neisseria.},
journal = {mSphere},
volume = {8},
number = {6},
pages = {e0044123},
pmid = {37850911},
issn = {2379-5042},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Neisseria/genetics ; Doxycycline ; Microbial Sensitivity Tests ; Plasmids/genetics ; *Gonorrhea/microbiology ; Neisseria gonorrhoeae/genetics ; *Neisseria meningitidis/genetics ; },
abstract = {Horizontal gene transfer (HGT) is a major influence in driving the spread of antimicrobial resistance (AMR) in many bacteria. A conjugative plasmid which is widespread in Neisseria gonorrhoeae, pConj, prevented the use of tetracycline/doxycycline for treating gonococcal infection. Here, we show that pConj evolved in the related pathogen, Neisseria meningitidis, and has been acquired by the gonococcus from the meningococcus on multiple occasions. Following its initial acquisition, pConj spread to different gonococcal lineages; changes in the plasmid's conjugation machinery associated with another transfer event limit spread in the gonococcal populations. Our findings have important implications for the use of doxycycline to prevent bacterial sexually transmitted disease which is likely to exacerbate the spread of AMR through HGT in pathogenic bacteria.},
}
@article {pmid37850800,
year = {2023},
author = {Giengkam, S and Kullapanich, C and Wongsantichon, J and Adcox, HE and Gillespie, JJ and Salje, J},
title = {Orientia tsutsugamushi: comprehensive analysis of the mobilome of a highly fragmented and repetitive genome reveals the capacity for ongoing lateral gene transfer in an obligate intracellular bacterium.},
journal = {mSphere},
volume = {8},
number = {6},
pages = {e0026823},
pmid = {37850800},
issn = {2379-5042},
support = {/WT_/Wellcome Trust/United Kingdom ; R21 AI156762/AI/NIAID NIH HHS/United States ; R21 AI166832/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Orientia tsutsugamushi/genetics/metabolism ; *Scrub Typhus/genetics/microbiology ; Gene Transfer, Horizontal ; Genome, Bacterial ; Longitudinal Studies ; },
abstract = {Obligate intracellular bacteria, or those only capable of growth inside other living cells, have limited opportunities for horizontal gene transfer with other microbes due to their isolated replicative niche. The human pathogen Ot, an obligate intracellular bacterium causing scrub typhus, encodes an unusually high copy number of a ~40 gene mobile genetic element that typically facilitates genetic transfer across microbes. This proliferated element is heavily degraded in Ot and previously assumed to be inactive. Here, we conducted a detailed analysis of this element in eight Ot strains and discovered two strains with at least one intact copy. This implies that the element is still capable of moving across Ot populations and suggests that the genome of this bacterium may be even more dynamic than previously appreciated. Our work raises questions about intracellular microbial evolution and sounds an alarm for gene-based efforts focused on diagnosing and combatting scrub typhus.},
}
@article {pmid37849012,
year = {2023},
author = {Wei, Y and Gong, Z and Han, GZ},
title = {Plants acquired mitochondrial linear plasmids horizontally from fungi likely during the conquest of land.},
journal = {Mobile DNA},
volume = {14},
number = {1},
pages = {15},
pmid = {37849012},
issn = {1759-8753},
support = {31922001//National Natural Science Foundation of China/ ; },
abstract = {Mitochondrial linear plasmids have been sporadically reported in fungi and plants. Yet, much remains obscure about the diversity, distribution, and evolution of mitochondrial linear plasmids. Here, through phylogenomic analyses across 7,163 cellular organisms (including 991 plants), we find that mitochondrial linear plasmids are widely present in land plants and fungi. Phylogenetic analyses indicate that plants are likely to have acquired mitochondrial linear plasmids horizontally from fungi before or during the conquest of terrestrial environments by plants. Gene content analyses show that mitochondrial linear plasmids harbor a highly dynamic and promiscuous repertoire of genes. Our study refines the understanding of the origin and evolution of mitochondrial linear plasmids.},
}
@article {pmid37848554,
year = {2023},
author = {Lücking, D and Mercier, C and Alarcón-Schumacher, T and Erdmann, S},
title = {Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {112},
pmid = {37848554},
issn = {2730-6151},
support = {Max Planck Research Group Archaeal Virology//Max-Planck-Gesellschaft (Max Planck Society)/ ; Max Planck Research Group Archaeal Virology//Max-Planck-Gesellschaft (Max Planck Society)/ ; Max Planck Research Group Archaeal Virology//Max-Planck-Gesellschaft (Max Planck Society)/ ; Max Planck Research Group Archaeal Virology//Max-Planck-Gesellschaft (Max Planck Society)/ ; },
abstract = {Environmental virus metagenomes, commonly referred to as "viromes", are typically generated by physically separating virus-like particles (VLPs) from the microbial fraction based on their size and mass. However, most methods used to purify VLPs, enrich extracellular vesicles (EVs) and gene transfer agents (GTAs) simultaneously. Consequently, the sequence space traditionally referred to as a "virome" contains host-associated sequences, transported via EVs or GTAs. We therefore propose to call the genetic material isolated from size-fractionated (0.22 µm) and DNase-treated samples protected environmental DNA (peDNA). This sequence space contains viral genomes, DNA transduced by viruses and DNA transported in EVs and GTAs. Since there is no genetic signature for peDNA transported in EVs, GTAs and virus particles, we rely on the successful removal of contaminating remaining cellular and free DNA when analyzing peDNA. Using marine samples collected from the North Sea, we generated a thoroughly purified peDNA dataset and developed a bioinformatic pipeline to determine the potential origin of the purified DNA. This pipeline was applied to our dataset as well as existing global marine "viromes". Through this pipeline, we identified known GTA and EV producers, as well as organisms with actively transducing proviruses as the source of the peDNA, thus confirming the reliability of our approach. Additionally, we identified novel and widespread EV producers, and found quantitative evidence suggesting that EV-mediated gene transfer plays a significant role in driving horizontal gene transfer (HGT) in the world's oceans.},
}
@article {pmid37845226,
year = {2023},
author = {Gonzalez-Serrano, R and Rosselli, R and Roda-Garcia, JJ and Martin-Cuadrado, AB and Rodriguez-Valera, F and Dunne, M},
title = {Distantly related Alteromonas bacteriophages share tail fibers exhibiting properties of transient chaperone caps.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {6517},
pmid = {37845226},
issn = {2041-1723},
mesh = {Humans ; *Bacteriophages/metabolism ; *Alteromonas/genetics/metabolism ; Molecular Chaperones/genetics/metabolism ; Carrier Proteins/metabolism ; Genome, Viral ; },
abstract = {The host recognition modules encoding the injection machinery and receptor binding proteins (RBPs) of bacteriophages are predisposed to mutation and recombination to maintain infectivity towards co-evolving bacterial hosts. In this study, we reveal how Alteromonas mediterranea schitovirus A5 shares its host recognition module, including tail fiber and cognate chaperone, with phages from distantly related families including Alteromonas myovirus V22. While the V22 chaperone is essential for producing active tail fibers, here we demonstrate production of functional A5 tail fibers regardless of chaperone co-expression. AlphaFold-generated models of tail fiber and chaperone pairs from phages A5, V22, and other Alteromonas phages reveal how amino acid insertions within both A5-like proteins results in a knob domain duplication in the tail fiber and a chaperone β-hairpin "tentacle" extension. These structural modifications are linked to differences in chaperone dependency between the A5 and V22 tail fibers. Structural similarity between the chaperones and intramolecular chaperone domains of other phage RBPs suggests an additional function of these chaperones as transient fiber "caps". Finally, our identification of homologous host recognition modules from morphologically distinct phages implies that horizontal gene transfer and recombination events between unrelated phages may be a more common process than previously thought among Caudoviricetes phages.},
}
@article {pmid37843655,
year = {2023},
author = {Sudhakari, PA and Ramisetty, BCM},
title = {An Eco-evolutionary Model on Surviving Lysogeny Through Grounding and Accumulation of Prophages.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {3068-3081},
pmid = {37843655},
issn = {1432-184X},
mesh = {Humans ; Lysogeny ; Prophages/genetics ; Escherichia coli/genetics ; *Superinfection/genetics ; Wastewater ; *Bacteriophages/genetics ; Genome, Bacterial ; },
abstract = {Temperate phages integrate into the bacterial genomes propagating along with the bacterial genomes. Multiple phage elements, representing diverse prophages, are present in most bacterial genomes. The evolutionary events and the ecological dynamics underlying the accumulation of prophage elements in bacterial genomes have yet to be understood. Here, we show that the local wastewater had 7% of lysogens (hosting mitomycin C-inducible prophages), and they showed resistance to superinfection by their corresponding lysates. Genomic analysis of four lysogens and four non-lysogens revealed the presence of multiple prophages (belonging to Myoviridae and Siphoviridae) in both lysogens and non-lysogens. For large-scale comparison, 2180 Escherichia coli genomes isolated from various sources across the globe and 523 genomes specifically isolated from diverse wastewaters were analyzed. A total of 15,279 prophages were predicted among 2180 E. coli genomes and 2802 prophages among 523 global wastewater isolates, with a mean of ~ 5 prophages per genome. These observations indicate that most putative prophages are relics of past bacteria-phage conflicts; they are "grounded" prophages that cannot excise from the bacterial genome. Prophage distribution analysis based on the sequence homology suggested the random distribution of E. coli prophages within and between E. coli clades. The independent occurrence pattern of these prophages indicates extensive horizontal transfers across the genomes. We modeled the eco-evolutionary dynamics to reconstruct the events that could have resulted in the prophage accumulation accounting for infection, superinfection immunity, and grounding. In bacteria-phage conflicts, the bacteria win by grounding the prophage, which could confer superinfection immunity.},
}
@article {pmid37842006,
year = {2023},
author = {López-Pérez, J and Otero, J and Sánchez-Osuna, M and Erill, I and Cortés, P and Llagostera, M},
title = {Impact of mutagenesis and lateral gene transfer processes in bacterial susceptibility to phage in food biocontrol and phage therapy.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1266685},
pmid = {37842006},
issn = {2235-2988},
mesh = {Animals ; *Bacteriophages/genetics ; *Salmonella Phages/genetics ; *Phage Therapy ; Chickens ; Gene Transfer, Horizontal ; Mutagenesis ; Bacteria ; },
abstract = {INTRODUCTION: The emergence of resistance and interference mechanisms to phage infection can hinder the success of bacteriophage-based applications, but the significance of these mechanisms in phage therapy has not been determined. This work studies the emergence of Salmonella isolates with reduced susceptibility to a cocktail of three phages under three scenarios: i) Salmonella cultures (LAB), ii) biocontrol of cooked ham slices as a model of food safety (FOOD), and iii) oral phage therapy in broilers (PT).<br><br>METHODS: S. Typhimurium ATCC 14028 RifR variants with reduced phage susceptibility were isolated from the three scenarios and conventional and molecular microbiology techniques were applied to study them.<br><br>RESULTS AND DISCUSSION: In LAB, 92% of Salmonella isolates lost susceptibility to all three phages 24 h after phage infection. This percentage was lower in FOOD, with 4.3% of isolates not susceptible to at least two of the three phages after seven days at 4&#xb0;C following phage treatment. In PT, 9.7% and 3.3 % of isolates from untreated and treated broilers, respectively, displayed some mechanism of interference with the life cycle of some of the phages. In LAB and FOOD scenarios, resistant variants carrying mutations in rfc and rfaJ genes involved in lipopolysaccharide synthesis (phage receptor) were identified. However, in PT, the significant decrease of EOP, ECOI, and burst size observed in isolates was prompted by lateral gene transfer of large IncI1 plasmids, which may encode phage defense mechanisms. These data indicate that the acquisition of specific conjugative plasmids has a stronger impact than mutagenesis on the emergence of reduced phage-susceptibility bacteria in certain environments. In spite of this, neither mechanism seems to significantly impair the success of Salmonella biocontrol and oral phage therapy.},
}
@article {pmid37841331,
year = {2023},
author = {Asif, M and Li-Qun, Z and Zeng, Q and Atiq, M and Ahmad, K and Tariq, A and Al-Ansari, N and Blom, J and Fenske, L and Alodaini, HA and Hatamleh, AA},
title = {Comprehensive genomic analysis of Bacillus paralicheniformis strain BP9, pan-genomic and genetic basis of biocontrol mechanism.},
journal = {Computational and structural biotechnology journal},
volume = {21},
number = {},
pages = {4647-4662},
pmid = {37841331},
issn = {2001-0370},
abstract = {Many Bacillus species are essential antibacterial agents, but their antibiosis potential still needs to be elucidated to its full extent. Here, we isolated a soil bacterium, BP9, which has significant antibiosis activity against fungal and bacterial pathogens. BP9 improved the growth of wheat seedlings via active colonization and demonstrated effective biofilm and swarming activity. BP9 sequenced genome contains 4282 genes with a mean G-C content of 45.94% of the whole genome. A single copy concatenated 802 core genes of 28 genomes, and their calculated average nucleotide identity (ANI) discriminated the strain BP9 from Bacillus licheniformis and classified it as Bacillus paralicheniformis. Furthermore, a comparative pan-genome analysis of 40 B. paralicheniformis strains suggested that the genetic repertoire of BP9 belongs to open-type genome species. A comparative analysis of a pan-genome dataset using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cluster of Orthologous Gene groups (COG) revealed the diversity of secondary metabolic pathways, where BP9 distinguishes itself by exhibiting a greater prevalence of loci associated with the metabolism and transportation of organic and inorganic substances, carbohydrate and amino acid for effective inhabitation in diverse environments. The primary secondary metabolites and their genes involved in synthesizing bacillibactin, fencing, bacitracin, and lantibiotics were identified as acquired through a recent Horizontal gene transfer (HGT) event, which contributes to a significant part of the strain`s antimicrobial potential. Finally, we report some genes essential for plant-host interaction identified in BP9, which reduce spore germination and virulence of multiple fungal and bacterial species. The effective colonization, diverse predicted metabolic pathways and secondary metabolites (antibiotics) suggest testing the suitability of strain BP9 as a potential bio-preparation in agricultural fields.},
}
@article {pmid37840734,
year = {2023},
author = {Li, Y and Fan, Y and Ma, X and Wang, Y and Liu, J},
title = {Metagenomic survey reveals global distribution and evolution of microbial sialic acid catabolism.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1267152},
pmid = {37840734},
issn = {1664-302X},
abstract = {Sialic acids comprise a varied group of nine-carbon amino sugars found mostly in humans and other higher metazoans, playing major roles in cell interactions with external environments as well as other cells. Microbial sialic acid catabolism (SAC) has long been considered a virulence determinant, and appears to be mainly the purview of pathogenic and commensal bacterial species associated with eukaryotic hosts. Here, we used 2,521 (pre-)assembled metagenomes to evaluate the distribution of SAC in microbial communities from diverse ecosystems and human body parts. Our results demonstrated that microorganisms possessing SAC globally existed in non-host associated environments, although much less frequently than in mammal hosts. We also showed that the ecological significance and taxonomic diversity of microbial SAC have so far been largely underestimated. Phylogenetic analysis revealed a strong signal of horizontal gene transfer among distinct taxa and habitats, and also suggested a specific ecological pressure and a relatively independent evolution history in environmental communities. Our study expanded the known diversity of microbial SAC, and has provided the backbone for further studies on its ecological roles and potential pathogenesis.},
}
@article {pmid37838320,
year = {2023},
author = {Wang, L and Hu, T and Li, Y and Zhao, Z and Zhu, M},
title = {Unraveling the interplay between antibiotic resistance genes and microbial communities in water and sediments of the intensive tidal flat aquaculture.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {339},
number = {},
pages = {122734},
doi = {10.1016/j.envpol.2023.122734},
pmid = {37838320},
issn = {1873-6424},
mesh = {*Anti-Bacterial Agents/pharmacology ; Water ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Aquaculture ; *Microbiota ; China ; },
abstract = {Tidal flats are formed valuably resources by the interaction of terrestrial and marine processes. Aquaculture on tidal flats has brought significant economic profits, but the over usage of antibiotics has resulted in the prevalence antibiotic resistance genes (ARGs) which pose serious threats to ecosystems. However, ARG abundances and bacterial community assemblies in the overlying water and sediments of tidal flat aquaculture areas have not been fully explored. Thus, antibiotic concentrations, ARG abundances, microbial communities and the influences of environmental factors in the Jiangsu tidal flat aquaculture ponds were investigated using high-throughput sequencing and qPCR. The concentrations of antibiotics at sampling ranged from not detectable to 2322.4 ng g[-1], and sulfamethazine and ciprofloxacin were the dominant antibiotics. The sul1 and sul2 abundances were highest and the ARG abundances were higher in sediment than in water. Meanwhile, bacterial community diversities and structures were significantly different (P < 0.05) between water and sediment samples. Network analysis identified Sphingomonadacear, Pseudomonas, and Xanthobacteraceae as potential ARG-carrying pathogens. A positive correlation between ARGs and intI1 indicated that horizontal gene transfer occurred in water, while antibiotics and TN significantly influenced ARG abundances in sediment. Neutral modeling showed that deterministic and stochastic processes contributed most to the bacterial community assemblies of water and sediment samples, respectively. This study comprehensively illustrates the prevalence of ARGs in intensive tidal flat aquaculture regions and provides an effective foundation for the management of antibiotics usage.},
}
@article {pmid37833945,
year = {2023},
author = {Kuznetsova, MV and Pospelova, JS and Maslennikova, IL and Starčič Erjavec, M},
title = {Dual-Species Biofilms: Biomass, Viable Cell Ratio/Cross-Species Interactions, Conjugative Transfer.},
journal = {International journal of molecular sciences},
volume = {24},
number = {19},
pages = {},
pmid = {37833945},
issn = {1422-0067},
support = {No. 19-44-590014 r_a.//Goverment of Perm Krai/ ; AAAA-A19-119112290009-1//Russian Foundation for Basic Research/ ; },
mesh = {*Escherichia coli/genetics ; Biomass ; *Biofilms ; Plasmids/genetics ; Cell Communication ; },
abstract = {Biofilms as a form of adaptation are beneficial for bacterial survival and may be hot spots for horizontal gene transfer, including conjugation. The aim of this research was to characterize the biofilm biomass, viable cell ratios and conjugative transfer of the pOX38 plasmid, an F-plasmid derivative, from the Escherichia coli N4i pOX38 strain (donor) into a uropathogenic E. coli DL82 strain (recipient) within dual-species biofilms with one of the following opportunistic pathogenic bacteria: Klebsiella pneumoniae, Enterococcus faecalis or Pseudomonas aeruginosa. Dual-species biofilms of E. coli with K. pneumoniae or P. aeruginosa but not E. faecalis were more massive and possessed more exopolysaccharide matrix compared to single-species biofilms of donor and recipient cells. Correlation between biofilm biomass and exopolysaccharide matrix was rs = 0.888 in dual-species biofilms. In dual-species biofilm with E. faecalis the proportion of E. coli was the highest, while in the biofilm with P. aeruginosa and K. pneumoniae, the E. coli was less abundant. The conjugative frequencies of plasmid transfer in dual-species biofilms of E. coli with E. faecalis and P. aeruginosa were reduced. A decrease in conjugative frequency was also observed when cell-free supernatants (CFSs) of E. faecalis and P. aeruginosa were added to the E. coli conjugation mixture. Further, the activity of the autoinducer AI-2 in the CFSs of the E. coli conjugation mixture was reduced when bacteria or CFSs of E. faecalis and P. aeruginosa were added to the E. coli conjugation mixture. Hence, the intercellular and interspecies interactions in dual-species biofilms depend on the partners involved.},
}
@article {pmid37832298,
year = {2023},
author = {Chu, K and Liu, Y and Hua, Z and Lu, Y and Ye, F},
title = {Spatio-temporal distribution and dynamics of antibiotic resistance genes in a water-diversion lake, China.},
journal = {Journal of environmental management},
volume = {348},
number = {},
pages = {119232},
doi = {10.1016/j.jenvman.2023.119232},
pmid = {37832298},
issn = {1095-8630},
mesh = {*Genes, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Water ; Drug Resistance, Microbial/genetics ; China ; },
abstract = {The distribution and dynamics of antibiotic resistance genes (ARGs) in water-diversion lakes are poorly understood. In this study, two comparative in situ investigations of ARG profiles targeting water diversion (DP) and non-diversion periods (NDP) were conducted in Luoma Lake, a vital transfer node for the eastern route of the South-to-North Water Diversion Project in China. The results demonstrated significant spatiotemporal variations in ARG contamination and notable differences in the co-occurrence patterns of ARGs and bacterial communities between DP and NDP. Correlations among ARGs with the 16 S rRNA, and mobile genetic elements indicate that horizontal gene transfer (HGT) and vertical gene transfer (VGT) in NDP, but only HGT in DP, were the primary mechanisms of ARG proliferation and spread, implying that water diversion could be an essential control of the transfer pattern of ARGs in a lake environment. The null model analysis indicated that stochastic processes, with predominant driver of ecological drift in the lake mainly drove the assembly of ARGs. Partial least squares structural equation modeling was developed to analyze the causal effects of the factors in shaping ARG dynamics and identify the major driving forces in the DP and NDP.},
}
@article {pmid37832249,
year = {2023},
author = {Wang, C and Yang, H and Liu, H and Zhang, XX and Ma, L},
title = {Anthropogenic contributions to antibiotic resistance gene pollution in household drinking water revealed by machine-learning-based source-tracking.},
journal = {Water research},
volume = {246},
number = {},
pages = {120682},
doi = {10.1016/j.watres.2023.120682},
pmid = {37832249},
issn = {1879-2448},
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Drinking Water ; Drug Resistance, Microbial/genetics ; Machine Learning ; },
abstract = {Although the presence of antibiotic resistance genes (ARGs) in drinking water and their potential horizontal gene transfer to pathogenic microbes are known to pose a threat to human health, their pollution levels and potential anthropogenic sources are poorly understood. In this study, broad-spectrum ARG profiling combined with machine-learning-based source classification SourceTracker was performed to investigate the pollution sources of ARGs in household drinking water collected from 95 households in 47 cities of eight countries/regions. In total, 451 ARG subtypes belonging to 19 ARG types were detected with total abundance in individual samples ranging from 1.4 × 10[-4] to 1.5 × 10° copies per cell. Source tracking analysis revealed that many ARGs were highly contributed by anthropogenic sources (37.1%), mainly wastewater treatment plants. The regions with the highest detected ARG contribution from wastewater (∼84.3%) used recycled water as drinking water, indicating the need for better ARG control strategies to ensure safe water quality in these regions. Among ARG types, sulfonamide, rifamycin and tetracycline resistance genes were mostly anthropogenic in origin. The contributions of anthropogenic sources to the 20 core ARGs detected in all of the studied countries/regions varied from 36.6% to 84.1%. Moreover, the anthropogenic contribution of 17 potential mobile ARGs identified in drinking water was significantly higher than other ARGs, and metagenomic assembly revealed that these mobile ARGs were carried by diverse potential pathogens. These results indicate that human activities have exacerbated the constant input and transmission of ARGs in drinking water. Our further risk classification framework revealed three ARGs (sul1, sul2 and aadA) that pose the highest risk to public health given their high prevalence, anthropogenic sources and mobility, facilitating accurate monitoring and control of anthropogenic pollution in drinking water.},
}
@article {pmid37831481,
year = {2023},
author = {Morgene, F and Rizoug Zeghlache, C and Feng, SY and Hauck, Y and Mirouze, N},
title = {Natural transformation and cell division delay in competent Staphylococcus aureus.},
journal = {Microbiology spectrum},
volume = {11},
number = {6},
pages = {e0280723},
pmid = {37831481},
issn = {2165-0497},
support = {ANR-18-CE35-0004//Agence Nationale de la Recherche (ANR)/ ; //China Scholarship Council (CSC)/ ; },
mesh = {Humans ; *Staphylococcus aureus/genetics/metabolism ; *Gene Transfer, Horizontal ; Bacteria/metabolism ; Bacterial Proteins/genetics/metabolism ; Cell Division ; },
abstract = {Natural transformation, considered one of the three main mechanisms leading to horizontal gene transfer in bacteria, is able to promote genomic plasticity and foster antibiotic resistance spreading. Conserved machinery and actors required to perform natural transformation have been shown to accumulate at different cellular localizations depending on the model organism considered. Here, we show in the human pathogen Staphylococcus aureus that DNA binding, uptake, and recombination are spatially and temporally coordinated to ensure S. aureus natural transformation. We also reveal that localization of natural transformation proteins occurs in the vicinity of the division septum allowing S. aureus competent cells to block cell division to ensure the success of natural transformation before the final constriction of the cytokinetic ring.},
}
@article {pmid37828802,
year = {2024},
author = {Zhao, J and Feng, T and An, X and Chen, X and Han, N and Wang, J and Chang, G and Hou, X},
title = {Livestock grazing is associated with the gut microbiota and antibiotic resistance genes in sympatric plateau pika (Ochotona curzoniae).},
journal = {Integrative zoology},
volume = {19},
number = {4},
pages = {646-661},
doi = {10.1111/1749-4877.12778},
pmid = {37828802},
issn = {1749-4877},
support = {2019QZKK0501//Second Tibetan Plateau Scientific Expedition&#xa0;and Research Program (STEP)/ ; 32172436//National Natural Science Foundation of&#xa0;China/ ; 2022K-16//Science and Technology Program of Shaanxi Academy&#xa0;of Science/ ; 2019QZKK0501//Scond Tibetan Plateau Scientific Expedition and Research/ ; 32172436//National Natural Science Foundation of China/ ; 2022K-16//Science and Technology Program of Shaanxi Academy of Science/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Lagomorpha/genetics ; *Drug Resistance, Microbial/genetics ; Herbivory ; Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Livestock/microbiology ; Genes, Bacterial ; },
abstract = {With the overuse of antibiotics in health care and animal husbandry, antibiotic resistance becomes a serious threat to public health. Antibiotic residues from veterinary medicine have increased the dissemination of antibiotic resistance genes (ARGs) by horizontal gene transfer globally, leading to the enrichment of ARGs in wildlife. Plateau pika (Ochotona curzoniae) is a small herbivore endemic to the Qinghai-Tibetan Plateau. Previous studies reveal that pika evolves a coprophagy behavior toward cohabitated yak, which makes the pika population a potential reservoir of ARGs. Yet, little is known about the resistome of pika under different grazing intensities. Here, we sampled the cecum content of pika from three different grazing intensity areas in the Qinghai-Tibetan Plateau to evaluate the effect of grazing on its gut microbiota and resistome. By using the 16S full-length amplicon and metagenomic sequencing, our study revealed that livestock grazing significantly altered the gut microbial community of plateau pika as compared to prohibited grazing areas. We found bacterial lineage Prevotellaceae, Lachnospirales, and RF39 increased in grazing areas. Analysis of the resistome revealed that pika from continuous grazing areas enriched a higher abundance of colistin (MCR) and streptogramin (vat) resistance genes. Moreover, we observed significant correlations between the gut microbial community, ARGs, and mobile genetic element profiles, hinting that pika gut microbiota was an important shaping force of the resistome. In future studies, the continuous monitoring of wildlife gut resistome and environmental antibiotic residues is imperative for a better understanding and for tackling the horizontal gene transfer of ARGs across the wildlife-livestock interface.},
}
@article {pmid37820728,
year = {2023},
author = {Weiss, A and Wang, T and You, L},
title = {Promotion of plasmid maintenance by heterogeneous partitioning of microbial communities.},
journal = {Cell systems},
volume = {14},
number = {10},
pages = {895-905.e5},
pmid = {37820728},
issn = {2405-4720},
support = {R01 AI125604/AI/NIAID NIH HHS/United States ; R01 EB031869/EB/NIBIB NIH HHS/United States ; R01 GM098642/GM/NIGMS NIH HHS/United States ; },
mesh = {Plasmids/genetics ; *Microbiota/genetics ; Escherichia coli/genetics ; },
abstract = {Transferable plasmids play a critical role in shaping the functions of microbial communities. Previous studies suggested multiple mechanisms underlying plasmid persistence and abundance. Here, we focus on the interplay between heterogeneous community partitioning and plasmid fates. Natural microbiomes often experience partitioning that creates heterogeneous local communities with reduced population sizes and biodiversity. Little is known about how population partitioning affects the plasmid fate through the modulation of community structure. By modeling and experiments, we show that heterogeneous community partitioning can paradoxically promote the persistence of a plasmid that would otherwise not persist in a global community. Among the local communities created by partitioning, a minority will primarily consist of members able to transfer the plasmid fast enough to support its maintenance by serving as a local plasmid haven. Our results provide insights into plasmid maintenance and suggest a generalizable approach to modulate plasmid persistence for engineering and medical applications.},
}
@article {pmid37819078,
year = {2023},
author = {Svet, L and Parijs, I and Isphording, S and Lories, B and Marchal, K and Steenackers, HP},
title = {Competitive interactions facilitate resistance development against antimicrobials.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {10},
pages = {e0115523},
pmid = {37819078},
issn = {1098-5336},
mesh = {*Anti-Infective Agents/pharmacology ; Biofilms ; Bacteria/genetics ; Phenotype ; Sulfathiazoles/pharmacology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {While the evolution of antimicrobial resistance is well studied in free-living bacteria, information on resistance development in dense and diverse biofilm communities is largely lacking. Therefore, we explored how the social interactions in a duo-species biofilm composed of the brewery isolates Pseudomonas rhodesiae and Raoultella terrigena influence the adaptation to the broad-spectrum antimicrobial sulfathiazole. Previously, we showed that the competition between these brewery isolates enhances the antimicrobial tolerance of P. rhodesiae. Here, we found that this enhanced tolerance in duo-species biofilms is associated with a strongly increased antimicrobial resistance development in P. rhodesiae. Whereas P. rhodesiae was not able to evolve resistance against sulfathiazole in monospecies conditions, it rapidly evolved resistance in the majority of the duo-species communities. Although the initial presence of R. terrigena was thus required for P. rhodesiae to acquire resistance, the resistance mechanisms did not depend on the presence of R. terrigena. Whole genome sequencing of resistant P. rhodesiae clones showed no clear mutational hot spots. This indicates that the acquired resistance phenotype depends on complex interactions between low-frequency mutations in the genetic background of the strains. We hypothesize that the increased tolerance in duo-species conditions promotes resistance by enhancing the selection of partially resistant mutants and opening up novel evolutionary trajectories that enable such genetic interactions. This hypothesis is reinforced by experimentally excluding potential effects of increased initial population size, enhanced mutation rate, and horizontal gene transfer. Altogether, our observations suggest that the community mode of life and the social interactions therein strongly affect the accessible evolutionary pathways toward antimicrobial resistance.IMPORTANCEAntimicrobial resistance is one of the most studied bacterial properties due to its enormous clinical and industrial relevance; however, most research focuses on resistance development of a single species in isolation. In the present study, we showed that resistance evolution of brewery isolates can differ greatly between single- and mixed-species conditions. Specifically, we observed that the development of antimicrobial resistance in certain species can be significantly enhanced in co-culture as compared to the single-species conditions. Overall, the current study emphasizes the need of considering the within bacterial interactions in microbial communities when evaluating antimicrobial treatments and resistance evolution.},
}
@article {pmid37814055,
year = {2023},
author = {Wang, Y and Gai, J and Hou, Q and Zhao, H and Shan, C and Guo, Z},
title = {Ultra-high-depth macrogenomic sequencing revealed differences in microbial composition and function between high temperature and medium-high temperature Daqu.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {39},
number = {12},
pages = {337},
pmid = {37814055},
issn = {1573-0972},
support = {2023//Science and technology plan project of Xinjiang Production and Construction Corps/ ; 2023//Science and technology plan project of Xinjiang Production and Construction Corps/ ; 2020kypytd009//Hubei university of arts and science cultivation fund for teachers' scientific research ability: technological innovation team/ ; },
mesh = {*Alcoholic Beverages/microbiology ; Temperature ; Bacteria/genetics ; *Microbiota ; Fermentation ; },
abstract = {Complex microorganisms in Daqu of different temperatures play a vital role in the taste, flavor and quality of Baijiu during fermentation. However, understanding the functional diversity of the whole microbial community between the Daqus of two different temperatures (high temperature Daqu, HD and medium-high temperature Daqu, MD) remains a major challenge. Here, a systematic study of the microbial diversity, functions as well as physiological and biochemical indexes of Daqu are described. The results revealed that the Daqu exhibited unique characteristics. In particular, the diversity of microorganisms in HD and MD was high, with 44 species including 14 novel species (Sphingomonas sp. is the main novel species) detected in all samples. Their profiles of carbohydrate-active enzymes and specific functional components supported the fact that these species were involved in flavor formation. The Daqu microbiome consisted of a high proportion of phage, providing evidence of phage infection/genome integration and horizontal gene transfer from phage to bacteria. Such processes would also regulate Daqu microbiomes and thus flavor quality. These results enrich current knowledge of Daqu and can be used to promote the development of Baijiu fermentation technology.},
}
@article {pmid37808307,
year = {2023},
author = {Sharma, A and Singh, RN and Song, XP and Singh, RK and Guo, DJ and Singh, P and Verma, KK and Li, YR},
title = {Genome analysis of a halophilic Virgibacillus halodenitrificans ASH15 revealed salt adaptation, plant growth promotion, and isoprenoid biosynthetic machinery.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1229955},
pmid = {37808307},
issn = {1664-302X},
abstract = {Globally, due to widespread dispersion, intraspecific diversity, and crucial ecological components of halophilic ecosystems, halophilic bacteria is considered one of the key models for ecological, adaptative, and biotechnological applications research in saline environments. With this aim, the present study was to enlighten the plant growth-promoting features and investigate the systematic genome of a halophilic bacteria, Virgibacillus halodenitrificans ASH15, through single-molecule real-time (SMRT) sequencing technology. Results showed that strain ASH15 could survive in high salinity up to 25% (w/v) NaCl concentration and express plant growth-promoting traits such as nitrogen fixation, plant growth hormones, and hydrolytic enzymes, which sustain salt stress. The results of pot experiment revealed that strain ASH15 significantly enhanced sugarcane plant growth (root shoot length and weight) under salt stress conditions. Moreover, the sequencing analysis of the strain ASH15 genome exhibited that this strain contained a circular chromosome of 3,832,903 bp with an average G+C content of 37.54%: 3721 predicted protein-coding sequences (CDSs), 24 rRNA genes, and 62 tRNA genes. Genome analysis revealed that the genes related to the synthesis and transport of compatible solutes (glycine, betaine, ectoine, hydroxyectoine, and glutamate) confirm salt stress as well as heavy metal resistance. Furthermore, functional annotation showed that the strain ASH15 encodes genes for root colonization, biofilm formation, phytohormone IAA production, nitrogen fixation, phosphate metabolism, and siderophore production, which are beneficial for plant growth promotion. Strain ASH15 also has a gene resistance to antibiotics and pathogens. In addition, analysis also revealed that the genome strain ASH15 has insertion sequences and CRISPRs, which suggest its ability to acquire new genes through horizontal gene transfer and acquire immunity to the attack of viruses. This work provides knowledge of the mechanism through which V. halodenitrificans ASH15 tolerates salt stress. Deep genome analysis, identified MVA pathway involved in biosynthesis of isoprenoids, more precisely "Squalene." Squalene has various applications, such as an antioxidant, anti-cancer agent, anti-aging agent, hemopreventive agent, anti-bacterial agent, adjuvant for vaccines and drug carriers, and detoxifier. Our findings indicated that strain ASH15 has enormous potential in industries such as in agriculture, pharmaceuticals, cosmetics, and food.},
}
@article {pmid37806594,
year = {2024},
author = {Li, N and Zheng, N and Pan, J and An, Q and Li, X and Sun, S and Chen, C and Zhu, H and Li, Z and Ji, Y},
title = {Distribution and major driving elements of antibiotic resistance genes in the soil-vegetable system under microplastic stress.},
journal = {The Science of the total environment},
volume = {906},
number = {},
pages = {167619},
doi = {10.1016/j.scitotenv.2023.167619},
pmid = {37806594},
issn = {1879-1026},
mesh = {*Vegetables ; *Microplastics ; Genes, Bacterial ; Soil ; Plastics ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Lactuca ; Polyethylenes ; },
abstract = {Microplastics (MPs) and antibiotic resistance genes (ARGs) are both enriched in soil-vegetable systems as a consequence of the prolonged use of agricultural mulches. MPs can form unique bacterial communities and provide potential hosts for ARGs. Therefore, MPs stress may promote the spread of ARGs from soil to crops. Increasing ARGs pollution in soil-vegetable system. In our research, we investigated the distribution and major driving elements of antibiotic resistance genes in the soil-vegetable system under microplastic stress. The results showed that MPs treatment decreased the relative abundance of ARGs in non-rhizosphere soil. High concentrations of MPs promoted the enrichment of tetracycline antibiotic resistance genes in rhizosphere soil. MPs treatment promoted the enrichment of ARGs and mobile genetic elements (MGEs) in lettuce tissues, and the overall abundance of ARGs in root after 0.5 %, 1 %, and 2 % (w/w, dry weight) polyethylene (PE) administration was considerably higher compared to that in the untreated group (p < 0.05). At the same time, high PE concentrations promoted the spread of sulfa ARGs from root to leaf. MPs also impacted the bacterial communities in the soil-plant system, and the changes in ARGs as well as MGEs in each part of the soil-vegetable system were significantly correlated with the bacterial diversity index (p < 0.05). Correlation analysis and network analysis showed that bacterial communities and MGEs were the main drivers of ARGs variation in soil-lettuce systems.},
}
@article {pmid37805184,
year = {2023},
author = {Roh, H and Kannimuthu, D},
title = {Comparative resistome analysis of Aeromonas species in aquaculture reveals antibiotic resistance patterns and phylogeographic distribution.},
journal = {Environmental research},
volume = {239},
number = {Pt 2},
pages = {117273},
doi = {10.1016/j.envres.2023.117273},
pmid = {37805184},
issn = {1096-0953},
mesh = {*Aeromonas/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial ; Aquaculture ; North America ; Genes, Bacterial ; },
abstract = {The overuse of antibiotics in aquaculture drives the emergence of multi-drug-resistant bacteria, and antibiotic-resistant genes (ARGs) can be disseminated to other bacteria through vertical- and horizontal gene transfer (VGT and HGT) under selective pressure. Profiling the antibiotic resistome and understanding the global distribution of ARGs constitutes the first step in developing a control strategy. Hence, this study utilized extensive genomic data from hundreds of Aeromonas strains in aquaculture to profile resistome patterns and explores their association with isolation year, country, and species characteristics. Overall, ∼400 Aeromonas genomes were used to predict the ARGs from A. salmonicida, A. hydrophila, A. veronii, A. media, and A. sobria. ARGs such as sul1, tet(A), and tet(D), which display a similar proportion of positive strains among species, were subjected to phylodynamic and phylogeographic analyses. More than a hundred ARGs were identified, some of which exhibited either species-specific or non-species-specific patterns. A. salmonicida and A. media were found to have a higher proportion of species-specific ARGs than other strains, which might lead to more distinct patterns of ARG acquisition. Overall, ∼25% of strains have either sul1, tet(A), or tet(D) gene(s), but no significant difference was observed in the proportion of positive strains by species. Phylogeographic analysis revealed that the abundant numbers of sul1, tet(A), and/or tet(D) introduced in a few East Asian and North American countries could spread to both adjacent and faraway countries. In recent years, the proportions of these ARGs have dramatically increased, particularly in strains sourced from aquatic environments, suggesting control is required of the overuse of antibiotics in aquaculture. The findings of this research offer significant insights into the global dissemination of ARGs.},
}
@article {pmid37804807,
year = {2023},
author = {Xue, YM and Wang, YC and Lin, YT and Jiang, GY and Chen, R and Qin, RL and Jia, XQ and Wang, C},
title = {Engineering a Pseudomonas putida as living quorum quencher for biofilm formation inhibition, benzenes degradation, and environmental risk evaluation.},
journal = {Water research},
volume = {246},
number = {},
pages = {120690},
doi = {10.1016/j.watres.2023.120690},
pmid = {37804807},
issn = {1879-2448},
mesh = {*Sewage/microbiology ; *Pseudomonas putida/genetics ; Benzene ; Biofilms ; Quorum Sensing/physiology ; Bioreactors/microbiology ; },
abstract = {Bacterial communication interruption based on quorum quenching (QQ) has been proven its potential in biofilm formation inhibition and biofouling control. However, it would be more satisfying if QQ could be combined with the efficient degradation of contaminants in environmental engineering. In this study, we engineered a biofilm of Pseudomonas putida through introducing a QQ synthetic gene, which achieved both biofilm formation inhibition and efficient degradation of benzene series in wastewater. The aiiO gene introduced into the P. putida by heat shock method was highly expressed to produce QQ enzyme to degrade AHL-based signal molecules. The addition of this engineered P. putida reduced the AHLs concentration, quorum sensing gene expression, and connections of the microbial community network in activated sludge and therefore inhibited the biofilm formation. Meanwhile, the sodium benzoate degradation assay indicated an enhanced benzene series removal ability of the engineering bacteria on activated sludge. Besides, we also demonstrated a controllable environmental risk of this engineered bacteria through monitoring its abundance and horizontal gene transfer test. Overall, the results of this study suggest an alternative strategy to solve multiple environmental problems through genetic engineering means and provide support for the application of engineered bacteria in environmental biotechnology.},
}
@article {pmid37804524,
year = {2023},
author = {Wang, YZ and Ye, YX and Lu, JB and Wang, X and Lu, HB and Zhang, ZL and Ye, ZX and Lu, YW and Sun, ZT and Chen, JP and Li, JM and Zhang, CX and Huang, HJ},
title = {Horizontally Transferred Salivary Protein Promotes Insect Feeding by Suppressing Ferredoxin-Mediated Plant Defenses.},
journal = {Molecular biology and evolution},
volume = {40},
number = {10},
pages = {},
pmid = {37804524},
issn = {1537-1719},
mesh = {Animals ; Ferredoxins/metabolism ; Plants/metabolism ; *Hemiptera/genetics ; Nicotiana/genetics/metabolism ; *Aphids/metabolism ; Salivary Proteins and Peptides/genetics ; },
abstract = {Herbivorous insects such as whiteflies, planthoppers, and aphids secrete abundant orphan proteins to facilitate feeding. Yet, how these genes are recruited and evolve to mediate plant-insect interaction remains unknown. In this study, we report a horizontal gene transfer (HGT) event from fungi to an ancestor of Aleyrodidae insects approximately 42 to 190 million years ago. BtFTSP1 is a salivary protein that is secreted into host plants during Bemisia tabaci feeding. It targets a defensive ferredoxin 1 in Nicotiana tabacum (NtFD1) and disrupts the NtFD1-NtFD1 interaction in plant cytosol, leading to the degradation of NtFD1 in a ubiquitin-dependent manner. Silencing BtFTSP1 has negative effects on B. tabaci feeding while overexpressing BtFTSP1 in N. tabacum benefits insects and rescues the adverse effect caused by NtFD1 overexpression. The association between BtFTSP1 and NtFD1 is newly evolved after HGT, with the homologous FTSP in its fungal donor failing to interact and destabilize NtFD1. Our study illustrates the important roles of horizontally transferred genes in plant-insect interactions and suggests the potential origin of orphan salivary genes.},
}
@article {pmid37803310,
year = {2023},
author = {Kawabe, Y and Du, Q and Narita, TB and Bell, C and Schilde, C and Kin, K and Schaap, P},
title = {Emerging roles for diguanylate cyclase during the evolution of soma in dictyostelia.},
journal = {BMC ecology and evolution},
volume = {23},
number = {1},
pages = {60},
pmid = {37803310},
issn = {2730-7182},
support = {/WT_/Wellcome Trust/United Kingdom ; 100293/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; BB/K000799/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Dictyostelium/genetics/metabolism ; Ammonia/metabolism ; Phosphorus-Oxygen Lyases/genetics/metabolism ; *Dictyosteliida/metabolism ; Oxygen/metabolism ; },
abstract = {BACKGROUND: Cyclic di-guanylate (c-di-GMP), synthesized by diguanylate cyclase, is a major second messenger in prokaryotes, where it triggers biofilm formation. The dictyostelid social amoebas acquired diguanylate cyclase (dgcA) by horizontal gene transfer. Dictyostelium discoideum (Ddis) in taxon group 4 uses c-di-GMP as a secreted signal to induce differentiation of stalk cells, the ancestral somatic cell type that supports the propagating spores. We here investigated how this role for c-di-GMP evolved in Dictyostelia by exploring dgcA function in the group 2 species Polysphondylium pallidum (Ppal) and in Polysphondylium violaceum (Pvio), which resides in a small sister clade to group 4.<br><br>RESULTS: Similar to Ddis, dgcA is upregulated after aggregation in Ppal and Pvio and predominantly expressed in the anterior region and stalks of emerging fruiting bodies. DgcA null mutants in Ppal and Pvio made fruiting bodies with very long and thin stalks and only few spores and showed delayed aggregation and larger aggregates, respectively. Ddis dgcA- cells cannot form stalks at all, but showed no aggregation defects. The long, thin stalks of Ppal and Pvio dgcA- mutants were also observed in acaA- mutants in these species. AcaA encodes adenylate cyclase A, which mediates the effects of c-di-GMP on stalk induction in Ddis. Other factors that promote stalk formation in Ddis are DIF-1, produced by the polyketide synthase StlB, low ammonia, facilitated by the ammonia transporter AmtC, and high oxygen, detected by the oxygen sensor PhyA (prolyl 4-hydroxylase). We deleted the single stlB, amtC and phyA genes in Pvio wild-type and dgcA- cells. Neither of these interventions affected stalk formation in Pvio wild-type and not or very mildly exacerbated the long thin stalk phenotype of Pvio dgcA- cells.<br><br>CONCLUSIONS: The study reveals a novel role for c-di-GMP in aggregation, while the reduced spore number in Pvio and Ppal dgcA- is likely an indirect effect, due to depletion of the cell pool by the extended stalk formation. The results indicate that in addition to c-di-GMP, Dictyostelia ancestrally used an as yet unknown factor for induction of stalk formation. The activation of AcaA by c-di-GMP is likely conserved throughout Dictyostelia.},
}
@article {pmid37801563,
year = {2023},
author = {Liu, L and Zhang, QH and Li, RT},
title = {In Situ and Individual-Based Analysis of the Influence of Polystyrene Microplastics on Escherichia coli Conjugative Gene Transfer at the Single-Cell Level.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {42},
pages = {15936-15944},
doi = {10.1021/acs.est.3c05476},
pmid = {37801563},
issn = {1520-5851},
mesh = {*Escherichia coli/genetics ; Plasmids ; *Microplastics ; Plastics ; Polystyrenes ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; },
abstract = {The impact of microplastic particles of micro- and nanometer sizes on microbial horizontal gene transfer (HGT) remains a controversial topic. Existing studies rely on traditional approaches, which analyze population behavior, leading to conflicting conclusions and a limited understanding. The present study addressed these limitations by employing a novel microfluidic chamber system for in situ visualization and precise quantification of the effects of different concentrations of polystyrene (PS) microbeads on microbial HGT at the single-cell level. The statistical analysis indicated no significant difference in the division times of both the donor and recipient bacteria across different PS microbead concentrations. However, as the concentration of PS microbeads increased from 0 to 2000 mg L[-1], the average conjugation frequency of Escherichia coli decreased from 0.028 ± 0.015 to 0.004 ± 0.003. Our observations from the microfluidic experiments revealed that 500 nm PS microbeads created a barrier effect on bacterial conjugative transfer. The presence of microbeads resulted in reduced contact and interaction between the donor and recipient strains, thereby causing a decrease in the conjugation transfer frequency. These findings were validated by an individual-based modeling framework parameterized by the data from the individual-level microfluidic experiments. Overall, this study offers a fresh perspective and strategy for investigating the risks associated with the dissemination of antibiotic resistance genes related to microplastics.},
}
@article {pmid37797823,
year = {2024},
author = {Lagune, M and Kremer, L and Herrmann, JL},
title = {Mycobacterium abscessus, a complex of three fast-growing subspecies sharing virulence traits with slow-growing mycobacteria.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {30},
number = {6},
pages = {726-731},
doi = {10.1016/j.cmi.2023.08.036},
pmid = {37797823},
issn = {1469-0691},
mesh = {*Mycobacterium abscessus/genetics/pathogenicity/classification ; Humans ; *Virulence Factors/genetics ; Virulence/genetics ; *Mycobacterium Infections, Nontuberculous/microbiology ; Animals ; Genome, Bacterial ; Cystic Fibrosis/microbiology ; },
abstract = {BACKGROUND: Mycobacterium abscessus belongs to the largest group of mycobacteria, the rapid-growing saprophytic mycobacteria, and is one of the most difficult-to-treat opportunistic pathogen. Several features pertain to the high adaptability of M. abscessus to the host. These include the capacity to survive and persist within amoebae, to transition from a smooth to a rough morphotype that occurs during the course of the disease and to express of a wide array of virulence factors.<br><br>OBJECTIVES: The main objective of this narrative review consists to report major assets of M.&#xa0;abscessus that contribute to the virulence of these rapid-growing saprophytic mycobacteria. Strikingly, many of these determinants, whether they are from a mycobacterial origin or acquired by horizontal gene transfer, are known virulence factors found in slow-growing and strict pathogens for humans and animals.<br><br>SOURCES: In the light of recent published work in the field we attempted to highlight major features characterizing M. abscessus pathogenicity and to explain why this led to the emergence of this mycobacterial species in patients with cystic fibrosis.<br><br>CONTENT: M. abscessus genome plasticity, the smooth-to-rough transition, and the expression of a panel of enzymes associated with virulence in other bacteria are key players in M.&#xa0;abscessus virulence. In addition, the very large repertoire of lipid transporters, known as mycobacterial membrane protein large and small (MmpL and MmpS respectively), deeply influences the pathogenicity of M. abscessus, as exemplified here for some of them.<br><br>IMPLICATIONS: All these traits largely contribute to make M. abscessus a unique mycobacterium regarding to its pathophysiological processes, ranging from the early colonization steps to the establishment of severe and chronic pulmonary diseases.},
}
@article {pmid37797771,
year = {2024},
author = {Liu, Q and Li, Y and Sun, Y and Xie, K and Zeng, Q and Hao, Y and Yang, Q and Pu, Y and Shi, S and Gong, Z},
title = {Deterioration of sludge characteristics and promotion of antibiotic resistance genes spread with the co-existing of polyvinylchloride microplastics and tetracycline in the sequencing batch reactor.},
journal = {The Science of the total environment},
volume = {906},
number = {},
pages = {167544},
doi = {10.1016/j.scitotenv.2023.167544},
pmid = {37797771},
issn = {1879-1026},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Sewage ; Wastewater ; Microplastics ; Plastics ; Genes, Bacterial ; Tetracycline/pharmacology ; Phenol ; Phenols ; Drug Resistance, Microbial/genetics ; },
abstract = {With the continuous increase in microplastics (MPs) and tetracycline (TC) entering wastewater treatment plants (WWTPs) along with sewage, the co-existence of MPs and TC in the biological treatment of wastewater has attracted extensive attention. This study investigated the effect of 1 mg/L polyvinyl chloride (PVC) MPs and 100 ng/L TC co-existing on sequencing batch reactors (SBRs) (S2) treating phenol wastewater in contrast to the control with TC alone (S1). The phenol removal efficiency was significantly inhibited by the co-existence of PVC MPs and TC. Sludge characteristics were also distinctively influenced. The decreased zone sludge velocity (ZSV) and increased sludge volume index (SVI) indicated that the combined effect of PVC MPs and TC deteriorated sludge settleability, which had positive and negative linear correlations with extracellular polymeric substances (EPS) content and the protein (PN)/polysaccharide (PS) ratio, respectively. Moreover, the decreased and increased relative abundances of potential phenol-degraders and antibiotic resistance gene (ARG) carriers may elucidate the inhibition of phenol removal and promotion of ARGs propagation with the co-occurrence of PVC MPs and TC. In addition, the enhanced potential ARGs hosts, loss of the EPS protective effect, and increased membrane permeability induced by reactive oxygen species (ROS) jointly promoted ARGs dissemination in the co-existence of PVC MPs and TC. Notably, the co-occurrence of ARGs and mobile genetic element (MGEs) indicated that the co-existence of PVC MPs and TC promoted the spread of some transposase-associated ARGs mediated by horizontal gene transfer (HGT).},
}
@article {pmid37796811,
year = {2023},
author = {Teixeira, M and Pillay, S and Urhan, A and Abeel, T},
title = {SHIP: identifying antimicrobial resistance gene transfer between plasmids.},
journal = {Bioinformatics (Oxford, England)},
volume = {39},
number = {10},
pages = {},
pmid = {37796811},
issn = {1367-4811},
mesh = {*Anti-Bacterial Agents/pharmacology ; Phylogeny ; *Drug Resistance, Bacterial/genetics ; Plasmids/genetics ; Escherichia coli/genetics ; Integrons/genetics ; Gene Transfer, Horizontal ; },
abstract = {MOTIVATION: Plasmids are carriers for antimicrobial resistance (AMR) genes and can exchange genetic material with other structures, contributing to the spread of AMR. There is no reliable approach to identify the transfer of AMR genes across plasmids. This is mainly due to the absence of a method to assess the phylogenetic distance of plasmids, as they show large DNA sequence variability. Identifying and quantifying such transfer can provide novel insight into the role of small mobile elements and resistant plasmid regions in the spread of AMR.<br><br>RESULTS: We developed SHIP, a novel method to quantify plasmid similarity based on the dynamics of plasmid evolution. This allowed us to find conserved fragments containing AMR genes in structurally different and phylogenetically distant plasmids, which is evidence for lateral transfer. Our results show that regions carrying AMR genes are highly mobilizable between plasmids through transposons, integrons, and recombination events, and contribute to the spread of AMR. Identified transferred fragments include a multi-resistant complex class 1 integron in Escherichia coli and Klebsiella pneumoniae, and a region encoding tetracycline resistance transferred through recombination in Enterococcus faecalis.<br><br>The code developed in this work is available at https://github.com/AbeelLab/plasmidHGT.},
}
@article {pmid37796250,
year = {2023},
author = {Jung, H and Lee, D and Lee, S and Kong, HJ and Park, J and Seo, YS},
title = {Comparative genomic analysis of Chryseobacterium species: deep insights into plant-growth-promoting and halotolerant capacities.},
journal = {Microbial genomics},
volume = {9},
number = {10},
pages = {},
pmid = {37796250},
issn = {2057-5858},
mesh = {*Chryseobacterium/genetics ; Phylogeny ; Comparative Genomic Hybridization ; Genomics ; Soil ; },
abstract = {Members of the genus Chryseobacterium have attracted great interest as beneficial bacteria that can promote plant growth and biocontrol. Given the recent risks of climate change, it is important to develop tolerance strategies for efficient applications of plant-beneficial bacteria in saline environments. However, the genetic determinants of plant-growth-promoting and halotolerance effects in Chryseobacterium have not yet been investigated at the genomic level. Here, a comparative genomic analysis was conducted with seven Chryseobacterium species. Phylogenetic and phylogenomic analyses revealed niche-specific evolutionary distances between soil and freshwater Chryseobacterium species, consistent with differences in genomic statistics, indicating that the freshwater bacteria have smaller genome sizes and fewer genes than the soil bacteria. Phosphorus- and zinc-cycling genes (required for nutrient acquisition in plants) were universally present in all species, whereas nitrification and sulphite reduction genes (required for nitrogen- and sulphur-cycling, respectively) were distributed only in soil bacteria. A pan-genome containing 6842 gene clusters was constructed, which reflected the general features of the core, accessory and unique genomes. Halotolerant species with an accessory genome shared a Kdp potassium transporter and biosynthetic pathways for branched-chain amino acids and the carotenoid lycopene, which are associated with countermeasures against salt stress. Protein-protein interaction network analysis was used to define the genetic determinants of Chryseobacterium salivictor NBC122 that reduce salt damage in bacteria and plants. Sixteen hub genes comprised the aromatic compound degradation and Por secretion systems, which are required to cope with complex stresses associated with saline environments. Horizontal gene transfer and CRISPR-Cas analyses indicated that C. salivictor NBC122 underwent more evolutionary events when interacting with different environments. These findings provide deep insights into genomic adaptation to dynamic interactions between plant-growth-promoting Chryseobacterium and salt stress.},
}
@article {pmid37793435,
year = {2023},
author = {Raimondeau, P and Bianconi, ME and Pereira, L and Parisod, C and Christin, PA and Dunning, LT},
title = {Lateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage.},
journal = {The New phytologist},
volume = {240},
number = {5},
pages = {2072-2084},
doi = {10.1111/nph.19272},
pmid = {37793435},
issn = {1469-8137},
support = {NE/T011025/1//Natural Environment Research Council/ ; NE/V000012/1//Natural Environment Research Council/ ; URF/R/180022//Royal Society/ ; },
mesh = {Humans ; Phylogeny ; *Poaceae/genetics ; *Gene Transfer, Horizontal ; Genome ; Evolution, Molecular ; },
abstract = {Lateral gene transfer (LGT) is the movement of DNA between organisms without sexual reproduction. The acquired genes represent genetic novelties that have independently evolved in the donor's genome. Phylogenetic methods have shown that LGT is widespread across the entire grass family, although we know little about the underlying dynamics. We identify laterally acquired genes in five de novo reference genomes from the same grass genus (four Alloteropsis semialata and one Alloteropsis angusta). Using additional resequencing data for a further 40 Alloteropsis individuals, we place the acquisition of each gene onto a phylogeny using stochastic character mapping, and then infer rates of gains and losses. We detect 168 laterally acquired genes in the five reference genomes (32-100 per genome). Exponential decay models indicate that the rate of LGT acquisitions (6-28 per Ma) and subsequent losses (11-24% per Ma) varied significantly among lineages. Laterally acquired genes were lost at a higher rate than vertically inherited loci (0.02-0.8% per Ma). This high turnover creates intraspecific gene content variation, with a preponderance of them occurring as accessory genes in the Alloteropsis pangenome. This rapid turnover generates standing variation that can ultimately fuel local adaptation.},
}
@article {pmid37792894,
year = {2023},
author = {Pompei, S and Bella, E and Weitz, JS and Grilli, J and Lagomarsino, MC},
title = {Metacommunity structure preserves genome diversity in the presence of gene-specific selective sweeps under moderate rates of horizontal gene transfer.},
journal = {PLoS computational biology},
volume = {19},
number = {10},
pages = {e1011532},
pmid = {37792894},
issn = {1553-7358},
mesh = {Humans ; *Gene Transfer, Horizontal/genetics ; *Bacteria/genetics ; Biological Evolution ; Genome ; },
abstract = {The horizontal transfer of genes is fundamental for the eco-evolutionary dynamics of microbial communities, such as oceanic plankton, soil, and the human microbiome. In the case of an acquired beneficial gene, classic population genetics would predict a genome-wide selective sweep, whereby the genome spreads clonally within the community and together with the beneficial gene, removing genome diversity. Instead, several sources of metagenomic data show the existence of "gene-specific sweeps", whereby a beneficial gene spreads across a bacterial community, maintaining genome diversity. Several hypotheses have been proposed to explain this process, including the decreasing gene flow between ecologically distant populations, frequency-dependent selection from linked deleterious allelles, and very high rates of horizontal gene transfer. Here, we propose an additional possible scenario grounded in eco-evolutionary principles. Specifically, we show by a mathematical model and simulations that a metacommunity where species can occupy multiple patches, acting together with a realistic (moderate) HGT rate, helps maintain genome diversity. Assuming a scenario of patches dominated by single species, our model predicts that diversity only decreases moderately upon the arrival of a new beneficial gene, and that losses in diversity can be quickly restored. We explore the generic behaviour of diversity as a function of three key parameters, frequency of insertion of new beneficial genes, migration rates and horizontal transfer rates.Our results provides a testable explanation for how diversity can be maintained by gene-specific sweeps even in the absence of high horizontal gene transfer rates.},
}
@article {pmid37791787,
year = {2023},
author = {Taton, A and Gilderman, TS and Ernst, DC and Omaga, CA and Cohen, LA and Rey-Bedon, C and Golden, JW and Golden, SS},
title = {Synechococcus elongatus Argonaute reduces natural transformation efficiency and provides immunity against exogenous plasmids.},
journal = {mBio},
volume = {14},
number = {5},
pages = {e0184323},
pmid = {37791787},
issn = {2150-7511},
support = {R01 GM118815/GM/NIGMS NIH HHS/United States ; R35 GM118290/GM/NIGMS NIH HHS/United States ; },
mesh = {*Synechococcus/genetics ; Plasmids/genetics ; *Circadian Clocks ; Genetic Engineering ; Bacterial Proteins/genetics ; },
abstract = {S. elongatus is an important cyanobacterial model organism for the study of its prokaryotic circadian clock, photosynthesis, and other biological processes. It is also widely used for genetic engineering to produce renewable biochemicals. Our findings reveal an SeAgo-based defense mechanism in S. elongatus against the horizontal transfer of genetic material. We demonstrate that deletion of the ago gene facilitates genetic studies and genetic engineering of S. elongatus.},
}
@article {pmid37788575,
year = {2023},
author = {Coluzzi, C and Guillemet, M and Mazzamurro, F and Touchon, M and Godfroid, M and Achaz, G and Glaser, P and Rocha, EPC},
title = {Chance Favors the Prepared Genomes: Horizontal Transfer Shapes the Emergence of Antibiotic Resistance Mutations in Core Genes.},
journal = {Molecular biology and evolution},
volume = {40},
number = {10},
pages = {},
pmid = {37788575},
issn = {1537-1719},
mesh = {Plasmids ; *Escherichia coli/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; *Quinolones/pharmacology ; Mutation ; Gene Transfer, Horizontal ; },
abstract = {Bacterial lineages acquire novel traits at diverse rates in part because the genetic background impacts the successful acquisition of novel genes by horizontal transfer. Yet, how horizontal transfer affects the subsequent evolution of core genes remains poorly understood. Here, we studied the evolution of resistance to quinolones in Escherichia coli accounting for population structure. We found 60 groups of genes whose gain or loss induced an increase in the probability of subsequently becoming resistant to quinolones by point mutations in the gyrase and topoisomerase genes. These groups include functions known to be associated with direct mitigation of the effect of quinolones, with metal uptake, cell growth inhibition, biofilm formation, and sugar metabolism. Many of them are encoded in phages or plasmids. Although some of the chronologies may reflect epidemiological trends, many of these groups encoded functions providing latent phenotypes of antibiotic low-level resistance, tolerance, or persistence under quinolone treatment. The mutations providing resistance were frequent and accumulated very quickly. Their emergence was found to increase the rate of acquisition of other antibiotic resistances setting the path for multidrug resistance. Hence, our findings show that horizontal gene transfer shapes the subsequent emergence of adaptive mutations in core genes. In turn, these mutations further affect the subsequent evolution of resistance by horizontal gene transfer. Given the substantial gene flow within bacterial genomes, interactions between horizontal transfer and point mutations in core genes may be a key to the success of adaptation processes.},
}
@article {pmid37786731,
year = {2023},
author = {Liao, J and Wei, X and Tao, K and Deng, G and Shu, J and Qiao, Q and Chen, G and Wei, Z and Fan, M and Saud, S and Fahad, S and Chen, S},
title = {Phenoloxidases: catechol oxidase - the temporary employer and laccase - the rising star of vascular plants.},
journal = {Horticulture research},
volume = {10},
number = {7},
pages = {uhad102},
pmid = {37786731},
issn = {2662-6810},
abstract = {Phenolics are vital for the adaptation of plants to terrestrial habitats and for species diversity. Phenoloxidases (catechol oxidases, COs, and laccases, LACs) are responsible for the oxidation and polymerization of phenolics. However, their origin, evolution, and differential roles during plant development and land colonization are unclear. We performed the phylogeny, domain, amino acids, compositional biases, and intron analyses to clarify the origin and evolution of COs and LACs, and analysed the structure, selective pressure, and chloroplast targeting to understand the species-dependent distribution of COs. We found that Streptophyta COs were not homologous to the Chlorophyta tyrosinases (TYRs), and might have been acquired by horizontal gene transfer from bacteria. COs expanded in bryophytes. Structural-functionality and selective pressure were partially responsible for the species-dependent retention of COs in embryophytes. LACs emerged in Zygnemaphyceae, having evolved from ascorbate oxidases (AAOs), and prevailed in the vascular plants and strongly expanded in seed plants. COs and LACs coevolved with the phenolic metabolism pathway genes. These results suggested that TYRs and AAOs were the first-stage phenoloxidases in Chlorophyta. COs might be the second key for the early land colonization. LACs were the third one (dominating in the vascular plants) and might be advantageous for diversified phenol substrates and the erect growth of plants. This work provided new insights into how phenoloxidases evolved and were devoted to plant evolution.},
}
@article {pmid37786723,
year = {2023},
author = {Mukherjee, A and Kizziah, JL and Hawkins, NC and Nasef, MO and Parker, LK and Dokland, T},
title = {Structure of the portal complex from Staphylococcus aureus pathogenicity island 1 transducing particles in situ and in solution.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37786723},
issn = {2692-8205},
support = {R01 AI083255/AI/NIAID NIH HHS/United States ; S10 OD024978/OD/NIH HHS/United States ; U24 GM116789/GM/NIGMS NIH HHS/United States ; },
abstract = {Staphylococcus aureus is an important human pathogen, and the prevalence of antibiotic resistance is a major public health concern. The evolution of pathogenicity and resistance in S. aureus often involves acquisition of mobile genetic elements (MGEs). Bacteriophages play an especially important role, since transduction represents the main mechanism for horizontal gene transfer. S. aureus pathogenicity islands (SaPIs), including SaPI1, are MGEs that carry genes encoding virulence factors, and are mobilized at high frequency through interactions with specific "helper" bacteriophages, such as 80α, leading to packaging of the SaPI genomes into virions made from structural proteins supplied by the helper. Among these structural proteins is the portal protein, which forms a ring-like portal at a fivefold vertex of the capsid, through which the DNA is packaged during virion assembly and ejected upon infection of the host. We have used high-resolution cryo-electron microscopy to determine structures of the S. aureus bacteriophage 80α portal in solution and in situ in the empty and full SaPI1 virions, and show how the portal interacts with the capsid. These structures provide a basis for understanding portal and capsid assembly and the conformational changes that occur upon DNA packaging and ejection.},
}
@article {pmid37779688,
year = {2023},
author = {González, D and Morales-Olavarria, M and Vidal-Veuthey, B and Cárdenas, JP},
title = {Insights into early evolutionary adaptations of the Akkermansia genus to the vertebrate gut.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1238580},
pmid = {37779688},
issn = {1664-302X},
abstract = {Akkermansia, a relevant mucin degrader from the vertebrate gut microbiota, is a member of the deeply branched Verrucomicrobiota, as well as the only known member of this phylum to be described as inhabitants of the gut. Only a few Akkermansia species have been officially described so far, although there is genomic evidence addressing the existence of more species-level variants for this genus. This niche specialization makes Akkermansia an interesting model for studying the evolution of microorganisms to their adaptation to the gastrointestinal tract environment, including which kind of functions were gained when the Akkermansia genus originated or how the evolutionary pressure functions over those genes. In order to gain more insight into Akkermansia adaptations to the gastrointestinal tract niche, we performed a phylogenomic analysis of 367 high-quality Akkermansia isolates and metagenome-assembled genomes, in addition to other members of Verrucomicrobiota. This work was focused on three aspects: the definition of Akkermansia genomic species clusters and the calculation and functional characterization of the pangenome for the most represented species; the evolutionary relationship between Akkermansia and their closest relatives from Verrucomicrobiota, defining the gene families which were gained or lost during the emergence of the last Akkermansia common ancestor (LAkkCA) and; the evaluation of the evolutionary pressure metrics for each relevant gene family of main Akkermansia species. This analysis found 25 Akkermansia genomic species clusters distributed in two main clades, divergent from their non-Akkermansia relatives. Pangenome analyses suggest that Akkermansia species have open pangenomes, and the gene gain/loss model indicates that genes associated with mucin degradation (both glycoside hydrolases and peptidases), (micro)aerobic metabolism, surface interaction, and adhesion were part of LAkkCA. Specifically, mucin degradation is a very ancestral innovation involved in the origin of Akkermansia. Horizontal gene transfer detection suggests that Akkermansia could receive genes mostly from unknown sources or from other Gram-negative gut bacteria. Evolutionary metrics suggest that Akkemansia species evolved differently, and even some conserved genes suffered different evolutionary pressures among clades. These results suggest a complex evolutionary landscape of the genus and indicate that mucin degradation could be an essential feature in Akkermansia evolution as a symbiotic species.},
}
@article {pmid37768051,
year = {2023},
author = {Li, L and Liu, Z and Meng, D and Liu, Y and Liu, T and Jiang, C and Yin, H},
title = {Sequence similarity network and protein structure prediction offer insights into the evolution of microbial pathways for ferrous iron oxidation.},
journal = {mSystems},
volume = {8},
number = {5},
pages = {e0072023},
pmid = {37768051},
issn = {2379-5077},
support = {2022SK2076//KEY RESEARCH AND DEVELOPMENT OF HUNAN PROVINCE, CHINA/ ; },
mesh = {*Iron/metabolism ; *Ferrous Compounds/metabolism ; Artificial Intelligence ; Oxidation-Reduction ; Anaerobiosis ; },
abstract = {Microbial Fe(II) oxidation is a crucial process that harnesses and converts the energy available in Fe, contributing significantly to global element cycling. However, there are still many aspects of this process that remain unexplored. In this study, we utilized a combination of comparative genomics, sequence similarity network analysis, and artificial intelligence-driven structure modeling methods to address the lack of structural information on Fe(II) oxidation proteins and offer a comprehensive perspective on the evolution of Fe(II) oxidation pathways. Our findings suggest that several microbial Fe(II) oxidation pathways currently known may have originated within classes Gammaproteobacteria and Betaproteobacteria.},
}
@article {pmid37762674,
year = {2023},
author = {Iasakov, T},
title = {Evolution End Classification of tfd Gene Clusters Mediating Bacterial Degradation of 2,4-Dichlorophenoxyacetic Acid (2,4-D).},
journal = {International journal of molecular sciences},
volume = {24},
number = {18},
pages = {},
pmid = {37762674},
issn = {1422-0067},
support = {23-24-00480//Russian Science Foundation (RSF)/ ; },
mesh = {Phylogeny ; Multigene Family ; *Alphaproteobacteria ; Catechols ; *Herbicides ; Phenoxyacetates ; 2,4-Dichlorophenoxyacetic Acid ; },
abstract = {The tfd (tfdI and tfdII) are gene clusters originally discovered in plasmid pJP4 which are involved in the bacterial degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) via the ortho-cleavage pathway of chlorinated catechols. They share this activity, with respect to substituted catechols, with clusters tcb and clc. Although great effort has been devoted over nearly forty years to exploring the structural diversity of these clusters, their evolution has been poorly resolved to date, and their classification is clearly obsolete. Employing comparative genomic and phylogenetic approaches has revealed that all tfd clusters can be classified as one of four different types. The following four-type classification and new nomenclature are proposed: tfdI, tfdII, tfdIII and tfdIV(A,B,C). Horizontal gene transfer between Burkholderiales and Sphingomonadales provides phenomenal linkage between tfdI, tfdII, tfdIII and tfdIV type clusters and their mosaic nature. It is hypothesized that the evolution of tfd gene clusters proceeded within first (tcb, clc and tfdI), second (tfdII and tfdIII) and third (tfdIV(A,B,C)) evolutionary lineages, in each of which, the genes were clustered in specific combinations. Their clustering is discussed through the prism of hot spots and driving forces of various models, theories, and hypotheses of cluster and operon formation. Two hypotheses about series of gene deletions and displacements are also proposed to explain the structural variations across members of clusters tfdII and tfdIII, respectively. Taking everything into account, these findings reconstruct the phylogeny of tfd clusters, have delineated their evolutionary trajectories, and allow the contribution of various evolutionary processes to be assessed.},
}
@article {pmid37760664,
year = {2023},
author = {Xia, X},
title = {Horizontal Gene Transfer and Drug Resistance Involving Mycobacterium tuberculosis.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {9},
pages = {},
pmid = {37760664},
issn = {2079-6382},
support = {RGPIN/2018-03878//Natural Sciences and Engineering Research Council/ ; },
abstract = {Mycobacterium tuberculosis (Mtb) acquires drug resistance at a rate comparable to that of bacterial pathogens that replicate much faster and have a higher mutation rate. One explanation for this rapid acquisition of drug resistance in Mtb is that drug resistance may evolve in other fast-replicating mycobacteria and then be transferred to Mtb through horizontal gene transfer (HGT). This paper aims to address three questions. First, does HGT occur between Mtb and other mycobacterial species? Second, what genes after HGT tend to survive in the recipient genome? Third, does HGT contribute to antibiotic resistance in Mtb? I present a conceptual framework for detecting HGT and analyze 39 ribosomal protein genes, 23S and 16S ribosomal RNA genes, as well as several genes targeted by antibiotics against Mtb, from 43 genomes representing all major groups within Mycobacterium. I also included mgtC and the insertion sequence IS6110 that were previously reported to be involved in HGT. The insertion sequence IS6110 shows clearly that the Mtb complex participates in HGT. However, the horizontal transferability of genes depends on gene function, as was previously hypothesized. HGT is not observed in functionally important genes such as ribosomal protein genes, rRNA genes, and other genes chosen as drug targets. This pattern can be explained by differential selection against functionally important and unimportant genes after HGT. Functionally unimportant genes such as IS6110 are not strongly selected against, so HGT events involving such genes are visible. For functionally important genes, a horizontally transferred diverged homologue from a different species may not work as well as the native counterpart, so the HGT event involving such genes is strongly selected against and eliminated, rendering them invisible to us. In short, while HGT involving the Mtb complex occurs, antibiotic resistance in the Mtb complex arose from mutations in those drug-targeted genes within the Mtb complex and was not gained through HGT.},
}
@article {pmid37760663,
year = {2023},
author = {Al-Sarawi, HA and Habibi, N and Uddin, S and Jha, AN and Al-Sarawi, MA and Lyons, BP},
title = {Antibiotic Resistance Mediated by Escherichia coli in Kuwait Marine Environment as Revealed through Genomic Analysis.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {9},
pages = {},
pmid = {37760663},
issn = {2079-6382},
abstract = {Antibiotic-resistance gene elements (ARGEs) such as antibiotic-resistance genes (ARGs), integrons, and plasmids are key to the spread of antimicrobial resistance (AMR) in marine environments. Kuwait's marine area is vulnerable to sewage contaminants introduced by numerous storm outlets and indiscriminate waste disposal near recreational beaches. Therefore, it has become a significant public health issue and warrants immediate investigation. Coliforms, especially Gram-negative Escherichia coli, have been regarded as significant indicators of recent fecal pollution and carriers of ARGEs. In this study, we applied a genome-based approach to identify ARGs' prevalence in E. coli isolated from mollusks and coastal water samples collected in a previous study. In addition, we investigated the plasmids and intl1 (class 1 integron) genes coupled with the ARGs, mediating their spread within the Kuwait marine area. Whole-genome sequencing (WGS) identified genes resistant to the drug classes of beta-lactams (blaCMY-150, blaCMY-42, blaCTX-M-15, blaDHA-1, blaMIR-1, blaOKP-B-15, blaOXA-1, blaOXA-48, blaTEM-1B, blaTEM-35), trimethoprim (dfrA14, dfrA15, dfrA16, dfrA1, dfrA5, dfrA7), fluroquinolone (oqxA, oqxB, qnrB38, qnrB4, qnrS1), aminoglycoside (aadA2, ant(3'')-Ia, aph(3'')-Ib, aph(3')-Ia, aph(6)-Id), fosfomycin (fosA7, fosA_6, fosA, fosB1), sulfonamide (sul1, sul2, sul3), tetracycline (tet-A, tet-B), and macrolide (mph-A). The MFS-type drug efflux gene mdf-A is also quite common in E. coli isolates (80%). The plasmid ColRNAI was also found to be prevalent in E. coli. The integron gene intI1 and gene cassettes (GC) were reported to be in 36% and 33%, respectively, of total E. coli isolates. A positive and significant (p < 0.001) correlation was observed between phenotypic AMR-intl1 (r = 0.311) and phenotypic AMR-GC (r = 0.188). These findings are useful for the surveillance of horizontal gene transfer of AMR in the marine environments of Kuwait.},
}
@article {pmid37759643,
year = {2023},
author = {Li, J and Cullis, C},
title = {Comparative Analysis of Tylosema esculentum Mitochondrial DNA Revealed Two Distinct Genome Structures.},
journal = {Biology},
volume = {12},
number = {9},
pages = {},
pmid = {37759643},
issn = {2079-7737},
support = {No Grant Number//Department of Biology, Case Western Reserve University./ ; },
abstract = {Tylosema esculentum, commonly known as the marama bean, is an underutilized legume with nutritious seeds, holding potential to enhance food security in southern Africa due to its resilience to prolonged drought and heat. To promote the selection of this agronomically valuable germplasm, this study assembled and compared the mitogenomes of 84 marama individuals, identifying variations in genome structure, single-nucleotide polymorphisms (SNPs), insertions/deletions (indels), heteroplasmy, and horizontal transfer. Two distinct germplasms were identified, and a novel mitogenome structure consisting of three circular molecules and one long linear chromosome was discovered. The structural variation led to an increased copy number of specific genes, nad5, nad9, rrnS, rrn5, trnC, and trnfM. The two mitogenomes also exhibited differences at 230 loci, with only one notable nonsynonymous substitution in the matR gene. Heteroplasmy was concentrated at certain loci on chromosome LS1 (OK638188). Moreover, the marama mitogenome contained an over 9 kb insertion of cpDNA, originating from chloroplast genomes, but had accumulated mutations and lost gene functionality. The evolutionary and comparative genomics analysis indicated that mitogenome divergence in marama might not be solely constrained by geographical factors. Additionally, marama, as a member from the Cercidoideae subfamily, tends to possess a more complete set of mitochondrial genes than Faboideae legumes.},
}
@article {pmid37759383,
year = {2024},
author = {Hafez, M and Gourlie, R and McDonald, M and Telfer, M and Carmona, MA and Sautua, FJ and Moffat, CS and Moolhuijzen, PM and See, PT and Aboukhaddour, R},
title = {Evolution of the Toxb Gene in Pyrenophora tritici-repentis and Related Species.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {37},
number = {3},
pages = {327-337},
doi = {10.1094/MPMI-08-23-0114-FI},
pmid = {37759383},
issn = {0894-0282},
mesh = {Phylogeny ; *Fungal Proteins/genetics/metabolism ; *Ascomycota/genetics/metabolism ; Triticum/genetics/microbiology ; },
abstract = {Pyrenophora tritici-repentis (tan spot) is a destructive foliar pathogen of wheat with global impact. This ascomycete fungus possesses a highly plastic open pangenome shaped by the gain and loss of effector genes. This study investigated the allelic variations in the chlorosis-encoding gene ToxB across 422 isolates representing all identified pathotypes and worldwide origins. To gain better insights into ToxB evolution, we examined its presence and variability in other Pyrenophora spp. A ToxB haplotype network was constructed, revealing the evolutionary relationships of this gene (20 haplotypes) across four Pyrenophora species. Notably, toxb, the homolog of ToxB, was detected for the first time in the barley pathogen Pyrenophora teres. The ToxB/toxb genes display evidence of selection that is characterized by loss of function, duplication, and diverse mutations. Within the ToxB/toxb open reading frame, 72 mutations were identified, including 14 synonymous, 55 nonsynonymous, and 3 indel mutations. Remarkably, a, ∼5.6-kb Copia-like retrotransposon, named Copia-1_Ptr, was found inserted in the toxb gene of a race 3 isolate. This insert disrupted the ToxB gene's function, a first case of effector gene disruption by a transposable element in P. tritici-repentis. Additionally, a microsatellite with 25 nucleotide repeats (0 to 10) in the upstream region of ToxB suggested a potential mechanism influencing ToxB expression and regulation. Exploring ToxB-like protein distribution in other ascomycetes revealed the presence of ToxB-like proteins in 19 additional species, including the Leotiomycetes class for the first time. The presence/absence pattern of ToxB-like proteins defied species relatedness compared with a phylogenetic tree, suggesting a past horizontal gene transfer event during the evolution of the ToxB gene. [Formula: see text] Copyright © 2024 His Majesty the King in Right of Canada, as represented by the Minister of Agriculture and Agri-Food. This is an open access article distributed under the CC BY-NC-ND 4.0 International license.},
}
@article {pmid37757562,
year = {2024},
author = {Sharma, M and Singh, DN and Uttam, G and Sharma, P and Meena, SA and Verma, AK and Negi, RK},
title = {Adaptive evolution of Sphingopyxis sp. MC4 conferred degradation potential for persistent β- and δ-Hexachlorocyclohexane (HCH) isomers.},
journal = {Journal of hazardous materials},
volume = {461},
number = {},
pages = {132545},
doi = {10.1016/j.jhazmat.2023.132545},
pmid = {37757562},
issn = {1873-3336},
mesh = {Ecosystem ; Hexachlorocyclohexane/metabolism ; *Sphingomonadaceae/genetics/metabolism ; *Pesticides/metabolism ; Biodegradation, Environmental ; },
abstract = {Hexachlorocyclohexane (HCH), an organochlorine pesticide imposes several harmful impacts on the ecosystem. β- and δ-isomers of HCH are highly toxic, persistent, and recalcitrant to biodegradation, slow and incomplete degradation of β- and δ- isomers have been reported in a few strains. We have isolated a strain designated as Sphingopyxis strain MC4 that can tolerate and degrade high concentrations of α-, β-, γ- and δ-HCH isomers. To date, no other Sphingopyxis strain has been reported to degrade β- and δ-isomers. To understand the underlying genetic makeup contributing to adaptations, the whole genome of strain MC4 was sequenced. Comparative genome analysis showed that strain MC4 harbors the complete pathway (lin genes) required for HCH degradation. Genetic footprints such as presence of lin genes on genomic islands, IS6100 elements in close proximity of lin genes, and synteny in lin flanking regions with other strains reflects the horizontal gene transfer in strain MC4. Positive selection and HGT drive the adaptive evolution of strain MC4 under the pressure of HCH contamination that it experienced in its surrounding niche. In silico analyses showed efficient binding of β- and δ-isomers with enzymes leading to rapid degradation that need further validation by cloning and biochemical experiments.},
}
@article {pmid37755994,
year = {2023},
author = {Shikov, AE and Savina, IA and Nizhnikov, AA and Antonets, KS},
title = {Recombination in Bacterial Genomes: Evolutionary Trends.},
journal = {Toxins},
volume = {15},
number = {9},
pages = {},
pmid = {37755994},
issn = {2072-6651},
support = {075-15-2021-1055//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {Bacterial organisms have undergone homologous recombination (HR) and horizontal gene transfer (HGT) multiple times during their history. These processes could increase fitness to new environments, cause specialization, the emergence of new species, and changes in virulence. Therefore, comprehensive knowledge of the impact and intensity of genetic exchanges and the location of recombination hotspots on the genome is necessary for understanding the dynamics of adaptation to various conditions. To this end, we aimed to characterize the functional impact and genomic context of computationally detected recombination events by analyzing genomic studies of any bacterial species, for which events have been detected in the last 30 years. Genomic loci where the transfer of DNA was detected pertained to mobile genetic elements (MGEs) housing genes that code for proteins engaged in distinct cellular processes, such as secretion systems, toxins, infection effectors, biosynthesis enzymes, etc. We found that all inferences fall into three main lifestyle categories, namely, ecological diversification, pathogenesis, and symbiosis. The latter primarily exhibits ancestral events, thus, possibly indicating that adaptation appears to be governed by similar recombination-dependent mechanisms.},
}
@article {pmid37754684,
year = {2023},
author = {Zhang, Y and Kitazumi, A and Liao, Y-T and de Los Reyes, BG and Wu, VCH},
title = {Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem.},
journal = {Microbiology spectrum},
volume = {11},
number = {5},
pages = {e0022623},
pmid = {37754684},
issn = {2165-0497},
support = {2030-42000-0055-000-D//USDA | Agricultural Research Service (ARS)/ ; },
mesh = {*Bacteriophages/genetics ; *Gene Transfer, Horizontal ; *Metagenomics ; *Agriculture ; *Bacteria/genetics/virology/drug effects ; *Microbiota/genetics ; Metagenome ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Ecosystem ; Drug Resistance, Bacterial/genetics ; Soil Microbiology ; },
abstract = {Antibiotic resistance has become a serious health concern worldwide. The potential impact of viruses, bacteriophages in particular, on spreading antibiotic resistance genes is still controversial due to the complexity of bacteriophage-bacterial interactions within diverse environments. In this study, we determined the microbiome profiles and the potential antibiotic resistance gene (ARG) transfer between bacterial and viral populations in different agricultural samples using a high-resolution analysis of the metagenomes. The results of this study provide compelling genetic evidence for ARG transfer through bacteriophage-bacteria interactions, revealing the inherent risks associated with bacteriophage-mediated ARG transfer across the agricultural microbiome.},
}
@article {pmid37754275,
year = {2023},
author = {Ma, J and Zhao, H and Mo, S and Li, J and Ma, X and Tang, Y and Li, H and Liu, Z},
title = {Acquisition of Type I methyltransferase via horizontal gene transfer increases the drug resistance of Aeromonas veronii.},
journal = {Microbial genomics},
volume = {9},
number = {9},
pages = {},
pmid = {37754275},
issn = {2057-5858},
mesh = {*Gene Transfer, Horizontal ; *Aeromonas veronii/genetics ; *Methyltransferases/genetics ; Drug Resistance, Bacterial/genetics ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Humans ; Genome, Bacterial ; Virulence/genetics ; Bacterial Proteins/genetics ; Gram-Negative Bacterial Infections/microbiology ; Animals ; DNA Methylation ; },
abstract = {Aeromonas veronii is an opportunistic pathogen that affects both fish and mammals, including humans, leading to bacteraemia, sepsis, meningitis and even death. The increasing virulence and drug resistance of A. veronii are of significant concern and pose a severe risk to public safety. The Type I restriction-modification (RM) system, which functions as a bacterial defence mechanism, can influence gene expression through DNA methylation. However, little research has been conducted to explore its origin, evolutionary path, and relationship to virulence and drug resistance in A. veronii. In this study, we analysed the pan-genome of 233 A. veronii strains, and the results indicated that it was 'open', meaning that A. veronii has acquired additional genes from other species. This suggested that A. veronii had the potential to adapt and evolve rapidly, which might have contributed to its drug resistance. One Type I methyltransferase (MTase) and two complete Type I RM systems were identified, namely AveC4I, AveC4II and AveC4III in A. veronii strain C4, respectively. Notably, AveC4I was exclusive to A. veronii C4. Phylogenetic analysis revealed that AveC4I was derived from horizontal gene transfer from Thiocystis violascens and exchanged genes with the human pathogen Comamonas kerstersii. Single molecule real-time sequencing was applied to identify the motif methylated by AveC4I, which was unique and not recognized by any reported MTases in the REBASE database. We also annotated the functions and pathways of the genes containing the motif, revealing that AveC4I may control drug resistance in A. veronii C4. Our findings provide new insight on the mechanisms underlying drug resistance in pathogenic bacteria. By identifying the specific genes and pathways affected by AveC4I, this study may aid in the development of new therapeutic approaches to combat A. veronii infections.},
}
@article {pmid37752971,
year = {2023},
author = {Tekle, YI and Tran, H and Wang, F and Singla, M and Udu, I},
title = {Omics of an Enigmatic Marine Amoeba Uncovers Unprecedented Gene Trafficking from Giant Viruses and Provides Insights into Its Complex Life Cycle.},
journal = {Microbiology research},
volume = {14},
number = {2},
pages = {656-672},
pmid = {37752971},
issn = {2036-7473},
support = {R15 GM116103/GM/NIGMS NIH HHS/United States ; },
abstract = {Amoebozoa include lineages of diverse ecology, behavior, and morphology. They are assumed to encompass members with the largest genome sizes of all living things, yet genomic studies in the group are limited. Trichosphaerium, a polymorphic, multinucleate, marine amoeba with a complicated life cycle, has puzzled experts for over a century. In an effort to explore the genomic diversity and investigate extraordinary behavior observed among the Amoebozoa, we used integrated omics approaches to study this enigmatic marine amoeba. Omics data, including single-cell transcriptomics and cytological data, demonstrate that Trichosphaerium sp. possesses the complete meiosis toolkit genes. These genes are expressed in life stages of the amoeba including medium and large cells. The life cycle of Trichosphaerium sp. involves asexual processes via binary fission and multiple fragmentation of giant cells, as well as sexual-like processes involving genes implicated in sexual reproduction and polyploidization. These findings are in stark contrast to a life cycle previously reported for this amoeba. Despite the extreme morphological plasticity observed in Trichosphaerium, our genomic data showed that populations maintain a species-level intragenomic variation. A draft genome of Trichosphaerium indicates elevated lateral gene transfer (LGT) from bacteria and giant viruses. Gene trafficking in Trichosphaerium is the highest within Amoebozoa and among the highest in microbial eukaryotes.},
}
@article {pmid37752398,
year = {2023},
author = {Liu, H and Shi, B and Liu, W and Wang, L and Zhu, L and Wang, J and Kim, YM and Wang, J},
title = {Effects of magnesium-modified biochar on antibiotic resistance genes and microbial communities in chicken manure composting.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {50},
pages = {108553-108564},
pmid = {37752398},
issn = {1614-7499},
support = {42277039//National Natural Science Foundation of China/ ; 42207026//National Natural Science Foundation of China/ ; ZR202111290386//Natural Science Foundation of Shandong Province/ ; },
mesh = {Animals ; Genes, Bacterial ; Manure/microbiology ; *Composting ; Chickens/genetics ; Magnesium ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Firmicutes ; Proteobacteria/genetics ; *Microbiota ; },
abstract = {Abatement of antibiotic resistance genes (ARGs) in livestock manure by composting has attracted attention. This study investigated the effect of adding magnesium-modified biochar (MBC) on ARGs and microbial communities in chicken manure composting. Twelve genes for tetracyclines, sulfonamides, and macrolides, and mobile genetic elements were measured in the compost pile. The results showed that after 45 days of the composting, the treatment groups of MBC had longer high temperature periods, significantly higher germination indices (GI) and lower phytotoxicity. There were four major dominant phyla (Firmicutes, Actinobacteriota, Proteobacteria, and Bacteroidota) in the compost. The abundance of Firmicutes decreased significantly during the compost cooling period; tetracycline resistance genes demonstrated an extremely significant positive correlation with Firmicutes, showing a trend of the same increase and decrease with composting time; tetT, tetO, tetM, tetW, ermB, and intI2 were reduced in the MBC group; the total abundance of resistance genes in the 2% MBC addition group was 0.67 times that of the control; Proteobacteria and Chloroflexi were also significantly lower than the other treatment groups. Most ARGs were significantly associated with mobile genetic elements (MGEs); MBC can reduce the spread and diffusion of ARGs by reducing the abundance of MGEs and inhibiting horizontal gene transfer (HGT).},
}
@article {pmid37748307,
year = {2024},
author = {Gao, J and Xing, X and Cai, W and Li, Z and Shi, G and Chen, Y and Liang, H and Chen, C and Ma, K and Chen, J and Hu, C},
title = {Effect of micropollutants on disinfection byproducts and antibiotic resistance genes in drinking water in the process of biological activated carbon treatment.},
journal = {Journal of hazardous materials},
volume = {461},
number = {},
pages = {132304},
doi = {10.1016/j.jhazmat.2023.132304},
pmid = {37748307},
issn = {1873-3336},
mesh = {Disinfection ; *Drinking Water ; Charcoal ; Extracellular Polymeric Substance Matrix/chemistry ; Anti-Bacterial Agents ; *Water Purification ; *Water Pollutants, Chemical/toxicity/analysis ; *Disinfectants/pharmacology ; },
abstract = {The biofilm stress response of biological activated carbon (BAC) was investigated under prolonged exposure to sulfadiazine and 2,4-Dichlorophenoxyacetic acid, simulating complex emerging organic contaminants (EOCs) that are mainly involved in the formation of nitrogenous disinfection byproducts (N-DBPs) and antibiotic resistance genes (ARGs). Under trace complex EOCs condition (2 µg/L), N-DBP precursors and abundance of ARGs increased significantly in BAC effluent. The total formation potential of haloacetonitriles (HANs) and halonitromethanes (HNMs) was 751.47 ± 2.98 ng/L, which was much higher than the control group (440.67 ± 13.38 ng/L without EOCs). Similarly, the relative abundance of ARGs was more than twice that in the control group. The complex EOCs induce excessive extracellular polymeric substance secretion (EPS), thereby causing more N-DBP precursors and stronger horizontal gene transfer. Metagenome analysis revealed that functional amino acid and protein biosynthesis genes were overexpressed compared to the control group, causing more EPS to be secreted into the external environment. Complex EOCs promote Cobetia, Clostridium, and Streptomyces dominance, contributing to the production of N-DBP precursors and ARGs. For the first time, in addition to the direct hazards of the EOCs, this study successfully revealed the indirect water quality risks of complex EOCs from the microbial stress response during BAC treatment. Synergistic regulation of EOCs and microorganisms is important for tap water security.},
}
@article {pmid37746224,
year = {2022},
author = {Schalamun, M and Schmoll, M},
title = {Trichoderma - genomes and genomics as treasure troves for research towards biology, biotechnology and agriculture.},
journal = {Frontiers in fungal biology},
volume = {3},
number = {},
pages = {1002161},
pmid = {37746224},
issn = {2673-6128},
support = {P 30893/FWF_/Austrian Science Fund FWF/Austria ; P 31464/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {The genus Trichoderma is among the best studied groups of filamentous fungi, largely because of its high relevance in applications from agriculture to enzyme biosynthesis to biofuel production. However, the physiological competences of these fungi, that led to these beneficial applications are intriguing also from a scientific and ecological point of view. This review therefore summarizes recent developments in studies of fungal genomes, updates on previously started genome annotation efforts and novel discoveries as well as efforts towards bioprospecting for enzymes and bioactive compounds such as cellulases, enzymes degrading xenobiotics and metabolites with potential pharmaceutical value. Thereby insights are provided into genomes, mitochondrial genomes and genomes of mycoviruses of Trichoderma strains relevant for enzyme production, biocontrol and mycoremediation. In several cases, production of bioactive compounds could be associated with responsible genes or clusters and bioremediation capabilities could be supported or predicted using genome information. Insights into evolution of the genus Trichoderma revealed large scale horizontal gene transfer, predominantly of CAZyme genes, but also secondary metabolite clusters. Investigation of sexual development showed that Trichoderma species are competent of repeat induced point mutation (RIP) and in some cases, segmental aneuploidy was observed. Some random mutants finally gave away their crucial mutations like T. reesei QM9978 and QM9136 and the fertility defect of QM6a was traced back to its gene defect. The Trichoderma core genome was narrowed down to 7000 genes and gene clustering was investigated in the genomes of multiple species. Finally, recent developments in application of CRISPR/Cas9 in Trichoderma, cloning and expression strategies for the workhorse T. reesei as well as the use genome mining tools for bioprospecting Trichoderma are highlighted. The intriguing new findings on evolution, genomics and physiology highlight emerging trends and illustrate worthwhile perspectives in diverse fields of research with Trichoderma.},
}
@article {pmid37745407,
year = {2023},
author = {Gonçalves, C and Harrison, MC and Steenwyk, JL and Opulente, DA and LaBella, AL and Wolters, JF and Zhou, X and Shen, XX and Groenewald, M and Hittinger, CT and Rokas, A},
title = {Diverse signatures of convergent evolution in cacti-associated yeasts.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37745407},
issn = {2692-8205},
support = {R01 AI153356/AI/NIAID NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; },
abstract = {Many distantly related organisms have convergently evolved traits and lifestyles that enable them to live in similar ecological environments. However, the extent of phenotypic convergence evolving through the same or distinct genetic trajectories remains an open question. Here, we leverage a comprehensive dataset of genomic and phenotypic data from 1,049 yeast species in the subphylum Saccharomycotina (Kingdom Fungi, Phylum Ascomycota) to explore signatures of convergent evolution in cactophilic yeasts, ecological specialists associated with cacti. We inferred that the ecological association of yeasts with cacti arose independently ~17 times. Using machine-learning, we further found that cactophily can be predicted with 76% accuracy from functional genomic and phenotypic data. The most informative feature for predicting cactophily was thermotolerance, which is likely associated with duplication and altered evolutionary rates of genes impacting the cell envelope in several cactophilic lineages. We also identified horizontal gene transfer and duplication events of plant cell wall-degrading enzymes in distantly related cactophilic clades, suggesting that putatively adaptive traits evolved through disparate molecular mechanisms. Remarkably, multiple cactophilic lineages and their close relatives are emerging human opportunistic pathogens, suggesting that the cactophilic lifestyle-and perhaps more generally lifestyles favoring thermotolerance-may preadapt yeasts to cause human disease. This work underscores the potential of a multifaceted approach involving high throughput genomic and phenotypic data to shed light onto ecological adaptation and highlights how convergent evolution to wild environments could facilitate the transition to human pathogenicity.},
}
@article {pmid37743870,
year = {2023},
author = {Palanisamy, V and Bosilevac, JM and Barkhouse, DA and Velez, SE and Chitlapilly Dass, S},
title = {Shotgun-metagenomics reveals a highly diverse and communal microbial network present in the drains of three beef-processing plants.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1240138},
pmid = {37743870},
issn = {2235-2988},
mesh = {*Metagenomics ; *Microbiota/genetics ; *Biofilms/growth &amp; development ; Cattle ; Animals ; Red Meat/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; Food Handling/methods ; Food Microbiology ; Food-Processing Industry ; },
abstract = {BACKGROUND: Multi-species biofilms pose a problem in various environments, especially food-processing environments. The diversity of microorganisms in these biofilms plays a critical role in their integrity and protection against external biotic and abiotic factors. Compared to single-species biofilms, mixed-species biofilms are more resistant to various stresses, including antimicrobials like sanitizers. Therefore, understanding the microbiome composition and diversity in biofilms and their metabolic potential is a priority when developing intervention techniques to combat foodborne pathogens in food processing environments.<br><br>METHODS: This study aimed to describe and compare the microbiome profile of 75 drain biofilm samples obtained from five different locations (Hotscale, Hotbox, Cooler, Processing, &amp; Grind room) of three beef-processing plants (Plant A, B &amp; C) taken over two timepoints 2017-18 (T1) and 2021 (T2) by shotgun sequencing.<br><br>RESULTS: Core microbiome analysis found Pseudomonas, Psychrobacter, and Acinetobacter to be the top three prevalent genera among the plants and locations. Alpha diversity analysis demonstrated a high diversity of microbiome present in all the plants and locations across the time points. Functional analysis showed the high metabolic potential of the microbial community with abundance of genes in metabolism, cell-adhesion, motility, and quorum sensing. Moreover, Quaternary Ammonium Compound (QAC) resistance genes were also observed, this is significant as QAC sanitizers are commonly used in many food processing facilities. Multi-functional genes such as transposases, polymerases, permeases, flagellar proteins, and Mobile Genetic Elements (MGEs) were found suggesting these are dynamic microbial communities that work together to protect themselves against environmental stresses through multiple defense mechanisms.<br><br>CONCLUSION: This study provides a framework for understanding the collective microbial network spanning a beef processing system. The results can be used to develop intervention strategies to best control these highly communicative microbial networks.},
}
@article {pmid37742882,
year = {2023},
author = {Gu, X},
title = {Genome distance and phylogenetic inference accommodating gene duplication, loss and new gene input.},
journal = {Molecular phylogenetics and evolution},
volume = {189},
number = {},
pages = {107916},
doi = {10.1016/j.ympev.2023.107916},
pmid = {37742882},
issn = {1095-9513},
mesh = {Phylogeny ; *Gene Duplication ; *Genome/genetics ; Biological Evolution ; Computer Simulation ; Evolution, Molecular ; },
abstract = {With the rapid growth of entire genome data, phylogenomics focuses on analyzing evolutionary histories and relationships of species, i.e., the tree of life. For decades it has been realized that the genome-wide phylogenetic inference can be approached based upon the dynamic pattern of gene content (the presence/absence of gene families), or extended gene content (absence, presence as a single-copy, or duplicates). Those methods, conceptually or technically, invoked the birth-and-death process to model the evolutionary process (gene duplication or gene loss. One common drawback is that the mechanism of new gene input, including de novo origin of new genes and the lateral gene transfer, has not been explicitly considered. In this paper, the author developed a new genome distance approach for genome phylogeny inference under the origin-birth-death stochastic process. The model takes gene duplication, gene loss and new gene input into account simultaneously. Computer simulations found that the two-genome approach is statistically difficult to distinguish between two proliferation parameters, i.e., the rate of gene duplication and the rate of new gene input. Nevertheless, it has also demonstrated the statistical feasibility for using the loss-genome distance to infer the genome phylogeny, which can avoid the large sampling problem. The strategy to study the universal tree of life was discussed and exemplified by an example.},
}
@article {pmid37741386,
year = {2023},
author = {Shen, Y and Liu, Y and Du, Y and Wang, X and Guan, J and Jia, X and Xu, F and Song, Z and Gao, H and Zhang, B and Guo, P},
title = {Transfer of antibiotic resistance genes from soil to wheat: Role of host bacteria, impact on seed-derived bacteria, and affecting factors.},
journal = {The Science of the total environment},
volume = {905},
number = {},
pages = {167279},
doi = {10.1016/j.scitotenv.2023.167279},
pmid = {37741386},
issn = {1879-1026},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Triticum ; Soil ; Genes, Bacterial ; Soil Microbiology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Seeds ; Manure/microbiology ; },
abstract = {The transfer of antibiotic resistance genes (ARGs) from soils to plants is poorly understood, especially the role of host bacteria in soils and its impact on seed-derived bacteria. Wheat (Triticum aestivum L.) was thus used to fill the gap by conducting pot experiments, with target ARGs and bacterial community analyzed. Results showed that the relative abundances of target ARGs gradually decreased during transfer of ARGs from the rhizosphere soil to root and shoot. Host bacteria in the rhizosphere soil were the primary source of ARGs in wheat. The 38, 21, and 19 potential host bacterial genera of target ARGs and intI1 in the rhizosphere soil, root, and shoot were identified, respectively, and they mainly belonged to phylum Proteobacteria. The abundance of ARGs carried by pathogenic Corynebacterium was reduced in sequence. During transfer of ARGs from the rhizosphere soil to root and shoot, some seed-derived bacteria and pathogenic Acinetobacter obtained ARGs through horizontal gene transfer and became potential host bacteria. Furthermore, total organic carbon, available nitrogen of the rhizosphere soil, water use efficiency, vapor pressure deficit, and superoxide dismutase of plants were identified as the key factors affecting potential host bacteria transfer in soils to wheat. This work provides important insights into transfer of ARGs and deepens our understanding of potential health risks of ARGs from soils to plants.},
}
@article {pmid37739550,
year = {2023},
author = {Khambhati, K and Bhattacharjee, G and Gohil, N and Maurya, R and Singh, V},
title = {Exploring the potential of phage and their applications.},
journal = {Progress in molecular biology and translational science},
volume = {200},
number = {},
pages = {1-12},
doi = {10.1016/bs.pmbts.2023.04.001},
pmid = {37739550},
issn = {1878-0814},
mesh = {Humans ; *Bacteriophages ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Food ; Mutation ; },
abstract = {Antibiotic resistant microorganisms are significantly increasing due to horizontal gene transfer, mutation and overdose of antibiotics leading to serious health conditions globally. Several multidrug resistant microorganisms have shown resistance to even the last line of antibiotics making it very difficult to treat them. Besides using antibiotics, an alternative approach to treat such resistant bacterial pathogens through the use of bacteriophage (phage) was used in the early 1900s which however declined and vanished after the discovery of antibiotics. In recent times, phage has emerged and gained interest as an alternative approach to antibiotics to treat MDR pathogens. Phage can self-replicate by utilizing cellular machinery of bacterial host by following lytic and lysogenic life cycles and therefore suitable for rapid regeneration. Application of phage for detection of bacterial pathogens, elimination of bacteria, agents for controlling food spoilage, treating human disease and several others entitles phage as a futuristic antibacterial armamentarium.},
}
@article {pmid37739079,
year = {2023},
author = {Wu, L and Wu, Q and Xu, J and Rong, L and Yu, X and Cai, C and Huang, X and Zou, X},
title = {Responses of antibiotic resistance genes in the enhanced biological phosphorus removal system under various antibiotics: Mechanisms and implications.},
journal = {The Science of the total environment},
volume = {905},
number = {},
pages = {167247},
doi = {10.1016/j.scitotenv.2023.167247},
pmid = {37739079},
issn = {1879-1026},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Sewage/microbiology ; },
abstract = {The effects of antibiotics on the proliferation of antibiotic resistant genes (ARGs) in WWTPs have drawn great attention in recent years. The effects of antibiotics on ARGs in the enhanced biological phosphorus removal (EBPR) system and its mechanisms, however, are still not well understood. In this study, EBPR systems were constructed using activated sludge to investigate the effects of ten commonly detected antibiotics in the environment on the proliferation of ARGs and the mechanisms involved. The results showed that the total abundance of ARGs increased to varying degrees with the addition of different antibiotics (0.05 mmol/L), and the top 30 ARGs increased by 271.1 % to 370.0 %. Mobile genetic elements (MGEs), functional modules, and the bacteria community were consistently related to the changes in ARGs. Refractory antibiotics, in particular, have a stronger promoting effect on transduction in the EBPR system. The insertion sequence common region (ISCR) and transposon (Tnp) were identified as crucial factors in the proliferation of ARGs. Moreover, the risk of polyphosphate accumulating organisms (PAOs) carrying ARGs in the presence of antibiotics should not be ignored. Our findings emphasize the potential efficacy of employing strategies that target the reduction of MGEs, regulation of cellular communication, and management of microbial communities to effectively mitigate the risks associated with ARGs.},
}
@article {pmid37738943,
year = {2023},
author = {Zhang, J and Xu, Z and Chu, W and Ju, F and Jin, W and Li, P and Xiao, R},
title = {Residual chlorine persistently changes antibiotic resistance gene composition and increases the risk of antibiotic resistance in sewer systems.},
journal = {Water research},
volume = {245},
number = {},
pages = {120635},
doi = {10.1016/j.watres.2023.120635},
pmid = {37738943},
issn = {1879-2448},
abstract = {During the COVID-19 pandemic, excessive amounts of disinfectants and their transformation products entered sewer systems worldwide, which was an extremely rare occurrence before. The stress of residual chlorine and disinfection by-products is not only likely to promote the spread of antibiotic resistance genes (ARGs), but also leads to the enrichment of chlorine-resistant bacteria that may also be resistant to antibiotics. Therefore, the potential impact of such discharge on ARG composition should be studied and the health risks should be assessed. Thus, this study combined high-throughput 16S rRNA gene amplicon sequencing and metagenomic analysis with long-term batch tests that involved two stages of stress and recovery to comprehensively evaluate the impact of residual chlorine on the microbial community and ARG compositions in sewer systems. The tests demonstrated that the disturbance of the microbial community structure by residual chlorine was reversible, but the change in ARG composition was persistent. This study found that vertical propagation and horizontal gene transfer jointly drove ARG composition succession in the biofilm, while the driving force was mainly horizontal gene transfer in the sediment. In this process, the biocide resistance gene (BRG) subtype chtR played an important role in promoting co-selection with ARGs through plasmids and integrative and conjugative elements. Moreover, it was further shown that the addition of sodium hypochlorite increased the risk of ARGs to human health, even after discontinuation of dosing, signifying that the impact was persistent. In general, this study strengthens the co-selection theory of ARGs and BRGs, and calls for improved disinfection strategies and more environmentally friendly disinfectants.},
}
@article {pmid37734313,
year = {2024},
author = {Wang, YZ and An, XL and Fan, XT and Pu, Q and Li, H and Liu, WZ and Chen, Z and Su, JQ},
title = {Visible light-activated photosensitizer inhibits the plasmid-mediated horizontal gene transfer of antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {461},
number = {},
pages = {132564},
doi = {10.1016/j.jhazmat.2023.132564},
pmid = {37734313},
issn = {1873-3336},
mesh = {*Photosensitizing Agents/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Escherichia coli/genetics ; Plasmids/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; },
abstract = {Inhibition of plasmid transfer, including transformation and conjugation, is essential to prevent the spread of plasmid-encoded antimicrobial resistance. Photosensitizers have been successfully used in the treatment of serious infectious diseases, however, the effects of photosensitizers on the plasmid transfer are still elusive. In this study, we determined the transformation and conjugation efficiency of plasmid pUC19 and pRP4, respectively, when exposed to a photosensitizer (Visible Light-activated Rose Bengal, VLRB). The results showed that the activation of VLRB resulted in up to a 580-fold decrease in the transformation frequency of pUC19 and a 10-fold decrease in the conjugation frequency of pRP4 compared with the non-VLRB control. The inhibition of pUC19 transformation by VLRB exhibited a dose-dependent manner and was attributed to the changes in the plasmid conformation. The inhibition of pRP4 conjugation was associated with the generation of extracellular free radicals, induced oxidative stress, suppression of the mating pair formation gene (trbBp) and DNA transfer and replication gene (trfAp), and enhanced expression of the global regulatory genes (korA, korB, and trbA). These findings highlight the potential of visible light-activated photosensitizer for mitigating the dissemination of plasmid-encoded antibiotic resistance genes.},
}
@article {pmid37733747,
year = {2023},
author = {Caygill, S and Dolan, L},
title = {ATP binding cassette transporters and uridine diphosphate glycosyltransferases are ancient protein families that evolved roles in herbicide resistance through exaptation.},
journal = {PloS one},
volume = {18},
number = {9},
pages = {e0287356},
pmid = {37733747},
issn = {1932-6203},
mesh = {*Glycosyltransferases/genetics ; *ATP-Binding Cassette Transporters/genetics ; Herbicide Resistance/genetics ; Phylogeny ; Amino Acid Sequence ; Plant Weeds ; },
abstract = {ATP-binding cassette (ABC) transporters actively transport various substances across membranes, while uridine diphosphate (UDP) glycosyltransferases (UGTs) are proteins that catalyse the chemical modification of various organic compounds. Both of these protein superfamilies have been associated with conferring herbicide resistance in weeds. Little is known about the evolutionary history of these protein families in the Archaeplastida. To infer the evolutionary histories of these protein superfamilies, we compared protein sequences collected from 10 species which represent distinct lineages of the Archaeplastida-the lineage including glaucophyte algae, rhodophyte algae, chlorophyte algae and the streptophytes-and generated phylogenetic trees. We show that ABC transporters were present in the last common ancestor of the Archaeplastida which lived 1.6 billion years ago, and the major clades identified in extant plants were already present then. Conversely, we only identified UGTs in members of the streptophyte lineage, which suggests a loss of these proteins in earlier diverging Archaeplastida lineages or arrival of UGTs into a common ancestor of the streptophyte lineage through horizontal gene transfer from a non-Archaeplastida eukaryote lineage. We found that within the streptophyte lineage, most diversification of the UGT protein family occurred in the vascular lineage, with 17 of the 20 clades identified in extant plants present only in vascular plants. Based on our findings, we conclude that ABC transporters and UGTs are ancient protein families which diversified during Archaeplastida evolution, which may have evolved for developmental functions as plants began to occupy new environmental niches and are now being selected to confer resistance to a diverse range of herbicides in weeds.},
}
@article {pmid37733635,
year = {2023},
author = {Luo, T and Dai, X and Wei, W and Xu, Q and Ni, BJ},
title = {Microplastics Enhance the Prevalence of Antibiotic Resistance Genes in Anaerobic Sludge Digestion by Enriching Antibiotic-Resistant Bacteria in Surface Biofilm and Facilitating the Vertical and Horizontal Gene Transfer.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {39},
pages = {14611-14621},
doi = {10.1021/acs.est.3c02815},
pmid = {37733635},
issn = {1520-5851},
mesh = {Humans ; *Sewage/microbiology ; *Microplastics ; Plastics ; Genes, Bacterial ; Anaerobiosis ; Gene Transfer, Horizontal ; Prevalence ; Angiotensin Receptor Antagonists ; Polyethylene ; Anti-Bacterial Agents/pharmacology ; Angiotensin-Converting Enzyme Inhibitors ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Digestion ; },
abstract = {Antibiotic resistance genes (ARGs) and microplastics (MPs) are recognized as emerging contaminants and threats to global human health. Despite both of them being significantly detected in their "hotspots", i.e., waste activated sludge (WAS), rare studies on how MPs affect ARGs and antibiotic-resistant bacteria (ARB) in anaerobic sludge digestion are available. Herein, the fate of ARGs and ARB after exposure to MPs of three dosages (10, 30, and 80 particles/g-TS), three polymer types (LDPE, PET, and PS), and three branching extents (LDPE, LLDPE, and HDPE) in anaerobic sludge digestion was investigated. Metagenomic results indicated that all variants of MPs resulted in an increase of the relative abundance of ARGs in the digester compared to the control. The abundance of ARGs demonstrated a dosage-dependent relationship within the range from 10 to 80 particles/g-TS, resulting in an increase from 4.5 to 27.9% compared to the control. Branching structure and polymer type influence ARG level in the sludge digester as well. Mechanism studies revealed that LDPE selectively enriched potential ARB and ARGs in the surface biofilm, possibly creating a favorable environment for ARB proliferation and ARG exchange. Furthermore, vertical transfer of ARGs was facilitated by LDPE through increasing bacterial cell proliferation accompanied by the enhancement of relevant functional genes. The elevated abundance of mobile genetic elements (MGEs) and ARGs-carrying plasmids also demonstrated that MGE-mediated horizontal transfer was promoted by LDPE at 80 particles/g-TS. This effect was compounded by increased oxidative stress, cell membrane permeability, and cell cohesion, collectively facilitating horizontal ARG transfer. Consequently, both vertical and horizontal transfer of ARGs could be concurrently promoted by LDPE an in anaerobic sludge digester.},
}
@article {pmid37732760,
year = {2023},
author = {Wirth, NT and Rohr, K and Danchin, A and Nikel, PI},
title = {Recursive genome engineering decodes the evolutionary origin of an essential thymidylate kinase activity in Pseudomonas putida KT2440.},
journal = {mBio},
volume = {14},
number = {5},
pages = {e0108123},
pmid = {37732760},
issn = {2150-7511},
support = {NNF20CC0035580//Novo Nordisk Fonden (NNF)/ ; NNF18OC0034818//Novo Nordisk Fonden (NNF)/ ; NNF21OC0067996//Novo Nordisk Fonden (NNF)/ ; 814418//EC | H2020 | IL | LEIT | H2020 LEIT Biotechnology (BIOTEC)/ ; },
mesh = {*Pseudomonas putida/genetics/metabolism ; Genomic Islands ; Biotechnology ; },
abstract = {Investigating fundamental aspects of metabolism is vital for advancing our understanding of the diverse biochemical capabilities and biotechnological applications of bacteria. The origin of the essential thymidylate kinase function in the model bacterium Pseudomonas putida KT2440, seemingly interrupted due to the presence of a large genomic island that disrupts the cognate gene, eluded a satisfactory explanation thus far. This is a first-case example of an essential metabolic function, likely acquired by horizontal gene transfer, which "landed" in a locus encoding the same activity. As such, foreign DNA encoding an essential dNMPK could immediately adjust to the recipient host-instead of long-term accommodation and adaptation. Understanding how these functions evolve is a major biological question, and the work presented here is a decisive step toward this direction. Furthermore, identifying essential and accessory genes facilitates removing those deemed irrelevant in industrial settings-yielding genome-reduced cell factories with enhanced properties and genetic stability.},
}
@article {pmid37730038,
year = {2023},
author = {Shen, M and Zhao, Y and Liu, S and Tao, S and Li, T and Long, H},
title = {Can microplastics and disinfectant resistance genes pose conceivable threats to water disinfection process?.},
journal = {The Science of the total environment},
volume = {905},
number = {},
pages = {167192},
doi = {10.1016/j.scitotenv.2023.167192},
pmid = {37730038},
issn = {1879-1026},
mesh = {*Disinfectants/analysis ; Disinfection ; Microplastics ; Plastics ; Water ; Bacteria/genetics ; },
abstract = {Microplastic pollution in the environment has aroused widespread concerns, however, the potential environmental risks caused by excessive use of disinfectants are still unknown. Disinfectants with doses below the threshold can enhance the communication of resistance genes in pathogenic microorganisms, promoting the development and spread of antimicrobial activity. Problematically, the intensification of microplastic pollution and the increase of disinfectant consumption will become a key driving force for the growth of disinfectant resistance bacteria (DRB) and disinfectant resistance genes (DRGs) in the environment. Disinfection plays a crucial role in ensuring water safety, however, the presence of microplastics and DRGs seriously disturb the water disinfection process. Microplastics can reduce the concentration of disinfectant in the local environment around microorganisms and improve their tolerance. Microorganisms can improve their resistance to disinfectants or generate resistance genes via phenotypic adaptation, gene mutations, and horizontal gene transfer. However, very limited information is available on the impact of DRB and DRGs on disinfection process. In this paper, the contribution of microplastics to the migration and transmission of DRGs was analyzed. The challenges posed by the presence of microplastics and DRGs on conventional disinfection were thoroughly discussed. The knowledge gaps faced by relevant current research and further research priorities have been proposed in order to provide a scientific basis in the future.},
}
@article {pmid37728942,
year = {2023},
author = {Subirats, J and Sharpe, H and Tai, V and Fruci, M and Topp, E},
title = {Metagenome meta-analysis reveals an increase in the abundance of some multidrug efflux pumps and mobile genetic elements in chemically polluted environments.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {10},
pages = {e0104723},
pmid = {37728942},
issn = {1098-5336},
mesh = {Humans ; *Metagenome ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Interspersed Repetitive Sequences ; *Petroleum ; },
abstract = {Many human activities contaminate terrestrial and aquatic environments with numerous chemical pollutants that not only directly alter the environment but also affect microbial communities in ways that are potentially concerning to human health, such as selecting for the spread of antibiotic-resistance genes (ARGs) through horizontal gene transfer. In the present study, metagenomes available in the public domain from polluted (with antibiotics, with petroleum, with metal mining, or with coal-mining effluents) and unpolluted terrestrial and aquatic environments were compared to examine whether pollution has influenced the abundance and composition of ARGs and mobile elements, with specific focus on IS26 and class 1 integrons (intI1). When aggregated together, polluted environments had a greater relative abundance of ARGs than unpolluted environments and a greater relative abundance of IS26 and intI1. In general, chemical pollution, notably with petroleum, was associated with an increase in the prevalence of ARGs linked to multidrug efflux pumps. Included in the suite of efflux pumps were mexK, mexB, mexF, and mexW that are polyspecific and whose substrate ranges include multiple classes of critically important antibiotics. Also, in some instances, β-lactam resistance (TEM181 and OXA-541) genes increased, and genes associated with rifampicin resistance (RNA polymerases subunits rpoB and rpoB2) decreased in relative abundance. This meta-analysis suggests that different types of chemical pollution can enrich populations that carry efflux pump systems associated with resistance to multiple classes of medically critical antibiotics.IMPORTANCEThe United Nations has identified chemical pollution as being one of the three greatest threats to environmental health, through which the evolution of antimicrobial resistance, a seminally important public health challenge, may be favored. While this is a very plausible outcome of continued chemical pollution, there is little evidence or research evaluating this risk. The objective of the present study was to examine existing metagenomes from chemically polluted environments and evaluate whether there is evidence that pollution increases the relative abundance of genes and mobile genetic elements that are associated with antibiotic resistance. The key finding is that for some types of pollution, particularly in environments exposed to petroleum, efflux pumps are enriched, and these efflux pumps can confer resistance to multiple classes of medically important antibiotics that are typically associated with Pseudomonas spp. or other Gram-negative bacteria. This finding makes clear the need for more investigation on the impact of chemical pollution on the environmental reservoir of ARGs and their association with mobile genetic elements that can contribute to horizontal gene transfer events.},
}
@article {pmid37724865,
year = {2023},
author = {Sabatino, R and Sbaffi, T and Sivalingam, P and Corno, G and Fontaneto, D and Di Cesare, A},
title = {Bacteriophages limitedly contribute to the antimicrobial resistome of microbial communities in wastewater treatment plants.},
journal = {Microbiology spectrum},
volume = {11},
number = {5},
pages = {e0110123},
pmid = {37724865},
issn = {2165-0497},
abstract = {Bacteriophages are known as players in the transmission of antimicrobial resistance genes (ARGs) by horizontal gene transfer. In this study, we characterized the bacteriophage community and the associated ARGs to estimate the potential for phages to spread ARGs in aquatic ecosystems analyzing the intra- and extracellular DNA isolated from two wastewater treatment plants (WWTPs) by shotgun metagenomics. We compared the phage antimicrobial resistome with the bacterial resistome and investigated the effect of the final disinfection treatment on the phage community and its resistome. Phage community was mainly composed by Siphoviridae and other members of the order Caudovirales. The final disinfection only marginally affected the composition of the phage community, and it was not possible to measure its effect on the antimicrobial resistome. Indeed, only three phage metagenome-assembled genomes (pMAGs) annotated as Siphoviridae, Padoviridae, and Myoviridae were positive for putative ARGs. Among the detected ARGs, i.e., dfrB6, rpoB mutants, and EF-Tu mutants, the first one was not annotated in the bacterial MAGs. Overall, these results demonstrate that bacteriophages limitedly contribute to the whole antimicrobial resistome. However, in order to obtain a comprehensive understanding of the antimicrobial resistome within a microbial community, the role of bacteriophages needs to be investigated. IMPORTANCE WWTPs are considered hotspots for the spread of ARGs by horizontal gene transfer. In this study, we evaluated the phage composition and the associated antimicrobial resistome by shotgun metagenomics of samples collected before and after the final disinfection treatment. Only a few bacteriophages carried ARGs. However, since one of the detected genes was not found in the bacterial metagenome-assembled genomes, it is necessary to investigate the phage community in order to gain a comprehensive overview of the antimicrobial resistome. This investigation could help assess the potential threats to human health.},
}
@article {pmid37724858,
year = {2023},
author = {Derbyshire, KM and Salfinger, M},
title = {Plasmid-mediated drug resistance in mycobacteria: the tip of the iceberg?.},
journal = {Journal of clinical microbiology},
volume = {61},
number = {10},
pages = {e0062823},
pmid = {37724858},
issn = {1098-660X},
mesh = {Humans ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Mycobacterium chelonae/drug effects/genetics ; Macrolides/pharmacology ; Drug Resistance, Bacterial/genetics/drug effects ; Clarithromycin/therapeutic use ; *Mycobacterium/genetics/drug effects ; *Mycobacterium Infections, Nontuberculous/microbiology ; Nontuberculous Mycobacteria/isolation &amp; purification ; Chromosomes/drug effects ; },
abstract = {Macrolides, such as clarithromycin, are crucial in the treatment of nontuberculous mycobacteria (NTM). NTM are notoriously innately drug resistant, which has made the dependence on macrolides for their treatment even more important. Not surprisingly, resistance to macrolides has been documented in some NTM, including Mycobacterium avium and Mycobacterium abscessus, which are the two NTM species most often identified in clinical isolates. Resistance is mediated by point mutations in the 23S ribosomal RNA or by methylation of the rRNA by a methylase (encoded by an erm gene). Chromosomally encoded erm genes have been identified in many of the macrolide-resistant isolates, but not in Mycobacterium chelonae. Now, Brown-Elliott et al. (J Clin Microbiol 61:e00428-23, 2023, https://doi.org/10.1128/JCM.00428-23) describe the identification of a new erm variant, erm(55), which was found either on the chromosome or on a plasmid in highly macrolide-resistant clinical isolates of M. chelonae. The chromosomal erm(55) gene appears to be associated with mobile elements; one gene is within a putative transposon and the second is in a large (37 kb) insertion/deletion. The plasmid carrying erm(55) also encodes type IV and type VII secretion systems, which are often linked on large mycobacterial plasmids and are hypothesized to mediate plasmid transfer. While the conjugative transfer of the erm(55)-containing plasmid between NTM has yet to be demonstrated, the inferences are clear, as evidenced by the dissemination of plasmid-mediated drug resistance in other medically important bacteria. Here, we discuss the findings of Brown-Elliott et al., and the potential ramifications on treatment of NTM infections.},
}
@article {pmid37720149,
year = {2023},
author = {Bhat, BA and Mir, RA and Qadri, H and Dhiman, R and Almilaibary, A and Alkhanani, M and Mir, MA},
title = {Integrons in the development of antimicrobial resistance: critical review and perspectives.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1231938},
pmid = {37720149},
issn = {1664-302X},
abstract = {Antibiotic resistance development and pathogen cross-dissemination are both considered essential risks to human health on a worldwide scale. Antimicrobial resistance genes (AMRs) are acquired, expressed, disseminated, and traded mainly through integrons, the key players capable of transferring genes from bacterial chromosomes to plasmids and their integration by integrase to the target pathogenic host. Moreover, integrons play a central role in disseminating and assembling genes connected with antibiotic resistance in pathogenic and commensal bacterial species. They exhibit a large and concealed diversity in the natural environment, raising concerns about their potential for comprehensive application in bacterial adaptation. They should be viewed as a dangerous pool of resistance determinants from the "One Health approach." Among the three documented classes of integrons reported viz., class-1, 2, and 3, class 1 has been found frequently associated with AMRs in humans and is a critical genetic element to serve as a target for therapeutics to AMRs through gene silencing or combinatorial therapies. The direct method of screening gene cassettes linked to pathogenesis and resistance harbored by integrons is a novel way to assess human health. In the last decade, they have witnessed surveying the integron-associated gene cassettes associated with increased drug tolerance and rising pathogenicity of human pathogenic microbes. Consequently, we aimed to unravel the structure and functions of integrons and their integration mechanism by understanding horizontal gene transfer from one trophic group to another. Many updates for the gene cassettes harbored by integrons related to resistance and pathogenicity are extensively explored. Additionally, an updated account of the assessment of AMRs and prevailing antibiotic resistance by integrons in humans is grossly detailed-lastly, the estimation of AMR dissemination by employing integrons as potential biomarkers are also highlighted. The current review on integrons will pave the way to clinical understanding for devising a roadmap solution to AMR and pathogenicity. Graphical AbstractThe graphical abstract displays how integron-aided AMRs to humans: Transposons capture integron gene cassettes to yield high mobility integrons that target res sites of plasmids. These plasmids, in turn, promote the mobility of acquired integrons into diverse bacterial species. The acquisitions of resistant genes are transferred to humans through horizontal gene transfer.},
}
@article {pmid37718237,
year = {2023},
author = {You, L and Jin, H and Kwok, LY and Lv, R and Zhao, Z and Bilige, M and Sun, Z and Liu, W and Zhang, H},
title = {Intraspecific microdiversity and ecological drivers of lactic acid bacteria in naturally fermented milk ecosystem.},
journal = {Science bulletin},
volume = {68},
number = {20},
pages = {2405-2417},
doi = {10.1016/j.scib.2023.09.001},
pmid = {37718237},
issn = {2095-9281},
mesh = {Animals ; Milk/microbiology ; *Lactobacillales/genetics ; Lactobacillus/genetics ; Ecosystem ; Phylogeny ; *Lactobacillus delbrueckii/genetics ; *Lactococcus lactis ; },
abstract = {Traditional fermented milks are produced by inoculating technique, which selects well-adapted microorganisms that have been passed on through generations. Few reports have used naturally fermented milks as model ecosystems to investigate the mechanism of formation of intra-species microbial diversity. Here, we isolated and whole-genome-sequenced a total of 717 lactic acid bacterial isolates obtained from 12 independent naturally fermented milks collect from 12 regions across five countries. We further analyzed the within-sample intra-species phylogenies of 214 Lactobacillus helveticus isolates, 97 Lactococcus lactis subsp. lactis isolates, and 325 Lactobacillus delbrueckii subsp. bulgaricus isolates. We observed a high degree of intra-species genomic and functional gene diversity within-/between-sample(s). Single nucleotide polymorphism-based phylogenetic reconstruction revealed great within-sample intra-species heterogeneity, evolving from multiple lineages. Further phylogenetic reconstruction (presence-absence gene profile) revealed within-sample inter-clade functional diversity (based on carbohydrate-active enzyme- and peptidase-encoding genes) in all three investigated species/subspecies. By identifying and mapping clade-specific genes of intra-sample clades of the three species/subspecies to the respective fermented milk metagenome, we found extensive potential inter-/intra-species horizontal gene transfer events. Finally, the microbial composition of the samples is closely linked to the nucleotide diversity of the respective species/subspecies. Overall, our results contribute to the conservation of lactic acid bacteria resources, providing ecological insights into the microbial ecosystem of naturally fermented dairy products.},
}
@article {pmid37716694,
year = {2023},
author = {Savin, M and Hammerl, JA and Hassa, J and Hembach, N and Kalinowski, J and Schwartz, T and Droop, F and Mutters, NT},
title = {Free-floating extracellular DNA (exDNA) in different wastewaters: Status quo on exDNA-associated antimicrobial resistance genes.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {337},
number = {},
pages = {122560},
doi = {10.1016/j.envpol.2023.122560},
pmid = {37716694},
issn = {1873-6424},
mesh = {*Wastewater ; Anti-Bacterial Agents ; Genes, Bacterial ; Waste Disposal, Fluid/methods ; RNA, Ribosomal, 16S ; Angiotensin Receptor Antagonists ; Drug Resistance, Bacterial/genetics ; Angiotensin-Converting Enzyme Inhibitors ; DNA ; *Ozone/analysis ; },
abstract = {Wastewater treatment plants (WWTPs) have been reported as major anthropogenic reservoirs for the spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) into the environment, worldwide. While most studies mainly focus on the intracellular DNA (iDNA), extracellular DNA (exDNA) accounting for a significant proportion of the total DNA in wastewater, was usually neglected. Following the One Health approach, this study focuses on wastewaters of municipal, clinical, and livestock origins (n = 45) that undergo different treatment processes (i.e., conventional activated sludge, ultrafiltration, and ozonation). Water samples were analysed for 12 ARGs as indicators of the different compartments associated with iDNA and exDNA by quantitative real-time PCR (qPCR). Taxonomic profiling of exDNA-fractions, obtained using nucleic acid adsorption particles, was conducted by sequencing the V3-V4 hypervariable regions of the 16S rRNA gene. Notified exDNA concentrations varied between on-site WWTPs and treatment stages, and ranged from 314.0 ± 70.2 ng/mL in untreated livestock wastewater down to 0.7 ± 0.1 ng/mL in effluents after ultrafiltration. In general, influents exhibited higher concentrations compared to effluents, while wastewater treated by advanced treatment processes (i.e., ultrafiltration and ozonation) showed the lowest exDNA concentrations. Despite the lower concentrations, free-floating exDNA accounted for up to 80.0 ± 5.8% of the total DNA in effluents. Target ARGs were more common in the iDNA (100%, n = 45/45), compared to the exDNA-fractions (51.1%, n = 23/45), whereas exDNA-ARGs were mostly detected in clinical and slaughterhouse wastewaters as well as in the municipal influents. Compared to the iDNA-ARGs, the concentrations of exDNA-ARGs were in general lower. Nevertheless, significant higher concentrations for exDNA-associated genes were measured in clinical wastewaters for blaNDM (4.07 ± 0.15 log gene copies (GC)/L) and blaVIM-2 (6.0 ± 0.2 log GC/L). Overall, our results suggest that depending on the origin of wastewater and its treatment methods, exDNA represents an important reservoir for ARGs, particularly in clinical wastewater.},
}
@article {pmid37716437,
year = {2023},
author = {Rodríguez-Pallares, S and Mateo-Vargas, MA and Rodríguez-Iglesias, MA and Galán-Sánchez, F},
title = {Molecular characterization of consecutive isolates of OXA-48-producing Klebsiella pneumoniae: changes in the virulome using next-generation sequencing (NGS).},
journal = {Microbes and infection},
volume = {25},
number = {8},
pages = {105217},
doi = {10.1016/j.micinf.2023.105217},
pmid = {37716437},
issn = {1769-714X},
mesh = {Humans ; *Bacterial Proteins/genetics ; beta-Lactamases/genetics ; Klebsiella pneumoniae ; Multilocus Sequence Typing ; *Klebsiella Infections ; Virulence Factors/genetics ; Microbial Sensitivity Tests ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/pharmacology/therapeutic use ; },
abstract = {Little is known about the clonality of consecutive OXA-48 producing-Klebsiella pneumoniae isolates from the same patient and the possibility of changes in their virulomes over time. We studied the molecular characteristics of twenty OXA-48-producing K. pneumoniae consecutive isolates from six patients using whole-genome sequencing. The genomes were screened for antimicrobial resistance and virulence factor genes and for replicon groups. MLST and SNPs analysis was performed. MLST analysis found 3 STs: ST11 (n = 13; 65.0%); ST4975 (n = 5, 25.0%); ST307 (n = 2; 10.0%). AcrAb efflux pump, siderophore enterobactin and rcsAB capsule synthesis regulator were detected in all sequenced isolates. The regulator of mucoid phenotype A (rmpA) and rmpA2 were not detected. Isolates also carried type 3 fimbriae (n = 19; 95.0%), yersiniabactin (n = 15; 75.0%) and type 1 fimbriae (7; 35.0%). Type 3 fimbriae and yersiniabactin were lost and recovered in consecutive isolates of two patients, probably acquired by horizontal gene transfer. Our findings reveal that recurrent infections are due to the same isolate, with an average of 2.69 SNPs per month, with different virulence profiles, and that the acquisition of virulence factor genes over time is possible.},
}
@article {pmid37715312,
year = {2023},
author = {Xi, Y and Zhao, J and Zhang, J and Jin, Y and Yang, H and Duan, G and Chen, S and Long, J},
title = {Analysis of the features of 105 confirmed CRISPR loci in 487 Klebsiella variicola.},
journal = {Letters in applied microbiology},
volume = {76},
number = {9},
pages = {},
doi = {10.1093/lambio/ovad108},
pmid = {37715312},
issn = {1472-765X},
support = {2022M712859//China Postdoctoral Science Foundation/ ; 2018ZX10301407//National Science and Technology Specific Project of China/ ; },
mesh = {Humans ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Klebsiella/genetics ; Plasmids/genetics ; *Bacteriophages/genetics ; Klebsiella pneumoniae/genetics ; },
abstract = {Klebsiella variicola, an emerging human pathogen, poses a threat to public health. The horizontal gene transfer (HGT) of plasmids is an important driver of the emergence of multiple antibiotic-resistant K. variicola. Clustered regularly interspersed short palindromic repeats (CRISPR) coupled with CRISPR-associated genes (CRISPR/Cas) constitute an adaptive immune system in bacteria, and can provide acquired immunity against HGT. However, the information about the CRISPR/Cas system in K. variicola is still limited. In this study, 487 genomes of K. variicola obtained from the National Center for Biotechnology Information database were used to analyze the characteristics of CRISPR/Cas systems. Approximately 21.56% of genomes (105/487) harbor at least one confirmed CRISPR array. Three types of CRISPR/Cas systems, namely the type I-E, I-E*, and IV-A systems, were identified among 105 strains. Spacer origin analysis further revealed that approximately one-third of spacers significantly match plasmids or phages, which demonstrates the implication of CRISPR/Cas systems in controlling HGT. Moreover, spacers in K. variicola tend to target mobile genetic elements from K. pneumoniae. This finding provides new evidence of the interaction of K. variicola and K. pneumoniae during their evolution. Collectively, our results provide valuable insights into the role of CRISPR/Cas systems in K. variicola.},
}
@article {pmid37705515,
year = {2023},
author = {Abdelbary, ER and Elsaghier, AM and Abd El-Baky, RM and Waly, NGFM and Ramadan, M and Abd-Elsamea, FS and Ali, ME and Alzahrani, HA and Salah, M},
title = {First Emergence of NDM-5 and OqxAB Efflux Pumps Among Multidrug-Resistant Klebsiella pneumoniae Isolated from Pediatric Patients in Assiut, Egypt.},
journal = {Infection and drug resistance},
volume = {16},
number = {},
pages = {5965-5976},
pmid = {37705515},
issn = {1178-6973},
abstract = {INTRODUCTION: New Delhi metallo-β-lactamase (NDM)-producing K. pneumoniae poses a high risk, especially among Egyptian pediatric patients who consume carbapenems antibiotics very widely and without adequate diagnostic sources. In addition, presence of efflux pump genes such as OqxAB increases resistance against many groups of antimicrobials which exacerbates the problem faced for human health. This study aimed to determine NDM variants among K. pneumoniae strains isolated from pediatric patients in Egypt, analyze the presence of OqxAB genes, and molecular characterization of blaNDM-5-positive K. pneumoniae.<br><br>METHODS: Fifty-six K. pneumoniae&#xa0;isolates were recovered from pediatric patients, and tested for carbapenemase by modified carbapenem inactivation methods (mCIM) test. Minimum inhibitory concentrations of meropenem and colistin were determined by meropenem E-test strips and broth microdilution, respectively. PCR was used for the detection of the resistant genes (ESBL gene (blaCTX-M), carbapenemase genes (blaNDM, blaKPC) colistin resistant (mcr1, mcr2)) and genes for efflux pump (oqxA and oqxB). BlaNDM was sequenced. The effect of efflux pump in NDM-5-producing isolates was assessed by measuring MIC of ciprofloxacin and meropenem before and after exposure to the carbonyl cyanide 3-chlorophenylhydrazone (CCCP). The horizontal gene transfer ability of&#xa0;blaNDM-5 was determined using liquid mating assay and PCR-based replicon typing (PBRT) was done to determine the major plasmid incompatibility group.<br><br>RESULTS: Twenty-nine isolates were positive for blaNDM-1, nine isolates were positive for blaNDM-5, and 15 isolates were positive for blaKPC. There is a significant increase of meropenem MIC of NDM-5-positive isolates compared with NDM-1-positive isolates. In addition, 38 isolates were positive for CTX-M, and 15 isolates were positive for mcr1. Both OqxA and OqxB were detected in 26 isolates and 13 isolates were positive for OqxA while 11 isolates were positive for OqxB only. All NDM-5-producing isolates except one isolate could transfer their plasmids by conjugation to their corresponding transconjugants (E. coli J53). Plasmid replicon typing showed that FII was predominant in NDM-5-producing K. pneumoniae. Similar strains were found between the three isolates and similarity was also detected between the two isolates.<br><br>CONCLUSION: The highly resistant K. pneumoniae producing blaNDM-5 type was firstly isolated from pediatric patients. The association of efflux pump genes such as OqxAB is involved in resistance to ciprofloxacin. This highlighted the severity risk of&#xa0;blaNDM-5-positive&#xa0;K. pneumonia as it could transfer blaNDM-5 to other bacteria and has more resistance against carbapenems. This underlines the importance of continuous monitoring of infection control guidelines, and the urgent need for a national antimicrobial stewardship plan in Egyptian hospitals.},
}
@article {pmid37700871,
year = {2023},
author = {Nasir, A and Caetano-Anollés, G and Claverie, JM},
title = {Editorial: Viruses, genetic exchange, and the tree of life, volume II.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1271181},
pmid = {37700871},
issn = {1664-302X},
}
@article {pmid37700035,
year = {2023},
author = {Lin, X and Zhang, C and Han, R and Li, S and Peng, H and Zhou, X and Huang, L and Xu, Y},
title = {Oxytetracycline and heavy metals promote the migration of resistance genes in the intestinal microbiome by plasmid transfer.},
journal = {The ISME journal},
volume = {17},
number = {11},
pages = {2003-2013},
pmid = {37700035},
issn = {1751-7370},
mesh = {Animals ; Humans ; *Oxytetracycline/pharmacology ; *Gastrointestinal Microbiome ; Genes, Bacterial ; *Metals, Heavy/toxicity ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Microbiota ; Plasmids/genetics ; Gene Transfer, Horizontal ; },
abstract = {Horizontal gene transfer (HGT) has been considered the most important pathway to introduce antibiotic resistance genes (ARGs), which seriously threatens human health and biological security. The presence of ARGs in the aquatic environment and their effect on the intestinal micro-ecosystem of aquatic animals can occur easily. To investigate the HGT potential and rule of exogenous ARGs in the intestinal flora, a visual conjugative model was developed, including the donor of dual-fluorescent bacterium and the recipient of Xenopus tropicalis intestinal microbiome. Some common pollutants of oxytetracycline (OTC) and three heavy metals (Zn, Cu and Pb) were selected as the stressor. The multi-techniques of flow cytometry (FCM), scanning electron microscopy (SEM), atomic force microscopy (AFM), single-cell Raman spectroscopy with sorting (SCRSS) and indicator analysis were used in this study. The results showed that ARG transfer could occur more easily under stressors. Moreover, the conjugation efficiency mainly depended on the viability of the intestinal bacteria. The mechanisms of OTC and heavy metal stressing conjugation included the upregulation of ompC, traJ, traG and the downregulation of korA gene. Moreover, the enzymatic activities of SOD, CAT, GSH-PX increased and the bacterial surface appearance also changed. The predominant recipient was identified as Citrobacter freundi by SCRSS, in which the abundance and quantity of ARG after conjugation were higher than those before. Therefore, since the diversity of potential recipients in the intestine are very high, the migration of invasive ARGs in the microbiome should be given more attention to prevent its potential risks to public health.},
}
@article {pmid37697273,
year = {2023},
author = {El-Sabeh, A and Mlesnita, AM and Munteanu, IT and Honceriu, I and Kallabi, F and Boiangiu, RS and Mihasan, M},
title = {Characterisation of the Paenarthrobacter nicotinovorans ATCC 49919 genome and identification of several strains harbouring a highly syntenic nic-genes cluster.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {536},
pmid = {37697273},
issn = {1471-2164},
support = {PN-III-P4-ID-PCE-2020-0656//Romanian Ministry of Education and Research/ ; PN-III-P4-ID-PCE-2020-0656//Romanian Ministry of Education and Research/ ; PN-III-P4-ID-PCE-2020-0656//Romanian Ministry of Education and Research/ ; PN-III-P4-ID-PCE-2020-0656//Romanian Ministry of Education and Research/ ; PN-III-P4-ID-PCE-2020-0656//Romanian Ministry of Education and Research/ ; },
mesh = {*Nicotine ; *Micrococcaceae ; Soil ; DNA ; },
abstract = {BACKGROUND: Paenarthrobacter nicotinovorans ATCC 49919 uses the pyridine-pathway to degrade nicotine and could provide a renewable source of precursors from nicotine-containing waste as well as a model for studying the molecular evolution of catabolic pathways and their spread by horizontal gene transfer via soil bacterial plasmids.<br><br>RESULTS: In the present study, the strain was sequenced using the Illumina NovaSeq 6000 and Oxford Nanopore Technology (ONT) MinION platforms. Following hybrid assembly with Unicycler, the complete genome sequence of the strain was obtained and used as reference for whole-genome-based phylogeny analyses. A total of 64 related genomes were analysed; five Arthrobacter strains showed both digital DNA-DNA hybridization and average nucleotide identity values over the species threshold when compared to P. nicotinovorans ATCC 49919. Five plasmids and two contigs belonging to Arthrobacter and Paenarthrobacter strains were shown to be virtually identical with the pAO1 plasmid of Paenarthrobacter nicotinovorans ATCC 49919. Moreover, a highly syntenic nic-genes cluster was identified on five plasmids, one contig and three chromosomes. The nic-genes cluster contains two major locally collinear blocks that appear to form a putative catabolic transposon. Although the origins of the nic-genes cluster and the putative transposon still elude us, we hypothesise here that the ATCC 49919 strain most probably evolved from Paenarthrobacter sp. YJN-D or a very closely related strain by acquiring the pAO1 megaplasmid and the nicotine degradation pathway.<br><br>CONCLUSIONS: The data presented here offers another snapshot into the evolution of plasmids harboured by Arthrobacter and Paenarthrobacter species and their role in the spread of metabolic traits by horizontal gene transfer among related soil bacteria.},
}
@article {pmid37693864,
year = {2023},
author = {Doughty, EL and Liu, H and Moran, RA and Hua, X and Ba, X and Guo, F and Chen, X and Zhang, L and Holmes, M and van Schaik, W and McNally, A and Yu, Y},
title = {Endemicity and diversification of carbapenem-resistant Acinetobacter baumannii in an intensive care unit.},
journal = {The Lancet regional health. Western Pacific},
volume = {37},
number = {},
pages = {100780},
pmid = {37693864},
issn = {2666-6065},
support = {MR/S013660/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {BACKGROUND: Carbapenem-resistant Acinetobacter baumannii (CRAB) is a major public health concern globally. Often studied in the context of hospital outbreaks, little is known about the persistence and evolutionary dynamics of endemic CRAB populations.<br><br>METHODS: A three-month cross-sectional observational study was conducted in a 28-bed intensive care unit (ICU) in Hangzhou, China. A total of 5068 samples were collected from the hospital environment (n&#xa0;=&#xa0;3985), patients (n&#xa0;=&#xa0;964) and staff (n&#xa0;=&#xa0;119). CRAB isolates were obtained from 10.5% of these samples (n&#xa0;=&#xa0;532). All of these isolates, plus an additional 19 from clinical infections, were characterised through whole-genome sequencing.<br><br>FINDINGS: The ICU CRAB population was dominated by OXA-23-producing global clone 2 isolates (99.3% of all isolates) that could be divided into 20 distinct clusters, defined through genome sequencing. CRAB was persistently present in the ICU, driven by regular introductions of distinct clusters. The hospital environment was heavily contaminated, with CRAB isolated from bed units on 183/335 (54.6%) sampling occasions but from patients on only 72/299 (24.1%) occasions. CRAB was spread to adjacent bed units and rooms, and following re-location of patients within the ICU. We also observed three horizontal gene transfer events between CRAB strains in the ICU, involving three different plasmids.<br><br>INTERPRETATION: The epidemiology of CRAB in this setting contrasted with previously described clonal outbreaks in high-income countries, highlighting the importance of environmental CRAB reservoirs in ICU epidemiology and the unique challenges in containing the spread of CRAB in ICUs where this important multidrug-resistant pathogen is endemic.<br><br>FUNDING: This work was undertaken as part of the DETECTIVE research project funded by the Medical Research Council (MR/S013660/1), National Natural Science Foundation of China (81861138054, 32011530116, 31970128, 31770142), Zhejiang Province Medical Platform Backbone Talent Plan (2020RC075), and the National Key Research and Development Program of China grant (2018YFE0102100). W.v.S was also supported by a Wolfson Research Merit Award (WM160092).},
}
@article {pmid37693574,
year = {2023},
author = {Fox, BW and Helf, MJ and Burkhardt, RN and Artyukhin, AB and Curtis, BJ and Palomino, DF and Chaturbedi, A and Tauffenberger, A and Wrobel, CJJ and Zhang, YK and Lee, SS and Schroeder, FC},
title = {Evolutionarily related host and microbial pathways regulate fat desaturation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37693574},
issn = {2692-8205},
support = {P40 OD010440/OD/NIH HHS/United States ; R35 GM131877/GM/NIGMS NIH HHS/United States ; T32 GM138826/GM/NIGMS NIH HHS/United States ; },
abstract = {Fatty acid desaturation is central to metazoan lipid metabolism and provides building blocks of membrane lipids and precursors of diverse signaling molecules. Nutritional conditions and associated microbiota regulate desaturase expression[1-4], but the underlying mechanisms have remained unclear. Here, we show that endogenous and microbiota-dependent small molecule signals promote lipid desaturation via the nuclear receptor NHR-49/PPARα in C. elegans. Untargeted metabolomics of a β-oxidation mutant, acdh-11, in which expression of the stearoyl-CoA desaturase FAT-7/SCD1 is constitutively increased, revealed accumulation of a β-cyclopropyl fatty acid, becyp#1, that potently activates fat-7 expression via NHR-49. Biosynthesis of becyp#1 is strictly dependent on expression of cyclopropane synthase by associated bacteria, e.g., E. coli. Screening for structurally related endogenous metabolites revealed a β-methyl fatty acid, bemeth#1, whose activity mimics that of microbiota-dependent becyp#1, but is derived from a methyltransferase, fcmt-1, that is conserved across Nematoda and likely originates from bacterial cyclopropane synthase via ancient horizontal gene transfer. Activation of fat-7 expression by these structurally similar metabolites is controlled by distinct mechanisms, as microbiota-dependent becyp#1 is metabolized by a dedicated β-oxidation pathway, while the endogenous bemeth#1 is metabolized via α-oxidation. Collectively, we demonstrate that evolutionarily related biosynthetic pathways in metazoan host and associated microbiota converge on NHR-49/PPARα to regulate fat desaturation.},
}
@article {pmid37693541,
year = {2023},
author = {Li, Z and Xue, AZ and Maeda, GP and Li, Y and Nabity, PD and Moran, NA},
title = {Phylloxera and aphids show distinct features of genome evolution despite similar reproductive modes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.08.28.555181},
pmid = {37693541},
issn = {2692-8205},
abstract = {Genomes of aphids (family Aphididae) show several unusual evolutionary patterns. In particular, within the XO sex determination system of aphids, the X chromosome exhibits a lower rate of interchromosomal rearrangements, fewer highly expressed genes, and faster evolution at nonsynonymous sites compared to the autosomes. In contrast, other hemipteran lineages have similar rates of interchromosomal rearrangement for autosomes and X chromosomes. One possible explanation for these differences is the aphid's life cycle of cyclical parthenogenesis, where multiple asexual generations alternate with one sexual generation. If true, we should see similar features in the genomes of Phylloxeridae, an outgroup of aphids which also undergoes cyclical parthenogenesis. To investigate this, we generated a chromosome-level assembly for the grape phylloxera, an agriculturally important species of Phylloxeridae, and identified its single X chromosome. We then performed synteny analysis using the phylloxerid genome and 30 high-quality genomes of aphids and other hemipteran species. Unexpectedly, we found that the phylloxera does not share aphids' patterns of chromosome evolution. By estimating interchromosomal rearrangement rates on an absolute time scale, we found that rates are elevated for aphid autosomes compared to their X chromosomes, but this pattern does not extend to the phylloxera branch. Potentially, the conservation of X chromosome gene content is due to selection on XO males that appear in the sexual generation. We also examined gene duplication patterns across Hemiptera and uncovered horizontal gene transfer events contributing to phylloxera evolution.},
}
@article {pmid37692203,
year = {2023},
author = {Chang, H and Bai, J and Zhang, H and Huang, R and Chu, H and Wang, Q and Liu, H and Cheng, J and Jiang, H},
title = {Origin and evolution of the main starch biosynthetic enzymes.},
journal = {Synthetic and systems biotechnology},
volume = {8},
number = {3},
pages = {462-468},
pmid = {37692203},
issn = {2405-805X},
abstract = {Starch, a semi-crystalline energy storage form primarily found in plant plastids plays a crucial role in various food or no-food applications. Despite the starch biosynthetic pathway's main enzymes have been characterized, their origin and evolution remained a subject of debate. In this study, we conducted the comprehensive phylogenetic and structural analysis of three types of starch biosynthetic enzymes: starch synthase (SS), starch branching enzyme (SBE) and isoamylase-type debranching enzyme (ISA) from 51,151 annotated genomes. Our findings provide valuable insights into the possible scenario for the origin and evolution of the starch biosynthetic pathway. Initially, the ancestor of SBE can be traced back to an unidentified bacterium that existed before the formation of the last eukaryotic common ancestor (LECA) via horizontal gene transfer (HGT). This transfer event likely provided the eukaryote ancestor with the ability to synthesize glycogen. Furthermore, during the emergence of Archaeplastida, one clade of SS was transferred from Deltaproteobacteria by HGT, while ISA and the other clade of SS originated from Chlamydiae through endosymbiosis gene transfer (EGT). Both these transfer events collectively contributed to the establishment of the original starch biosynthetic pathway. Subsequently, after the divergence of Viridiplantae from Rhodophyta, all three enzymes underwent multiple duplications and N-terminus extension domain modifications, resulting in the formation of functionally specialized isoforms and ultimately leading to the complete starch biosynthetic pathway. By shedding light on the evolutionary origins of key enzymes involved in the starch biosynthetic pathway, this study provides important insights into the evolutionary events of plants.},
}
@article {pmid37690629,
year = {2023},
author = {Haghjooy Javanmard, S and Rafiee, L and Bahri Najafi, M and Khorsandi, D and Hasan, A and Vaseghi, G and Makvandi, P},
title = {Microfluidic-based technologies in cancer liquid biopsy: Unveiling the role of horizontal gene transfer (HGT) materials.},
journal = {Environmental research},
volume = {238},
number = {Pt 1},
pages = {117083},
doi = {10.1016/j.envres.2023.117083},
pmid = {37690629},
issn = {1096-0953},
mesh = {Humans ; *Microfluidics ; *Neoplasms ; Gene Transfer, Horizontal ; Precision Medicine ; Liquid Biopsy ; DNA ; },
abstract = {Liquid biopsy includes the isolating and analysis of non-solid biological samples enables us to find new ways for molecular profiling, prognostic assessment, and better therapeutic decision-making in cancer patients. Despite the conventional theory of tumor development, a non-vertical transmission of DNA has been reported among cancer cells and between cancer and normal cells. The phenomenon referred to as horizontal gene transfer (HGT) has the ability to amplify the advancement of tumors by disseminating genes that encode molecules conferring benefits to the survival or metastasis of cancer cells. Currently, common liquid biopsy approaches include the analysis of extracellular vesicles (EVs) and tumor-free DNA (tfDNA) derived from primary tumors and their metastatic sites, which are well-known HGT mediators in cancer cells. Current technological and molecular advances expedited the high-throughput and high-sensitive HGT materials analyses by using new technologies, such as microfluidics in liquid biopsies. This review delves into the convergence of microfluidic-based technologies and the investigation of Horizontal Gene Transfer (HGT) materials in cancer liquid biopsy. The integration of microfluidics offers unprecedented advantages such as high sensitivity, rapid analysis, and the ability to analyze rare cell populations. These attributes are instrumental in detecting and characterizing CTCs, circulating nucleic acids, and EVs, which are carriers of genetic cargo that could potentially undergo HGT. The phenomenon of HGT in cancer has raised intriguing questions about its role in driving genomic diversity and acquired drug resistance. By leveraging microfluidic platforms, researchers have been able to capture and analyze individual cells or genetic material with enhanced precision, shedding light on the potential transfer of genetic material between cancer cells and surrounding stromal cells. Furthermore, the application of microfluidics in single-cell sequencing has enabled the elucidation of the genetic changes associated with HGT events, providing insights into the evolution of tumor genomes. This review also discusses the challenges and opportunities in studying HGT materials using microfluidic-based technologies. In conclusion, microfluidic-based technologies have significantly advanced the field of cancer liquid biopsy, enabling the sensitive and accurate detection of HGT materials. As the understanding of HGT's role in tumor evolution and therapy resistance continues to evolve, the synergistic integration of microfluidics and HGT research promises to provide valuable insights into cancer biology, with potential implications for precision oncology and therapeutic strategies.},
}
@article {pmid37689422,
year = {2023},
author = {Hull, DM and Harrel, E and Harden, L and Thakur, S},
title = {Detection of resistance and virulence plasmids in Campylobacter coli and Campylobacter jejuni isolated from North Carolina food animal production, 2018-2019.},
journal = {Food microbiology},
volume = {116},
number = {},
pages = {104348},
doi = {10.1016/j.fm.2023.104348},
pmid = {37689422},
issn = {1095-9998},
mesh = {Animals ; Cattle ; Swine ; *Campylobacter coli/genetics ; *Campylobacter jejuni/genetics ; Virulence/genetics ; North Carolina ; Chickens ; *Campylobacter ; Virulence Factors/genetics ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; },
abstract = {Campylobacter remains the leading cause of bacterial foodborne illness in the U.S. and worldwide. Campylobacter plasmids may play a significant role in antimicrobial resistance (AMR) and virulence factor distribution, and potentially drive rapid adaptation. C. coli (n = 345) and C. jejuni (n = 199) isolates collected from live cattle, swine, turkey, and chickens, poultry carcasses at production, and retail meat in N.C. were analyzed to determine plasmid prevalence, extrachromosomal virulence and AMR genes, and the phylogeny of assembled plasmids. Putative plasmids ranging from <2 kb to 237kb were identified with virulence factors present in 66.1% (228/345) C. coli and 88.4% (176/199) C. jejuni plasmids (promoting adherence, invasion, exotoxin production, immune modulation, chemotaxis, mobility, and the type IV secretion system). AMR genes were identified in 21.2% (73/345) C. coli and 28.1% C. jejuni plasmids (conferring resistance to tetracyclines, aminoglycosides, beta-lactams, nucleosides, and lincosamides). Megaplasmids (>100 kb) were present in 25.7% (140/544) of the isolates and carried genes previously recognized to be involved with interspecies recombination. Our study highlights the extensive distribution and diversity of Campylobacter plasmids in food animal production and their role in the dissemination of biomedically important genes. Characterizing Campylobacter plasmids within the food animal production niche is important to understanding the epidemiology of potential emerging strains.},
}
@article {pmid37680975,
year = {2023},
author = {Ashy, RA},
title = {Functional analysis of bacterial genes accidentally packaged in rhizospheric phageome of the wild plant species Abutilon fruticosum.},
journal = {Saudi journal of biological sciences},
volume = {30},
number = {10},
pages = {103789},
pmid = {37680975},
issn = {1319-562X},
abstract = {The study aimed to reveal the structure and function of phageome existing in soil rhizobiome of Abutilon fruticosum in order to detect accidentally-packaged bacterial genes that encode Carbohydrate-Active enZymes (or CAZymes) and those that confer antibiotic resistance (e.g., antibiotic resistance genes or ARGs). Highly abundant genes were shown to mainly exist in members of the genera Pseudomonas, Streptomyces, Mycobacterium and Rhodococcus. Enriched CAZymes belong to glycoside hydrolase families GH4, GH6, GH12, GH15 and GH43 and mainly function in D-glucose biosynthesis via 10 biochemical passages. Another enriched CAZyme, e.g., alpha-galactosidase, of the GH4 family is responsible for the wealth of different carbohydrate forms in rhizospheric soil sink of A. fruticosum. ARGs of this phageome include the soxR and OleC genes that participate in the "antibiotic efflux pump" resistance mechanism, the parY mutant gene that participates in the "antibiotic target alteration" mechanism and the arr-1, iri, and AAC(3)-Ic genes that participate in the "antibiotic inactivation" mechanism. It is claimed that the genera Streptomyces, which harbors phages with oleC and parY mutant genes, and Pseudomonas, which harbors phages with soxR and AAC(3)-Ic genes, are approaching multidrug resistance via newly disseminating phages. These ARGs inhibit many antibiotics including oleandomycin, tetracycline, rifampin and aminoglycoside. The study highlights the possibility of accidental packaging of these ARGs in soil phageome and the risk of their horizontal transfer to human gut pathogens through the food chain as detrimental impacts of soil phageome of A. fruticosum. The study also emphasizes the beneficial impacts of phageome on soil microbiome and plant interacting in storing carbohydrates in the soil sink for use by the two entities upon carbohydrate deprivation.},
}
@article {pmid37676703,
year = {2023},
author = {Avontuur, JR and Wilken, PM and Palmer, M and Coetzee, MPA and Stępkowski, T and Venter, SN and Steenkamp, ET},
title = {Complex evolutionary history of photosynthesis in Bradyrhizobium.},
journal = {Microbial genomics},
volume = {9},
number = {9},
pages = {},
pmid = {37676703},
issn = {2057-5858},
mesh = {*Bradyrhizobium/genetics ; Photosynthesis/genetics ; },
abstract = {Bradyrhizobium comprises a diverse group of bacteria with various lifestyles. Although best known for their nodule-based nitrogen-fixation in symbiosis with legumes, a select group of bradyrhizobia are also capable of photosynthesis. This ability seems to be rare among rhizobia, and its origin and evolution in these bacteria remain a subject of substantial debate. Therefore, our aim here was to investigate the distribution and evolution of photosynthesis in Bradyrhizobium using comparative genomics and representative genomes from closely related taxa in the families Nitrobacteraceae, Methylobacteriaceae, Boseaceae and Paracoccaceae. We identified photosynthesis gene clusters (PGCs) in 25 genomes belonging to three different Bradyrhizobium lineages, notably the so-called Photosynthetic, B. japonicum and B. elkanii supergroups. Also, two different PGC architectures were observed. One of these, PGC1, was present in genomes from the Photosynthetic supergroup and in three genomes from a species in the B. japonicum supergroup. The second cluster, PGC2, was also present in some strains from the B. japonicum supergroup, as well as in those from the B. elkanii supergroup. PGC2 was largely syntenic to the cluster found in Rhodopseudomonas palustris and Tardiphaga . Bayesian ancestral state reconstruction unambiguously showed that the ancestor of Bradyrhizobium lacked a PGC and that it was acquired horizontally by various lineages. Maximum-likelihood phylogenetic analyses of individual photosynthesis genes also suggested multiple acquisitions through horizontal gene transfer, followed by vertical inheritance and gene losses within the different lineages. Overall, our findings add to the existing body of knowledge on Bradyrhizobium ’s evolution and provide a meaningful basis from which to explore how these PGCs and the photosynthesis itself impact the physiology and ecology of these bacteria.},
}
@article {pmid37670002,
year = {2023},
author = {Natarajan, S and Pucker, B and Srivastava, S},
title = {Genomic and transcriptomic analysis of camptothecin producing novel fungal endophyte: Alternaria burnsii NCIM 1409.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {14614},
pmid = {37670002},
issn = {2045-2322},
mesh = {*Camptothecin ; *Endophytes ; Transcriptome ; Alternaria ; Genomics ; },
abstract = {Camptothecin is an important anticancer alkaloid produced by particular plant species. No suitable synthetic route has been established for camptothecin production yet, imposing a stress on plant-based production systems. Endophytes associated with these camptothecin-producing plants have been reported to also produce camptothecin and other high-value phytochemicals. A previous study identified a fungal endophyte Alternaria burnsii NCIM 1409, isolated from Nothapodytes nimmoniana, to be a sustainable producer of camptothecin. Our study provides key insights on camptothecin biosynthesis in this recently discovered endophyte. The whole genome sequence of A. burnsii NCIM 1409 was assembled and screened for biosynthetic gene clusters. Comparative studies with related fungi supported the identification of candidate genes involved in camptothecin synthesis and also helped to understand some aspects of the endophyte's defense against the toxic effects of camptothecin. No evidence for horizontal gene transfer of the camptothecin biosynthetic genes from the host plant to the endophyte was detected suggesting an independent evolution of the camptothecin biosynthesis in this fungus.},
}
@article {pmid37665285,
year = {2024},
author = {Takahashi, T and Kim, H and Kim, HS and Kim, HS and Song, W and Kim, JS},
title = {Comparative Genomic Analysis of Staphylococcal Cassette Chromosome mec Type V Staphylococcus aureus Strains and Estimation of the Emergence of SCCmec V Clinical Isolates in Korea.},
journal = {Annals of laboratory medicine},
volume = {44},
number = {1},
pages = {47-55},
pmid = {37665285},
issn = {2234-3814},
mesh = {Humans ; Likelihood Functions ; *Methicillin-Resistant Staphylococcus aureus/genetics ; Phylogeny ; Staphylococcus aureus ; Genomics ; Staphylococcus ; Republic of Korea ; },
abstract = {BACKGROUND: Staphylococcal cassette chromosome mec type V (SCCmec V) methicillin-resistant Staphylococcus aureus (MRSA) has been recovered from patients and livestock. Using comparative genomic analyses, we evaluated the phylogenetic emergence of SCCmec V after transmission from overseas donor strains to Korean recipient strains.<br><br>METHODS: Sixty-three complete MRSA SCCmec V genomes (including six Korean clinical isolates) were used to construct a phylogenetic tree. Single-nucleotide polymorphisms were identified using Snippy, and a maximum-likelihood-based phylogenetic tree was constructed using RAxML. The possible emergence of the most common ancestor was estimated using BactDating. To estimate mecA horizontal gene transfer (HGT) events, Ranger-dtl was applied to 818 SCCmec V strains using publicly available whole-genome data.<br><br>RESULTS: The phylogenetic tree showed five major clades. German strains formed a major clade; their possible origin was traced to the 1980s. The emergence of Korean SCCmec V clinical isolates was traced to 2000-2010. mecA HGT events in Staphylococcus spp. were identified in seven strains. P7 (Hong Kong outbreak strain) served as the donor strain for two Korean sequence type (ST) 59 strains, whereas the other five recipient strains emerged from different SCCmec V donors.<br><br>CONCLUSIONS: Most Korean SCCmec V strains may have emerged during 2000-2010. A unique MRSA SCCmec V strain, ST72 (a Korean common type of community-associated MRSA), was also identified. The genomic dynamics of this clone with a zoonotic background should be monitored to accurately understand MRSA evolution.},
}
@article {pmid37664620,
year = {2023},
author = {Mao, C and Li, Q and Komijani, M and Huang, J and Li, T},
title = {Metagenomic analysis reveals the dissemination mechanisms and risks of resistance genes in plateau lakes.},
journal = {iScience},
volume = {26},
number = {9},
pages = {107508},
pmid = {37664620},
issn = {2589-0042},
abstract = {Antibiotic resistance genes (ARGs) are emerging as environmental pollutants that can persist and disseminate in aquatic environments. Lakes, as important sources of freshwater, also serve as potential natural reservoirs of ARGs. In this study, we analyzed the distribution and potential risks of resistance genes in five typical freshwater lakes on the Yunnan-Guizhou Plateau. Our findings revealed that multidrug and MLS ARGs dominated in the studied lakes. Notably, while Lugu Lake exhibited higher abundance of ARGs, mobile genetic elements (MGEs), and metal resistance genes (MRGs), a greater resistome risk was observed in the eutrophic Xingyun Lake. The dissemination processes of ARGs and MRGs are primarily driven by microbial communities and the horizontal gene transfer via MGEs. Limnohabitans, Flavobacterium, and Acinetobacter were identified as key players in the dissemination of ARGs. Our study highlights the persistence of ARGs and provides valuable baseline data and risk assessment of ARGs in plateau freshwater lakes.},
}
@article {pmid37662302,
year = {2023},
author = {Jeong, DE and Sundrani, S and Hall, RN and Krupovic, M and Koonin, EV and Fire, AZ},
title = {DNA polymerase diversity reveals multiple incursions of Polintons during nematode evolution.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.08.22.554363},
pmid = {37662302},
issn = {2692-8205},
abstract = {Polintons are dsDNA, virus-like self-synthesizing transposons widely found in eukaryotic genomes. Recent metagenomic discoveries of Polinton-like viruses are consistent with the hypothesis that Polintons invade eukaryotic host genomes through infectious viral particles. Nematode genomes contain multiple copies of Polintons and provide an opportunity to explore the natural distribution and evolution of Polintons during this process. We performed an extensive search of Polintons across nematode genomes, identifying multiple full-length Polinton copies in several species. We provide evidence of both ancient Polinton integrations and recent mobility in strains of the same nematode species. In addition to the major nematode Polinton family, we identified a group of Polintons that are overall closely related to the major family, but encode a distinct protein-primed B family DNA polymerase (pPolB) that is related to homologs from a different group of Polintons present outside of the Nematoda . Phylogenetic analyses on the pPolBs support the evolutionary scenarios in which these extrinsic pPolBs that seem to derive from Polinton families present in oomycetes and molluscs replaced the canonical pPolB in subsets of Polintons found in terrestrial and marine nematodes, respectively, suggesting inter-phylum horizontal gene transfers. The pPolBs of the terrestrial nematode and oomycete Polintons share a unique feature, an insertion of a HNH nuclease domain, whereas the pPolBs in the marine nematode Polintons share an insertion of a VSR nuclease domain with marine mollusc pPolBs. We hypothesize that horizontal gene transfer occurs among Polintons from widely different but cohabiting hosts.},
}
@article {pmid37662235,
year = {2023},
author = {Pandey, T and Kalluraya, C and Wang, B and Xu, T and Huang, X and Guang, S and Daugherty, MD and Ma, DK},
title = {Acquired stress resilience through bacteria-to-nematode horizontal gene transfer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37662235},
issn = {2692-8205},
support = {P40 OD010440/OD/NIH HHS/United States ; R35 GM133633/GM/NIGMS NIH HHS/United States ; R35 GM139618/GM/NIGMS NIH HHS/United States ; },
abstract = {Natural selection drives acquisition of organismal resilience traits to protect against adverse environments. Horizontal gene transfer (HGT) is an important evolutionary mechanism for the acquisition of novel traits, including metazoan acquisition of functions in immunity, metabolism, and reproduction via interdomain HGT (iHGT) from bacteria. We report that the nematode gene rml-3, which was acquired by iHGT from bacteria, enables exoskeleton resilience and protection against environmental toxins in C. elegans. Phylogenetic analysis reveals that diverse nematode RML-3 proteins form a single monophyletic clade most highly similar to bacterial enzymes that biosynthesize L-rhamnose to build cell wall polysaccharides. C. elegans rml-3 is regulated in developing seam cells by heat stress and stress-resistant dauer stage. Importantly, rml-3 deficiency impairs cuticle integrity, barrier functions and organismal stress resilience, phenotypes that are rescued by exogenous L-rhamnose. We propose that iHGT of an ancient bacterial rml-3 homolog enables L-rhamnose biosynthesis in nematodes that facilitates cuticle integrity and organismal resilience in adaptation to environmental stresses during evolution. These findings highlight the remarkable contribution of iHGT on metazoan evolution that is conferred by the domestication of bacterial genes.},
}
@article {pmid37662009,
year = {2023},
author = {Li, Z and Zhou, X and Liao, D and Liu, R and Zhao, X and Wang, J and Zhong, Q and Zeng, Z and Peng, Y and Tan, Y and Yang, Z},
title = {Comparative genomics and DNA methylation analysis of Pseudomonas aeruginosa clinical isolate PA3 by single-molecule real-time sequencing reveals new targets for antimicrobials.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1180194},
pmid = {37662009},
issn = {2235-2988},
mesh = {*Pseudomonas aeruginosa/genetics ; DNA Methylation ; Phylogeny ; Genomics ; *Anti-Infective Agents ; DNA ; },
abstract = {INTRODUCTION: Pseudomonas aeruginosa (P.aeruginosa) is an important opportunistic pathogen with broad environmental adaptability and complex drug resistance. Single-molecule real-time (SMRT) sequencing technique has longer read-length sequences, more accuracy, and the ability to identify epigenetic DNA alterations.<br><br>METHODS: This study applied SMRT technology to sequence a clinical strain P. aeruginosa PA3 to obtain its genome sequence and methylation modification information. Genomic, comparative, pan-genomic, and epigenetic analyses of PA3 were conducted.<br><br>RESULTS: General genome annotations of PA3 were discovered, as well as information about virulence factors, regulatory proteins (RPs), secreted proteins, type II toxin-antitoxin (TA) pairs, and genomic islands. A genome-wide comparison revealed that PA3 was comparable to other P. aeruginosa strains in terms of identity, but varied in areas of horizontal gene transfer (HGT). Phylogenetic analysis showed that PA3 was closely related to P. aeruginosa 60503 and P. aeruginosa 8380. P. aeruginosa's pan-genome consists of a core genome of roughly 4,300 genes and an accessory genome of at least 5,500 genes. The results of the epigenetic analysis identified one main methylation sites, N6-methyladenosine (m6A) and 1 motif (CATNNNNNNNTCCT/AGGANNNNNNNATG). 16 meaningful methylated sites were picked. Among these, purH, phaZ, and lexA are of great significance playing an important role in the drug resistance and biological environment adaptability of PA3, and the targeting of these genes may benefit further antibacterial studies.<br><br>DISUCSSION: This study provided a detailed visualization and DNA methylation information of the PA3 genome and set a foundation for subsequent research into the molecular mechanism of DNA methyltransferase-controlled P. aeruginosa pathogenicity.},
}
@article {pmid37658677,
year = {2023},
author = {Clark, JW},
title = {Genome evolution in plants and the origins of innovation.},
journal = {The New phytologist},
volume = {240},
number = {6},
pages = {2204-2209},
doi = {10.1111/nph.19242},
pmid = {37658677},
issn = {1469-8137},
support = {RPG-2019-004//Leverhulme Trust/ ; },
mesh = {*Plants/genetics ; *Evolution, Molecular ; Genome, Plant ; Gene Duplication ; Gene Transfer, Horizontal ; Phylogeny ; },
abstract = {Plant evolution has been characterised by a series of major novelties in their vegetative and reproductive traits that have led to greater complexity. Underpinning this diversification has been the evolution of the genome. When viewed at the scale of the plant kingdom, plant genome evolution has been punctuated by conspicuous instances of gene and whole-genome duplication, horizontal gene transfer and extensive gene loss. The periods of dynamic genome evolution often coincide with the evolution of key traits, demonstrating the coevolution of plant genomes and phenotypes at a macroevolutionary scale. Conventionally, plant complexity and diversity have been considered through the lens of gene duplication and the role of gene loss in plant evolution remains comparatively unexplored. However, in light of reductive evolution across multiple plant lineages, the association between gene loss and plant phenotypic diversity warrants greater attention.},
}
@article {pmid37657315,
year = {2023},
author = {Zhao, Y and Hu, Z and Xie, H and Wu, H and Wang, Y and Xu, H and Liang, S and Zhang, J},
title = {Size-dependent promotion of micro(nano)plastics on the horizontal gene transfer of antibiotic resistance genes in constructed wetlands.},
journal = {Water research},
volume = {244},
number = {},
pages = {120520},
doi = {10.1016/j.watres.2023.120520},
pmid = {37657315},
issn = {1879-2448},
mesh = {*Gene Transfer, Horizontal ; *Wetlands ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Escherichia coli/genetics ; Polystyrenes ; },
abstract = {Constructed wetlands (CWs) have been identified as significant sources of micro(nano)plastics (MPs/NPs) and antibiotic resistance genes (ARGs) in aquatic environments. However, little is known about the impact of MPs/NPs exposure on horizontal gene transfer (HGT) of ARGs and shaping the corresponding ARG hosts' community. Herein, the contribution of polystyrene (PS) particles (control, 4 mm, 100 μm, and 100 nm) to ARG transfer was investigated by adding an engineered fluorescent Escherichia coli harboring RP4 plasmid-encoded ARGs into CWs. It was found MPs/NPs significantly promoted ARG transfer in a size-dependent manner in each CW medium (p < 0.05). The 100 μm-sized PS exhibited the most significant promotion of ARG transfer (p < 0.05), whereas 100 nm-sized PS induced limited promotion due to its inhibitory activity on microbes. The altered RP4-carrying bacterial communities suggested that MPs/NPs, especially 100 µm-PS, could recruit pathogenic and nitrifying bacteria to acquire ARGs. The increased sharing of RP4-carrying core bacteria in CW medium further suggested that ARGs can spread into CW microbiome using MPs/NPs as carriers. Overall, our results highlight the high risks of ARG dissemination induced by MPs/NPs exposure and emphasize the need for better control of plastic disposal to prevent the potential health threats.},
}
@article {pmid37653049,
year = {2023},
author = {Johnson, ET and Bowman, MJ and Gomes, RP and Carneiro, LC and Dunlap, CA},
title = {Identification of 2,4-diacetylphloroglucinol production in the genus Chromobacterium.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {14292},
pmid = {37653049},
issn = {2045-2322},
mesh = {*Chromobacterium/genetics ; Phylogeny ; *Anti-Bacterial Agents/pharmacology ; Brazil ; Escherichia coli ; Pseudomonas ; },
abstract = {The compound 2,4-diacetylphloroglucinol (DAPG) is a broad-spectrum antibiotic that is primarily produced by Pseudomonas spp. DAPG plays an important role in the biocontrol disease suppressing activity of Pseudomonas spp. In the current study, we report the discovery of the DAPG biosynthetic cluster in strains of Chromobacterium vaccinii isolated from Brazilian aquatic environments and the distribution of the biosynthetic cluster in the Chromobacterium genus. Phylogenetic analysis of the phlD protein suggests the biosynthetic cluster probably entered the genus of Chromobacterium after a horizontal gene transfer event with a member of the Pseudomonas fluorescens group. We were able to detect trace amounts of DAPG in wild type cultures and confirm the function of the cluster with heterologous expression in Escherichia coli. In addition, we identified and verified the presence of other secondary metabolites in these strains. We also confirmed the ability of C. vaccinii strains to produce bioactive pigment violacein and bioactive cyclic depsipeptide FR900359. Both compounds have been reported to have antimicrobial and insecticidal activities. These compounds suggest strains of C. vaccinii should be further explored for their potential as biocontrol agents.},
}
@article {pmid37651790,
year = {2023},
author = {Katsburg, M and Brombach, J and Hanke, D and Aubry, E and Lübke-Becker, A and Fulde, M},
title = {New variant strain of Streptococcus canis with Lancefield group C isolated from canine otitis externa.},
journal = {Veterinary microbiology},
volume = {285},
number = {},
pages = {109869},
doi = {10.1016/j.vetmic.2023.109869},
pmid = {37651790},
issn = {1873-2542},
mesh = {Dogs ; Animals ; *Streptococcal Infections/veterinary/microbiology ; *Otitis Externa/veterinary ; Streptococcus/genetics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/veterinary ; *Dog Diseases/diagnosis/microbiology ; },
abstract = {Every basic course in microbiology teaches us, Streptococcus canis always tests positive for Lancefield group G. Surprisingly, we identified a strain of S. canis with Lancefield group C, cultured from a dog with otitis externa after lateral ear canal resection. Whole genome sequencing data and analysis points towards a horizontal gene transfer event between S. canis and S. dysgalactiae. Although these species are closely related, gene transfer in this region of the genome of S. canis has not been described before. The value of technologies as MALDI-TOF MS and sequencing in microbiological diagnostics will grow as more diverse streptococci arise that do not always conform anymore to the classical Lancefield group typing.},
}
@article {pmid37649002,
year = {2023},
author = {Ye, J and Jin, L and Li, Y and Xu, H and Lin, Y and Zhou, T and Zheng, B and Wang, M and Wang, Z},
title = {Complete-genome sequencing and comparative genomic characterization of blaNDM-5 carrying Citrobacter freundii isolates from a patient with multiple infections.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {506},
pmid = {37649002},
issn = {1471-2164},
support = {82102457//the National Natural Science Foundation of China/ ; LQ22H200004//the Zhejiang Provincial Natural Science Foundation of China/ ; Y20210110//the Planned Science and Technology Project of Wenzhou/ ; 2019QD011//Start-up Funding for Talent Research Program in the First Affiliated Hospital of Wenzhou Medical University/ ; 2023RC046//the Zhejiang Provincial Science and Technology Plan Project of China/ ; 2022E10022//Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province/ ; },
mesh = {Humans ; *Citrobacter freundii/genetics ; Chromosome Mapping ; Conserved Sequence ; *Carbapenems/pharmacology/therapeutic use ; Escherichia coli ; Genomics ; },
abstract = {BACKGROUND: The emergence and wide spread of carbapenemase-producing Enterobacteriaceae (CPE) poses a growing threat to global public health. However, clinically derived carbapenemase-producing Citrobacter causing multiple infections has rarely been investigated. Here we first report the isolation and comparative genomics of two blaNDM-5 carrying Citrobacter freundii (C. freundii) isolates from a patient with bloodstream and urinary tract infections.<br><br>RESULTS: Antimicrobial susceptibility testing showed that both blaNDM-5 carrying C. freundii isolates were multidrug-resistant. Positive modified carbapenem inactivation method (mCIM) and EDTA-carbapenem inactivation method (eCIM) results suggested metallo-carbapenemase production. PCR and sequencing confirmed that both metallo-carbapenemase producers were blaNDM-5 positive. Genotyping and comparative genomics analyses revealed that both isolates exhibited a high level of genetic similarity. Plasmid analysis confirmed that the blaNDM-5 resistance gene is located on IncX3 plasmid with a length of 46,161 bp, and could successfully be transferred to the recipient Escherichia coli EC600 strain. A conserved structure sequence (ISAba125-IS5-blaNDM-5-trpF-IS26-umuD-ISKox3) was found in the upstream and downstream of the blaNDM-5 gene.<br><br>CONCLUSIONS: The data presented in this study showed that the conjugative blaNDM-5 plasmid possesses a certain ability to horizontal transfer. The dissemination of NDM-5-producing C. freundii isolates should be of close concern in future clinical surveillance. To our knowledge, this is the first study to characterize C. freundii strains carrying the blaNDM-5 gene from one single patient with multiple infections.},
}
@article {pmid37648730,
year = {2023},
author = {Xiong, L and Li, Y and Yu, H and Wei, Y and Li, H and Ji, X},
title = {Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {14190},
pmid = {37648730},
issn = {2045-2322},
mesh = {*Wetlands ; *Bacteriophages ; Clustered Regularly Interspaced Short Palindromic Repeats ; Cold Temperature ; Pseudomonas/genetics ; },
abstract = {Microbial communities of wetlands play key roles in the earth's ecology and stability. To elucidate the cold adaptation mechanisms of bacteria in plateau wetlands, we conducted comparative genomic analyses of Pseudomonas sivasensis and closely related lineages. The genome of P. sivasensis W-6, a cold-adapted bacterium isolated from the Napahai plateau wetland, was sequenced and analyzed. The genome length was 6,109,123 bp with a G+C content of 59.5%. Gene prediction yielded 5360 protein-coding sequences, 70 tRNAs, 24 gene islands, and 2 CRISPR sequences. The isolate contained evidence of horizontal gene transfer events during its evolution. Two prophages were predicted and indicated that W-6 was a lysogen. The cold adaptation of the W-6 strain showed psychrophilic rather than psychrotrophic characteristics. Cold-adapted bacterium W-6 can utilize glycogen and trehalose as resources, associated with carbohydrate-active enzymes, and survive in a low-temperature environment. In addition, the cold-adapted mechanisms of the W-6 included membrane fluidity by changing the unsaturated fatty acid profile, the two-component regulatory systems, anti-sense transcription, the role played by rpsU genes in the translation process, etc. The genome-wide analysis of W-6 provided a deeper understanding of cold-adapted strategies of bacteria in environments. We elucidated the adaptive mechanism of the psychrophilic W-6 strain for survival in a cold environment, which provided a basis for further study on host-phage coevolution.},
}
@article {pmid37647945,
year = {2023},
author = {Goodman, RN and Tansirichaiya, S and Roberts, AP},
title = {Development of pBACpAK entrapment vector derivatives to detect intracellular transfer of mobile genetic elements within chloramphenicol resistant bacterial isolates.},
journal = {Journal of microbiological methods},
volume = {213},
number = {},
pages = {106813},
doi = {10.1016/j.mimet.2023.106813},
pmid = {37647945},
issn = {1872-8359},
support = {MR/W030578/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Chloramphenicol/pharmacology ; *Escherichia coli ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; Interspersed Repetitive Sequences ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; },
abstract = {Antimicrobial resistance disseminates throughout bacterial populations via horizontal gene transfer, driven mainly by mobile genetic elements (MGEs). Entrapment vectors are key tools in determining MGE movement within a bacterial cell between different replicons or between sites within the same replicon. The pBACpAK entrapment vector has been previously used to study intracellular transfer in Gram-negative bacteria however since pBACpAK contains a chloramphenicol resistance gene, it cannot be used in bacterial isolates which are already resistant to chloramphenicol. Therefore, we developed new derivatives of the pBACpAK entrapment vector to determine intracellular transfer of MGEs in an Escherichia coli DH5α transconjugant containing the chloramphenicol resistance plasmid pD25466. The catA1 of pBACpAK was replaced by both mcr-1 in pBACpAK-COL and aph(3')-Ia in pBACpAK-KAN, allowing it to be used in chloramphenicol resistant strains. The plasmid constructs were verified and then used to transform the E. coli DH5α/pD25466 transconjugants in order to detect intracellular movement of the MGEs associated with the pD25466 plasmid. Here we report on the validation of the expanded suite of pBACpAK vectors which can be used to study the intracellular transfer of MGEs between, and within, replicons in bacteria with different antimicrobial resistance profiles.},
}
@article {pmid37645846,
year = {2023},
author = {Youngblom, MA and Imhoff, MR and Smyth, LM and Mohamed, MA and Pepperell, CS},
title = {Portrait of a generalist bacterium: pathoadaptation, metabolic specialization and extreme environments shape diversity of Staphylococcus saprophyticus.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.08.18.553882},
pmid = {37645846},
issn = {2692-8205},
abstract = {UNLABELLED: Staphylococcus saprophyticus is a Gram-positive, coagulase-negative staphylococcus found in diverse environments including soil and freshwater, meat, and dairy foods. S. saprophyticus is also an important cause of urinary tract infections (UTIs) in humans, and mastitis in cattle. However, the genetic determinants of virulence have not yet been identified, and it remains unclear whether there are distinct sub-populations adapted to human and animal hosts. Using a diverse sample of S. saprophyticus isolates from food, animals, environmental sources, and human infections, we characterized the population structure and diversity of global populations of S. saprophyticus . We found that divergence of the two major clades of S. saprophyticus is likely facilitated by barriers to horizontal gene transfer (HGT) and differences in metabolism. Using genome-wide association study (GWAS) tools we identified the first Type VII secretion system (T7SS) described in S. saprophyticus and its association with bovine mastitis. Finally, we found that in general, strains of S. saprophyticus from different niches are genetically similar with the exception of built environments, which function as a 'sink' for S. saprophyticus populations. This work increases our understanding of the ecology of S. saprophyticus and of the genomics of bacterial generalists.<br><br>DATA SUMMARY: Raw sequencing data for newly sequenced S. saprophyticus isolates have been deposited to the NCBI SRA under the project accession PRJNA928770. A list of all genomes used in this work and their associated metadata are available in the supplementary material. Custom scripts used in the comparative genomics and GWAS analyses are available here: https://github.com/myoungblom/sapro_genomics .<br><br>IMPACT STATEMENT: It is not known whether human and cattle diseases caused by S. saprophyticus represent spillover events from a generalist adapted to survive in a range of environments, or whether the capacity to cause disease represents a specific adaptation. Seasonal cycles of S. saprophyticus UTIs and molecular epidemiological evidence suggest that these infections may be environmentally-acquired rather than via transmission from person to person. Using comparative genomics and genome wide association study tools, we found that S. saprophyticus appears adapted to inhabit a wide range of environments (generalist), with isolates from animals, food, natural environments and human infections being closely related. Bacteria that routinely switch environments, particularly between humans and animals, are of particular concern when it comes to the spread of antibiotic resistance from farm environments into human populations. This work provides a framework for comparative genomic analyses of bacterial generalists and furthers our understanding of how bacterial populations move between humans, animals, and the environment.},
}
@article {pmid37640834,
year = {2023},
author = {van Dijk, B and Buffard, P and Farr, AD and Giersdorf, F and Meijer, J and Dutilh, BE and Rainey, PB},
title = {Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {90},
pmid = {37640834},
issn = {2730-6151},
abstract = {Microbial evolution is driven by rapid changes in gene content mediated by horizontal gene transfer (HGT). While mobile genetic elements (MGEs) are important drivers of gene flux, the nanobiome-the zoo of Darwinian replicators that depend on microbial hosts-remains poorly characterised. New approaches are necessary to increase our understanding beyond MGEs shaping individual populations, towards their impacts on complex microbial communities. A bioinformatic pipeline (xenoseq) was developed to cross-compare metagenomic samples from microbial consortia evolving in parallel, aimed at identifying MGE dissemination, which was applied to compost communities which underwent periodic mixing of MGEs. We show that xenoseq can distinguish movement of MGEs from demographic changes in community composition that otherwise confounds identification, and furthermore demonstrate the discovery of various unexpected entities. Of particular interest was a nanobacterium of the candidate phylum radiation (CPR) which is closely related to a species identified in groundwater ecosystems (Candidatus Saccharibacterium), and appears to have a parasitic lifestyle. We also highlight another prolific mobile element, a 313 kb plasmid hosted by a Cellvibrio lineage. The host was predicted to be capable of nitrogen fixation, and acquisition of the plasmid coincides with increased ammonia production. Taken together, our data show that new experimental strategies combined with bioinformatic analyses of metagenomic data stand to provide insight into the nanobiome as a driver of microbial community evolution.},
}
@article {pmid37634776,
year = {2023},
author = {Zámocký, M and Ferianc, P},
title = {Discovering the deep evolutionary roots of serum amyloid A protein family.},
journal = {International journal of biological macromolecules},
volume = {252},
number = {},
pages = {126537},
doi = {10.1016/j.ijbiomac.2023.126537},
pmid = {37634776},
issn = {1879-0003},
mesh = {Animals ; *Serum Amyloid A Protein/genetics/metabolism ; Phylogeny ; *Bacteria/metabolism ; Genome, Bacterial ; Protein Isoforms/genetics ; },
abstract = {Deep evolutionary origin of the conserved animal serum amyloid A (SAA) apolipoprotein family leading to yet unknown highly similar SAA-like sequences occurring in certain bacterial genomes is demonstrated in this contribution. Horizontal gene transfer event of corresponding genes between gut bacteria and non-vertebrate animals was discovered in the reconstructed phylogenetic tree obtained with maximum likelihood and neighbor-joining methods, respectively. This detailed phylogeny based on totally 128 complete sequences comprised diverse serum amyloid A isoforms from various animal vertebrate and non-vertebrate phyla and also corresponding genes coding for highly similar proteins from animal gut bacteria. Typical largely conserved sequence motifs and a peculiar structural fold consisting mainly of four α-helices in a bundle within all reconstructed clades of the SAA protein family are discussed with respect to their supposed biological functions in various organisms that contain corresponding genes.},
}
@article {pmid37632379,
year = {2023},
author = {Sabar, MA and Van Huy, T and Sugie, Y and Wada, H and Zhao, B and Matsuura, N and Ihara, M and Watanabe, T and Tanaka, H and Honda, R},
title = {Antimicrobial resistome and mobilome in the urban river affected by combined sewer overflows and wastewater treatment effluent.},
journal = {Journal of water and health},
volume = {21},
number = {8},
pages = {1032-1050},
doi = {10.2166/wh.2023.073},
pmid = {37632379},
issn = {1477-8920},
mesh = {Rivers ; *Anti-Infective Agents ; Anti-Bacterial Agents/pharmacology ; Macrolides ; *Microbiota ; },
abstract = {The dissemination of antimicrobial resistance in the environment is an emerging global health problem. Wastewater treatment effluent and combined sewer overflows (CSOs) are major sources of antimicrobial resistance in urban rivers. This study aimed to clarify the effect of municipal wastewater treatment effluent and CSO on antimicrobial resistance genes (ARGs), mobile gene elements, and the microbial community in an urban river. The ARG abundance per 16S-based microbial population in the target river was 0.37-0.54 and 0.030-0.097 during the CSO event and dry weather, respectively. During the CSO event, the antimicrobial resistome in the river shifted toward a higher abundance of ARGs to clinically important drug classes, including macrolide, fluoroquinolone, and β-lactam, whereas ARGs to sulfonamide and multidrug by efflux pump were relatively abundant in dry weather. The abundance of intI1 and tnpA genes were highly associated with the total ARG abundance, suggesting their potential application as an indicator for estimating resistome contamination. Increase of prophage during the CSO event suggested that impact of CSO has a greater potential for horizontal gene transfer (HGT) via transduction. Consequently, CSO not only increases the abundance of ARGs to clinically important antimicrobials but also possibly enhances potential of HGT in urban rivers.},
}
@article {pmid37632043,
year = {2023},
author = {Kozlova, AP and Saksaganskaia, AS and Afonin, AM and Muntyan, VS and Vladimirova, ME and Dzyubenko, EA and Roumiantseva, ML},
title = {A Temperate Sinorhizobium Phage, AP-16-3, Closely Related to Phage 16-3: Mosaic Genome and Prophage Analysis.},
journal = {Viruses},
volume = {15},
number = {8},
pages = {},
pmid = {37632043},
issn = {1999-4915},
mesh = {Humans ; *Bacteriophages ; Prophages/genetics ; *Sinorhizobium ; *Siphoviridae ; Lysogeny ; },
abstract = {Soil Sinorhizobium phage AP-16-3, a strain phylogenetically close to Rhizobium phage 16-3, was isolated in a mountainous region of Dagestan, belonging to the origin of cultivated plants in the Caucasus, according to Vavilov N.I. The genome of phage AP-16-3 is 61 kbp in size and contains 62 ORFs, of which 42 ORFs have homologues in the genome of Rhizobium phage 16-3, which was studied in the 1960s-1980s. A search for Rhizobium phage 16-3-related sequences was performed in the genomes of modern strains of root nodule bacteria belonging to different species, genera, and families. A total of 43 prophages of interest were identified out of 437 prophages found in the genomes of 42 strains, of which 31 belonged to Sinorhizobium meliloti species. However, almost all of the mentioned prophages contained single ORFs, and only two prophages contained 51 and 39 ORFs homologous to phages related to 16-3. These prophages were detected in S. meliloti NV1.1.1 and Rh. leguminosarum OyaliB strains belonging to different genera; however, the similarity level of these two prophages did not exceed 14.7%. Analysis of the orphan genes in these prophages showed that they encoded predominantly virion structural elements, but also enzymes and an extensive group of hypothetical proteins belonging to the L, S, and E regions of viral genes of phage 16-3. The data obtained indicate that temperate phages related to 16-3 had high infectivity against nodule bacteria and participated in intragenomic recombination events involving other phages, and in horizontal gene transfer between rhizobia of different genera. According to the data obtained, it is assumed that the repetitive lysogenic cycle of temperate bacteriophages promotes the dissolution of the phage genetic material in the host bacterial genome, and radical updating of phage and host bacterial genomes takes place.},
}
@article {pmid37627664,
year = {2023},
author = {Bonsaglia, ECR and Calvo, GH and Sordelli, DO and Silva, NCC and Rall, VLM and Casas, A and Buzzola, F},
title = {The Impact of Low-Level Benzalkonium Chloride Exposure on Staphylococcus spp. Strains and Control by Photoinactivation.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {8},
pages = {},
pmid = {37627664},
issn = {2079-6382},
support = {PICT2019-2883//Agencia Nacional de Promoci&#xf3;n de la Ciencia y Tecnolog&#xed;a (ANPCyT)/ ; PIP2021-11220200102843CO and PUE085//CONICET/ ; },
abstract = {Exposure of bacteria to low concentrations of biocides can facilitate horizontal gene transfer, which may lead to bacterial adaptive responses and resistance to antimicrobial agents. The emergence of antibacterial resistance not only poses a significant concern to the dairy industry but also adds to the complexity and cost of mastitis treatment. This study was aimed to evaluate how selective stress induced by benzalkonium chloride (BC) promotes antibiotic non-susceptibility in Staphylococcus spp. In addition, we investigated the efficacy of photodynamic inactivation (PDI) in both resistant and susceptible strains. The study determined the minimum inhibitory concentration (MIC) of BC using the broth microdilution method for different Staphylococcus strains. The experiments involved pairing strains carrying the qacA/qacC resistance genes with susceptible strains and exposing them to subinhibitory concentrations of BC for 72 h. The recovered isolates were tested for MIC BC and subjected to disc diffusion tests to assess changes in susceptibility patterns. The results demonstrated that subinhibitory concentrations of BC could select strains with reduced susceptibility and antibiotic resistance, particularly in the presence of S. pasteuri. The results of PDI mediated by toluidine blue (100 µM) followed by 60 min irradiation (total light dose of 2.5 J/cm[2]) were highly effective, showing complete inactivation for some bacterial strains and a reduction of up to 5 logs in others.},
}
@article {pmid37616556,
year = {2023},
author = {Farrell, AA and Nesbø, CL and Zhaxybayeva, O},
title = {Early Divergence and Gene Exchange Highways in the Evolutionary History of Mesoaciditogales.},
journal = {Genome biology and evolution},
volume = {15},
number = {9},
pages = {},
pmid = {37616556},
issn = {1759-6653},
mesh = {Phylogeny ; *Biological Evolution ; *Bacteria ; Archaea ; Acclimatization ; },
abstract = {The placement of a nonhyperthermophilic order Mesoaciditogales as the earliest branching clade within the Thermotogota phylum challenges the prevailing hypothesis that the last common ancestor of Thermotogota was a hyperthermophile. Yet, given the long branch leading to the only two Mesoaciditogales described to date, the phylogenetic position of the order may be due to the long branch attraction artifact. By testing various models and applying data recoding in phylogenetic reconstructions, we observed that early branching of Mesoaciditogales within Thermotogota is strongly supported by the conserved marker genes assumed to be vertically inherited. However, based on the taxonomic content of 1,181 gene families and a phylogenetic analysis of 721 gene family trees, we also found that a substantial number of Mesoaciditogales genes are more closely related to species from the order Petrotogales. These genes contribute to coenzyme transport and metabolism, fatty acid biosynthesis, genes known to respond to heat and cold stressors, and include many genes of unknown functions. The Petrotogales comprise moderately thermophilic and mesophilic species with similar temperature tolerances to that of Mesoaciditogales. Our findings hint at extensive horizontal gene transfer (HGT) between, or parallel independent gene gains by, the two ecologically similar lineages and suggest that the exchanged genes may be important for adaptation to comparable temperature niches.},
}
@article {pmid37611393,
year = {2023},
author = {Deng, WK and He, JL and Chen, JY and Wu, RT and Xing, SC and Liao, XD},
title = {Effects of microplastics on functional genes related to CH4 and N2O metabolism in bacteriophages during manure composting and its planting applications.},
journal = {Journal of hazardous materials},
volume = {460},
number = {},
pages = {132288},
doi = {10.1016/j.jhazmat.2023.132288},
pmid = {37611393},
issn = {1873-3336},
mesh = {*Composting ; *Greenhouse Gases ; Manure ; Microplastics ; Plastics ; *Bacteriophages/genetics ; Soil ; },
abstract = {Microplastics (MPs), as a new type of pollutant, widely exist in livestock and poultry breeding and agricultural soils. However, research on MPs pollution on greenhouse gas emissions in combined planting and breeding systems is lacking, especially from the perspective of phage horizontal gene transfer. Therefore, this paper explores the effects of MPs on functional genes related to CH4 and N2O metabolism in bacteriophages during manure composting and its planting applications. The results of the study indicated that the addition of MPs had an impact on both the physicochemical properties and microbial community structure of manure during the composting process and on the compost-applied rhizosphere soil of lactuca (Lactuca sativa). Specifically, on day 7 of composting, mcrA/pmoA and (nirS+nirK) levels in bacteria in the MP group significantly increased. Additionally, it was observed that the MP group had higher average temperatures during the high-temperature period of composting, which led to a rapid reduction in phages. However, the phage levels quickly recovered during the cooling period. Furthermore, the addition of MPs to the rhizosphere soil resulted in higher levels of nirK. These changes may affect greenhouse gas emissions.},
}
@article {pmid37610250,
year = {2023},
author = {Zhao, Y and Kuang, W and An, Q and Li, J and Wang, Y and Deng, Z},
title = {Cryo-EM structures of African swine fever virus topoisomerase.},
journal = {mBio},
volume = {14},
number = {5},
pages = {e0122823},
pmid = {37610250},
issn = {2150-7511},
mesh = {Swine ; Animals ; *African Swine Fever Virus ; *African Swine Fever ; Cryoelectron Microscopy ; DNA Topoisomerases, Type II/genetics ; Catalytic Domain ; Saccharomyces cerevisiae/metabolism ; },
abstract = {African swine fever virus (ASFV) is a highly contagious virus that causes lethal hemorrhagic diseases known as African swine fever (ASF) with a case fatality rate of 100%. There is an urgent need to develop anti-ASFV drugs. We determine the first high-resolution structures of viral topoisomerase ASFV P1192R in both the closed and open C-gate forms. P1192R shows a similar overall architecture with eukaryotic and prokaryotic type II topoisomerases, which have been successful targets of many antimicrobials and anticancer drugs, with the most similarity to yeast topo II. P1192R also exhibits differences in the details of active site configuration, which are important to enzyme activity. These two structures offer useful structural information for antiviral drug design and provide structural evidence to support that eukaryotic type IIA topoisomerase likely originated from horizontal gene transfer from the virus.},
}
@article {pmid37609252,
year = {2023},
author = {Hsu, TY and Nzabarushimana, E and Wong, D and Luo, C and Beiko, RG and Langille, M and Huttenhower, C and Nguyen, LH and Franzosa, EA},
title = {Profiling novel lateral gene transfer events in the human microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37609252},
issn = {2692-8205},
support = {K23 DK125838/DK/NIDDK NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; T32 CA009001/CA/NCI NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; },
abstract = {Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial populations, including the human microbiome. While prior work has surveyed LGT events in human-associated microbial isolate genomes, the scope and dynamics of novel LGT events arising in personal microbiomes are not well understood, as there are no widely adopted computational methods to detect, quantify, and characterize LGT from complex microbial communities. We addressed this by developing, benchmarking, and experimentally validating a computational method (WAAFLE) to profile novel LGT events from assembled metagenomes. Applying WAAFLE to >2K human metagenomes from diverse body sites, we identified >100K putative high-confidence but previously uncharacterized LGT events (~2 per assembled microbial genome-equivalent). These events were enriched for mobile elements (as expected), as well as restriction-modification and transport functions typically associated with the destruction of foreign DNA. LGT frequency was quantifiably influenced by biogeography, the phylogenetic similarity of the involved taxa, and the ecological abundance of the donor taxon. These forces manifest as LGT networks in which hub species abundant in a community type donate unequally with their close phylogenetic neighbors. Our findings suggest that LGT may be a more ubiquitous process in the human microbiome than previously described. The open-source WAAFLE implementation, documentation, and data from this work are available at http://huttenhower.sph.harvard.edu/waafle.},
}
@article {pmid37605076,
year = {2023},
author = {Baig, MIR and Kadu, P and Bawane, P and Nakhate, KT and Yele, S and Ojha, S and Goyal, SN},
title = {Mechanisms of emerging resistance associated with non-antibiotic antimicrobial agents: a state-of-the-art review.},
journal = {The Journal of antibiotics},
volume = {76},
number = {11},
pages = {629-641},
pmid = {37605076},
issn = {1881-1469},
mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria ; *Anti-Infective Agents/pharmacology ; *Disinfectants/pharmacology ; Drug Resistance, Bacterial/genetics ; },
abstract = {Although the development of resistance by microorganisms to antimicrobial drugs has been recognized as a global public health concern, the contribution of various non-antibiotic antimicrobial agents to the development of antimicrobial resistance (AMR) remains largely neglected. The present review discusses various chemical substances and factors other than typical antibiotics, such as preservatives, disinfectants, biocides, heavy metals and improper chemical sterilization that contribute to the development of AMR. Furthermore, it encompasses the mechanisms like co-resistance and co-selection, horizontal gene transfer, changes in the composition and permeability of cell membrane, efflux pumps, transposons, biofilm formation and enzymatic degradation of antimicrobial chemicals which underlie the development of resistance to various non-antibiotic antimicrobial agents. In addition, the review addresses the resistance-associated changes that develops in microorganisms due to these agents, which ultimately contribute to the development of resistance to antibiotics. In order to prevent the indiscriminate use of chemical substances and create novel therapeutic agents to halt resistance development, a more holistic scientific approach might provide diversified views on crucial factors contributing to the persistence and spread of AMR. The review illustrates the common and less explored mechanisms contributing directly or indirectly to the development of AMR by non-antimicrobial agents that are commonly used.},
}
@article {pmid37595132,
year = {2023},
author = {Kobayashi, N and Dang, TA and Pham, KTM and Gómez Luciano, LB and Van Vu, B and Izumitsu, K and Shimizu, M and Ikeda, KI and Li, WH and Nakayashiki, H},
title = {Horizontally Transferred DNA in the Genome of the Fungus Pyricularia oryzae is Associated With Repressive Histone Modifications.},
journal = {Molecular biology and evolution},
volume = {40},
number = {9},
pages = {},
pmid = {37595132},
issn = {1537-1719},
mesh = {*Histone Code ; Histones/genetics ; Phylogeny ; DNA ; *Ascomycota/genetics ; Triticum ; },
abstract = {Horizontal gene transfer (HGT) is a means of exchanging genetic material asexually. The process by which horizontally transferred genes are domesticated by the host genome is of great interest but is not well understood. In this study, we determined the telomere-to-telomere genome sequence of the wheat-infecting Pyricularia oryzae strain Br48. SNP analysis indicated that the Br48 strain is a hybrid of wheat- and Brachiaria-infecting strains by a sexual or parasexual cross. Comparative genomic analysis identified several megabase-scale "insertions" in the Br48 genome, some of which were possibly gained by HGT-related events from related species, such as P. pennisetigena or P. grisea. Notably, the mega-insertions often contained genes whose phylogeny is not congruent with the species phylogeny. Moreover, some of the genes have a close homolog even in distantly related organisms, such as basidiomycetes or prokaryotes, implying the involvement of multiple HGT events. Interestingly, the levels of the silent epigenetic marks H3K9me3 and H3K27me3 in a genomic region tended to be negatively correlated with the phylogenetic concordance of genes in the same region, suggesting that horizontally transferred DNA is preferentially targeted for epigenetic silencing. Indeed, the putative HGT-derived genes were activated when MoKmt6, the gene responsible for H3K27me3 modification, was deleted. Notably, these genes also tended to be up-regulated during infection, suggesting that they are now under host control and have contributed to establishing a fungal niche. In conclusion, this study suggests that epigenetic modifications have played an important role in the domestication of HGT-derived genes in the P. oryzae genome.},
}
@article {pmid37594001,
year = {2023},
author = {Yang, C and Xiang, Y and Qiu, S},
title = {Resistance in Enteric Shigella and nontyphoidal Salmonella : emerging concepts.},
journal = {Current opinion in infectious diseases},
volume = {36},
number = {5},
pages = {360-365},
pmid = {37594001},
issn = {1473-6527},
mesh = {Humans ; *Azithromycin/pharmacology/therapeutic use ; Colistin ; *Shigella/genetics ; Salmonella/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Ciprofloxacin/pharmacology/therapeutic use ; },
abstract = {PURPOSE OF REVIEW: The emergence of globally resistant enteric Shigella and nontyphoidal Salmonella strains (NTS) has limited the selection of effective drugs, which has become a major challenge for the treatment of infections. The purpose of this review is to provide the current opinion on the antimicrobial-resistant enteric Shigella and nontyphoidal Salmonella .<br><br>RECENT FINDINGS: Enteric Shigella and NTS are resistant to almost all classes of antimicrobials in recent years. Those with co-resistance to ciprofloxacin, azithromycin and ceftriaxone, the first-line antibiotics for the treatment of infectious diarrhoea have emerged worldwide. Some of them have caused interregional and international spread by travel, trade, MSM, and polluted water sources. Several strains have even developed resistance to colistin, the last-resort antibiotic used for treatment of multidrug-resistant Gram-negative bacteria infections.<br><br>SUMMARY: The drug resistance of enteric Shigella and NTS is largely driven by the use of antibiotics and horizontal gene transfer of mobile genetic elements. These two species show various drug resistance patterns in different regions and serotypes. Hence treatment decisions for Shigella and Salmonella infections need to take into consideration prevalent antimicrobial drug resistance patterns. It is worth noting that the resistance genes such as blaCTX,mph, ermB , qnr and mcr , which can cause resistance to ciprofloxacin, cephalosporin, azithromycin and colistin are widespread because of transmission by IncFII, IncI1, IncI2 and IncB/O/K/Z plasmids. Therefore, continuous global monitoring of resistance in Shigella and Salmonella is imperative.},
}
@article {pmid37592233,
year = {2023},
author = {Zhang, X and Xiao, L and Liu, J and Tian, Q and Xie, J},
title = {Trade-off in genome turnover events leading to adaptive evolution of Microcystis aeruginosa species complex.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {462},
pmid = {37592233},
issn = {1471-2164},
support = {32101368//National Natural Science Foundation of China/ ; 2022YFE0119600//National Key Research and Development Program of China/ ; },
mesh = {*Microcystis/genetics ; Genome-Wide Association Study ; *Bacteriophages ; Energy Metabolism ; Evolution, Molecular ; },
abstract = {BACKGROUND: Numerous studies in the past have expanded our understanding of the genetic differences of global distributed cyanobacteria that originated around billions of years ago, however, unraveling how gene gain and loss drive the genetic evolution of cyanobacterial species, and the trade-off of these evolutionary forces are still the central but poorly understood issues.<br><br>RESULTS: To delineate the contribution of gene flow in mediating the hereditary differentiation and shaping the microbial evolution, a global genome-wide study of bloom-forming cyanobacterium, Microcystis aeruginosa species complex, provided robust evidence for genetic diversity, reflected by enormous variation in gene repertoire among various strains. Mathematical extrapolation showed an 'open' microbial pan-genome of M. aeruginosa species, since novel genes were predicted to be introduced after new genomes were sequenced. Identification of numerous horizontal gene transfer's signatures in genome regions of interest suggested that genome expansion via transformation and phage-mediated transduction across bacterial lineage as an evolutionary route may contribute to the differentiation of Microcystis functions (e.g., carbohydrate metabolism, amino acid metabolism, and energy metabolism). Meanwhile, the selective loss of some dispensable genes at the cost of metabolic versatility is as a mean of adaptive evolution that has the potential to increase the biological fitness.<br><br>CONCLUSIONS: Now that the recruitment of novel genes was accompanied by a parallel loss of some other ones, a trade-off in gene content may drive the divergent differentiation of M. aeruginosa genomes. Our study provides a genetic framework for the evolution of M. aeruginosa species and illustrates their possible evolutionary patterns.},
}
@article {pmid37586197,
year = {2023},
author = {Shen, C and He, M and Zhang, J and Liu, J and Su, J and Dai, J},
title = {Effects of the coexistence of antibiotics and heavy metals on the fate of antibiotic resistance genes in chicken manure and surrounding soils.},
journal = {Ecotoxicology and environmental safety},
volume = {263},
number = {},
pages = {115367},
doi = {10.1016/j.ecoenv.2023.115367},
pmid = {37586197},
issn = {1090-2414},
mesh = {Animals ; Female ; Anti-Bacterial Agents/pharmacology ; Chickens/genetics ; Manure/microbiology ; Soil/chemistry ; Genes, Bacterial ; *Metals, Heavy/analysis ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; *Chlortetracycline ; Soil Microbiology ; },
abstract = {Both heavy metals and antibiotics exert selection pressure on bacterial resistance, and as they are commonly co-contaminated in the environment, they may play a larger role in bacterial resistance. This study examined how breeding cycles affect antibiotic resistance genes (ARGs) in chicken manure and the surrounding topsoils at 20, 50, 100, 200, and 300 m from twelve typical laying hen farms in the Ningxia Hui Autonomous Region of northwest China. Six antibiotics, seven heavy metals, ten mobile genetic elements (MGEs), and microbial community affected the ARGs profile in chicken dung and soil samples. Tetracycline antibiotic residues were prevalent in chicken manure, as were relatively high content of aureomycin during each culture period. Zinc (Zn) content was highest among the seven heavy metals in chicken feces. Chicken dung also enriched aminoglycosides, MLSB, and tetracycline ARGs, notably during brooding and high production. The farm had a minimal influence on antibiotics in the surrounding soil, but its effect on ARGs and MGEs closer to the farm (50 m) was stronger, and several ARGs and MGEs increased with distance. Manure microbial composition differed dramatically throughout breeding cycles and sampling distances. ARGs were more strongly related with antibiotics and heavy metals in manure than soil, whereas MGEs were the reverse. Antibiotics, heavy metals, MGEs, and bacteria in manure accounted 12.28%, 22.25%, 0.74%, and 0.19% of ARGs composition variance, respectively, according to RDA and VPA. Bacteria (2.89%) and MGEs (2.82%) only affected soil ARGs composition. These findings showed that heavy metals and antibiotics are the main factors affecting faecal ARGs and bacteria and MGEs soil ARGs. This paper includes antibiotic resistance data for large-scale laying hen husbandry in northwest China and a theoretical framework for decreasing antibiotic resistance.},
}
@article {pmid37584599,
year = {2023},
author = {Mi-Ichi, F and Tsugawa, H and Yoshida, H and Arita, M},
title = {Unique features of Entamoeba histolytica glycerophospholipid metabolism; has the E. histolytica lipid metabolism network evolved through gene loss and gain to enable parasitic life cycle adaptation?.},
journal = {mSphere},
volume = {8},
number = {5},
pages = {e0017423},
pmid = {37584599},
issn = {2379-5042},
mesh = {Animals ; Humans ; *Entamoeba histolytica/genetics ; *Parasites ; Lipid Metabolism ; Life Cycle Stages ; Glycerophospholipids/metabolism ; },
abstract = {Entamoeba histolytica, a protozoan parasite, causes amoebiasis, which is a global public health problem. During the life cycle of this parasite, the properties of the cell membrane are changed markedly. To clarify the mechanism of membrane lipid changes, we exploited state-of-the-art untargeted lipidomic analysis, and atypical features of glycerophospholipids, lysoglycerophospholipids, and sphingolipids were observed compared with human equivalents. Here, we overview an entire E. histolytica glycerophospholipid metabolic pathway based on re-evaluated whole lipidome and genome along with the results of metabolic labeling experiments. We also discuss whether the E. histolytica lipid metabolism network, including the glycerophospholipid metabolic pathway, has unique features necessary for parasitic life cycle adaptation through gene loss and/or gain, and raise important questions involving biochemistry, molecular cell biology, and physiology underlying this network. Answering these questions will advance the understanding of Entamoeba physiology and will provide potential targets to develop new anti-amoebiasis drugs.},
}
@article {pmid37584505,
year = {2024},
author = {Boyer, C and Lefeuvre, P and Richard, D and Lobin, KK and Pruvost, O},
title = {Complete Genome Sequence of a Copper-Resistant Xanthomonas campestris pv. campestris Strain Isolated from Broccoli in Mauritius Suggests Adaptive Gene Gain Through Horizontal Gene Transfer.},
journal = {Phytopathology},
volume = {114},
number = {2},
pages = {328-333},
doi = {10.1094/PHYTO-05-23-0177-SC},
pmid = {37584505},
issn = {0031-949X},
mesh = {*Brassica ; Copper ; *Xanthomonas campestris/genetics ; Gene Transfer, Horizontal ; Mauritius ; Plant Diseases ; },
abstract = {Bacterial adaptation is facilitated by the presence of mobile genetic elements and horizontal gene transfer of genes, such as those coding for virulence factors or resistance to antimicrobial compounds. A hybrid assembly of Nanopore MinIon long-read and Illumina short-read data was produced from a copper-resistant Xanthomonas campestris pv. campestris strain isolated from symptomatic broccoli leaves in Mauritius. We obtained a 5.2-Mb high-quality chromosome and no plasmid. We found four genomic islands, three of which were characterized as integrative conjugative elements or integrative mobilizable elements. These genomic islands carried type III effectors and the copper resistance copLABMGF system involved in pathogenicity and environmental adaptation, respectively.},
}
@article {pmid37582866,
year = {2023},
author = {},
title = {Horizontal gene transfer explains unusual traits of Armillaria fungi.},
journal = {Nature microbiology},
volume = {8},
number = {9},
pages = {1617-1618},
pmid = {37582866},
issn = {2058-5276},
mesh = {*Armillaria/genetics ; Gene Transfer, Horizontal ; Fungi/genetics ; },
}
@article {pmid37578142,
year = {2023},
author = {Luo, G and Liang, B and Cui, H and Kang, Y and Zhou, X and Tao, Y and Lu, L and Fan, L and Guo, J and Wang, A and Gao, SH},
title = {Determining the Contribution of Micro/Nanoplastics to Antimicrobial Resistance: Challenges and Perspectives.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {33},
pages = {12137-12152},
doi = {10.1021/acs.est.3c01128},
pmid = {37578142},
issn = {1520-5851},
mesh = {*Anti-Bacterial Agents ; *Drug Resistance, Bacterial/genetics ; Microplastics ; Plastics ; Gene Transfer, Horizontal ; },
abstract = {Microorganisms colonizing the surfaces of microplastics form a plastisphere in the environment, which captures miscellaneous substances. The plastisphere, owning to its inherently complex nature, may serve as a "Petri dish" for the development and dissemination of antibiotic resistance genes (ARGs), adding a layer of complexity in tackling the global challenge of both microplastics and ARGs. Increasing studies have drawn insights into the extent to which the proliferation of ARGs occurred in the presence of micro/nanoplastics, thereby increasing antimicrobial resistance (AMR). However, a comprehensive review is still lacking in consideration of the current increasingly scattered research focus and results. This review focuses on the spread of ARGs mediated by microplastics, especially on the challenges and perspectives on determining the contribution of microplastics to AMR. The plastisphere accumulates biotic and abiotic materials on the persistent surfaces, which, in turn, offers a preferred environment for gene exchange within and across the boundary of the plastisphere. Microplastics breaking down to smaller sizes, such as nanoscale, can possibly promote the horizontal gene transfer of ARGs as environmental stressors by inducing the overgeneration of reactive oxygen species. Additionally, we also discussed methods, especially quantitatively comparing ARG profiles among different environmental samples in this emerging field and the challenges that multidimensional parameters are in great necessity to systematically determine the antimicrobial dissemination risk in the plastisphere. Finally, based on the biological sequencing data, we offered a framework to assess the AMR risks of micro/nanoplastics and biocolonizable microparticles that leverage multidimensional AMR-associated messages, including the ARGs' abundance, mobility, and potential acquisition by pathogens.},
}
@article {pmid37577532,
year = {2023},
author = {Wolters, JF and LaBella, AL and Opulente, DA and Rokas, A and Hittinger, CT},
title = {Mitochondrial Genome Diversity across the Subphylum Saccharomycotina.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37577532},
issn = {2692-8205},
support = {R01 AI153356/AI/NIAID NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; },
abstract = {Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available. By extracting mitochondrial assemblies from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades. Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera Metschnikowia and Saccharomyces trended larger, while several species in the order Saccharomycetales, which includes S. cerevisiae, exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but they were highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements. As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.},
}
@article {pmid37577448,
year = {2023},
author = {Bonatelli, ML and Rohwerder, T and Popp, D and Liu, Y and Akay, C and Schultz, C and Liao, KP and Ding, C and Reemtsma, T and Adrian, L and Kleinsteuber, S},
title = {Recently evolved combination of unique sulfatase and amidase genes enables bacterial degradation of the wastewater micropollutant acesulfame worldwide.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1223838},
pmid = {37577448},
issn = {1664-302X},
abstract = {Xenobiotics often challenge the principle of microbial infallibility. One example is acesulfame introduced in the 1980s as zero-calorie sweetener, which was recalcitrant in wastewater treatment plants until the early 2010s. Then, efficient removal has been reported with increasing frequency. By studying acesulfame metabolism in alphaproteobacterial degraders of the genera Bosea and Chelatococcus, we experimentally confirmed the previously postulated route of two subsequent hydrolysis steps via acetoacetamide-N-sulfonate (ANSA) to acetoacetate and sulfamate. Genome comparison of wildtype Bosea sp. 100-5 and an acesulfame degradation-defective mutant revealed the involvement of two plasmid-borne gene clusters. The acesulfame-hydrolyzing sulfatase is strictly manganese-dependent and belongs to the metallo beta-lactamase family. In all degraders analyzed, it is encoded on a highly conserved gene cluster embedded in a composite transposon. The ANSA amidase, on the other hand, is an amidase signature domain enzyme encoded in another gene cluster showing variable length among degrading strains. Transposition of the sulfatase gene cluster between chromosome and plasmid explains how the two catabolic gene clusters recently combined for the degradation of acesulfame. Searching available genomes and metagenomes for the two hydrolases and associated genes indicates that the acesulfame plasmid evolved and spread worldwide in short time. While the sulfatase is unprecedented and unique for acesulfame degraders, the amidase occurs in different genetic environments and likely evolved for the degradation of other substrates. Evolution of the acesulfame degradation pathway might have been supported by the presence of structurally related natural and anthropogenic compounds, such as aminoacyl sulfamate ribonucleotide or sulfonamide antibiotics.},
}
@article {pmid37574851,
year = {2023},
author = {Chandler, M and Ross, K and Varani, AM},
title = {The insertion sequence excision enhancer: A PrimPol-based primer invasion system for immobilizing transposon-transmitted antibiotic resistance genes.},
journal = {Molecular microbiology},
volume = {120},
number = {5},
pages = {658-669},
doi = {10.1111/mmi.15140},
pmid = {37574851},
issn = {1365-2958},
mesh = {Humans ; *DNA Transposable Elements/genetics ; *Anti-Bacterial Agents/pharmacology ; Regulatory Sequences, Nucleic Acid ; Bacteria/genetics ; Drug Resistance, Microbial ; DNA-Directed DNA Polymerase/genetics ; DNA Primase/genetics ; Multifunctional Enzymes/genetics ; },
abstract = {Evolutionary studies often identify genes that have been exchanged between different organisms and the phrase Lateral or Horizontal Gene Transfer is often used in this context. However, they rarely provide any mechanistic information concerning how these gene transfers might have occurred. With the astonishing increase in the number of sequences in public databases over the past two or three decades, identical antibiotic resistance genes have been identified in many different sequence contexts. One explanation for this would be that genes are initially transmitted by transposons which have subsequently decayed and can no longer be detected. Here, we provide an overview of a protein, IEE (Insertion Sequence Excision Enhancer) observed to facilitate high-frequency excision of IS629 from clinically important Escherichia coli O157:H7 and subsequently shown to affect a large class of bacterial insertion sequences which all transpose using the copy-out-paste-in transposition mechanism. Excision depends on both IEE and transposase indicating association with the transposition process itself. We review genetic and biochemical data and propose that IEE immobilizes genes carried by compound transposons by removing the flanking insertion sequence (IS) copies. The biochemical activities of IEE as a primase with the capacity to recognize DNA microhomologies and the observation that its effect appears restricted to IS families which use copy-out-paste-in transposition, suggests IS deletion occurs by abortive transposition involving strand switching (primer invasion) during the copy-out step. This reinforces the proposal made for understanding the widespread phenomenon loss of ISApl1 flanking mcr-1 in the compound transposon Tn6330 which we illustrate with a detailed model. This model also provides a convincing way to explain the high levels of IEE-induced precise IS excision.},
}
@article {pmid37567328,
year = {2023},
author = {Andrade-Oliveira, AL and Lacerda-Rodrigues, G and Pereira, MF and Bahia, AC and Machado, EA and Rossi, CC and Giambiagi-deMarval, M},
title = {Tenebrio molitor as a model system to study Staphylococcus spp virulence and horizontal gene transfer.},
journal = {Microbial pathogenesis},
volume = {183},
number = {},
pages = {106304},
doi = {10.1016/j.micpath.2023.106304},
pmid = {37567328},
issn = {1096-1208},
mesh = {Animals ; Virulence/genetics ; *Tenebrio/microbiology ; Staphylococcus/genetics ; Staphylococcus aureus/genetics ; Gene Transfer, Horizontal ; Larva/microbiology ; },
abstract = {Invertebrates can provide a valuable alternative to traditional vertebrate animal models for studying bacterial and fungal infections. This study aimed to establish the larvae of the coleoptera Tenebrio molitor (mealworm) as an in vivo model for evaluating virulence and horizontal gene transfer between Staphylococcus spp. After identifying the best conditions for rearing T. molitor, larvae were infected with different Staphylococcus species, resulting in dose-dependent killing curves. All species tested killed the insects at higher doses, with S. nepalensis and S. aureus being the most and least virulent, respectively. However, only S. nepalensis was able to kill more than 50% of larvae 72 h post-infection at a low amount of 10[5] CFU. Staphylococcus infection also stimulated an increase in the concentration of hemocytes present in the hemolymph, which was proportional to the virulence. To investigate T. molitor's suitability as an in vivo model for plasmid transfer studies, we used S. aureus strains as donor and recipient of a plasmid containing the gentamicin resistance gene aac(6')-aph(2″). By inoculating larvae with non-lethal doses of each, we observed conjugation, and obtained transconjugant colonies with a frequency of 1.6 × 10[-5] per donor cell. This study demonstrates the potential of T. molitor larvae as a reliable and cost-effective model for analyzing the virulence of Staphylococcus and, for the first time, an optimal environment for the plasmid transfer between S. aureus carrying antimicrobial resistance genes.},
}
@article {pmid37565764,
year = {2023},
author = {Yin, L and Wang, X and Xu, H and Yin, B and Wang, X and Zhang, Y and Li, X and Luo, Y and Chen, Z},
title = {Unrecognized risk of perfluorooctane sulfonate in promoting conjugative transfers of bacterial antibiotic resistance genes.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {9},
pages = {e0053323},
pmid = {37565764},
issn = {1098-5336},
mesh = {Humans ; *Escherichia coli/genetics ; Drug Resistance, Bacterial/genetics ; *Fluorocarbons/pharmacology ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Soil ; Genes, Bacterial ; Plasmids/genetics ; Gene Transfer, Horizontal ; },
abstract = {Antibiotic resistance is a major global health crisis facing humanity, with horizontal gene transfer (HGT) as a principal dissemination mechanism in the natural and clinical environments. Perfluoroalkyl substances (PFASs) are emerging contaminants of global concern due to their high persistence in the environment and adverse effects on humans. However, it is unknown whether PFASs affect the HGT of bacterial antibiotic resistance. Using a genetically engineered Escherichia coli MG1655 as the donor of plasmid-encoded antibiotic resistance genes (ARGs), E. coli J53 and soil bacterial community as two different recipients, this study demonstrated that the conjugation frequency of ARGs between two E. coli strains was (1.45 ± 0.17) × 10[-5] and perfluorooctane sulfonate (PFOS) at environmentally relevant concentrations (2-50 μg L[-1]) increased conjugation transfer between E. coli strains by up to 3.25-fold. Increases in reactive oxygen species production, cell membrane permeability, biofilm formation capacity, and cell contact in two E. coli strains were proposed as major promotion mechanisms from PFOS exposure. Weighted gene co-expression network analysis of transcriptome data identified a series of candidate genes whose expression changes could contribute to the increase in conjugation transfer induced by PFOS. Furthermore, PFOS also generally increased the ARG transfer into the studied soil bacterial community, although the uptake ability of different community members of the plasmid either increased or decreased upon PFOS exposure depending on specific bacterial taxa. Overall, this study reveals an unrecognized risk of PFOS in accelerating the dissemination of antibiotic resistance. IMPORTANCE Perfluoroalkyl substances (PFASs) are emerging contaminants of global concern due to their high persistence in the environment and adverse health effects. Although the influence of environmental pollutants on the spread of antibiotic resistance, one of the biggest threats to global health, has attracted increasing attention in recent years, it is unknown whether environmental residues of PFASs affect the dissemination of bacterial antibiotic resistance. Considering PFASs, often called "forever" compounds, have significantly higher environmental persistence than most emerging organic contaminants, exploring the effect of PFASs on the spread of antibiotic resistance is more environmentally relevant and has essential ecological and health significance. By systematically examining the influence of perfluorooctane sulfonate on the antibiotic resistance gene conjugative transfer, not only at the single-strain level but also at the community level, this study has uncovered an unrecognized risk of PFASs in promoting conjugative transfers of bacterial antibiotic resistance genes, which could be incorporated into the risk assessment framework of PFASs.},
}
@article {pmid37561843,
year = {2023},
author = {Cooper, RM and Wright, JA and Ng, JQ and Goyne, JM and Suzuki, N and Lee, YK and Ichinose, M and Radford, G and Ryan, FJ and Kumar, S and Thomas, EM and Vrbanac, L and Knight, R and Woods, SL and Worthley, DL and Hasty, J},
title = {Engineered bacteria detect tumor DNA.},
journal = {Science (New York, N.Y.)},
volume = {381},
number = {6658},
pages = {682-686},
pmid = {37561843},
issn = {1095-9203},
support = {R01 CA241728/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Humans ; Mice ; *Colorectal Neoplasms/diagnosis/genetics ; *DNA, Neoplasm/analysis ; Mutation ; *Acinetobacter/genetics ; *Cell-Free Nucleic Acids/analysis ; Bioengineering ; *Biosensing Techniques ; },
abstract = {Synthetic biology has developed sophisticated cellular biosensors to detect and respond to human disease. However, biosensors have not yet been engineered to detect specific extracellular DNA sequences and mutations. Here, we engineered naturally competent Acinetobacter baylyi to detect donor DNA from the genomes of colorectal cancer (CRC) cells, organoids, and tumors. We characterized the functionality of the biosensors in vitro with coculture assays and then validated them in vivo with sensor bacteria delivered to mice harboring colorectal tumors. We observed horizontal gene transfer from the tumor to the sensor bacteria in our mouse model of CRC. This cellular assay for targeted, CRISPR-discriminated horizontal gene transfer (CATCH) enables the biodetection of specific cell-free DNA.},
}
@article {pmid37557975,
year = {2023},
author = {Weaver, RJ and McDonald, AE},
title = {Mitochondrial alternative oxidase across the tree of life: Presence, absence, and putative cases of lateral gene transfer.},
journal = {Biochimica et biophysica acta. Bioenergetics},
volume = {1864},
number = {4},
pages = {149003},
doi = {10.1016/j.bbabio.2023.149003},
pmid = {37557975},
issn = {1879-2650},
mesh = {Animals ; *Gene Transfer, Horizontal ; *Plant Proteins/genetics ; Oxidoreductases/genetics ; Mitochondria/genetics ; Plants ; Eukaryota/genetics ; },
abstract = {The alternative oxidase (AOX) is a terminal oxidase in the electron transport system that plays a role in mitochondrial bioenergetics. The past 20 years of research shows AOX has a wide yet patchy distribution across the tree of life. AOX has been suggested to have a role in stress tolerance, growth, and development in plants, but less is known about its function in other groups, including animals. In this study, we analyzed the taxonomic distribution of AOX across >2800 species representatives from prokaryotes and eukaryotes and developed a standardized workflow for finding and verifying the authenticity of AOX sequences. We found that AOX is limited to proteobacteria among prokaryotes, but is widely distributed in eukaryotes, with the highest prevalence in plants, fungi, and protists. AOX is present in many invertebrates, but is absent in others including most arthropods, and is absent from vertebrates. We found aberrant AOX sequences associated with some animal groups. Some of these aberrant AOXs were contaminants, but we also found putative cases of lateral gene transfer of AOX from fungi and protists to nematodes, springtails, fungus gnats, and rotifers. Our findings provide a robust and detailed analysis of the distribution of AOX and a method for identifying and verifying putative AOX sequences, which will be useful as more sequence data becomes available on public repositories.},
}
@article {pmid37557016,
year = {2023},
author = {Veremeichik, GN and Gorpenchenko, TY and Rusapetova, TV and Brodovskaya, EV and Tchernoded, GK and Bulgakov, DV and Shkryl, YN and Bulgakov, VP},
title = {Auxin-dependent regulation of growth via rolB-induced modulation of the ROS metabolism in the long-term cultivated pRiA4-transformed Rubiacordifolia L. calli.},
journal = {Plant physiology and biochemistry : PPB},
volume = {202},
number = {},
pages = {107932},
doi = {10.1016/j.plaphy.2023.107932},
pmid = {37557016},
issn = {1873-2690},
mesh = {Reactive Oxygen Species/metabolism ; Indoleacetic Acids/pharmacology ; Plant Cells ; *Cell Culture Techniques/methods ; *Botany/methods ; Transformation, Genetic ; Agrobacterium ; Plant Growth Regulators/metabolism ; *Rubia/chemistry/metabolism ; Anthraquinones/metabolism ; },
abstract = {Gene transfer from Agrobacterium to plants is the best studied example of horizontal gene transfer (HGT) between prokaryotes and eukaryotes. The rol genes of A. rhizogenes (Rhizobium rhizogenes) provide uncontrolled root growth, or "hairy root" syndrome, the main diagnostic feature. In the present study, we investigated the stable pRiA4-transformed callus culture of Rubia cordifolia L. While untransformed callus cultures need PGRs (plant growth regulators) as an obligatory supplement, pRiA4 calli is able to achieve long-term PGR-free cultivation. For the first time, we described the pRiA4-transformed callus cultures' PGR-dependent ROS status, growth, and specialized metabolism. As we have shown, expression of the rolA and rolB but not the rolC genes is contradictory in a PGR-dependent manner. Moreover, a PGR-free pRiA4 transformed cell line is characterised as more anthraquinone (AQ) productive than an untransformed cell culture. These findings pertain to actual plant biotechnology: it could be the solution to troubles in choosing the best PGR combination for the cultivation of some rare, medicinal, and woody plants; wild-type Ri-plants and tissue cultures may become freed from legal controls on genetically modified organisms in the future. We propose possible PGR-dependent relationships between rolA and rolB as well as ROS signalling targets. The present study highlighted the high importance of the rolA gene in the regulation of combined rol gene effects and the large knowledge gap in rolA action.},
}
@article {pmid37550759,
year = {2023},
author = {Pas, C and Latka, A and Fieseler, L and Briers, Y},
title = {Phage tailspike modularity and horizontal gene transfer reveals specificity towards E. coli O-antigen serogroups.},
journal = {Virology journal},
volume = {20},
number = {1},
pages = {174},
pmid = {37550759},
issn = {1743-422X},
mesh = {Humans ; Serogroup ; *Escherichia coli Infections/microbiology ; O Antigens/genetics/metabolism ; Gene Transfer, Horizontal ; Phylogeny ; *Shiga-Toxigenic Escherichia coli/genetics ; Feces/microbiology ; },
abstract = {BACKGROUND: The interaction between bacteriophages and their hosts is intricate and highly specific. Receptor-binding proteins (RBPs) of phages such as tail fibers and tailspikes initiate the infection process. These RBPs bind to diverse outer membrane structures, including the O-antigen, which is a serogroup-specific sugar-based component of the outer lipopolysaccharide layer of Gram-negative bacteria. Among the most virulent Escherichia coli strains is the Shiga toxin-producing E. coli (STEC) pathotype dominated by a subset of O-antigen serogroups.<br><br>METHODS: Extensive phylogenetic and structural analyses were used to identify and validate specificity correlations between phage RBP subtypes and STEC O-antigen serogroups, relying on the principle of horizontal gene transfer as main driver for RBP evolution.<br><br>RESULTS: We identified O-antigen specific RBP subtypes for seven out of nine most prevalent STEC serogroups (O26, O45, O103, O104, O111, O145 and O157) and seven additional E. coli serogroups (O2, O8, O16, O18, 4s/O22, O77 and O78). Eight phage genera (Gamaleya-, Justusliebig-, Kaguna-, Kayfuna-, Kutter-, Lederberg-, Nouzilly- and Uetakeviruses) emerged for their high proportion of serogroup-specific RBPs. Additionally, we reveal sequence motifs in the RBP region, potentially serving as recombination hotspots between lytic phages.<br><br>CONCLUSION: The results contribute to a better understanding of mosaicism of phage RBPs, but also demonstrate a method to identify and validate new RBP subtypes for current and future emerging serogroups.},
}
@article {pmid37550506,
year = {2023},
author = {Sahu, N and Indic, B and Wong-Bajracharya, J and Merényi, Z and Ke, HM and Ahrendt, S and Monk, TL and Kocsubé, S and Drula, E and Lipzen, A and Bálint, B and Henrissat, B and Andreopoulos, B and Martin, FM and Bugge Harder, C and Rigling, D and Ford, KL and Foster, GD and Pangilinan, J and Papanicolaou, A and Barry, K and LaButti, K and Virágh, M and Koriabine, M and Yan, M and Riley, R and Champramary, S and Plett, KL and Grigoriev, IV and Tsai, IJ and Slot, J and Sipos, G and Plett, J and Nagy, LG},
title = {Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria.},
journal = {Nature microbiology},
volume = {8},
number = {9},
pages = {1668-1681},
pmid = {37550506},
issn = {2058-5276},
support = {758161/ERC_/European Research Council/International ; },
mesh = {*Armillaria/genetics/metabolism ; Biomass ; Gene Transfer, Horizontal ; Ecosystem ; Plants ; },
abstract = {The fungal genus Armillaria contains necrotrophic pathogens and some of the largest terrestrial organisms that cause tremendous losses in diverse ecosystems, yet how they evolved pathogenicity in a clade of dominantly non-pathogenic wood degraders remains elusive. Here we show that Armillaria species, in addition to gene duplications and de novo gene origins, acquired at least 1,025 genes via 124 horizontal gene transfer events, primarily from Ascomycota. Horizontal gene transfer might have affected plant biomass degrading and virulence abilities of Armillaria, and provides an explanation for their unusual, soft rot-like wood decay strategy. Combined multi-species expression data revealed extensive regulation of horizontally acquired and wood-decay related genes, putative virulence factors and two novel conserved pathogenicity-induced small secreted proteins, which induced necrosis in planta. Overall, this study details how evolution knitted together horizontally and vertically inherited genes in complex adaptive traits of plant biomass degradation and pathogenicity in important fungal pathogens.},
}
@article {pmid37549546,
year = {2023},
author = {Ren, CY and Xu, QJ and Alvarez, PJJ and Zhu, L and Zhao, HP},
title = {Simultaneous antibiotic removal and mitigation of resistance induction by manganese bio-oxidation process.},
journal = {Water research},
volume = {244},
number = {},
pages = {120442},
doi = {10.1016/j.watres.2023.120442},
pmid = {37549546},
issn = {1879-2448},
mesh = {*Manganese ; *Anti-Bacterial Agents/pharmacology ; Escherichia coli/metabolism ; Oxidation-Reduction ; Oxides/metabolism ; Manganese Compounds/metabolism ; Tetracycline ; },
abstract = {Microbial degradation to remove residual antibiotics in wastewater is of growing interest. However, biological treatment of antibiotics may cause resistance dissemination by mutations and horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). In this study, a Mn(Ⅱ)-oxidizing bacterium (MnOB), Pseudomonas aeruginosa MQ2, simultaneously degraded antibiotics, decreased HGT, and mitigated antibiotic resistance mutation. Intracellular Mn(II) levels increased during manganese oxidation, and biogenic manganese oxides (BioMnOx, including Mn(II), Mn(III) and Mn(IV)) tightly coated the cell surface. Mn(II) bio-oxidation mitigated antibiotic resistance acquisition from an E. coli ARG donor and mitigated antibiotic resistance inducement by decreasing conjugative transfer and mutation, respectively. BioMnOx also oxidized ciprofloxacin (1 mg/L) and tetracycline (5 mg/L), respectively removing 93% and 96% within 24 h. Transcriptomic analysis revealed that two new multicopper oxidase and one peroxidase genes are involved in Mn(II) oxidation. Downregulation of SOS response, multidrug resistance and type Ⅳ secretion system related genes explained that Mn(II) and BioMnOx decreased HGT and mitigated resistance mutation by alleviating oxidative stress, which makes recipient cells more vulnerable to ARG acquisition and mutation. A manganese bio-oxidation based reactor was constructed and completely removed tetracycline with environmental concentration within 4-hour hydraulic retention time. Overall, this study suggests that Mn (II) bio-oxidation process could be exploited to control antibiotic contamination and mitigate resistance propagation during water treatment.},
}
@article {pmid37548082,
year = {2023},
author = {Zackova Suchanova, J and Bilcke, G and Romanowska, B and Fatlawi, A and Pippel, M and Skeffington, A and Schroeder, M and Vyverman, W and Vandepoele, K and Kröger, N and Poulsen, N},
title = {Diatom adhesive trail proteins acquired by horizontal gene transfer from bacteria serve as primers for marine biofilm formation.},
journal = {The New phytologist},
volume = {240},
number = {2},
pages = {770-783},
doi = {10.1111/nph.19145},
pmid = {37548082},
issn = {1469-8137},
mesh = {*Diatoms/metabolism ; Adhesives/metabolism ; Gene Transfer, Horizontal ; Biofilms ; Bacteria ; },
abstract = {Biofilm-forming benthic diatoms are key primary producers in coastal habitats, where they frequently dominate sunlit intertidal substrata. The development of gliding motility in raphid diatoms was a key molecular adaptation that contributed to their evolutionary success. However, the structure-function correlation between diatom adhesives utilized for gliding and their relationship to the extracellular matrix that constitutes the diatom biofilm is unknown. Here, we have used proteomics, immunolocalization, comparative genomics, phylogenetics and structural homology analysis to investigate the evolutionary history and function of diatom adhesive proteins. Our study identified eight proteins from the adhesive trails of Craspedostauros australis, of which four form a new protein family called Trailins that contain an enigmatic Choice-of-Anchor A (CAA) domain, which was acquired through horizontal gene transfer from bacteria. Notably, the CAA-domain shares a striking structural similarity with one of the most widespread domains found in ice-binding proteins (IPR021884). Our work offers new insights into the molecular basis for diatom biofilm formation, shedding light on the function and evolution of diatom adhesive proteins. This discovery suggests that there is a transition in the composition of biomolecules required for initial surface colonization and those utilized for 3D biofilm matrix formation.},
}
@article {pmid37541538,
year = {2023},
author = {Nielsen, TK and Winther-Have, CS and Thomsen, IM and Jackson, RW and Rabiey, M and Hennessy, RC and Bak, F and Kot, W and Nicolaisen, MH and Carstens, AB and Hansen, LH},
title = {Genetic rearrangements in Pseudomonas amygdali pathovar aesculi shape coronatine plasmids.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {113},
number = {},
pages = {105486},
doi = {10.1016/j.meegid.2023.105486},
pmid = {37541538},
issn = {1567-7257},
mesh = {*Pseudomonas/genetics/metabolism ; Plasmids/genetics ; *Virulence Factors/genetics/metabolism ; },
abstract = {Plant pathogenic Pseudomonas species use multiple classes of toxins and virulence factors during host infection. The genes encoding these pathogenicity factors are often located on plasmids and other mobile genetic elements, suggesting that they are acquired through horizontal gene transfer to confer an evolutionary advantage for successful adaptation to host infection. However, the genetic rearrangements that have led to mobilization of the pathogenicity genes are not fully understood. In this study, we have sequenced and analyzed the complete genome sequences of four Pseudomonas amygdali pv. aesculi (Pae), which infect European horse chestnut trees (Aesculus hippocastanum) and belong to phylogroup 3 of the P. syringae species complex. The four investigated genomes contain six groups of plasmids that all encode pathogenicity factors. Effector genes were found to be mostly associated with insertion sequence elements, suggesting that virulence genes are generally mobilized and potentially undergo horizontal gene transfer after transfer to a conjugative plasmid. We show that the biosynthetic gene cluster encoding the phytotoxin coronatine was recently transferred from a chromosomal location to a mobilizable plasmid that subsequently formed a co-integrate with a conjugative plasmid.},
}
@article {pmid37541493,
year = {2023},
author = {Li, S and Li, X and Chang, H and Zhong, N and Ren, N and Ho, SH},
title = {Comprehensive insights into antibiotic resistance gene migration in microalgal-bacterial consortia: Mechanisms, factors, and perspectives.},
journal = {The Science of the total environment},
volume = {901},
number = {},
pages = {166029},
doi = {10.1016/j.scitotenv.2023.166029},
pmid = {37541493},
issn = {1879-1026},
abstract = {With the overuse of antibiotics, antibiotic resistance gene (ARG) prevalence is gradually increasing. ARGs are considered emerging contaminants that are broadly concentrated and dispersed in most aquatic environments. Recently, interest in microalgal-bacterial biotreatment of antibiotics has increased, as eukaryotes are not the primary target of antimicrobial drugs. Moreover, research has shown that microalgal-bacterial consortia can minimize the transmission of antibiotic resistance in the environment. Unfortunately, reviews surrounding the ARG migration mechanism in microalgal-bacterial consortia have not yet been performed. This review briefly introduces the migration of ARGs in aquatic environments. Additionally, an in-depth summary of horizontal gene transfer (HGT) between cyanobacteria and bacteria and from bacteria to eukaryotic microalgae is presented. Factors influencing gene transfer in microalgal-bacterial consortia are discussed systematically, including bacteriophage abundance, environmental conditions (temperature, pH, and nutrient availability), and other selective pressure conditions including nanomaterials, heavy metals, and pharmaceuticals and personal care products. Furthermore, considering that quorum sensing could be involved in DNA transformation by affecting secondary metabolites, current knowledge surrounding quorum sensing regulation of HGT of ARGs is summarized. In summary, this review gives valuable information to promote the development of practical and innovative techniques for ARG removal by microalgal-bacterial consortia.},
}
@article {pmid37537271,
year = {2023},
author = {Lund, D and Coertze, RD and Parras-Moltó, M and Berglund, F and Flach, CF and Johnning, A and Larsson, DGJ and Kristiansson, E},
title = {Extensive screening reveals previously undiscovered aminoglycoside resistance genes in human pathogens.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {812},
pmid = {37537271},
issn = {2399-3642},
mesh = {Humans ; *Aminoglycosides/pharmacology ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology/metabolism ; Genome, Bacterial ; Escherichia coli/metabolism ; },
abstract = {Antibiotic resistance is a growing threat to human health, caused in part by pathogens accumulating antibiotic resistance genes (ARGs) through horizontal gene transfer. New ARGs are typically not recognized until they have become widely disseminated, which limits our ability to reduce their spread. In this study, we use large-scale computational screening of bacterial genomes to identify previously undiscovered mobile ARGs in pathogens. From ~1 million genomes, we predict 1,071,815 genes encoding 34,053 unique aminoglycoside-modifying enzymes (AMEs). These cluster into 7,612 families (<70% amino acid identity) of which 88 are previously described. Fifty new AME families are associated with mobile genetic elements and pathogenic hosts. From these, 24 of 28 experimentally tested AMEs confer resistance to aminoglycoside(s) in Escherichia coli, with 17 providing resistance above clinical breakpoints. This study greatly expands the range of clinically relevant aminoglycoside resistance determinants and demonstrates that computational methods enable early discovery of potentially emerging ARGs.},
}
@article {pmid37533411,
year = {2023},
author = {Groisman, EA and Choi, J},
title = {Advancing evolution: Bacteria break down gene silencer to express horizontally acquired genes.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {45},
number = {10},
pages = {e2300062},
pmid = {37533411},
issn = {1521-1878},
support = {R01 AI049561/AI/NIAID NIH HHS/United States ; },
mesh = {*DNA-Binding Proteins/genetics ; *Bacterial Proteins/genetics/metabolism ; Bacteria/metabolism ; Salmonella typhimurium/genetics/metabolism ; DNA-Directed RNA Polymerases/genetics ; Gene Expression Regulation, Bacterial/genetics ; },
abstract = {Horizontal gene transfer advances bacterial evolution. To benefit from horizontally acquired genes, enteric bacteria must overcome silencing caused when the widespread heat-stable nucleoid structuring (H-NS) protein binds to AT-rich horizontally acquired genes. This ability had previously been ascribed to both anti-silencing proteins outcompeting H-NS for binding to AT-rich DNA and RNA polymerase initiating transcription from alternative promoters. However, we now know that pathogenic Salmonella enterica serovar Typhimurium and commensal Escherichia coli break down H-NS when this silencer is not bound to DNA. Curiously, both species use the same protease - Lon - to destroy H-NS in distinct environments. Anti-silencing proteins promote the expression of horizontally acquired genes without binding to them by displacing H-NS from AT-rich DNA, thus leaving H-NS susceptible to proteolysis and decreasing H-NS amounts overall. Conserved amino acid sequences in the Lon protease and H-NS cleavage site suggest that diverse bacteria degrade H-NS to exploit horizontally acquired genes.},
}
@article {pmid37533217,
year = {2023},
author = {Shin, NR and Pauchet, Y},
title = {First evidence of a horizontally-acquired GH-7 cellobiohydrolase from a longhorned beetle genome.},
journal = {Archives of insect biochemistry and physiology},
volume = {114},
number = {2},
pages = {1-14},
doi = {10.1002/arch.22039},
pmid = {37533217},
issn = {1520-6327},
support = {//Max Planck Society/ ; PA2808/4-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; *Coleoptera/metabolism ; Cellulose 1,4-beta-Cellobiosidase/genetics/chemistry/metabolism ; Phylogeny ; Glycoside Hydrolases/genetics/metabolism ; Polysaccharides ; Cellulose ; },
abstract = {Xylophagous larvae of longhorned beetles (Coleoptera; Cerambycidae) efficiently break down polysaccharides of the plant cell wall, which make the bulk of their food, using a range of carbohydrate-active enzymes (CAZymes). In this study, we investigated the function and evolutionary history of the first identified example of insect-encoded members of glycoside hydrolase family 7 (GH7) derived from the Lamiinae Exocentrus adspersus. The genome of this beetle contained two genes encoding GH7 proteins located in tandem and flanked by transposable elements. Phylogenetic analysis revealed that the GH7 sequences of E. adspersus were closely related to those of Ascomycete fungi, suggesting that they were acquired through horizontal gene transfer (HGT) from fungi. However, they were more distantly related to those encoded by genomes of Crustacea and of protist symbionts of termites and cockroaches, supporting that the same enzyme family was recruited several times independently in Metazoa during the course of their evolution. The recombinant E. adspersus GH7 was found to primarily break down cellulose polysaccharides into cellobiose, indicating that it is a cellobiohydrolase, and could also use smaller cellulose oligomers as substrates. Additionally, the cellobiohydrolase activity was boosted by the presence of calcium chloride. Our findings suggest that the combination of GH7 cellobiohydrolases with other previously characterized endo-β-1,4-glucanases and β-glucosidases allows longhorned beetles like E. adspersus to efficiently break down cellulose into monomeric glucose.},
}
@article {pmid37531380,
year = {2023},
author = {Pinder, C and Lebedinec, R and Levine, TP and Birch, M and Oliver, JD},
title = {Characterisation of putative class 1A DHODH-like proteins from Mucorales and dematiaceous mould species.},
journal = {PloS one},
volume = {18},
number = {8},
pages = {e0289441},
pmid = {37531380},
issn = {1932-6203},
mesh = {Dihydroorotate Dehydrogenase ; Saccharomyces cerevisiae/metabolism ; *Mucorales ; *Oxidoreductases Acting on CH-CH Group Donors/genetics/metabolism ; Pyrimidines/pharmacology ; },
abstract = {Olorofim is a new antifungal in clinical development which has a novel mechanism of action against dihydroorotate dehydrogenase (DHODH). DHODH form a ubiquitous family of enzymes in the de novo pyrimidine biosynthetic pathway and are split into class 1A, class 1B and class 2. Olorofim specifically targets the fungal class 2 DHODH present in a range of pathogenic moulds. The nature and number of DHODH present in many fungal species have not been addressed for large clades of this kingdom. Mucorales species do not respond to olorofim; previous work suggests they have only class 1A DHODH and so lack the class 2 target that olorofim inhibits. The dematiaceous moulds have mixed susceptibility to olorofim, yet previous analyses imply that they have class 2 DHODH. As this is at odds with their intermediate susceptibility to olorofim, we hypothesised that these pathogens may maintain a second class of DHODH, facilitating pyrimidine biosynthesis in the presence of olorofim. The aim of this study was to investigate the DHODH repertoire of clinically relevant species of Mucorales and dematiaceous moulds to further characterise these pathogens and understand variations in olorofim susceptibility. Using bioinformatic analysis, S. cerevisiae complementation and biochemical assays of recombinant protein, we provide the first evidence that two representative members of the Mucorales have only class 1A DHODH, substantiating a lack of olorofim susceptibility. In contrast, bioinformatic analyses initially suggested that seven dematiaceous species appeared to harbour both class 1A-like and class 2-like DHODH genes. However, further experimental investigation of the putative class 1A-like genes through yeast complementation and biochemical assays characterised them as dihydrouracil oxidases rather than DHODHs. These data demonstrate variation in dematiaceous mould olorofim susceptibility is not due to a secondary DHODH and builds on the growing picture of fungal dihydrouracil oxidases as an example of horizontal gene transfer.},
}
@article {pmid37526972,
year = {2023},
author = {Winter, M and Harms, K and Johnsen, PJ and Buckling, A and Vos, M},
title = {Testing for the fitness benefits of natural transformation during community-embedded evolution.},
journal = {Microbiology (Reading, England)},
volume = {169},
number = {8},
pages = {},
pmid = {37526972},
issn = {1465-2080},
mesh = {*DNA ; DNA, Bacterial/genetics ; *Bacteria/genetics ; Transformation, Bacterial/genetics ; Adaptation, Physiological ; },
abstract = {Natural transformation is a process where bacteria actively take up DNA from the environment and recombine it into their genome or reconvert it into extra-chromosomal genetic elements. The evolutionary benefits of transformation are still under debate. One main explanation is that foreign allele and gene uptake facilitates natural selection by increasing genetic variation, analogous to meiotic sex. However, previous experimental evolution studies comparing fitness gains of evolved transforming- and isogenic non-transforming strains have yielded mixed support for the 'sex hypothesis.' Previous studies testing the sex hypothesis for natural transformation have largely ignored species interactions, which theory predicts provide conditions favourable to sex. To test for the adaptive benefits of bacterial transformation, the naturally transformable wild-type Acinetobacter baylyi and a transformation-deficient ∆comA mutant were evolved for 5 weeks. To provide strong and potentially fluctuating selection, A. baylyi was embedded in a community of five other bacterial species. DNA from a pool of different Acinetobacter strains was provided as a substrate for transformation. No effect of transformation ability on the fitness of evolved populations was found, with fitness increasing non-significantly in most treatments. Populations showed fitness improvement in their respective environments, with no apparent costs of adaptation to competing species. Despite the absence of fitness effects of transformation, wild-type populations evolved variable transformation frequencies that were slightly greater than their ancestor which potentially could be caused by genetic drift.},
}
@article {pmid37526649,
year = {2023},
author = {Rodrigues, JA and Blankenship, HM and Cha, W and Mukherjee, S and Sloup, RE and Rudrik, JT and Soehnlen, M and Manning, SD},
title = {Pangenomic analyses of antibiotic-resistant Campylobacter jejuni reveal unique lineage distributions and epidemiological associations.},
journal = {Microbial genomics},
volume = {9},
number = {8},
pages = {},
pmid = {37526649},
issn = {2057-5858},
support = {U01 CK000510/CK/NCEZID CDC HHS/United States ; U01CK000510/ACL/ACL HHS/United States ; },
mesh = {Animals ; Cattle ; Anti-Bacterial Agents/pharmacology ; *Campylobacter jejuni/genetics ; *Campylobacter Infections/epidemiology ; Phylogeny ; Multilocus Sequence Typing ; },
abstract = {Application of whole-genome sequencing (WGS) to characterize foodborne pathogens has advanced our understanding of circulating genotypes and evolutionary relationships. Herein, we used WGS to investigate the genomic epidemiology of Campylobacter jejuni, a leading cause of foodborne disease. Among the 214 strains recovered from patients with gastroenteritis in Michigan, USA, 85 multilocus sequence types (STs) were represented and 135 (63.1 %) were phenotypically resistant to at least one antibiotic. Horizontally acquired antibiotic resistance genes were detected in 128 (59.8 %) strains and the genotypic resistance profiles were mostly consistent with the phenotypes. Core-gene phylogenetic reconstruction identified three sequence clusters that varied in frequency, while a neighbour-net tree detected significant recombination among the genotypes (pairwise homoplasy index P<0.01). Epidemiological analyses revealed that travel was a significant contributor to pangenomic and ST diversity of C. jejuni, while some lineages were unique to rural counties and more commonly possessed clinically important resistance determinants. Variation was also observed in the frequency of lineages over the 4 year period with chicken and cattle specialists predominating. Altogether, these findings highlight the importance of geographically specific factors, recombination and horizontal gene transfer in shaping the population structure of C. jejuni. They also illustrate the usefulness of WGS data for predicting antibiotic susceptibilities and surveillance, which are important for guiding treatment and prevention strategies.},
}
@article {pmid37517232,
year = {2023},
author = {Zheng, Z and Huang, Y and Liu, L and Wang, L and Tang, J},
title = {Interaction between microplastic biofilm formation and antibiotics: Effect of microplastic biofilm and its driving mechanisms on antibiotic resistance gene.},
journal = {Journal of hazardous materials},
volume = {459},
number = {},
pages = {132099},
doi = {10.1016/j.jhazmat.2023.132099},
pmid = {37517232},
issn = {1873-3336},
mesh = {*Microplastics ; Plastics ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Drug Resistance, Microbial/genetics ; Biofilms ; *Environmental Pollutants ; },
abstract = {As two pollutants with similar transport pathways, microplastics (MPs) and antibiotics (ATs) inevitably co-exist in water environments, and their interaction has become a topic of intense research interest for scholars over the past few years. This paper comprehensively and systematically reviews the current interaction between MPs and ATs, in particular, the role played by biofilm developed MPs (microplastic biofilm). A summary of the formation process of microplastic biofilm and its unique microbial community structure is presented in the paper. The formation of microplastic biofilm can enhance the adsorption mechanisms of ATs on primary MPs. Moreover, microplastic biofilm system is a diverse and vast reservoir of genetic material, and this paper reviews the mechanisms by which microplastics with biofilm drive the production of antibiotic resistance genes (ARGs) and the processes that selectively enrich for more ARGs. Meanwhile, the enrichment of ARGs may lead to the development of microbial resistance and the gradual loss of the antimicrobial effect of ATs. The transfer pathways of ARGs affected by microplastic biofilm are outlined, and ARGs dependent transfer of antibiotic resistance bacteria (ARB) is mainly through horizontal gene transfer (HGT). Furthermore, the ecological implications of the interaction between microplastic biofilm and ATs and perspectives for future research are reviewed. This review contributes to a new insight into the aquatic ecological environmental risks and the fate of contaminants (MPs, ATs), and is of great significance for controlling the combined pollution of these two pollutants.},
}
@article {pmid37513735,
year = {2023},
author = {Nath, J and De, J and Sur, S and Banerjee, P},
title = {Interaction of Microbes with Microplastics and Nanoplastics in the Agroecosystems-Impact on Antimicrobial Resistance.},
journal = {Pathogens (Basel, Switzerland)},
volume = {12},
number = {7},
pages = {},
pmid = {37513735},
issn = {2076-0817},
support = {2020-70020-33033//National Institute of Food and Agriculture/ ; 2022-70020-37590//National Institute of Food and Agriculture/ ; },
abstract = {Microplastics (MPs) and nanoplastics (NPs) are hotspots for the exchange of antimicrobial resistance genes (ARGs) between different bacterial taxa in the environment. Propagation of antimicrobial resistance (AMR) is a global public health issue that needs special attention concerning horizontal gene transfer (HGT) under micro-nano plastics (MNPs) pressure. Interactions between MNPs and microbes, or mere persistence of MNPs in the environment (either water or soil), influence microbial gene expressions, affecting autochthonous microbiomes, their resistomes, and the overall ecosystem. The adsorption of a range of co-contaminants on MNPs leads to the increased interaction of pollutants with microbes resulting in changes in AMR, virulence, toxin production, etc. However, accurately estimating the extent of MNP infestation in agroecosystems remains challenging. The main limitation in estimating the level of MNPs contamination in agroecosystems, surface and subsurface waters, or sediments is the lack of standardized protocols for extraction of MPs and analytical detection methods from complex high organic content matrices. Nonetheless, recent advances in MPs detection from complex matrices with high organic matter content are highly promising. This review aims to provide an overview of relevant information available to date and summarize the already existing knowledge about the mechanisms of MNP-microbe interactions including the different factors with influence on HGT and AMR. In-depth knowledge of the enhanced ARGs propagation in the environment under the influence of MNPs could raise the needed awareness, about future consequences and emergence of multidrug-resistant bacteria.},
}
@article {pmid37513616,
year = {2023},
author = {Fan, X and Lu, Y and Zhao, Y and Miao, H and Qi, K and Wang, R},
title = {An Insight into the Exploration of Antibiotic Resistance Genes in Calorie Restricted Diet Fed Mice.},
journal = {Nutrients},
volume = {15},
number = {14},
pages = {},
pmid = {37513616},
issn = {2072-6643},
support = {7212143//Natural Science Foundation of Beijing/ ; 81803214, 81800750, 82003432//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Mice ; *Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Caloric Restriction ; Manure/microbiology ; Drug Resistance, Microbial/genetics ; },
abstract = {Antibiotic resistance genes (ARGs) threaten the success of modern drugs against multidrug resistant infections. ARGs can be transferred to opportunistic pathogens by horizontal gene transfer (HGT). Many studies have investigated the characteristics of ARGs in various chemical stressors. Studies on the effects of dietary nutrition and dietary patterns on ARGs are rare. The study first demonstrated the effect of calorie restricted (CR) diet on the ARGs and mobile genetic elements (MGEs) in mouse feces and explored their relationship with gut microbiota and their functions. The results showed that the abundance of the total ARGs in mouse feces of the CR group increased, especially tetracycline ARGs (tetW-01). The abundance of the MLSB ARGs (ermB) decreased evidently in mouse feces of the CR group. In addition, the total abundance of MGEs decreased evidently in the CR group, especially tnpA-03. In the meantime, the abundance of Lactobacillus and Bifidobacterium in mouse feces of the CR group increased remarkably. The Spearman correlation analysis between gut microbiota and ARGs showed that several probiotics were significantly positively correlated with ARGs (tetW-01), which might be the main contribution to the increase in ARGs of the CR group.},
}
@article {pmid37513002,
year = {2023},
author = {Gryganskyi, AP and Golan, J and Muszewska, A and Idnurm, A and Dolatabadi, S and Mondo, SJ and Kutovenko, VB and Kutovenko, VO and Gajdeczka, MT and Anishchenko, IM and Pawlowska, J and Tran, NV and Ebersberger, I and Voigt, K and Wang, Y and Chang, Y and Pawlowska, TE and Heitman, J and Vilgalys, R and Bonito, G and Benny, GL and Smith, ME and Reynolds, N and James, TY and Grigoriev, IV and Spatafora, JW and Stajich, JE},
title = {Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned?.},
journal = {Microorganisms},
volume = {11},
number = {7},
pages = {},
pmid = {37513002},
issn = {2076-2607},
support = {R01 AI039115/AI/NIAID NIH HHS/United States ; R01 AI050113/AI/NIAID NIH HHS/United States ; },
abstract = {The first genome sequenced of a eukaryotic organism was for Saccharomyces cerevisiae, as reported in 1996, but it was more than 10 years before any of the zygomycete fungi, which are the early-diverging terrestrial fungi currently placed in the phyla Mucoromycota and Zoopagomycota, were sequenced. The genome for Rhizopus delemar was completed in 2008; currently, more than 1000 zygomycete genomes have been sequenced. Genomic data from these early-diverging terrestrial fungi revealed deep phylogenetic separation of the two major clades-primarily plant-associated saprotrophic and mycorrhizal Mucoromycota versus the primarily mycoparasitic or animal-associated parasites and commensals in the Zoopagomycota. Genomic studies provide many valuable insights into how these fungi evolved in response to the challenges of living on land, including adaptations to sensing light and gravity, development of hyphal growth, and co-existence with the first terrestrial plants. Genome sequence data have facilitated studies of genome architecture, including a history of genome duplications and horizontal gene transfer events, distribution and organization of mating type loci, rDNA genes and transposable elements, methylation processes, and genes useful for various industrial applications. Pathogenicity genes and specialized secondary metabolites have also been detected in soil saprobes and pathogenic fungi. Novel endosymbiotic bacteria and viruses have been discovered during several zygomycete genome projects. Overall, genomic information has helped to resolve a plethora of research questions, from the placement of zygomycetes on the evolutionary tree of life and in natural ecosystems, to the applied biotechnological and medical questions.},
}
@article {pmid37512869,
year = {2023},
author = {Zinno, P and Perozzi, G and Devirgiliis, C},
title = {Foodborne Microbial Communities as Potential Reservoirs of Antimicrobial Resistance Genes for Pathogens: A Critical Review of the Recent Literature.},
journal = {Microorganisms},
volume = {11},
number = {7},
pages = {},
pmid = {37512869},
issn = {2076-2607},
abstract = {Antimicrobial resistance (AMR) is a global and increasing threat to human health. Several genetic determinants of AMR are found in environmental reservoirs, including bacteria naturally associated with widely consumed fermented foods. Through the food chain, these bacteria can reach the gut, where horizontal gene transfer (HGT) can occur within the complex and populated microbial environment. Numerous studies on this topic have been published over the past decades, but a conclusive picture of the potential impact of the non-pathogenic foodborne microbial reservoir on the spread of AMR to human pathogens has not yet emerged. This review critically evaluates a comprehensive list of recent experimental studies reporting the isolation of AMR bacteria associated with fermented foods, focusing on those reporting HGT events, which represent the main driver of AMR spread within and between different bacterial communities. Overall, our analysis points to the methodological heterogeneity as a major weakness impairing determination or a causal relation between the presence of AMR determinants within the foodborne microbial reservoir and their transmission to human pathogens. The aim is therefore to highlight the main gaps and needs to better standardize future studies addressing the potential role of non-pathogenic bacteria in the spread of AMR.},
}
@article {pmid37512822,
year = {2023},
author = {Di Pierro, F and Campedelli, I and De Marta, P and Fracchetti, F and Del Casale, A and Cavecchia, I and Matera, M and Cazzaniga, M and Bertuccioli, A and Guasti, L and Zerbinati, N},
title = {Bifidobacterium breve PRL2020: Antibiotic-Resistant Profile and Genomic Detection of Antibiotic Resistance Determinants.},
journal = {Microorganisms},
volume = {11},
number = {7},
pages = {},
pmid = {37512822},
issn = {2076-2607},
abstract = {Antibiotics are one of the greatest scientific achievements of modern medicine, but excessive use is creating challenges for the future of medicine. Antibiotic resistance (AR) is thought to cause changes in bowel habits and an increased risk of gastroenteritis, but it may also increase the risk of overweight, obesity, autoimmune and atopic diseases, and a low response to vaccines and cancer, likely mediated by antibiotic-induced gut dysbiosis. Probiotic add-on therapy could partially prevent antibiotic-induced gut dysbiosis, but their antibiotic sensitivity features likely limits this potential. The EFSA (European Food Safety Authority) guidelines consider the use of probiotics whose antibiotic-resistant profile could be transferable an important hazard. Recently, a strain of B. breve (PRL2020) has shown to be resistant to amoxicillin and amoxicillin-clavulanate (AC) by applying the microdilution protocol according EFSA guidelines. After verifying that horizontal gene transfer is unlikely to take place, this feature suggests its concomitant use with these specific antibiotics. The results of our tests demonstrated that the strain PRL2020 is indeed endowed with amoxicillin- and AC-resistant properties and that it is also insensitive to ampicillin. In-depth analysis of the annotated genome sequence of B. breve PRL2020 was employed to query the Comprehensive Antibiotic Resistance Database (CARD) using Resistance Gene Identifier (RGI) software (version 5.2.1). The similarity among the AR determinants found was studied through nucleotide sequence alignment, and it was possible to verify not only the absence of genes explaining these features in the flanking regions but also the presence of genetic sequences (rpoB and erm(X)) putatively responsible for rifampicin and erythromycin resistance. Both features are not phenotypically expressed, and for these antibiotics, the strain is within the EFSA limits. Analysis of the flanking regions of these genes revealed possible mobile elements upstream and downstream only in the case of the erm(X) gene, but the features of the Insertion Sequences (IS) are described as not to cause horizontal transfer. Our findings on strain PRL2020 demonstrate that its AR profile is compatible with antibiotics when taken with the aim of reducing the risk of dysbiosis.},
}
@article {pmid37511529,
year = {2023},
author = {Kordiš, D and Turk, V},
title = {Origin and Early Diversification of the Papain Family of Cysteine Peptidases.},
journal = {International journal of molecular sciences},
volume = {24},
number = {14},
pages = {},
pmid = {37511529},
issn = {1422-0067},
support = {P1-0207, P1-0140, J1-2473//Slovenian Research Agency/ ; },
mesh = {*Papain/genetics/metabolism ; Cysteine/metabolism ; Evolution, Molecular ; Phylogeny ; Eukaryota/genetics ; Archaea/genetics ; *Cysteine Proteases/metabolism ; Peptide Hydrolases/metabolism ; },
abstract = {Peptidases of the papain family play a key role in protein degradation, regulated proteolysis, and the host-pathogen arms race. Although the papain family has been the subject of many studies, knowledge about its diversity, origin, and evolution in Eukaryota, Bacteria, and Archaea is limited; thus, we aimed to address these long-standing knowledge gaps. We traced the origin and expansion of the papain family with a phylogenomic analysis, using sequence data from numerous prokaryotic and eukaryotic proteomes, transcriptomes, and genomes. We identified the full complement of the papain family in all prokaryotic and eukaryotic lineages. Analysis of the papain family provided strong evidence for its early diversification in the ancestor of eukaryotes. We found that the papain family has undergone complex and dynamic evolution through numerous gene duplications, which produced eight eukaryotic ancestral paralogous C1A lineages during eukaryogenesis. Different evolutionary forces operated on C1A peptidases, including gene duplication, horizontal gene transfer, and gene loss. This study challenges the current understanding of the origin and evolution of the papain family and provides valuable insights into their early diversification. The findings of this comprehensive study provide guidelines for future structural and functional studies of the papain family.},
}
@article {pmid37511216,
year = {2023},
author = {Kim, YK and Jo, S and Cheon, SH and Hong, JR and Kim, KJ},
title = {Ancient Horizontal Gene Transfers from Plastome to Mitogenome of a Nonphotosynthetic Orchid, Gastrodia pubilabiata (Epidendroideae, Orchidaceae).},
journal = {International journal of molecular sciences},
volume = {24},
number = {14},
pages = {},
pmid = {37511216},
issn = {1422-0067},
support = {NRF-2021R1A2C1013731//National Research Foundation of Korea/ ; NRF-2020R1A6A3A01100512//National Research Foundation of Korea/ ; },
mesh = {*Orchidaceae/genetics ; *Gastrodia/genetics ; *Genome, Mitochondrial ; Gene Transfer, Horizontal ; Phylogeny ; *Magnoliopsida/genetics ; },
abstract = {Gastrodia pubilabiata is a nonphotosynthetic and mycoheterotrophic orchid belonging to subfamily Epidendroideae. Compared to other typical angiosperm species, the plastome of G. pubilabiata is dramatically reduced in size to only 30,698 base pairs (bp). This reduction has led to the loss of most photosynthesis-related genes and some housekeeping genes in the plastome, which now only contains 19 protein coding genes, three tRNAs, and three rRNAs. In contrast, the typical orchid species contains 79 protein coding genes, 30 tRNAs, and four rRNAs. This study decoded the entire mitogenome of G. pubilabiata, which consisted of 44 contigs with a total length of 867,349 bp. Its mitogenome contained 38 protein coding genes, nine tRNAs, and three rRNAs. The gene content of G. pubilabiata mitogenome is similar to the typical plant mitogenomes even though the mitogenome size is twice as large as the typical ones. To determine possible gene transfer events between the plastome and the mitogenome individual BLASTN searches were conducted, using all available orchid plastome sequences and flowering plant mitogenome sequences. Plastid rRNA fragments were found at a high frequency in the mitogenome. Seven plastid protein coding gene fragments (ndhC, ndhJ, ndhK, psaA, psbF, rpoB, and rps4) were also identified in the mitogenome of G. pubilabiata. Phylogenetic trees using these seven plastid protein coding gene fragments suggested that horizontal gene transfer (HGT) from plastome to mitogenome occurred before losses of photosynthesis related genes, leading to the lineage of G. pubilabiata. Compared to species phylogeny of the lineage of orchid, it was estimated that HGT might have occurred approximately 30 million years ago.},
}
@article {pmid37508388,
year = {2023},
author = {Zuber, NE and Fornasero, LV and Erdozain Bagolín, SA and Lozano, MJ and Sanjuán, J and Del Papa, MF and Lagares, A},
title = {Diversity, Genomics and Symbiotic Characteristics of Sinorhizobia That Nodulate Desmanthus spp. in Northwest Argentina.},
journal = {Biology},
volume = {12},
number = {7},
pages = {},
pmid = {37508388},
issn = {2079-7737},
support = {PICT-2019-01021//Ministerio de Ciencia Tecnololog&#xed;a e Innovaci&#xf3;n Productiva - MinCyT, Argentina/ ; PIP 2022-2024-11220210100367CO//Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas - CONICET, Argentina/ ; ATN-RF-18786-RG//FONTAGRO/ ; },
abstract = {Desmanthus spp. are legumes with the ability to associate with diverse α-proteobacteria-a microsymbiont-in order to establish nitrogen-fixing root nodules. A previous investigation from our laboratory revealed that the main bacteria associated with Desmanthus paspalaceus in symbiosis in central Argentina (Province of Santa Fe) were quite diverse and belonged to the genera Rhizobium and Mesorhizobium. To achieve a more extensive view of the local microsymbionts associated with Desmanthus spp., we sampled three different sites in Jujuy and Salta, in northwest Argentina. Matrix-assisted Laser-Desorption-Ionization Time-of-Flight mass spectrometry (MALDI-TOF) typing, 16S-rDNA analysis, and genome sequencing demonstrated that the dominant root-nodule microsymbionts belonged to the genus Sinorhizobium, with some sequenced genomes related to Sinorhizobium mexicanum, Sinorhizobium chiapanecum, and Sinorhizobium psoraleae. An analysis of nodA and nodC markers indicated that, in some of the isolates, horizontal gene transfer appeared to be responsible for the lack of congruence between the phylogenies of the chromosome and of the symbiotic region. These results revealed diverse evolutionary strategies for reaching the current Desmanthus-microsymbiont diversity. What is remarkable beside their observed genetic diversity is that the tolerance profiles of these isolates to abiotic stresses (temperature, salt concentration, pH) were quite coincident with the separation of the sinorhizobia according to place of origin, suggesting possible ecoedaphic adaptations. This observation, together with the higher aerial dry-weight matter that some isolates generated in Desmanthus virgatus cv. Marc when compared to the biomass generated by the commercial strain Sinorhizobium terangae CB3126, distinguish the collected sinorhizobia as constituting valuable germplasm for evaluation in local fields to select for more efficient symbiotic pairs.},
}
@article {pmid37508321,
year = {2023},
author = {Zaghen, F and Sora, VM and Meroni, G and Laterza, G and Martino, PA and Soggiu, A and Bonizzi, L and Zecconi, A},
title = {Epidemiology of Antimicrobial Resistance Genes in Staphyloccocus aureus Isolates from a Public Database in a One Health Perspective-Sample Characteristics and Isolates' Sources.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {7},
pages = {},
pmid = {37508321},
issn = {2079-6382},
support = {Programma di Sviluppo Rurale 2014-2020 Misura 16.1 project MOOH//FEASR/ ; 2017MZ5KWM_001 project "SAFE MILK: OMICS SCIENCE FOR MILK SAFETY AND QUALITY"//PRIN/ ; PSR2021 line 6 One Health Action Hub//University of Milan/ ; },
abstract = {Staphylococcus aureus is considered one of the most widespread bacterial pathogens for both animals and humans, being the causative agent of various diseases like food poisoning, respiratory tract infections, nosocomial bacteremia, and surgical site and cardiovascular infections in humans, as well as clinical and subclinical mastitis, dermatitis, and suppurative infections in animals. Thanks to their genetic flexibility, several virulent and drug-resistant strains have evolved mainly due to horizontal gene transfer and insurgence of point mutations. Infections caused by the colonization of such strains are particularly problematic due to frequently occurring antibiotic resistance, particulary methicillin-resistant S. aureus (MRSA), and are characterized by increased mortality, morbidity, and hospitalization rates compared to those caused by methicillin-sensitive S. aureus (MSSA). S. aureus infections in humans and animals are a prime example of a disease that may be managed by a One Health strategy. In fact, S. aureus is a significant target for control efforts due to its zoonotic potential, the frequency of its illnesses in both humans and animals, and the threat posed by S. aureus antibiotic resistance globally. The results of an epidemiological analysis on a worldwide public database (NCBI Pathogen Detection Isolate Browser; NPDIB) of 35,026 S. aureus isolates were described. We considered the diffusion of antibiotic resistance genes (ARGs), in both human and animal setting, and the results may be considered alarming. The result of this study allowed us to identify the presence of clusters with specific ARG patterns, and that these clusters are associated with different sources of isolation (e.g., human, non-human).},
}
@article {pmid37508250,
year = {2023},
author = {Liu, S and Liu, B and Zhu, Y and Qiu, Y and Li, B},
title = {The Spatial-Temporal Effects of Bacterial Growth Substrates on Antibiotic Resistance Gene Spread in the Biofilm.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {7},
pages = {},
pmid = {37508250},
issn = {2079-6382},
support = {2020YFC19092-05, 2022YFC32031-04//Ministry of Science and Technology/ ; FRF-TP-20-011A3//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Biofilm is considered as the hotspot of antibiotic resistance gene (ARG) dissemination. Bacterial growth substrates are important factors for biofilm formation, but its spatial-temporal effects on ARG spread in biofilm is still unclear. In this study, microfluidics combined with microscopic observation were used to reveal spatial-temporal effects of bacterial growth substrates on ARG transfer at real time. The initial horizontal gene transfer events were found to be independent of substrate levels. However, subsequent transfer processes varied greatly depending on the availability of growth substrates. The proportion of transconjugants was much higher (~12%) when observed in substrate-rich regions (under the channel) at 24 h, followed by an exponential decline, with the distance far from the channel. Furthermore, three-dimensional observation revealed that vertical gene transfer influenced by the concentrations of bacterial growth substrates was important for ARG spread in biofilm. The transfer frequency was 8.2 times higher in the high substrate concentration (50×) compared to low concentration (0.5×) in simulated sewage, underscoring the substantial impact of bacterial growth substrate variability on ARG dissemination. This study is helpful for in-depth understanding of ARG dissemination through biofilms and indicates that reducing pollutant emission is important for ARG control in the environment.},
}
@article {pmid37508224,
year = {2023},
author = {Guidotti-Takeuchi, M and Melo, RT and Ribeiro, LNM and Dumont, CF and Ribeiro, RAC and Brum, BA and de Amorim Junior, TLIF and Rossi, DA},
title = {Interference with Bacterial Conjugation and Natural Alternatives to Antibiotics: Bridging a Gap.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {7},
pages = {},
pmid = {37508224},
issn = {2079-6382},
abstract = {Horizontal gene transfer (HGT) in food matrices has been investigated under conditions that favor gene exchange. However, the major challenge lies in determining the specific conditions pertaining to the adapted microbial pairs associated with the food matrix. HGT is primarily responsible for enhancing the microbial repertoire for the evolution and spread of antimicrobial resistance and is a major target for controlling pathogens of public health concern in food ecosystems. In this study, we investigated Salmonella Heidelberg (SH) and Escherichia coli (EC) regarding gene exchange under conditions mimicking the industrial environment, with the coproducts whey (SL) and chicken juice (CJ). The S. Heidelberg strain was characterized by antibiotic susceptibility standards and PCR to detect the blaTEM gene. A concentration of 0.39 mg/mL was determined to evaluate the anti-conjugation activity of nanostructured lipid nanocarriers (NLCs) of essential oils to mitigate β-lactam resistance gene transfer. The results showed that the addition of these coproducts promoted an increase of more than 3.5 (whey) and 2.5 (chicken juice) orders of magnitude in the conjugation process (p < 0.01), and NLCs of sage essential oil significantly reduced the conjugation frequency (CF) by 74.90, 90.6, and 124.4 times when compared to the transfers in the absence of coproducts and the presence of SL and CJ, respectively. For NLCs from olibanum essential oil, the decrease was 4.46-fold for conjugations without inhibitors and 3.12- and 11.3-fold in the presence of SL and CJ. NLCs associated with sage and olibanum essential oils effectively control the transfer of antibiotic resistance genes and are a promising alternative for use at industrial levels.},
}
@article {pmid37508213,
year = {2023},
author = {Anyanwu, MU and Jaja, IF and Okpala, COR and Njoga, EO and Okafor, NA and Oguttu, JW},
title = {Mobile Colistin Resistance (mcr) Gene-Containing Organisms in Poultry Sector in Low- and Middle-Income Countries: Epidemiology, Characteristics, and One Health Control Strategies.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {7},
pages = {},
pmid = {37508213},
issn = {2079-6382},
abstract = {Mobile colistin resistance (mcr) genes (mcr-1 to mcr-10) are plasmid-encoded genes that threaten the clinical utility of colistin (COL), one of the highest-priority critically important antibiotics (HP-CIAs) used to treat infections caused by multidrug-resistant and extensively drug-resistant bacteria in humans and animals. For more than six decades, COL has been used largely unregulated in the poultry sector in low- and middle-income countries (LMICs), and this has led to the development/spread of mcr gene-containing bacteria (MGCB). The prevalence rates of mcr-positive organisms from the poultry sector in LMICs between January 1970 and May 2023 range between 0.51% and 58.8%. Through horizontal gene transfer, conjugative plasmids possessing insertion sequences (ISs) (especially ISApl1), transposons (predominantly Tn6330), and integrons have enhanced the spread of mcr-1, mcr-2, mcr-3, mcr-4, mcr-5, mcr-7, mcr-8, mcr-9, and mcr-10 in the poultry sector in LMICs. These genes are harboured by Escherichia, Klebsiella, Proteus, Salmonella, Cronobacter, Citrobacter, Enterobacter, Shigella, Providencia, Aeromonas, Raoultella, Pseudomonas, and Acinetobacter species, belonging to diverse clones. The mcr-1, mcr-3, and mcr-10 genes have also been integrated into the chromosomes of these bacteria and are mobilizable by ISs and integrative conjugative elements. These bacteria often coexpress mcr with virulence genes and other genes conferring resistance to HP-CIAs, such as extended-spectrum cephalosporins, carbapenems, fosfomycin, fluoroquinolone, and tigecycline. The transmission routes and dynamics of MGCB from the poultry sector in LMICs within the One Health triad include contact with poultry birds, feed/drinking water, manure, poultry farmers and their farm workwear, farming equipment, the consumption and sale of contaminated poultry meat/egg and associated products, etc. The use of pre/probiotics and other non-antimicrobial alternatives in the raising of birds, the judicious use of non-critically important antibiotics for therapy, the banning of nontherapeutic COL use, improved vaccination, biosecurity, hand hygiene and sanitization, the development of rapid diagnostic test kits, and the intensified surveillance of mcr genes, among others, could effectively control the spread of MGCB from the poultry sector in LMICs.},
}
@article {pmid37505810,
year = {2023},
author = {Dewan, I and Uecker, H},
title = {A mathematician's guide to plasmids: an introduction to plasmid biology for modellers.},
journal = {Microbiology (Reading, England)},
volume = {169},
number = {7},
pages = {},
pmid = {37505810},
issn = {1465-2080},
mesh = {Humans ; Plasmids/genetics ; *Bacteria/genetics ; *Biology ; Gene Transfer, Horizontal ; },
abstract = {Plasmids, extrachromosomal DNA molecules commonly found in bacterial and archaeal cells, play an important role in bacterial genetics and evolution. Our understanding of plasmid biology has been furthered greatly by the development of mathematical models, and there are many questions about plasmids that models would be useful in answering. In this review, we present an introductory, yet comprehensive, overview of the biology of plasmids suitable for modellers unfamiliar with plasmids who want to get up to speed and to begin working on plasmid-related models. In addition to reviewing the diversity of plasmids and the genes they carry, their key physiological functions, and interactions between plasmid and host, we also highlight selected plasmid topics that may be of particular interest to modellers and areas where there is a particular need for theoretical development. The world of plasmids holds a great variety of subjects that will interest mathematical biologists, and introducing new modellers to the subject will help to expand the existing body of plasmid theory.},
}
@article {pmid37503831,
year = {2023},
author = {Sanchez-Puerta, MV and Ceriotti, LF and Gatica-Soria, LM and Roulet, ME and Garcia, LE and Sato, HA},
title = {Invited Review Beyond parasitic convergence: unravelling the evolution of the organellar genomes in holoparasites.},
journal = {Annals of botany},
volume = {132},
number = {5},
pages = {909-928},
pmid = {37503831},
issn = {1095-8290},
support = {PICT2020-01018//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; 06/A092-T1//Universidad Nacional de Cuyo/ ; },
mesh = {*Magnoliopsida/genetics ; Plants/genetics ; *Genome, Mitochondrial/genetics ; Evolution, Molecular ; Plastids ; Phylogeny ; },
abstract = {BACKGROUND: The molecular evolution of organellar genomes in angiosperms has been studied extensively, with some lineages, such as parasitic ones, displaying unique characteristics. Parasitism has emerged 12 times independently in angiosperm evolution. Holoparasitism is the most severe form of parasitism, and is found in ~10 % of parasitic angiosperms. Although a few holoparasitic species have been examined at the molecular level, most reports involve plastomes instead of mitogenomes. Parasitic plants establish vascular connections with their hosts through haustoria to obtain water and nutrients, which facilitates the exchange of genetic information, making them more susceptible to horizontal gene transfer (HGT). HGT is more prevalent in the mitochondria than in the chloroplast or nuclear compartments.<br><br>SCOPE: This review summarizes current knowledge on the plastid and mitochondrial genomes of holoparasitic angiosperms, compares the genomic features across the different lineages, and discusses their convergent evolutionary trajectories and distinctive features. We focused on Balanophoraceae (Santalales), which exhibits extraordinary traits in both their organelles.<br><br>CONCLUSIONS: Apart from morphological similarities, plastid genomes of holoparasitic plants also display other convergent features, such as rampant gene loss, biased nucleotide composition and accelerated evolutionary rates. In addition, the plastomes of Balanophoraceae have extremely low GC and gene content, and two unexpected changes in the genetic code. Limited data on the mitochondrial genomes of holoparasitic plants preclude thorough comparisons. Nonetheless, no obvious genomic features distinguish them from the mitochondria of free-living angiosperms, except for a higher incidence of HGT. HGT appears to be predominant in holoparasitic angiosperms with a long-lasting endophytic stage. Among the Balanophoraceae, mitochondrial genomes exhibit disparate evolutionary paths with notable levels of heteroplasmy in Rhopalocnemis and unprecedented levels of HGT in Lophophytum. Despite their differences, these Balanophoraceae share a multichromosomal mitogenome, a feature also found in a few free-living angiosperms.},
}
@article {pmid37502928,
year = {2023},
author = {Hu, K and Chia-Wei, C and Wilke, CO and Finkelstein, IJ},
title = {Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37502928},
issn = {2692-8205},
support = {R01 GM088344/GM/NIGMS NIH HHS/United States ; R01 GM124141/GM/NIGMS NIH HHS/United States ; },
abstract = {CRISPR-associated transposons (CASTs) co-opt CRISPR-Cas proteins and Tn7-family transposons for RNA-guided vertical and horizontal transmission. CASTs encode minimal CRISPR arrays but can't acquire new spacers. Here, we show that CASTs instead co-opt defense-associated CRISPR arrays for horizontal transmission. A bioinformatic analysis shows that all CAST sub-types co-occur with defense-associated CRISPR-Cas systems. Using an E. coli quantitative transposition assay, we show that CASTs use CRISPR RNAs (crRNAs) from these defense systems for horizontal gene transfer. A high-resolution structure of the type I-F CAST-Cascade in complex with a type III-B crRNA reveals that Cas6 recognizes direct repeats via sequence-independent π - π interactions. In addition to using heterologous CRISPR arrays, type V CASTs can also transpose via a crRNA-independent unguided mechanism, even when the S15 co-factor is over-expressed. Over-expressing S15 and the trans-activating CRISPR RNA (tracrRNA) or a single guide RNA (sgRNA) reduces, but does not abrogate, off-target integration for type V CASTs. Exploiting new spacers in defense-associated CRISPR arrays explains how CASTs horizontally transfer to new hosts. More broadly, this work will guide further efforts to engineer the activity and specificity of CASTs for gene editing applications.},
}
@article {pmid37499542,
year = {2023},
author = {Chen, X and Zhu, Y and Chen, J and Yan, S and Xie, S},
title = {Multi-omic profiling of a novel activated sludge strain Sphingobacterium sp. WM1 reveals the mechanism of tetracycline biodegradation and its merits of potential application.},
journal = {Water research},
volume = {243},
number = {},
pages = {120397},
doi = {10.1016/j.watres.2023.120397},
pmid = {37499542},
issn = {1879-2448},
mesh = {*Sewage/microbiology ; *Sphingobacterium/metabolism ; Multiomics ; Anti-Bacterial Agents/metabolism ; Tetracycline/metabolism ; Bacteria/metabolism ; Biodegradation, Environmental ; },
abstract = {As an emerging pollutant, the antibiotic tetracycline (TC) has been consistently detected in wastewater and activated sludge. Biodegradation represents a potentially crucial pathway to dissipate TC contamination. However, few efficient TC-degrading bacteria have been isolated and a comprehensive understanding of the molecular mechanisms underlying TC degradation is still lacking. In this study, a novel TC-degrading bacterium, designated as Sphingobacterium sp. WM1, was successfully isolated from activated sludge. Strain WM1 exhibited a remarkable performance in degrading 50 mg/L TC within 1 day under co-metabolic conditions. Genomic analysis of the strain WM1 unveiled the presence of three functional tetX genes. Unraveling the complex molecular mechanisms, transcriptome analysis highlighted the role of upregulated transmembrane transport and accelerated electron transport in facilitating TC degradation. Proteomics confirmed the up-regulation of proteins involved in cellular biosynthesis/metabolism and ribosomal processes. Crucially, the tetX gene-encoding protein showed a significant upregulation, indicating its role in TC degradation. Heterologous expression of the tetX gene resulted in TC dissipation from an initial 51.9 mg/L to 4.2 mg/L within 24 h. The degradation pathway encompassed TC hydroxylation, transforming into TP461 and subsequent metabolites, which effectively depleted TC's inhibitory activity. Notably, the tetX genes in strain WM1 showed limited potential for horizontal gene transfer. Collectively, strain WM1's potent TC degradation capacity signals a promise for enhancing TC clean-up strategies.},
}
@article {pmid37499413,
year = {2023},
author = {Ma, R and Wang, J and Liu, Y and Wang, G and Yang, Y and Liu, Y and Kong, Y and Lin, J and Li, Q and Li, G and Yuan, J},
title = {Dynamics of antibiotic resistance genes and bacterial community during pig manure, kitchen waste, and sewage sludge composting.},
journal = {Journal of environmental management},
volume = {345},
number = {},
pages = {118651},
doi = {10.1016/j.jenvman.2023.118651},
pmid = {37499413},
issn = {1095-8630},
mesh = {Animals ; Swine ; *Anti-Bacterial Agents/pharmacology ; Sewage ; Tetracycline ; *Composting ; Manure/microbiology ; Genes, Bacterial ; Drug Resistance, Bacterial ; Macrolides ; Bacteria ; Sulfanilamide ; },
abstract = {Organic solid wastes (OSWs) are important reservoirs for antibiotic resistance genes (ARGs). Aerobic composting transforms OSWs into fertilizers. In this study, we investigated ARGs dynamics and their driving mechanisms in three OSW composts: pig manure (PM), kitchen waste (KC), and sewage sludge (SG). The dominant ARGs were different in each OSW, namely tetracycline, aminoglycoside, and macrolide resistance (PM); tetracyclines and aminoglycosides (KC); and sulfonamides (SG). ARGs abundance decreased in PM (71%) but increased in KC (5.9-fold) and SG (1.3-fold). Interestingly, the ARGs abundance was generally similar in all final composts, which was contributed to the similar bacterial community in final composts. In particular, sulfonamide and β-lactam resistant genes removed (100%) in PM, while sulfonamide in KC (38-fold) and tetracycline in SG (5-fold) increased the most. Additionally, ARGs abundance rebounded during the maturation period in all treatments. Firmicutes, Proteobacteria, and Actinobacteria were the main ARGs hosts. Several persistent and high-risk genes included tetW, aadA, aadE, tetX, strB, tetA, mefA, intl1, and intl2. The structural equation models showed ARGs removal was mainly affected by physicochemical parameters and bacterial communities in PM, the ARGs enrichment in KC composting correlated with increased mobile genetic elements (MGEs). In general, thermophilic aerobic composting can inhibit the vertical gene transfer (VGT) of pig manure and horizontal gene transfer (HGT) of sludge, but it increases the HGT of kitchen waste, resulting in a dramatic increase of ARGs in KC compost. More attention should be paid to the ARGs risk of kitchen waste composting.},
}
@article {pmid37495486,
year = {2023},
author = {Soler-Bistué, A},
title = {Restriction-methylation systems regulate transformation in Acinetobacter baumannii.},
journal = {Trends in microbiology},
volume = {31},
number = {9},
pages = {879-881},
doi = {10.1016/j.tim.2023.07.009},
pmid = {37495486},
issn = {1878-4380},
mesh = {*Acinetobacter baumannii/genetics ; Methylation ; Anti-Bacterial Agents ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; },
abstract = {Antimicrobial resistance in Acinetobacter baumannii is a major concern. Natural transformation remains understudied as a horizontal gene transfer (HGT) mechanism for the spread of resistance genes. Recent work (Vesel et al.) reveals a profound impact of the state of donor DNA methylation with strong implications for HGT of resistance determinants in this worrisome pathogen.},
}
@article {pmid37494793,
year = {2023},
author = {Wang, H and Xu, K and Wang, J and Feng, C and Chen, Y and Shi, J and Ding, Y and Deng, C and Liu, X},
title = {Microplastic biofilm: An important microniche that may accelerate the spread of antibiotic resistance genes via natural transformation.},
journal = {Journal of hazardous materials},
volume = {459},
number = {},
pages = {132085},
doi = {10.1016/j.jhazmat.2023.132085},
pmid = {37494793},
issn = {1873-3336},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Extracellular Polymeric Substance Matrix ; Plastics ; Microplastics ; Biofilms ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; },
abstract = {Microplastic (MP) biofilms provide a specific microniche for microbial life and are a potential hotspot for the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Nevertheless, the acquisition of ARGs in MP biofilms via natural transformation mediated by extracellular DNA (eDNA) has been rarely explored. This study demonstrated that MP biofilms promoted the natural transformation of extracellular ARGs at the single-cell and multi-species levels, compared to natural substrate (NS) biofilms and bacterioplankton. The transformation frequency on MP biofilms was up to 1000-fold compare to that on NS. The small MPs and aged MPs enhanced the ARG transformation frequencies up to 77.16-fold and 32.05-fold, respectively, compared with the large MPs and pristine MPs. The transformation frequencies on MP biofilms were significantly positively correlated with the bacterial density and extracellular polymeric substance (EPS) content (P < 0.05). Furthermore, MPs significantly increased the expression of the biofilm formation related genes (motA and pgaA) and DNA uptake related genes (pilX and comA) compared to NS and bacterioplankton. The more transformants colonized on MPs contributed to the enhanced transformation frequencies at the community-wide level. Overall, eDNA-mediated transformation in MP biofilms may be an important path of ARG spread, which was promoted by heterogeneous biofilm.},
}
@article {pmid37486104,
year = {2023},
author = {Hallal Ferreira Raro, O and Poirel, L and Tocco, M and Nordmann, P},
title = {Impact of veterinary antibiotics on plasmid-encoded antibiotic resistance transfer.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {78},
number = {9},
pages = {2209-2216},
pmid = {37486104},
issn = {1460-2091},
support = {/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Oxytetracycline/pharmacology ; Edaravone/pharmacology ; Reactive Oxygen Species ; Escherichia coli/genetics ; Plasmids/genetics ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; },
abstract = {OBJECTIVES: Resistance genes can be genetically transmitted and exchanged between commensal and pathogenic bacterial species, and in different compartments including the environment, or human and animal guts (One Health concept). The aim of our study was to evaluate whether subdosages of antibiotics administered in veterinary medicine could enhance plasmid transfer and, consequently, resistance gene exchange in gut microbiota.<br><br>METHODS: Conjugation frequencies were determined with Escherichia coli strains carrying IncL- (blaOXA-48) or IncI1-type (blaCTX-M-1) plasmids subjected to a series of subinhibitory concentrations of antibiotics used in veterinary medicine, namely amoxicillin, ceftiofur, apramycin, neomycin, enrofloxacin, colistin, erythromycin, florfenicol, lincomycin, oxytetracycline, sulfamethazine, tiamulin and the ionophore narasin. Treatments with subinhibitory dosages were performed with and without supplementation with the antioxidant edaravone, known as a mitigator of the inducibility effect of several antibiotics on plasmid conjugation frequency (PCF). Expression of SOS-response associated genes and fluorescence-based reactive oxygen species (ROS) detection assays were performed to evaluate the stress oxidative response.<br><br>RESULTS: Increased PCFs were observed for both strains when treating with florfenicol and oxytetracycline. Increased expression of the SOS-associated recA gene also occurred concomitantly, as well as increased ROS production. Addition of edaravone to the treatments reduced their PCF and also showed a decreasing effect on SOS and ROS responses for both plasmid scaffolds.<br><br>CONCLUSIONS: We showed here that some antibiotics used in veterinary medicine may induce transfer of plasmid-encoded resistance and therefore may contribute to the worldwide spread of antibiotic resistance genes.},
}
@article {pmid37485539,
year = {2023},
author = {Li, L and Liu, Y and Xiao, Q and Xiao, Z and Meng, D and Yang, Z and Deng, W and Yin, H and Liu, Z},
title = {Dissecting the HGT network of carbon metabolic genes in soil-borne microbiota.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1173748},
pmid = {37485539},
issn = {1664-302X},
abstract = {The microbiota inhabiting soil plays a significant role in essential life-supporting element cycles. Here, we investigated the occurrence of horizontal gene transfer (HGT) and established the HGT network of carbon metabolic genes in 764 soil-borne microbiota genomes. Our study sheds light on the crucial role of HGT components in microbiological diversification that could have far-reaching implications in understanding how these microbial communities adapt to changing environments, ultimately impacting agricultural practices. In the overall HGT network of carbon metabolic genes in soil-borne microbiota, a total of 6,770 nodes and 3,812 edges are present. Among these nodes, phyla Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes are predominant. Regarding specific classes, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Bacteroidia, Actinomycetia, Betaproteobacteria, and Clostridia are dominant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) functional assignments of glycosyltransferase (18.5%), glycolysis/gluconeogenesis (8.8%), carbohydrate-related transporter (7.9%), fatty acid biosynthesis (6.5%), benzoate degradation (3.1%) and butanoate metabolism (3.0%) are primarily identified. Glycosyltransferase involved in cell wall biosynthesis, glycosylation, and primary/secondary metabolism (with 363 HGT entries), ranks first overwhelmingly in the list of most frequently identified carbon metabolic HGT enzymes, followed by pimeloyl-ACP methyl ester carboxylesterase, alcohol dehydrogenase, and 3-oxoacyl-ACP reductase. Such HGT events mainly occur in the peripheral functions of the carbon metabolic pathway instead of the core section. The inter-microbe HGT genetic traits in soil-borne microbiota genetic sequences that we recognized, as well as their involvement in the metabolism and regulation processes of carbon organic, suggest a pervasive and substantial effect of HGT on the evolution of microbes.},
}
@article {pmid37483384,
year = {2023},
author = {Wang, M},
title = {Editorial: Antimicrobial resistance dissemination and horizontal gene transfer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1240680},
pmid = {37483384},
issn = {2235-2988},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Bacteria/genetics ; },
}
@article {pmid37478933,
year = {2023},
author = {Yan, Q and Xu, Y and Zhong, Z and Xu, Y and Lin, X and Cao, Z and Feng, G},
title = {Insights into antibiotic resistance-related changes in microbial communities, resistome and mobilome in paddy irrigated with reclaimed wastewater.},
journal = {The Science of the total environment},
volume = {900},
number = {},
pages = {165672},
doi = {10.1016/j.scitotenv.2023.165672},
pmid = {37478933},
issn = {1879-1026},
mesh = {*Wastewater ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology/analysis ; Soil ; *Microbiota ; Drug Resistance, Microbial/genetics ; },
abstract = {Reclaimed wastewater (reclaimed wastewater, RWW) from municipal wastewater treatment plants for paddy irrigation is a well-established practice to alleviate water scarcity. However, the reuse may result in the persistent exposure of the paddy to residual antibiotics in RWW. Continuous presence of even low-level antibiotics can exert selective pressure on microbiota, resulting in the proliferation and dissemination of antibiotic resistance genes (ARGs) in paddy. In this study, metagenomic analysis was applied to firstly deciphered the effects of residual antibiotics on microbiome and resistome in constructed mesocosm-scale paddy soils. The diversity and abundance of ARG have remarkably risen with the increasing antibiotic concentration in RWW. Network analysis revealed that 28 genera belonging to six phyla were considered as the potential ARG hosts, and their abundances were enhanced with increasing antibiotic concentrations. A partial least-squares path model indicated that the microbial community was the principal direct driver of the ARG abundance and the resistome alteration in paddy soil under long-term RWW irrigation. Microbes may acquire ARGs via horizontal gene transfer. IntI1 could play an essential role in the propagation and spread of ARGs. Functional analysis suggested that enhanced SOS response and T4SSs (Type IV secretion systems) modules could stimulate horizontal transfer potential and promote the ARG abundance. The obtained results provide a scientific decision for assessing the ecological risk of RWW application.},
}
@article {pmid37478352,
year = {2023},
author = {Deng, Z and Chen, H and Wang, J and Zhang, N and Han, Z and Xie, Y and Zhang, X and Fang, X and Yu, H and Zhang, D and Yue, Z and Zhang, C},
title = {Marine Dehalogenator and Its Chaperones: Microbial Duties and Responses in 2,4,6-Trichlorophenol Dechlorination.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {30},
pages = {11300-11312},
doi = {10.1021/acs.est.3c03738},
pmid = {37478352},
issn = {1520-5851},
abstract = {Marine environments contain diverse halogenated organic compounds (HOCs), both anthropogenic and natural, nourishing a group of versatile organohalide-respiring bacteria (OHRB). Here, we identified a novel OHRB (Peptococcaceae DCH) with conserved motifs but phylogenetically diverse reductive dehalogenase catalytic subunit (RdhAs) from marine enrichment culture. Further analyses clearly demonstrate the horizontal gene transfer of rdhAs among marine OHRB. Moreover, 2,4,6-trichlorophenol (TCP) was dechlorinated to 2,4-dichlorophenol and terminated at 4-chlorophenol in culture. Dendrosporobacter and Methanosarcina were the two dominant genera, and the constructed and verified metabolic pathways clearly demonstrated that the former provided various substrates for other microbes, while the latter drew nutrients, but might provide little benefit to microbial dehalogenation. Furthermore, Dendrosporobacter could readily adapt to TCP, and sporulation-related proteins of Dendrosporobacter were significantly upregulated in TCP-free controls, whereas other microbes (e.g., Methanosarcina and Aminivibrio) became more active, providing insights into how HOCs shape microbial communities. Additionally, sulfate could affect the dechlorination of Peptococcaceae DCH, but not debromination. Considering their electron accessibility and energy generation, the results clearly demonstrate that bromophenols are more suitable than chlorophenols for the enrichment of OHRB in marine environments. This study will greatly enhance our understanding of marine OHRB (rdhAs), auxiliary microbes, and microbial HOC adaptive mechanisms.},
}
@article {pmid37476668,
year = {2023},
author = {Agarwal, V and Stubits, R and Nassrullah, Z and Dillon, MM},
title = {Pangenome insights into the diversification and disease specificity of worldwide Xanthomonas outbreaks.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1213261},
pmid = {37476668},
issn = {1664-302X},
abstract = {The bacterial genus Xanthomonas is responsible for disease outbreaks in several hundred plant species, many of them economically important crops. In the era of next-generation sequencing, thousands of strains from this genus have now been sequenced as part of isolated studies that focus on outbreak characterization, host range, diversity, and virulence factor identification. However, these data have not been synthesized and we lack a comprehensive phylogeny for the genus, with some species designations in public databases still relying on phenotypic similarities and representative sequence typing. The extent of genetic cohesiveness among Xanthomonas strains, the distribution of virulence factors across strains, and the impact of evolutionary history on host range across the genus are also poorly understood. In this study, we present a pangenome analysis of 1,910 diverse Xanthomonas genomes, highlighting their evolutionary relationships, the distribution of virulence-associated genes across strains, and rates of horizontal gene transfer. We find a number of broadly conserved classes of virulence factors and considerable diversity in the Type 3 Secretion Systems (T3SSs) and Type 3 Secreted Effector (T3SE) repertoires of different Xanthomonas species. We also use these data to re-assign incorrectly classified strains to phylogenetically informed species designations and find evidence of both monophyletic host specificity and convergent evolution of phylogenetically distant strains to the same host. Finally, we explore the role of recombination in maintaining genetic cohesion within the Xanthomonas genus as a result of both ancestral and recent recombination events. Understanding the evolutionary history of Xanthomonas species and the relationship of key virulence factors with host-specificity provides valuable insight into the mechanisms through which Xanthomonas species shift between hosts and will enable us to develop more robust resistance strategies against these highly virulent pathogens.},
}
@article {pmid37475746,
year = {2023},
author = {Bhatia, RP and Kirit, HA and Lewis, CM and Sankaranarayanan, K and Bollback, JP},
title = {Evolutionary barriers to horizontal gene transfer in macrophage-associated Salmonella.},
journal = {Evolution letters},
volume = {7},
number = {4},
pages = {227-239},
pmid = {37475746},
issn = {2056-3744},
abstract = {Horizontal gene transfer (HGT) is a powerful evolutionary force facilitating bacterial adaptation and emergence of novel phenotypes. Several factors, including environmental ones, are predicted to restrict HGT, but we lack systematic and experimental data supporting these predictions. Here, we address this gap by measuring the relative fitness of 44 genes horizontally transferred from Escherichia coli to Salmonella enterica in infection-relevant environments. We estimated the distribution of fitness effects in each environment and identified that dosage-dependent effects across different environments are a significant barrier to HGT. The majority of genes were found to be deleterious. We also found longer genes had stronger negative fitness consequences than shorter ones, showing that gene length was negatively associated with HGT. Furthermore, fitness effects of transferred genes were found to be environmentally dependent. In summary, a substantial fraction of transferred genes had a significant fitness cost on the recipient, with both gene characteristics and the environment acting as evolutionary barriers to HGT.},
}
@article {pmid37475130,
year = {2023},
author = {Yang, G and Cao, JM and Cui, HL and Zhan, XM and Duan, G and Zhu, YG},
title = {Artificial Sweetener Enhances the Spread of Antibiotic Resistance Genes During Anaerobic Digestion.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {30},
pages = {10919-10928},
doi = {10.1021/acs.est.2c08673},
pmid = {37475130},
issn = {1520-5851},
mesh = {*Sweetening Agents/pharmacology ; Drug Resistance, Microbial/drug effects/genetics ; Anaerobiosis/drug effects ; Genes, Bacterial ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; },
abstract = {Artificial sweeteners have been frequently detected in the feedstocks of anaerobic digestion. As these sweeteners can lead to the shift of anaerobic microbiota in the gut similar to that caused by antibiotics, we hypothesize that they may have an antibiotic-like impact on antibiotic resistance genes (ARGs) in anaerobic digestion. However, current understanding on this topic is scarce. This investigation aimed to examine the potential impact of acesulfame, a typical artificial sweetener, on ARGs in anaerobic digestion by using metagenomics sequencing and qPCR. It was found that acesulfame increased the number of detected ARG classes and the abundance of ARGs during anaerobic digestion. The abundance of typical mobile genetic elements (MGEs) and the number of potential hosts of ARGs also increased under acesulfame exposure, suggesting the enhanced potential of horizontal gene transfer of ARGs, which was further confirmed by the correlation analysis between absolute abundances of the targeted ARGs and MGEs. The increased horizontal dissemination of ARGs may be associated with the SOS response induced by the increased ROS production, and the increased cellular membrane permeability. These findings indicate that artificial sweeteners may accelerate ARG spread through digestate disposal, thus corresponding strategies should be considered to prevent potential risks in practice.},
}
@article {pmid37468904,
year = {2023},
author = {Liu, B and Warnow, T},
title = {Weighted ASTRID: fast and accurate species trees from weighted internode distances.},
journal = {Algorithms for molecular biology : AMB},
volume = {18},
number = {1},
pages = {6},
pmid = {37468904},
issn = {1748-7188},
abstract = {BACKGROUND: Species tree estimation is a basic step in many biological research projects, but is complicated by the fact that gene trees can differ from the species tree due to processes such as incomplete lineage sorting (ILS), gene duplication and loss (GDL), and horizontal gene transfer (HGT), which can cause different regions within the genome to have different evolutionary histories (i.e., "gene tree heterogeneity"). One approach to estimating species trees in the presence of gene tree heterogeneity resulting from ILS operates by computing trees on each genomic region (i.e., computing "gene trees") and then using these gene trees to define a matrix of average internode distances, where the internode distance in a tree T between two species x and y is the number of nodes in T between the leaves corresponding to x and y. Given such a matrix, a tree can then be computed using methods such as neighbor joining. Methods such as ASTRID and NJst (which use this basic approach) are provably statistically consistent, very fast (low degree polynomial time) and have had high accuracy under many conditions that makes them competitive with other popular species tree estimation methods. In this study, inspired by the very recent work of weighted ASTRAL, we present weighted ASTRID, a variant of ASTRID that takes the branch uncertainty on the gene trees into account in the internode distance.<br><br>RESULTS: Our experimental study evaluating weighted ASTRID typically shows improvements in accuracy compared to the original (unweighted) ASTRID, and shows competitive accuracy against weighted ASTRAL, the state of the art. Our re-implementation of ASTRID also improves the runtime, with marked improvements on large datasets.<br><br>CONCLUSIONS: Weighted ASTRID is a new and very fast method for species tree estimation that typically improves upon ASTRID and has comparable accuracy to weighted ASTRAL, while remaining much faster. Weighted ASTRID is available at https://github.com/RuneBlaze/internode .},
}
@article {pmid37467272,
year = {2023},
author = {Li, XL and Sun, Y and Yin, Y and Zhan, S and Wang, C},
title = {A bacterial-like Pictet-Spenglerase drives the evolution of fungi to produce β-carboline glycosides together with separate genes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {30},
pages = {e2303327120},
pmid = {37467272},
issn = {1091-6490},
mesh = {Animals ; Carbolines ; *Alkaloids ; Cytochrome P-450 Enzyme System/genetics ; Multigene Family ; Fungi/genetics ; *Beauveria/genetics ; },
abstract = {Diverse β-carboline (βC) alkaloids are produced by microbes, plants, and animals with myriad bioactivities and drug potentials. However, the biosynthetic mechanism of βCs remains largely elusive, especially regarding the hydroxyl and glucosyl modifications of βCs. Here, we report the presence of the bacterial-like Pictet-Spenglerase gene Fcs1 in the entomopathogenic Beauveria fungi that can catalyze the biosynthesis of the βC skeleton. The overexpression of Fcs1 in Beauveria bassiana led to the identification of six βC methyl glycosides, termed bassicarbosides (BCSs) A-F. We verified that the cytochrome P450 (CYP) genes adjacent to Fcs1 cannot oxidize βCs. Alternatively, the separated CYP684B2 family gene Fcs2 was identified to catalyze βC hydroxylation together with its cofactor gene Fcs3. The functional homologue of Fcs2 is only present in the Fcs1-containing fungi and highly similar to the Fcs1-connected yet nonfunctional CYP. Both evolved quicker than those from fungi without Fcs1 homologues. Finally, the paired methyl/glucosyl transferase genes were verified to mediate the production of BCSs from hydroxy-βCs. All these functionally verified genes are located on different chromosomes of Beauveria, which is in contrast to the typical content-clustered feature of fungal biosynthetic gene clusters (BGCs). We also found that the production of BCSs selectively contributed to fungal infection of different insect species. Our findings shed light on the biosynthetic mechanism of βC glycosides, including the identification of a βC hydroxylase. The results of this study also propose an evolving process of fungal BGC formation following the horizontal transfer of a bacterial gene to fungi.},
}
@article {pmid37467082,
year = {2023},
author = {Jen, FE and Abrahams, JL and Schulz, BL and Lamelas, A and Pluschke, G and Jennings, MP},
title = {High-Frequency Changes in Pilin Glycosylation Patterns during Neisseria meningitidis Serogroup a Meningitis Outbreaks in the African Meningitis Belt.},
journal = {ACS infectious diseases},
volume = {9},
number = {8},
pages = {1451-1457},
pmid = {37467082},
issn = {2373-8227},
mesh = {Humans ; *Neisseria meningitidis/genetics ; Fimbriae Proteins/genetics ; Glycosylation ; Serogroup ; Disease Outbreaks ; *Meningitis ; Polysaccharides ; },
abstract = {In the meningitis belt of sub-Saharan Africa, there are cyclic meningococcal epidemics that coincide with clonal waves of Neisseria meningitidis carriage and invasive disease. In the framework of longitudinal colonization and disease studies in Ghana and Burkina Faso, meningococcal isolates belonging to the closely related hypervirulent A:ST-5, A:ST-7, and A:ST-2859 clones have been collected from 1998 to 2011 during meningococcal outbreaks. A comparative whole-genome sequencing study with 100 of these isolates identified the pilin glycosylation (pgl) locus as one hot spot of recombination. Frequent exchange of pgl genes in N. meningitidis by lateral gene transfer results in differences in the glycosylation patterns of pilin and other cell surface glycoproteins. In this study, we looked at both recombination and phase variation of the pgl genes of these clinical isolates and analyzed the glycan structures resulting from different pgl alleles and their variable expression. Our results indicate that the basal O-linked sugar of the glycans expressed by these isolates is masked by various additional mono- or disaccharide structures whose expression is highly variable due to the phase-variable expression of pgl genes. We also observed a distinct glycoform in two isolates with pgl loci that were modified by recombination. These data suggest that variation in N. meningitidis protein glycosylation could be crucial for bacterial adaptation to evade herd immunity in semi-immune populations. Investigating pilin glycosylation in N. meningitidis can shed light on the mechanisms by which this pathogen evades the host immune response, and may help identify potential targets for novel therapies and vaccines.},
}
@article {pmid37462915,
year = {2024},
author = {Alav, I and Buckner, MMC},
title = {Non-antibiotic compounds associated with humans and the environment can promote horizontal transfer of antimicrobial resistance genes.},
journal = {Critical reviews in microbiology},
volume = {50},
number = {6},
pages = {993-1010},
pmid = {37462915},
issn = {1549-7828},
support = {MR/V009885/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Gene Transfer, Horizontal ; Humans ; *Plasmids/genetics ; *Bacteria/genetics/drug effects/metabolism ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Environmental Pollutants/metabolism ; Conjugation, Genetic ; },
abstract = {Horizontal gene transfer plays a key role in the global dissemination of antimicrobial resistance (AMR). AMR genes are often carried on self-transmissible plasmids, which are shared amongst bacteria primarily by conjugation. Antibiotic use has been a well-established driver of the emergence and spread of AMR. However, the impact of commonly used non-antibiotic compounds and environmental pollutants on AMR spread has been largely overlooked. Recent studies found common prescription and over-the-counter drugs, artificial sweeteners, food preservatives, and environmental pollutants, can increase the conjugative transfer of AMR plasmids. The potential mechanisms by which these compounds promote plasmid transmission include increased membrane permeability, upregulation of plasmid transfer genes, formation of reactive oxygen species, and SOS response gene induction. Many questions remain around the impact of most non-antibiotic compounds on AMR plasmid conjugation in clinical isolates and the long-term impact on AMR dissemination. By elucidating the role of routinely used pharmaceuticals, food additives, and pollutants in the dissemination of AMR, action can be taken to mitigate their impact by closely monitoring use and disposal. This review will discuss recent progress on understanding the influence of non-antibiotic compounds on plasmid transmission, the mechanisms by which they promote transfer, and the level of risk they pose.},
}
@article {pmid37461575,
year = {2023},
author = {Asad, A and Jahan, I and Munni, MA and Begum, R and Mukta, MA and Saif, K and Faruque, SN and Hayat, S and Islam, Z},
title = {Increasing trend of antibiotic resistance in Shigella in Bangladesh: a plasmid-mediated transfer of mphA macrolide resistance gene.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {37461575},
issn = {2693-5015},
support = {D43 TW010540/TW/FIC NIH HHS/United States ; K43 TW011447/TW/FIC NIH HHS/United States ; },
abstract = {Shigellosis remains a common gastrointestinal disease mostly in children <5 years of age in developing countries. Azithromycin (AZM), a macrolide, is currently the first-line treatment for shigellosis in Bangladesh; ciprofloxacin (CIP) and ceftriaxone (CRO) are also used frequently. We aimed to evaluate the current epidemiology of antimicrobial resistance (AMR) and mechanism(s) of increasing macrolide resistance in Shigella in Bangladesh. A total of 2407 clinical isolates of Shigella from 2009 to 2016 were studied. Over the study period, Shigella sonnei was gradually increasing and become predominant (55%) over Shigella flexneri (36%) by 2016. We used CLSI-guided epidemiological cut-off value (ECV) for AZM in Shigella to set resistance breakpoints (zone-diameter ≤ 15 mm for S. flexneri and ≤ 11 mm for S. sonnei). Between 2009 and 2016, AZM resistance increased from 22% to approximately 60%, CIP resistance increased by 40%, and CRO resistance increased from zero to 15%. The mphA gene was the key macrolide resistance factor in Shigella; a 63MDa conjugative middle-range plasmid was harboring AZM and CRO resistance factors. Our findings show that, especially after 2014, there has been a rapid increase in resistance to the three most effective antibiotics. The rapid spread of macrolide (AZM) resistance genes among Shigella are driven by horizontal gene transfer rather than direct lineage.},
}
@article {pmid37460464,
year = {2023},
author = {Morreale, DP and Porsch, EA and Kern, BK and St Geme, JW and Planet, PJ},
title = {Acquisition, co-option, and duplication of the rtx toxin system and the emergence of virulence in Kingella.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {4281},
pmid = {37460464},
issn = {2041-1723},
support = {R01 AI121015/AI/NIAID NIH HHS/United States ; R01 AI172841/AI/NIAID NIH HHS/United States ; T32 AI141393/AI/NIAID NIH HHS/United States ; },
mesh = {Phylogeny ; Virulence/genetics ; *Bacterial Toxins/genetics ; Kingella/genetics ; *Kingella kingae/genetics ; },
abstract = {The bacterial genus Kingella includes two pathogenic species, namely Kingella kingae and Kingella negevensis, as well as strictly commensal species. Both K. kingae and K. negevensis secrete a toxin called RtxA that is absent in the commensal species. Here we present a phylogenomic study of the genus Kingella, including new genomic sequences for 88 clinical isolates, genotyping of another 131 global isolates, and analysis of 52 available genomes. The phylogenetic evidence supports that the toxin-encoding operon rtxCA was acquired by a common ancestor of the pathogenic Kingella species, and that a preexisting type-I secretion system was co-opted for toxin export. Subsequent genomic reorganization distributed the toxin machinery across two loci, with 30-35% of K. kingae strains containing two copies of the rtxA toxin gene. The rtxA duplication is largely clonal and is associated with invasive disease. Assays with isogenic strains show that a single copy of rtxA is associated with reduced cytotoxicity in vitro. Thus, our study identifies key steps in the evolutionary transition from commensal to pathogen, including horizontal gene transfer, co-option of an existing secretion system, and gene duplication.},
}
@article {pmid37459818,
year = {2023},
author = {Kelleher, ES},
title = {Jack of all trades versus master of one: how generalist versus specialist strategies of transposable elements relate to their horizontal transfer between lineages.},
journal = {Current opinion in genetics &amp; development},
volume = {81},
number = {},
pages = {102080},
pmid = {37459818},
issn = {1879-0380},
support = {R35 GM138112/GM/NIGMS NIH HHS/United States ; },
mesh = {*DNA Transposable Elements/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genomics ; },
abstract = {Transposable elements (TEs) are obligate genomic parasites, relying on host germline cells to ensure their replication and passage to future generations. While some TEs exhibit high fidelity to their host genome, being passed from parent to offspring through vertical transmission for millions of years, others frequently invade new and distantly related hosts through horizontal transfer. In this review, I highlight how the complexity of interactions between TE and host required for transposition may be an important determinant of horizontal transfer: with TEs with more complex regulatory requirements being less able to invade new host genomes.},
}
@article {pmid37452100,
year = {2023},
author = {Koch, L},
title = {Maverick - top gun of horizontal gene transfer.},
journal = {Nature reviews. Genetics},
volume = {24},
number = {9},
pages = {586},
pmid = {37452100},
issn = {1471-0064},
}
@article {pmid37450185,
year = {2023},
author = {Loret, S and Habib, B and Romain, P and Roba, A and Reboul, A},
title = {Prevention of horizontal transfer of laboratory plasmids to environmental bacteria: comparison of the effectiveness of a few disinfection approaches to degrade DNA.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {38},
pages = {89369-89380},
pmid = {37450185},
issn = {1614-7499},
support = {Grant Recipient/ Boutaina HABIB//UNamur GRant for Foreign PhD Students/ ; },
mesh = {*Disinfection/methods ; Wastewater ; Escherichia coli/genetics ; Laboratories ; Plasmids ; Bacteria/genetics ; DNA ; *Disinfectants/pharmacology ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; },
abstract = {The routine work of any molecular biology laboratory includes the daily use of microorganisms, including strains of E. coli, transformed with a variety of plasmids expressing at least one antibiotic resistance gene (ARG). Therefore, to avoid the accidental release of ARGs into environmental water, methods for disinfection of liquid laboratory waste must be effective in destroying nucleic acids. In support of this recommendation, the origin of replication of Enterobacteriaceae plasmids has been detected in strains of non-Enterobacteriaceae bacteria isolated from wastewater from laboratories and research institutes, suggesting that interspecific transfer of laboratory plasmids had occurred. Using quantitative polymerase chain reaction, we determined the decimal reduction value (D value, expressed as concentration of disinfectant or length of physical treatment) of several decontamination methods for their DNA degradation effect on cultures of E. coli Top10 transformed with a kanamycin resistant plasmid (pET28A + or pEGFP-C2). The estimated D values were 0.7 M for sulfuric acid, 6.3% for a commercial P3 disinfectant, 25 min for steam sterilization at 121 °C, and 49 min for disinfection by UVC. A 20-min treatment of bacteria cultures with a final concentration of 1-10% sodium hypochlorite was found to be ineffective in completely destroying a bacteria plasmid gene marker (coding for the pBR322 origin of replication). Residual DNA from NaClO-treated cells was 60%, while it decreased under 10% using the commercial disinfectant P3 diluted at 5%. As the degradation was incomplete in both cases, we recommend avoiding discharge of disinfected liquid waste to wastewater (even after chemical neutralization) without additional plasmid destruction treatment, to prevent horizontal transfer of laboratory ARGs to environmental bacteria.},
}
@article {pmid37445761,
year = {2023},
author = {Xiao, Y and Zhang, Y and Xie, F and Olsen, RH and Shi, L and Li, L},
title = {Inhibition of Plasmid Conjugation in Escherichia coli by Targeting rbsB Gene Using CRISPRi System.},
journal = {International journal of molecular sciences},
volume = {24},
number = {13},
pages = {},
pmid = {37445761},
issn = {1422-0067},
mesh = {Humans ; *Escherichia coli/metabolism ; *RNA, Guide, CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; },
abstract = {Bacterial conjugation constitutes a major horizontal gene transfer mechanism for the dissemination of antibiotic-resistant genes (ARGs) among human pathogens. The spread of ARGs can be halted or diminished by interfering with the conjugation process. In this study, we explored the possibility of using an rbsB gene as a single target to inhibit plasmid-mediated horizontal gene transfer in Escherichia coli by CRISPR interference (CRISPRi) system. Three single-guide RNAs (sgRNAs) were designed to target the rbsB gene. The transcriptional levels of the rbsB gene, the conjugation-related genes, and the conjugation efficiency in the CRISPRi strain were tested. We further explored the effect of the repressed expression of the rbsB gene on the quorum sensing (QS) system and biofilm formation. The results showed that the constructed CRISPRi system was effective in repressing the transcriptional level of the rbsB gene at a rate of 66.4%. The repressed expression of the rbsB gene resulted in the reduced conjugation rate of RP4 plasmid by 88.7%, which significantly inhibited the expression of the conjugation-related genes (trbBp, trfAp, traF and traJ) and increased the global regulator genes (korA, korB and trbA). The repressed rbsB gene expression reduced the depletion of autoinducer 2 signals (AI-2) by 12.8% and biofilm formation by a rate of 68.2%. The results of this study indicated the rbsB gene could be used as a universal target for the inhibition of conjugation. The constructed conjugative CRISPRi system has the potential to be used in ARG high-risk areas.},
}
@article {pmid37442321,
year = {2023},
author = {van Hamelsveld, S and Kurenbach, B and Paull, DJ and Godsoe, WA and Ferguson, GC and Heinemann, JA},
title = {Indigenous food sources as vectors of Escherichia coli and antibiotic resistance.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {334},
number = {},
pages = {122155},
doi = {10.1016/j.envpol.2023.122155},
pmid = {37442321},
issn = {1873-6424},
mesh = {Animals ; Humans ; Anti-Bacterial Agents/pharmacology ; *Bivalvia ; Drug Resistance, Microbial ; *Escherichia coli ; Maori People ; Plasmids ; *Water Microbiology ; *Food Contamination ; },
abstract = {The contamination of surface waters by fecal bacteria, measured by the number of Escherichia coli, is a significant public health issue. When these bacteria are also resistant to antimicrobials, infections are more complicated to treat. While water is regularly tested at recreational sites, wild-harvested foods, known as mahinga kai by the indigenous Māori people of Aotearoa New Zealand, are commonly overlooked as a source of exposure to potential pathogens and antimicrobial resistance (AMR). We investigate two likely sources of risk from harvesting aquatic wild foods. The first is water contact, and the second is contact with/ingestion of the harvest. We used E. coli as a proxy for microbial water quality at harvesting sites. Two popular mahinga kai species were also harvested and assessed. We found antibiotic-resistant bacteria on watercress (Nasturtium officinale) and cockles (Austrovenus stutchburyi). One-third of E. coli isolates were conjugative donors of at least one resistance phenotype. Tank experiments were used to track the internalization of E. coli by Greenshell/lip mussels (Perna canaliculus). Greenshell mussels kept at environmentally relevant concentrations of E. coli were colonized to levels considered unsafe for human consumption in 24 h. Finally, we measured horizontal gene transfer between bacteria within the shellfish, what we termed 'intra-shellular' conjugation. The transmission frequency of plasmid RP4 was significantly higher in mussels than in water alone. Our results indicate that shellfish could promote the dissemination of antibiotic resistance. They highlight the need to limit or reduce human pathogenic bacteria where food is gathered.},
}
@article {pmid37440893,
year = {2023},
author = {Brenner, E and Sreevatsan, S},
title = {Cold Cas: reevaluating the occurrence of CRISPR/Cas systems in Mycobacteriaceae.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1204838},
pmid = {37440893},
issn = {1664-302X},
support = {T15 LM009451/LM/NLM NIH HHS/United States ; },
abstract = {Bacterial CRISPR/Cas systems target foreign genetic elements such as phages and regulate gene expression by some pathogens, even in the host. The system is a marker for evolutionary history and has been used for inferences in Mycobacterium tuberculosis for 30 years. However, knowledge about mycobacterial CRISPR/Cas systems remains limited. It is believed that Type III-A Cas systems are exclusive to Mycobacterium canettii and the M. tuberculosis complex (MTBC) of organisms and that very few of the >200 diverse species of non-tuberculous mycobacteria (NTM) possess any CRISPR/Cas system. This study sought unreported CRISPR/Cas loci across NTM to better understand mycobacterial evolution, particularly in species phylogenetically near the MTBC. An analysis of available mycobacterial genomes revealed that Cas systems are widespread across Mycobacteriaceae and that some species contain multiple types. The phylogeny of Cas loci shows scattered presence in many NTM, with variation even within species, suggesting gains/losses of these loci occur frequently. Cas Type III-A systems were identified in pathogenic Mycobacterium heckeshornense and the geological environmental isolate Mycobacterium SM1. In summary, mycobacterial CRISPR/Cas systems are numerous, Type III-A systems are unreliable as markers for MTBC evolution, and mycobacterial horizontal gene transfer appears to be a frequent source of genetic variation.},
}
@article {pmid37440885,
year = {2023},
author = {Verhaegen, M and Bergot, T and Liebana, E and Stancanelli, G and Streissl, F and Mingeot-Leclercq, MP and Mahillon, J and Bragard, C},
title = {On the use of antibiotics to control plant pathogenic bacteria: a genetic and genomic perspective.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1221478},
pmid = {37440885},
issn = {1664-302X},
abstract = {Despite growing attention, antibiotics (such as streptomycin, oxytetracycline or kasugamycin) are still used worldwide for the control of major bacterial plant diseases. This raises concerns on their potential, yet unknown impact on antibiotic and multidrug resistances and the spread of their genetic determinants among bacterial pathogens. Antibiotic resistance genes (ARGs) have been identified in plant pathogenic bacteria (PPB), with streptomycin resistance genes being the most commonly reported. Therefore, the contribution of mobile genetic elements (MGEs) to their spread among PPB, as well as their ability to transfer to other bacteria, need to be further explored. The only well-documented example of ARGs vector in PPB, Tn5393 and its highly similar variants (carrying streptomycin resistance genes), is concerning because of its presence outside PPB, in Salmonella enterica and Klebsiella pneumoniae, two major human pathogens. Although its structure among PPB is still relatively simple, in human- and animal-associated bacteria, Tn5393 has evolved into complex associations with other MGEs and ARGs. This review sheds light on ARGs and MGEs associated with PPB, but also investigates the potential role of antibiotic use in resistance selection in plant-associated bacteria.},
}
@article {pmid37440531,
year = {2023},
author = {Gulay, A and Fournier, G and Smets, BF and Girguis, PR},
title = {Proterozoic Acquisition of Archaeal Genes for Extracellular Electron Transfer: A Metabolic Adaptation of Aerobic Ammonia-Oxidizing Bacteria to Oxygen Limitation.},
journal = {Molecular biology and evolution},
volume = {40},
number = {8},
pages = {},
pmid = {37440531},
issn = {1537-1719},
mesh = {Oxidation-Reduction ; *Ammonia/metabolism ; Electrons ; Phylogeny ; Oxygen ; Genes, Archaeal ; *Gammaproteobacteria/metabolism ; },
abstract = {Many aerobic microbes can utilize alternative electron acceptors under oxygen-limited conditions. In some cases, this is mediated by extracellular electron transfer (or EET), wherein electrons are transferred to extracellular oxidants such as iron oxide and manganese oxide minerals. Here, we show that an ammonia-oxidizer previously known to be strictly aerobic, Nitrosomonas communis, may have been able to utilize a poised electrode to maintain metabolic activity in anoxic conditions. The presence and activity of multiheme cytochromes in N. communis further suggest a capacity for EET. Molecular clock analysis shows that the ancestors of β-proteobacterial ammonia oxidizers appeared after Earth's atmospheric oxygenation when the oxygen levels were >10-4pO2 (present atmospheric level [PAL]), consistent with aerobic origins. Equally important, phylogenetic reconciliations of gene and species trees show that the multiheme c-type EET proteins in Nitrosomonas and Nitrosospira lineages were likely acquired by gene transfer from γ-proteobacteria when the oxygen levels were between 0.1 and 1 pO2 (PAL). These results suggest that β-proteobacterial EET evolved during the Proterozoic when oxygen limitation was widespread, but oxidized minerals were abundant.},
}
@article {pmid37439570,
year = {2023},
author = {Diorio-Toth, L and Wallace, MA and Farnsworth, CW and Wang, B and Gul, D and Kwon, JH and Andleeb, S and Burnham, CD and Dantas, G},
title = {Intensive care unit sinks are persistently colonized with multidrug resistant bacteria and mobilizable, resistance-conferring plasmids.},
journal = {mSystems},
volume = {8},
number = {4},
pages = {e0020623},
pmid = {37439570},
issn = {2379-5077},
support = {F30 AI157161/AI/NIAID NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; U01 AI123394/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Drug Resistance, Multiple, Bacterial/genetics ; Prospective Studies ; Plasmids/genetics ; *Intensive Care Units ; Bacteria/genetics ; Anti-Bacterial Agents ; },
abstract = {Contamination of hospital sinks with microbial pathogens presents a serious potential threat to patients, but our understanding of sink colonization dynamics is largely based on infection outbreaks. Here, we investigate the colonization patterns of multidrug-resistant organisms (MDROs) in intensive care unit sinks and water from two hospitals in the USA and Pakistan collected over 27 months of prospective sampling. Using culture-based methods, we recovered 822 bacterial isolates representing 104 unique species and genomospecies. Genomic analyses revealed long-term colonization by Pseudomonas spp. and Serratia marcescens strains across multiple rooms. Nanopore sequencing uncovered examples of long-term persistence of resistance-conferring plasmids in unrelated hosts. These data indicate that antibiotic resistance (AR) in Pseudomonas spp. is maintained both by strain colonization and horizontal gene transfer (HGT), while HGT maintains AR within Acinetobacter spp. and Enterobacterales, independent of colonization. These results emphasize the importance of proactive, genomic-focused surveillance of built environments to mitigate MDRO spread. IMPORTANCE Hospital sinks are frequently linked to outbreaks of antibiotic-resistant bacteria. Here, we used whole-genome sequencing to track the long-term colonization patterns in intensive care unit (ICU) sinks and water from two hospitals in the USA and Pakistan collected over 27 months of prospective sampling. We analyzed 822 bacterial genomes, representing over 100 different species. We identified long-term contamination by opportunistic pathogens, as well as transient appearance of other common pathogens. We found that bacteria recovered from the ICU had more antibiotic resistance genes (ARGs) in their genomes compared to matched community spaces. We also found that many of these ARGs are harbored on mobilizable plasmids, which were found shared in the genomes of unrelated bacteria. Overall, this study provides an in-depth view of contamination patterns for common nosocomial pathogens and identifies specific targets for surveillance.},
}
@article {pmid37437616,
year = {2023},
author = {Li, H and Wang, K and Xu, J and Wu, H and Ma, Y and Zou, R and Song, HL},
title = {Enhanced removal of antibiotic and antibiotic resistance genes by coupling biofilm electrode reactor and manganese ore substrate up-flow microbial fuel cell constructed wetland system.},
journal = {Chemosphere},
volume = {338},
number = {},
pages = {139461},
doi = {10.1016/j.chemosphere.2023.139461},
pmid = {37437616},
issn = {1879-1298},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Bioelectric Energy Sources/microbiology ; Manganese ; Wetlands ; Sulfadiazine ; Ciprofloxacin ; Bacteria/genetics ; Electrodes ; Biofilms ; Drug Resistance, Microbial/genetics ; },
abstract = {Manganese ore substrate up-flow microbial fuel cell constructed wetland (UCW-MFC(Mn)) as an innovative wastewater treatment technology for purifying antibiotics and electricity generation with few antibiotic resistance genes (ARGs) generation has attracted attention. However, antibiotic purifying effects should be further enhanced. In this study, a biofilm electrode reactor (BER) that needs direct current driving was powered by a Mn ore anode (UCW-MFC(Mn)) to form a coupled system without requiring direct-current source. Removal efficiencies of sulfadiazine (SDZ), ciprofloxacin (CIP) and the corresponding ARGs in the coupled system were compared with composite (BER was powered by direct-current source) and anaerobic systems (both of BER and UCW-MFC were in open circuit mode). The result showed that higher antibiotic removal efficiency (94% for SDZ and 99.1% for CIP) in the coupled system was achieved than the anaerobic system (88.5% for SDZ and 98.2% for CIP). Moreover, electrical stimulation reduced antibiotic selective pressure and horizontal gene transfer potential in BER, and UCW-MFC further reduced ARG abundances by strengthening the electro-adsorption of ARG hosts determined by Network analysis. Bacterial community diversity continuously decreased in BER while it increased in UCW-MFC, indicating that BER mitigated the toxicity of antibiotic. Degree of modularity, some functional bacteria (antibiotic degrading bacteria, fermentative bacteria and EAB), and P450 enzyme related to antibiotic and xenobiotics biodegradation genes were enriched in electric field existing UCW-MFC, accounting for the higher degradation efficiency. In conclusion, this study provided an effective strategy for removing antibiotics and ARGs in wastewater by operating a BER-UCW-MFC coupled system.},
}
@article {pmid37436868,
year = {2023},
author = {Mondal, A and Bansal, MS},
title = {Generalizing the Domain-Gene-Species Reconciliation Framework to Microbial Genes and Domains.},
journal = {IEEE/ACM transactions on computational biology and bioinformatics},
volume = {20},
number = {6},
pages = {3511-3522},
doi = {10.1109/TCBB.2023.3294480},
pmid = {37436868},
issn = {1557-9964},
mesh = {*Gene Duplication ; *Evolution, Molecular ; Phylogeny ; Algorithms ; Genes, Microbial ; Gene Transfer, Horizontal/genetics ; Models, Genetic ; },
abstract = {Protein domains play an important role in the function and evolution of many gene families. Previous studies have shown that domains are frequently lost or gained during gene family evolution. Yet, most computational approaches for studying gene family evolution do not account for domain-level evolution within genes. To address this limitation, a new three-level reconciliation framework, called the Domain-Gene-Species (DGS) reconciliation model, has been recently developed to simultaneously model the evolution of a domain family inside one or more gene families and the evolution of those gene families inside a species tree. However, the existing model applies only to multi-cellular eukaryotes where horizontal gene transfer is negligible. In this work, we generalize the existing DGS reconciliation model by allowing for the spread of genes and domains across species boundaries through horizontal transfer. We show that the problem of computing optimal generalized DGS reconciliations, though NP-hard, is approximable to within a constant factor, where the specific approximation ratio depends on the "event costs" used. We provide two different approximation algorithms for the problem and demonstrate the impact of the generalized framework using both simulated and real biological data. Our results show that our new algorithms result in highly accurate reconstructions of domain family evolution for microbes.},
}
@article {pmid37434470,
year = {2023},
author = {Bucknell, AH and McDonald, MC},
title = {That's no moon, it's a Starship: Giant transposons driving fungal horizontal gene transfer.},
journal = {Molecular microbiology},
volume = {120},
number = {4},
pages = {555-563},
doi = {10.1111/mmi.15118},
pmid = {37434470},
issn = {1365-2958},
support = {//Royal Society of Biology/ ; //the School of Biosciences at the University of Birmingham/ ; },
abstract = {To date, most reports of horizontal gene transfer (HGT) in fungi rely on genome sequence data and are therefore an indirect measure of HGT after the event has occurred. However, a novel group of class II-like transposons known as Starships may soon alter this status quo. Starships are giant transposable elements that carry dozens of genes, some of which are host-beneficial, and are linked to many recent HGT events in the fungal kingdom. These transposons remain active and mobile in many fungal genomes and their transposition has recently been shown to be driven by a conserved tyrosine-recombinase called 'Captain'. This perspective explores some of the remaining unanswered questions about how these Starship transposons move, both within a genome and between different species. We seek to outline several experimental approaches that can be used to identify the genes essential for Starship-mediated HGT and draw links to other recently discovered giant transposons outside of the fungal kingdom.},
}
@article {pmid37434168,
year = {2023},
author = {Li, KL and Nakashima, K and Hisata, K and Satoh, N},
title = {Expression and possible functions of a horizontally transferred glycosyl hydrolase gene, GH6-1, in Ciona embryogenesis.},
journal = {EvoDevo},
volume = {14},
number = {1},
pages = {11},
pmid = {37434168},
issn = {2041-9139},
abstract = {BACKGROUND: The Tunicata or Urochordata is the only animal group with the ability to synthesize cellulose directly and cellulose is a component of the tunic that covers the entire tunicate body. The genome of Ciona intestinalis type A contains a cellulose synthase gene, CesA, that it acquired via an ancient, horizontal gene transfer. CesA is expressed in embryonic epidermal cells and functions in cellulose production. Ciona CesA is composed of both a glycosyltransferase domain, GT2, and a glycosyl hydrolase domain, GH6, which shows a mutation at a key position and seems functionless. Interestingly, the Ciona genome contains a glycosyl hydrolase gene, GH6-1, in which the GH6 domain seems intact. This suggests expression and possible functions of GH6-1 during Ciona embryogenesis. Is GH6-1 expressed during embryogenesis? If so, in what tissues is the gene expressed? Does GH6-1 serve a function? If so, what is it? Answers to these questions may advance our understanding of evolution of this unique animal group.<br><br>RESULTS: Quantitative reverse transcription PCR and in situ hybridization revealed that GH6-1 is expressed in epidermis of tailbud embryos and in early swimming larvae, a pattern similar to that of CesA. Expression is downregulated at later stages and becomes undetectable in metamorphosed juveniles. The GH6-1 expression level is higher in the anterior-trunk region and caudal-tip regions of late embryos. Single-cell RNA sequencing analysis of the late tailbud stage showed that cells of three clusters with epidermal identity express GH6-1, and that some of them co-express CesA. TALEN-mediated genome editing was used to generate GH6-1 knockout Ciona larvae. Around half of TALEN-electroporated larvae showed abnormal development of adhesive papillae and altered distribution of surface cellulose. In addition, three-fourths of TALEN-electroporated animals failed to complete larval metamorphosis.<br><br>CONCLUSIONS: This study showed that tunicate GH6-1, a gene that originated by horizontal gene transfer of a prokaryote gene, is recruited into the ascidian genome, and that it is expressed and functions in epidermal cells of ascidian embryos. Although further research is required, this observation demonstrates that both CesA and GH6-1 are involved in tunicate cellulose metabolism, impacting tunicate morphology and ecology.},
}
@article {pmid37429971,
year = {2023},
author = {Heo, S and Oh, SE and Lee, G and Lee, J and Ha, NC and Jeon, CO and Jeong, K and Lee, JH and Jeong, DW},
title = {Staphylococcus equorum plasmid pKS1030-3 encodes auxiliary biofilm formation and trans-acting gene mobilization systems.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {11108},
pmid = {37429971},
issn = {2045-2322},
mesh = {*Staphylococcus aureus ; *Staphylococcus/genetics ; Plasmids/genetics ; Biofilms ; },
abstract = {The foodborne bacterium Staphylococcus equorum strain KS1030 harbours plasmid pSELNU1, which encodes a lincomycin resistance gene. pSELNU1 undergoes horizontal transfer between bacterial strains, thus spreading antibiotic resistance. However, the genes required for horizontal plasmid transfer are not encoded in pSELNU1. Interestingly, a relaxase gene, a type of gene related to horizontal plasmid transfer, is encoded in another plasmid of S. equorum KS1030, pKS1030-3. The complete genome of pKS1030-3 is 13,583 bp long and encodes genes for plasmid replication, biofilm formation (the ica operon), and horizontal gene transfer. The replication system of pKS1030-3 possesses the replication protein-encoding gene repB, a double-stranded origin of replication, and two single-stranded origins of replication. The ica operon, relaxase gene, and a mobilization protein-encoding gene were detected in pKS1030-3 strain-specifically. When expressed in S. aureus RN4220, the ica operon and relaxase operon of pKS1030-3 conferred biofilm formation ability and horizontal gene transfer ability, respectively. The results of our analyses show that the horizontal transfer of pSELNU1 of S. equorum strain KS1030 depends on the relaxase encoded by pKS1030-3, which is therefore trans-acting. Genes encoded in pKS1030-3 contribute to important strain-specific properties of S. equorum KS1030. These results could contribute to preventing the horizontal transfer of antibiotic resistance genes in food.},
}
@article {pmid37428925,
year = {2023},
author = {Walker, AA and Robinson, SD and Merritt, DJ and Cardoso, FC and Goudarzi, MH and Mercedes, RS and Eagles, DA and Cooper, P and Zdenek, CN and Fry, BG and Hall, DW and Vetter, I and King, GF},
title = {Horizontal gene transfer underlies the painful stings of asp caterpillars (Lepidoptera: Megalopygidae).},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {29},
pages = {e2305871120},
pmid = {37428925},
issn = {1091-6490},
mesh = {Animals ; Mice ; Gene Transfer, Horizontal ; *Moths/genetics ; *Bites and Stings ; Larva/genetics ; Venoms ; *Toxins, Biological ; Pain ; Mammals ; },
abstract = {Larvae of the genus Megalopyge (Lepidoptera: Zygaenoidea: Megalopygidae), known as asp or puss caterpillars, produce defensive venoms that cause severe pain. Here, we present the anatomy, chemistry, and mode of action of the venom systems of caterpillars of two megalopygid species, the Southern flannel moth Megalopyge opercularis and the black-waved flannel moth Megalopyge crispata. We show that megalopygid venom is produced in secretory cells that lie beneath the cuticle and are connected to the venom spines by canals. Megalopygid venoms consist of large aerolysin-like pore-forming toxins, which we have named megalysins, and a small number of peptides. The venom system differs markedly from those of previously studied venomous zygaenoids of the family Limacodidae, suggestive of an independent origin. Megalopygid venom potently activates mammalian sensory neurons via membrane permeabilization and induces sustained spontaneous pain behavior and paw swelling in mice. These bioactivities are ablated by treatment with heat, organic solvents, or proteases, indicating that they are mediated by larger proteins such as the megalysins. We show that the megalysins were recruited as venom toxins in the Megalopygidae following horizontal transfer of genes from bacteria to the ancestors of ditrysian Lepidoptera. Megalopygids have recruited aerolysin-like proteins as venom toxins convergently with centipedes, cnidarians, and fish. This study highlights the role of horizontal gene transfer in venom evolution.},
}
@article {pmid37427782,
year = {2023},
author = {Tang, X and Shang, J and Ji, Y and Sun, Y},
title = {PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer.},
journal = {Nucleic acids research},
volume = {51},
number = {15},
pages = {e83},
pmid = {37427782},
issn = {1362-4962},
mesh = {*Genome, Bacterial ; *Software ; Plasmids/genetics ; Metagenome ; Metagenomics/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Plasmids are mobile genetic elements that carry important accessory genes. Cataloging plasmids is a fundamental step to elucidate their roles in promoting horizontal gene transfer between bacteria. Next generation sequencing (NGS) is the main source for discovering new plasmids today. However, NGS assembly programs tend to return contigs, making plasmid detection difficult. This problem is particularly grave for metagenomic assemblies, which contain short contigs of heterogeneous origins. Available tools for plasmid contig detection still suffer from some limitations. In particular, alignment-based tools tend to miss diverged plasmids while learning-based tools often have lower precision. In this work, we develop a plasmid detection tool PLASMe that capitalizes on the strength of alignment and learning-based methods. Closely related plasmids can be easily identified using the alignment component in PLASMe while diverged plasmids can be predicted using order-specific Transformer models. By encoding plasmid sequences as a language defined on the protein cluster-based token set, Transformer can learn the importance of proteins and their correlation through positionally token embedding and the attention mechanism. We compared PLASMe and other tools on detecting complete plasmids, plasmid contigs, and contigs assembled from CAMI2 simulated data. PLASMe achieved the highest F1-score. After validating PLASMe on data with known labels, we also tested it on real metagenomic and plasmidome data. The examination of some commonly used marker genes shows that PLASMe exhibits more reliable performance than other tools.},
}
@article {pmid37425999,
year = {2023},
author = {Sun, D and Sun, X and Hu, Y and Yamaichi, Y},
title = {Editorial: Horizontal gene transfer mediated bacterial antibiotic resistance, volume II.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1221606},
pmid = {37425999},
issn = {1664-302X},
}
@article {pmid37425898,
year = {2023},
author = {Culbertson, EM and Levin, TC},
title = {Eukaryotic antiviral immune proteins arose via convergence, horizontal transfer, and ancient inheritance.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37425898},
issn = {2692-8205},
support = {R00 AI139344/AI/NIAID NIH HHS/United States ; R35 GM150681/GM/NIGMS NIH HHS/United States ; S10 OD028483/OD/NIH HHS/United States ; },
abstract = {Animals use a variety of cell-autonomous innate immune proteins to detect viral infections and prevent replication. Recent studies have discovered that a subset of mammalian antiviral proteins have homology to anti-phage defense proteins in bacteria, implying that there are aspects of innate immunity that are shared across the Tree of Life. While the majority of these studies have focused on characterizing the diversity and biochemical functions of the bacterial proteins, the evolutionary relationships between animal and bacterial proteins are less clear. This ambiguity is partly due to the long evolutionary distances separating animal and bacterial proteins, which obscures their relationships. Here, we tackle this problem for three innate immune families (CD-NTases [including cGAS], STINGs, and Viperins) by deeply sampling protein diversity across eukaryotes. We find that Viperins and OAS family CD-NTases are truly ancient immune proteins, likely inherited since the last eukaryotic common ancestor and possibly longer. In contrast, we find other immune proteins that arose via at least four independent events of horizontal gene transfer (HGT) from bacteria. Two of these events allowed algae to acquire new bacterial viperins, while two more HGT events gave rise to distinct superfamilies of eukaryotic CD-NTases: the Mab21 superfamily (containing cGAS) which has diversified via a series of animal-specific duplications, and a previously undefined eSMODS superfamily, which more closely resembles bacterial CD-NTases. Finally, we found that cGAS and STING proteins have substantially different histories, with STINGs arising via convergent domain shuffling in bacteria and eukaryotes. Overall, our findings paint a picture of eukaryotic innate immunity as highly dynamic, where eukaryotes build upon their ancient antiviral repertoires through the reuse of protein domains and by repeatedly sampling a rich reservoir of bacterial anti-phage genes.},
}
@article {pmid37424546,
year = {2023},
author = {Sharon, BM and Hulyalkar, NV and Zimmern, PE and Palmer, KL and De Nisco, NJ},
title = {Inter-species diversity and functional genomic analyses of closed genome assemblies of clinically isolated, megaplasmid-containing Enterococcus raffinosus Er676 and ATCC49464.},
journal = {Access microbiology},
volume = {5},
number = {6},
pages = {},
pmid = {37424546},
issn = {2516-8290},
support = {R01 AI116610/AI/NIAID NIH HHS/United States ; },
abstract = {Enterococcus raffinosus is an understudied member of its genus possessing a characteristic megaplasmid contributing to a large genome size. Although less commonly associated with human infection compared to other enterococci, this species can cause disease and persist in diverse niches such as the gut, urinary tract, blood and environment. Few complete genome assemblies have been published to date for E. raffinosus . In this study, we report the complete assembly of the first clinical urinary E. raffinosus strain, Er676, isolated from a postmenopausal woman with history of recurrent urinary tract infection. We additionally completed the assembly of clinical type strain ATCC49464. Comparative genomic analyses reveal inter-species diversity driven by large accessory genomes. The presence of a conserved megaplasmid indicates it is a ubiquitous and vital genetic feature of E. raffinosus . We find that the E. raffinosus chromosome is enriched for DNA replication and protein biosynthesis genes while the megaplasmid is enriched for transcription and carbohydrate metabolism genes. Prophage analysis suggests that diversity in the chromosome and megaplasmid sequences arises, in part, from horizontal gene transfer. Er676 demonstrated the largest genome size reported to date for E. raffinosus and the highest probability of human pathogenicity. Er676 also possesses multiple antimicrobial resistance genes, of which all but one are encoded on the chromosome, and has the most complete prophage sequences. Complete assembly and comparative analyses of the Er676 and ATCC49464 genomes provide important insight into the inter-species diversity of E. raffinosus that gives it its ability to colonize and persist in the human body. Investigating genetic factors that contribute to the pathogenicity of this species will provide valuable tools to combat diseases caused by this opportunistic pathogen.},
}
@article {pmid37424042,
year = {2023},
author = {Wang, B and Xu, J and Wang, Y and Stirling, E and Zhao, K and Lu, C and Tan, X and Kong, D and Yan, Q and He, Z and Ruan, Y and Ma, B},
title = {Tackling Soil ARG-Carrying Pathogens with Global-Scale Metagenomics.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {10},
number = {26},
pages = {e2301980},
pmid = {37424042},
issn = {2198-3844},
support = {42090060//National Natural Science Foundation of China/ ; 42277283//National Natural Science Foundation of China/ ; 41991334//National Natural Science Foundation of China/ ; 2023C02004//Key R&amp;D Program of Zhejjiang Province/ ; 2023C02015//Key R&amp;D Program of Zhejjiang Province/ ; },
mesh = {*Soil ; *Metagenomics ; Ecosystem ; Soil Microbiology ; Anti-Bacterial Agents ; },
abstract = {Antibiotic overuse and the subsequent environmental contamination of residual antibiotics poses a public health crisis via an acceleration in the spread of antibiotic resistance genes (ARGs) through horizontal gene transfer. Although the occurrence, distribution, and driving factors of ARGs in soils have been widely investigated, little is known about the antibiotic resistance of soilborne pathogens at a global scale. To explore this gap, contigs from 1643 globally sourced metagnomes are assembled, yielding 407 ARG-carrying pathogens (APs) with at least one ARG; APs are detected in 1443 samples (sample detection rate of 87.8%). The richness of APs is greater in agricultural soils (with a median of 20) than in non-agricultural ecosystems. Agricultural soils possess a high prevalence of clinical APs affiliated with Escherichia, Enterobacter, Streptococcus, and Enterococcus. The APs detected in agricultural soils tend to coexist with multidrug resistance genes and bacA. A global map of soil AP richness is generated, where anthropogenic and climatic factors explained AP hot spots in East Asia, South Asia, and the eastern United States. The results herein advance this understanding of the global distribution of soil APs and determine regions prioritized to control soilborne APs worldwide.},
}
@article {pmid37410611,
year = {2023},
author = {Shetty, VP and Akshay, SD and Rai, P and Deekshit, VK},
title = {Integrons as the potential targets for combating multidrug resistance in Enterobacteriaceae using CRISPR- Cas9 technique.},
journal = {Journal of applied microbiology},
volume = {134},
number = {7},
pages = {},
doi = {10.1093/jambio/lxad137},
pmid = {37410611},
issn = {1365-2672},
support = {AMR/DHR/GIA/3/ECD-II-2020//ICMR/ ; },
mesh = {*Enterobacteriaceae ; *Integrons ; CRISPR-Cas Systems ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {The emergence of multi-drug resistance (MDR) to pan-drug resistance (PDR) in Enterobacteriaceae has made treatment extremely challenging. Genetic mutations and horizontal gene transfer (HGT) through mobile genetic elements (MGEs) were frequently associated mechanisms of drug resistance in pathogens. However, transposons, plasmids, and integrons transfer MDR genes in bacterium via HGT much faster. Integrons are dsDNA segment that plays a crucial role in the adaptation and evolution of bacteria. They contain multiple gene cassettes that code for antibiotic resistance determinants that are expressed by a single promoter (Pc). Integrons are the cause of drug resistance in Enterobacteriaceae. Although alternatives to antibiotics such as bacteriophages, phage proteins, antimicrobial peptides, and natural compounds have been widely used to treat MDR infections, there have been limited efforts to reverse the antibiotic resistance ability of bacteria. Thus, silencing the genes harboured on MGEs achieved by Gene Editing Techniques (GETs) might prevent the spread of MDR. One such GETs, which has a simple design, good repeatability, low cost, and high efficiency, is CRISPR- Cas9 system. Thus, this review is a first of the kind that focuses on utilizing the structure of an integron to make it an ideal target for GETs like CRISPR- Cas9 systems.},
}
@article {pmid37409977,
year = {2023},
author = {Fan, Q and Zhang, J and Shi, H and Chang, S and Hou, F},
title = {Metagenomic Profiles of Yak and Cattle Manure Resistomes in Different Feeding Patterns before and after Composting.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {7},
pages = {e0064523},
pmid = {37409977},
issn = {1098-5336},
mesh = {Animals ; Humans ; Cattle ; *Genes, Bacterial ; *Composting ; Manure/microbiology ; Metagenomics ; Drug Resistance, Microbial/genetics ; Metals ; Anti-Bacterial Agents/pharmacology ; Livestock ; },
abstract = {Antibiotic resistance is a global threat to public health, with antibiotic resistance genes (ARGs) being one of the emerging contaminants; furthermore, animal manure is an important reservoir of biocide resistance genes (BRGs) and metal resistance genes (MRGs). However, few studies have reported differences in the abundance and diversity of BRGs and MRGs between different types of animal manure and the changes in BRGs and MRGs before and after composting. This study employed a metagenomics-based approach to investigate ARGs, BRGs, MRGs, and mobile genetic elements (MGEs) of yak and cattle manure before and after composting under grazing and intensive feeding patterns. The total abundances of ARGs, clinical ARGs, BRGs, MRGs, and MGEs were lower in the manure of grazing livestock than in the manure of the intensively fed group. After composting, the total abundances of ARGs, clinical ARGs, and MGEs in intensively fed livestock manure decreased, whereas those of ARGs, clinical ARGs, MRGs, and MGEs increased in grazing livestock manure. The synergy between MGEs mediated horizontal gene transfer and vertical gene transmission via host bacteria proliferation, which was the main driver that altered the abundance and diversity of ARGs, BRGs, and MRGs in livestock manure and compost. Additionally, tetQ, IS91, mdtF, and fabK were potential indicators for estimating the total abundance of clinical ARGs, BRGs, MRGs, and MGEs in livestock manure and compost. These findings suggest that grazing livestock manure can be directly discharged into the fields, whereas intensively fed livestock manure should be composted before returning to the field. IMPORTANCE The recent increase in the prevalence of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and metal resistance genes (MRGs) in livestock manure poses risks to human health. Composting is known to be a promising technology for reducing the abundance of resistance genes. This study investigated the differences and changes in the abundances of ARGs, BRGs, and MRGs between yak and cattle manure under grazing and intensive feeding patterns before and after composting. The results indicate that the feeding pattern significantly affected the abundances of resistance genes in livestock manure. Manure in intensive farming should be composted before being discharged into the field, while grazing livestock manure is not suitable for composting due to an increased number of resistance genes.},
}
@article {pmid37408640,
year = {2023},
author = {Kumari, K and Rawat, V and Shadan, A and Sharma, PK and Deb, S and Singh, RP},
title = {In-depth genome and pan-genome analysis of a metal-resistant bacterium Pseudomonas parafulva OS-1.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1140249},
pmid = {37408640},
issn = {1664-302X},
abstract = {A metal-resistant bacterium Pseudomonas parafulva OS-1 was isolated from waste-contaminated soil in Ranchi City, India. The isolated strain OS-1 showed its growth at 25-45°C, pH 5.0-9.0, and in the presence of ZnSO4 (upto 5 mM). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain OS-1 belonged to the genus Pseudomonas and was most closely related to parafulva species. To unravel the genomic features, we sequenced the complete genome of P. parafulva OS-1 using Illumina HiSeq 4,000 sequencing platform. The results of average nucleotide identity (ANI) analysis indicated the closest similarity of OS-1 to P. parafulva PRS09-11288 and P. parafulva DTSP2. The metabolic potential of P. parafulva OS-1 based on Clusters of Othologous Genes (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated a high number of genes related to stress protection, metal resistance, and multiple drug-efflux, etc., which is relatively rare in P. parafulva strains. Compared with other parafulva strains, P. parafulva OS-1 was found to have the unique β-lactam resistance and type VI secretion system (T6SS) gene. Additionally, its genomes encode various CAZymes such as glycoside hydrolases and other genes associated with lignocellulose breakdown, suggesting that strain OS-1 have strong biomass degradation potential. The presence of genomic complexity in the OS-1 genome indicates that horizontal gene transfer (HGT) might happen during evolution. Therefore, genomic and comparative genome analysis of parafulva strains is valuable for further understanding the mechanism of resistance to metal stress and opens a perspective to exploit a newly isolated bacterium for biotechnological applications.},
}
@article {pmid37406030,
year = {2023},
author = {Rhoads, DD and Pummil, J and Ekesi, NS and Alrubaye, AAK},
title = {Horizontal transfer of probable chicken-pathogenicity chromosomal islands between Staphylococcus aureus and Staphylococcus agnetis.},
journal = {PloS one},
volume = {18},
number = {7},
pages = {e0283914},
pmid = {37406030},
issn = {1932-6203},
mesh = {Phylogeny ; Gene Transfer, Horizontal ; *Staphylococcus aureus/genetics ; Staphylococcus ; Female ; Cattle ; Virulence/genetics ; Humans ; Genomic Islands/genetics ; *Staphylococcal Infections/veterinary/genetics ; Animals ; Chickens/genetics ; },
abstract = {Staphylococcus agnetis is an emerging pathogen in chickens but has been most commonly isolated from sub-clinical mastitis in bovines. Previous whole-genome analyses for known virulence genes failed to identify determinants for the switch from mild ductal infections in cattle to severe infections in poultry. We now report identification of a family of 15 kbp, 17-19 gene mobile genetic elements (MGEs) specific to chicken osteomyelitis and dermatitis isolates of S. agnetis. These MGEs can be present in multiple copies per genome. The MGE has been vectored on a Staphylococcus phage that separately lysogenized two S. agnetis osteomyelitis strains. The S. agnetis genome from a broiler breeder case of ulcerative dermatitis contains 2 orthologs of this MGE, not associated with a prophage. BLASTn and phylogenetic analyses show that there are closely related intact MGEs found in genomes of S. aureus. The genome from a 1980s isolate from chickens in Ireland contains 3 copies of this MGE. More recent chicken isolates descended from that genome (Poland 2009, Oklahoma 2010, and Arkansas 2018) contain 2 to 4 related copies. Many of the genes of this MGE can be identified in disparate regions of the genomes of other chicken isolates of S. aureus. BLAST searches of the NCBI databases detect no similar MGEs outside of S. aureus and S. agnetis. These MGEs encode no proteins related to those produced by Staphylococcus aureus Pathogenicity Islands, which have been associated with the transition of S. aureus from human to chicken hosts. Other than mobilization functions, most of the genes in these new MGEs annotate as hypothetical proteins. The MGEs we describe appear to represent a new family of Chromosomal Islands (CIs) shared amongst S. agnetis and S. aureus. Further work is needed to understand the role of these CIs/MGEs in pathogenesis. Analysis of horizontal transfer of genetic elements between isolates and species of Staphylococci provides clues to evolution of host-pathogen interactions as well as revealing critical determinants for animal welfare and human diseases.},
}
@article {pmid37404190,
year = {2023},
author = {Kosmopoulos, JC and Campbell, DE and Whitaker, RJ and Wilbanks, EG},
title = {Horizontal Gene Transfer and CRISPR Targeting Drive Phage-Bacterial Host Interactions and Coevolution in "Pink Berry" Marine Microbial Aggregates.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {7},
pages = {e0017723},
pmid = {37404190},
issn = {1098-5336},
support = {T32 DK077653-29//HHS | National Institutes of Health (NIH)/ ; },
mesh = {Humans ; *Bacteriophages/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Transfer, Horizontal ; Fruit ; Host Microbial Interactions ; },
abstract = {Bacteriophages (phages), which are viruses that infect bacteria, are the most abundant components of microbial communities and play roles in community dynamics and host evolution. However, the study of phage-host interactions is hindered by a paucity of model systems from natural environments. Here, we investigate phage-host interactions in the "pink berry" consortia, which are naturally occurring, low-diversity, macroscopic bacterial aggregates that are found in the Sippewissett Salt Marsh (Falmouth, MA, USA). We leverage metagenomic sequence data and a comparative genomics approach to identify eight compete phage genomes, infer their bacterial hosts from host-encoded clustered regularly interspaced short palindromic repeats (CRISPRs), and observe the potential evolutionary consequences of these interactions. Seven of the eight phages identified infect known pink berry symbionts, namely, Desulfofustis sp. PB-SRB1, Thiohalocapsa sp. PB-PSB1, and Rhodobacteraceae sp. A2, and they are largely divergent from known viruses. In contrast to the conserved bacterial community structure of pink berries, the distribution of these phages across aggregates is highly variable. Two phages persisted over a period of seven years with high sequence conservation, allowing us to identify gene gain and loss. Increased nucleotide variation in a conserved phage capsid gene that is commonly targeted by host CRISPR systems suggests that CRISPRs may drive phage evolution in pink berries. Finally, we identified a predicted phage lysin gene that was horizontally transferred to its bacterial host, potentially via a transposon intermediary. Taken together, our results demonstrate that pink berry consortia contain diverse and variable phages as well as provide evidence for phage-host coevolution via multiple mechanisms in a natural microbial system. IMPORTANCE Phages, which are viruses that infect bacteria, are important components of all microbial systems, in which they drive the turnover of organic matter by lysing host cells, facilitate horizontal gene transfer (HGT), and coevolve with their bacterial hosts. Bacteria resist phage infection, which is often costly or lethal, through a diversity of mechanisms. One of these mechanisms is CRISPR systems, which encode arrays of phage-derived sequences from past infections to block subsequent infection with related phages. Here, we investigate the bacteria and phage populations from a simple marine microbial community, known as "pink berries", found in salt marshes of Falmouth, Massachusetts, as a model of phage-host coevolution. We identify eight novel phages and characterize a case of putative CRISPR-driven phage evolution as well as an instance of HGT between a phage and its host, together suggesting that phages have large evolutionary impacts in a naturally occurring microbial community.},
}
@article {pmid37396349,
year = {2023},
author = {Chen, F and Wang, D and Lu, T and Li, S},
title = {Identification of a novel type II-C Cas9 from the fish pathogen Flavobacterium psychrophilum.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1181303},
pmid = {37396349},
issn = {1664-302X},
abstract = {Flavobacterium psychrophilum is the causative agent of rainbow trout fry syndrome and bacterial cold-water disease in salmonid fish worldwide. As an important fish pathogen, F. psychrophilum is frequently exposed to multiple invading genetic elements in natural environments. Endonuclease Cas9 provides bacteria with adaptive interference against invading genetic elements. Previous studies revealed that several F. psychrophilum strains harbored a type II-C Cas9 called Fp1Cas9, but little is known about the potential role of this endonuclease against invading genetic elements. In this work, we identified a gene encoding a novel type II-C Cas9 called Fp2Cas9 from F. psychrophilum strain CN46. Through bacterial RNA sequencing, we demonstrated active transcription of both Fp2Cas9 and pre-crRNAs in strain CN46. Bioinformatics analysis further revealed that the transcription of Fp2Cas9 and pre-crRNAs was driven by a newly integrated promoter sequence and a promoter element embedded within each CRISPR repeat, respectively. To formally demonstrate that Fp2Cas9 and associated crRNAs yielded functional interference in strain CN46, a plasmid interference assay was performed, resulting in adaptive immunity to target DNA sequences in Flavobacterium bacteriophages. Phylogenetic analysis demonstrated that Fp2Cas9 was present only in several F. psychrophilum isolates. Phylogenetic analysis revealed that this novel endonuclease was probably acquired through horizontal gene transfer from the CRISPR-Cas9 system in an unidentified Flavobacterium species. Comparative genomics analysis further showed that the Fp2Cas9 was integrated into the type II-C CRISPR-Cas locus in strain CN38 instead of the original Fp1Cas9. Taken together, our results shed light on the origin and evolution of Fp2Cas9 gene and demonstrated that this novel endonuclease provided adaptive interference against bacteriophage infections.},
}
@article {pmid37395521,
year = {2023},
author = {Meng, PQ and Zhang, Q and Ding, Y and Lin, JX and Chen, F},
title = {Evolutionary and Pan-genome Analysis of Three Important Black-pigmented Periodontal Pathogens.},
journal = {The Chinese journal of dental research},
volume = {26},
number = {2},
pages = {93-104},
doi = {10.3290/j.cjdr.b4128023},
pmid = {37395521},
issn = {1867-5646},
mesh = {*Prevotella/genetics/metabolism ; Phylogeny ; Prevotella intermedia/genetics/metabolism ; *Porphyromonas gingivalis/genetics/metabolism ; Prevotella nigrescens/genetics ; },
abstract = {OBJECTIVE: To analyse the pan-genome of three black-pigmented periodontal pathogens: Porphyromonas gingivalis, Prevotella intermedia and Prevotella nigrescens.<br><br>METHODS: Pan-genome analyses of 66, 33 and 5 publicly available whole-genome sequences of P. gingivalis, P. intermedia and P. nigrescens, respectively, were performed using Pan-genome Analysis Pipeline software (version 1.2.1; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, PR China). Phylogenetic trees were constructed based on the entire pan-genome and single nucleotide polymorphisms within the core genome. The distribution and abundance of virulence genes in the core and dispensable genomes were also compared in the three species.<br><br>RESULTS: All three species possess an open pan-genome. The core genome of P. gingivalis, P. intermedia and P. nigrescens included 1001, 1514 and 1745 orthologous groups, respectively, which were mainly related to basic cellular functions such as metabolism. The dispensable genome of P. gingivalis, P. intermedia and P. nigrescens was composed of 2814, 2689 and 906 orthologous groups, respectively, and it was enriched in genes involved in pathogenicity or with unknown functions. Phylogenetic trees presented a clear separation of P. gingivalis, P. intermedia and P. nigrescens, verifying the reclassification of the black-pigmented species. Furthermore, the three species shared almost the same virulence factors involved in adhesion, proteolysis and evasion of host defences. Some of these virulence genes were conserved across species whereas others belonged to the dispensable genome, which might be acquired through horizontal gene transfer.<br><br>CONCLUSION: This study highlighted the usefulness of pan-genome analysis to infer evolutionary cues for black-pigmented species, indicating their homology and phylogenomic diversity.},
}
@article {pmid37395112,
year = {2023},
author = {Lloyd, GS and Thomas, CM},
title = {Microbial Primer: The logic of bacterial plasmids.},
journal = {Microbiology (Reading, England)},
volume = {169},
number = {7},
pages = {},
doi = {10.1099/mic.0.001336},
pmid = {37395112},
issn = {1465-2080},
support = {BB/X512230/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Bacteria/genetics ; Conjugation, Genetic ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; *Logic ; Plasmids/genetics ; },
abstract = {This short primer is intended to give an overview of bacterial plasmids for those not yet familiar with these fascinating genetic elements. It covers their basic properties but does not attempt to cover the diversity of phenotypic properties that can be encoded by plasmids, and includes suggestions for further reading.},
}
@article {pmid37394915,
year = {2023},
author = {Pereira, L and Dunning, LT},
title = {Extrachromosomal circular DNA as a vehicle to gene transfer in plants.},
journal = {Plant physiology},
volume = {193},
number = {1},
pages = {172-173},
pmid = {37394915},
issn = {1532-2548},
mesh = {*DNA, Circular/genetics ; Gene Transfer, Horizontal ; *Plants/genetics ; },
}
@article {pmid37394042,
year = {2023},
author = {Mohammad Mirsoleimani Azizi, S and Zakaria, BS and Haffiez, N and Kumar, A and Ranjan Dhar, B},
title = {Pilot-scale investigation of conductive carbon cloth amendment for enhancing high-solids anaerobic digestion and mitigating antibiotic resistance.},
journal = {Bioresource technology},
volume = {385},
number = {},
pages = {129411},
doi = {10.1016/j.biortech.2023.129411},
pmid = {37394042},
issn = {1873-2976},
mesh = {*Carbon ; Anaerobiosis ; Electron Transport ; Drug Resistance, Microbial/genetics ; *Methane ; Bioreactors ; },
abstract = {This study examined the effectiveness of introducing conductive carbon cloth into a pilot-scale high-solids anaerobic digestion (HSAD) system. Adding carbon cloth increased methane production by 22 % and improved the maximum methane production rate by 39 %. Microbial community characterization indicated a possible direct interspecies electron transfer-based syntrophic association among microbes. Using carbon cloth also enhanced microbial richness, diversity, and evenness. Carbon cloth effectively reduced the total abundance of antibiotic resistance genes (ARGs) by 44.6 %, mainly by inhibiting horizontal gene transfer, as shown by the significant decrease in the relative abundance of integron genes (particularly intl1). The multivariate analysis further demonstrated strong correlations of intl1 with most of the targeted ARGs. These findings suggest that carbon cloth amendment can promote efficient methane production and attenuate the spread of ARGs in HSAD systems.},
}
@article {pmid37392596,
year = {2023},
author = {Evans, D and Sundermann, A and Griffith, M and Rangachar Srinivasa, V and Mustapha, M and Chen, J and Dubrawski, A and Cooper, V and Harrison, L and Van Tyne, D},
title = {Empirically derived sequence similarity thresholds to study the genomic epidemiology of plasmids shared among healthcare-associated bacterial pathogens.},
journal = {EBioMedicine},
volume = {93},
number = {},
pages = {104681},
pmid = {37392596},
issn = {2352-3964},
mesh = {Humans ; *Anti-Bacterial Agents ; Plasmids/genetics ; Genomics ; Bacteria/genetics ; *Cross Infection/epidemiology ; Genome, Bacterial ; },
abstract = {BACKGROUND: Healthcare-associated bacterial pathogens frequently carry plasmids that contribute to antibiotic resistance and virulence. The horizontal transfer of plasmids in healthcare settings has been previously documented, but genomic and epidemiologic methods to study this phenomenon remain underdeveloped. The objectives of this study were to apply whole-genome sequencing to systematically resolve and track plasmids carried by nosocomial pathogens in a single hospital, and to identify epidemiologic links that indicated likely horizontal plasmid transfer.<br><br>METHODS: We performed an observational study of plasmids circulating among bacterial isolates infecting patients at a large hospital. We first examined plasmids carried by isolates sampled from the same patient over time and isolates that caused clonal outbreaks in the same hospital to develop thresholds with which horizontal plasmid transfer within a tertiary hospital could be inferred. We then applied those sequence similarity thresholds to perform a systematic screen of 3074 genomes of nosocomial bacterial isolates from a single hospital for the presence of 89 plasmids. We also collected and reviewed data from electronic health records for evidence of geotemporal links between patients infected with bacteria encoding plasmids of interest.<br><br>FINDINGS: Our analyses determined that 95% of analyzed genomes maintained roughly 95% of their plasmid genetic content and accumulated fewer than 15 SNPs per 100&#xa0;kb of plasmid sequence. Applying these similarity thresholds to identify horizontal plasmid transfer identified 45 plasmids that potentially circulated among clinical isolates. Ten highly preserved plasmids met criteria for geotemporal links associated with horizontal transfer. Several plasmids with shared backbones also encoded different additional mobile genetic element content, and these elements were variably present among the sampled clinical isolate genomes.<br><br>INTERPRETATION: Evidence suggests that the horizontal transfer of plasmids among nosocomial bacterial pathogens appears to be frequent within hospitals and can be monitored with whole genome sequencing and comparative genomics approaches. These approaches should incorporate both nucleotide identity and reference sequence coverage to study the dynamics of plasmid transfer in the hospital.<br><br>FUNDING: This research was supported by the US National Institute of Allergy and Infectious Disease (NIAID) and the University of Pittsburgh School of Medicine.},
}
@article {pmid37389331,
year = {2023},
author = {Bromfield, ESP and Cloutier, S and Hynes, MF},
title = {Ensifer canadensis sp. nov. strain T173[T] isolated from Melilotus albus (sweet clover) in Canada possesses recombinant plasmid pT173b harbouring symbiosis and type IV secretion system genes apparently acquired from Ensifer medicae.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1195755},
pmid = {37389331},
issn = {1664-302X},
abstract = {A bacterial strain, designated T173[T], was previously isolated from a root-nodule of a Melilotus albus plant growing in Canada and identified as a novel Ensifer lineage that shared a clade with the non-symbiotic species, Ensifer adhaerens. Strain T173[T] was also previously found to harbour a symbiosis plasmid and to elicit root-nodules on Medicago and Melilotus species but not fix nitrogen. Here we present data for the genomic and taxonomic description of strain T173[T]. Phylogenetic analyses including the analysis of whole genome sequences and multiple locus sequence analysis (MLSA) of 53 concatenated ribosome protein subunit (rps) gene sequences confirmed placement of strain T173[T] in a highly supported lineage distinct from named Ensifer species with E. morelensis Lc04[T] as the closest relative. The highest digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of genome sequences of strain T173[T] compared with closest relatives (35.7 and 87.9%, respectively) are well below the respective threshold values of 70% and 95-96% for bacterial species circumscription. The genome of strain T173[T] has a size of 8,094,229 bp with a DNA G + C content of 61.0 mol%. Six replicons were detected: a chromosome (4,051,102 bp) and five plasmids harbouring plasmid replication and segregation (repABC) genes. These plasmids were also found to possess five apparent conjugation systems based on analysis of TraA (relaxase), TrbE/VirB4 (part of the Type IV secretion system (T4SS)) and TraG/VirD4 (coupling protein). Ribosomal RNA operons encoding 16S, 23S, and 5S rRNAs that are usually restricted to bacterial chromosomes were detected on plasmids pT173d and pT173e (946,878 and 1,913,930 bp, respectively) as well as on the chromosome of strain T173[T]. Moreover, plasmid pT173b (204,278 bp) was found to harbour T4SS and symbiosis genes, including nodulation (nod, noe, nol) and nitrogen fixation (nif, fix) genes that were apparently acquired from E. medicae by horizontal transfer. Data for morphological, physiological and symbiotic characteristics complement the sequence-based characterization of strain T173[T]. The data presented support the description of a new species for which the name Ensifer canadensis sp. nov. is proposed with strain T173[T] (= LMG 32374[T] = HAMBI 3766[T]) as the species type strain.},
}
@article {pmid37384706,
year = {2023},
author = {Widen, SA and Bes, IC and Koreshova, A and Pliota, P and Krogull, D and Burga, A},
title = {Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities.},
journal = {Science (New York, N.Y.)},
volume = {380},
number = {6652},
pages = {eade0705},
doi = {10.1126/science.ade0705},
pmid = {37384706},
issn = {1095-9203},
mesh = {Animals ; *Caenorhabditis/genetics ; *Gene Transfer, Horizontal ; *Viruses/genetics ; *DNA Transposable Elements ; Genetic Vectors ; *Biological Evolution ; },
abstract = {Horizontal gene transfer, the movement of genetic material between species, has been reported across all major eukaryotic lineages. However, the underlying mechanisms of transfer and their impact on genome evolution are still poorly understood. While studying the evolutionary origin of a selfish element in the nematode Caenorhabditis briggsae, we discovered that Mavericks, ancient virus-like transposons related to giant viruses and virophages, are one of the long-sought vectors of horizontal gene transfer. We found that Mavericks gained a novel herpesvirus-like fusogen in nematodes, leading to the widespread exchange of cargo genes between extremely divergent species, bypassing sexual and genetic barriers spanning hundreds of millions of years. Our results show how the union between viruses and transposons causes horizontal gene transfer and ultimately genetic incompatibilities in natural populations.},
}
@article {pmid37384391,
year = {2023},
author = {Römling, U and Cao, LY and Bai, FW},
title = {Evolution of cyclic di-GMP signalling on a short and long term time scale.},
journal = {Microbiology (Reading, England)},
volume = {169},
number = {6},
pages = {},
pmid = {37384391},
issn = {1465-2080},
mesh = {Humans ; *Signal Transduction ; *Second Messenger Systems ; Amino Acid Substitution ; Biofilms ; Gene Transfer, Horizontal ; },
abstract = {Diversifying radiation of domain families within specific lineages of life indicates the importance of their functionality for the organisms. The foundation for the diversifying radiation of the cyclic di-GMP signalling network that occurred within the bacterial kingdom is most likely based in the outmost adaptability, flexibility and plasticity of the system. Integrative sensing of multiple diverse extra- and intracellular signals is made possible by the N-terminal sensory domains of the modular cyclic di-GMP turnover proteins, mutations in the protein scaffolds and subsequent signal reception by diverse receptors, which eventually rewires opposite host-associated as well as environmental life styles including parallel regulated target outputs. Natural, laboratory and microcosm derived microbial variants often with an altered multicellular biofilm behaviour as reading output demonstrated single amino acid substitutions to substantially alter catalytic activity including substrate specificity. Truncations and domain swapping of cyclic di-GMP signalling genes and horizontal gene transfer suggest rewiring of the network. Presence of cyclic di-GMP signalling genes on horizontally transferable elements in particular observed in extreme acidophilic bacteria indicates that cyclic di-GMP signalling and biofilm components are under selective pressure in these types of environments. On a short and long term evolutionary scale, within a species and in families within bacterial orders, respectively, the cyclic di-GMP signalling network can also rapidly disappear. To investigate variability of the cyclic di-GMP signalling system on various levels will give clues about evolutionary forces and discover novel physiological and metabolic pathways affected by this intriguing second messenger signalling system.},
}
@article {pmid37379503,
year = {2023},
author = {Duan, JL and Ma, JY and Sun, XD and Liu, XY and Wang, Y and Du, L and Xia, PF and Yuan, XZ},
title = {Bubbles Expand the Dissemination of Antibiotic Resistance in the Aquatic Environment.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {27},
pages = {10079-10088},
doi = {10.1021/acs.est.3c02935},
pmid = {37379503},
issn = {1520-5851},
mesh = {Humans ; *Angiotensin Receptor Antagonists ; Pandemics ; Angiotensin-Converting Enzyme Inhibitors ; *COVID-19 ; Bacteria ; Drug Resistance, Microbial ; },
abstract = {Antibiotic resistance is a global health challenge, and the COVID-19 pandemic has amplified the urgency to understand its airborne transmission. The bursting of bubbles is a fundamental phenomenon in natural and industrial processes, with the potential to encapsulate or adsorb antibiotic-resistant bacteria (ARB). However, there is no evidence to date for bubble-mediated antibiotic resistance dissemination. Here, we show that bubbles can eject abundant bacteria to the air, form stable biofilms over the air-water interface, and provide opportunities for cell-cell contact that facilitates horizontal gene transfer at and over the air-liquid interface. The extracellular matrix (ECM) on bacteria can increase bubble attachment on biofilms, increase bubble lifetime, and, thus, produce abundant small droplets. We show through single-bubble probe atomic force microscopy and molecular dynamics simulations that hydrophobic interactions with polysaccharides control how the bubble interacts with the ECM. These results highlight the importance of bubbles and its physicochemical interaction with ECM in facilitating antibiotic resistance dissemination and fulfill the framework on antibiotic resistance dissemination.},
}
@article {pmid37378525,
year = {2023},
author = {Tan, Q and Li, R and Liu, L and Wang, D and Dai, XF and Song, LM and Zhang, DD and Kong, ZQ and Klosterman, SJ and Usami, T and Subbarao, KV and Liang, WX and Chen, JY},
title = {Functional Characterization of Verticillium dahliae Race 3-Specific Gene VdR3e in Virulence and Elicitation of Plant Immune Responses.},
journal = {Microbiology spectrum},
volume = {11},
number = {4},
pages = {e0108323},
pmid = {37378525},
issn = {2165-0497},
mesh = {Virulence/genetics ; *Verticillium/genetics ; *Ascomycota ; Plant Immunity ; Virulence Factors/genetics/metabolism ; Plant Diseases/microbiology ; },
abstract = {Verticillium dahliae is a soilborne fungal pathogen that causes disease on many economically important crops. Based on the resistance or susceptibility of differential cultivars in tomato, isolates of V. dahliae are divided into three races. Avirulence (avr) genes within the genomes of the three races have also been identified. However, the functional role of the avr gene in race 3 isolates of V. dahliae has not been characterized. In this study, bioinformatics analysis showed that VdR3e, a cysteine-rich secreted protein encoded by the gene characterizing race 3 in V. dahliae, was likely obtained by horizontal gene transfer from the fungal genus Bipolaris. We demonstrate that VdR3e causes cell death by triggering multiple defense responses. In addition, VdR3e localized at the periphery of the plant cell and triggered immunity depending on its subcellular localization and the cell membrane receptor BAK1. Furthermore, VdR3e is a virulence factor and shows differential pathogenicity in race 3-resistant and -susceptible hosts. These results suggest that VdR3e is a virulence factor that can also interact with BAK1 as a pathogen-associated molecular pattern (PAMP) to trigger immune responses. IMPORTANCE Based on the gene-for-gene model, research on the function of avirulence genes and resistance genes has had an unparalleled impact on breeding for resistance in most crops against individual pathogens. The soilborne fungal pathogen, Verticillium dahliae, is a major pathogen on many economically important crops. Currently, avr genes of the three races in V. dahliae have been identified, but the function of avr gene representing race 3 has not been described. We investigated the characteristics of VdR3e-mediated immunity and demonstrated that VdR3e acts as a PAMP to activate a variety of plant defense responses and induce plant cell death. We also demonstrated that the role of VdR3e in pathogenicity was host dependent. This is the first study to describe the immune and virulence functions of the avr gene from race 3 in V. dahliae, and we provide support for the identification of genes mediating resistance against race 3.},
}
@article {pmid37374993,
year = {2023},
author = {Caliskan-Aydogan, O and Alocilja, EC},
title = {A Review of Carbapenem Resistance in Enterobacterales and Its Detection Techniques.},
journal = {Microorganisms},
volume = {11},
number = {6},
pages = {},
pmid = {37374993},
issn = {2076-2607},
support = {1012975//United States Department of Agriculture/ ; 2022-67017-36982.//USDA-NIFA/ ; },
abstract = {Infectious disease outbreaks have caused thousands of deaths and hospitalizations, along with severe negative global economic impacts. Among these, infections caused by antimicrobial-resistant microorganisms are a major growing concern. The misuse and overuse of antimicrobials have resulted in the emergence of antimicrobial resistance (AMR) worldwide. Carbapenem-resistant Enterobacterales (CRE) are among the bacteria that need urgent attention globally. The emergence and spread of carbapenem-resistant bacteria are mainly due to the rapid dissemination of genes that encode carbapenemases through horizontal gene transfer (HGT). The rapid dissemination enables the development of host colonization and infection cases in humans who do not use the antibiotic (carbapenem) or those who are hospitalized but interacting with environments and hosts colonized with carbapenemase-producing (CP) bacteria. There are continuing efforts to characterize and differentiate carbapenem-resistant bacteria from susceptible bacteria to allow for the appropriate diagnosis, treatment, prevention, and control of infections. This review presents an overview of the factors that cause the emergence of AMR, particularly CRE, where they have been reported, and then, it outlines carbapenemases and how they are disseminated through humans, the environment, and food systems. Then, current and emerging techniques for the detection and surveillance of AMR, primarily CRE, and gaps in detection technologies are presented. This review can assist in developing prevention and control measures to minimize the spread of carbapenem resistance in the human ecosystem, including hospitals, food supply chains, and water treatment facilities. Furthermore, the development of rapid and affordable detection techniques is helpful in controlling the negative impact of infections caused by AMR/CRE. Since delays in diagnostics and appropriate antibiotic treatment for such infections lead to increased mortality rates and hospital costs, it is, therefore, imperative that rapid tests be a priority.},
}
@article {pmid37374909,
year = {2023},
author = {Harris, M and Fasolino, T and Ivankovic, D and Davis, NJ and Brownlee, N},
title = {Genetic Factors That Contribute to Antibiotic Resistance through Intrinsic and Acquired Bacterial Genes in Urinary Tract Infections.},
journal = {Microorganisms},
volume = {11},
number = {6},
pages = {},
pmid = {37374909},
issn = {2076-2607},
abstract = {The overprescribing and misuse of antibiotics have led to the rapid development of multidrug-resistant bacteria, such as those that cause UTIs. UTIs are the most common outpatient infections and are mainly caused by Escherichia coli and Klebsiella spp., although some Gram-positive bacteria, such as Pseudomonas aeruginosa, have been isolated in many cases. The rise of antimicrobial-resistant bacteria is a major public health concern, as it is predicted to lead to increased healthcare costs and poor patient outcomes and is expected to be the leading cause of global mortality by 2050. Antibiotic resistance among bacterial species can arise from a myriad of factors, including intrinsic and acquired resistance mechanisms, as well as mobile genetic elements, such as transposons, integrons, and plasmids. Plasmid-mediated resistance is of major concern as drug-resistance genes can quickly and efficiently spread across bacterial species via horizontal gene transfer. The emergence of extended-spectrum β-lactamases (ESBLs) such as NDM-1, OXA, KPC, and CTX-M family members has conferred resistance to many commonly used antibiotics in the treatment of UTIs, including penicillins, carbapenems, cephalosporins, and sulfamethoxazole. This review will focus on plasmid-mediated bacterial genes, especially those that encode ESBLs, and how they contribute to antibiotic resistance. Early clinical detection of these genes in patient samples will provide better treatment options and reduce the threat of antibiotic resistance.},
}
@article {pmid37372483,
year = {2023},
author = {Shymialevich, D and Wójcicki, M and Świder, O and Średnicka, P and Sokołowska, B},
title = {Characterization and Genome Study of a Newly Isolated Temperate Phage Belonging to a New Genus Targeting Alicyclobacillus acidoterrestris.},
journal = {Genes},
volume = {14},
number = {6},
pages = {},
pmid = {37372483},
issn = {2073-4425},
mesh = {*Alicyclobacillus/genetics ; *Bacteriophages/genetics ; Hot Temperature ; Temperature ; },
abstract = {The spoilage of juices by Alicyclobacillus spp. remains a serious problem in industry and leads to economic losses. Compounds such as guaiacol and halophenols, which are produced by Alicyclobacillus, create undesirable flavors and odors and, thus, decrease the quality of juices. The inactivation of Alicyclobacillus spp. constitutes a challenge because it is resistant to environmental factors, such as high temperatures, and active acidity. However, the use of bacteriophages seems to be a promising approach. In this study, we aimed to isolate and comprehensively characterize a novel bacteriophage targeting Alicyclobacillus spp. The Alicyclobacillus phage strain KKP 3916 was isolated from orchard soil against the Alicyclobacillus acidoterrestris strain KKP 3133. The bacterial host's range and the effect of phage addition at different rates of multiplicity of infections (MOIs) on the host's growth kinetics were determined using a Bioscreen C Pro growth analyzer. The Alicyclobacillus phage strain KKP 3916, retained its activity in a wide range of temperatures (from 4 °C to 30 °C) and active acidity values (pH from 3 to 11). At 70 °C, the activity of the phage decreased by 99.9%. In turn, at 80 °C, no activity against the bacterial host was observed. Thirty minutes of exposure to UV reduced the activity of the phages by almost 99.99%. Based on transmission-electron microscopy (TEM) and whole-genome sequencing (WGS) analyses, the Alicyclobacillus phage strain KKP 3916 was classified as a tailed bacteriophage. The genomic sequencing revealed that the newly isolated phage had linear double-stranded DNA (dsDNA) with sizes of 120 bp and 131 bp and 40.3% G+C content. Of the 204 predicted proteins, 134 were of unknown function, while the remainder were annotated as structural, replication, and lysis proteins. No genes associated with antibiotic resistance were found in the genome of the newly isolated phage. However, several regions, including four associated with integration into the bacterial host genome and excisionase, were identified, which indicates the temperate (lysogenic) life cycle of the bacteriophage. Due to the risk of its potential involvement in horizontal gene transfer, this phage is not an appropriate candidate for further research on its use in food biocontrol. To the best of our knowledge, this is the first article on the isolation and whole-genome analysis of the Alicyclobacillus-specific phage.},
}
@article {pmid37372055,
year = {2023},
author = {Gheibzadeh, MS and Manyumwa, CV and Tastan Bishop, &#xd6; and Shahbani Zahiri, H and Parkkila, S and Zolfaghari Emameh, R},
title = {Genome Study of α-, β-, and γ-Carbonic Anhydrases from the Thermophilic Microbiome of Marine Hydrothermal Vent Ecosystems.},
journal = {Biology},
volume = {12},
number = {6},
pages = {},
pmid = {37372055},
issn = {2079-7737},
support = {737//National Institute of Genetic Engineering and Biotechnology/ ; M/75137//Ministry of Science, Research and Technology/ ; 111212//National Research Foundation/ ; },
abstract = {Carbonic anhydrases (CAs) are metalloenzymes that can help organisms survive in hydrothermal vents by hydrating carbon dioxide (CO2). In this study, we focus on alpha (α), beta (β), and gamma (γ) CAs, which are present in the thermophilic microbiome of marine hydrothermal vents. The coding genes of these enzymes can be transferred between hydrothermal-vent organisms via horizontal gene transfer (HGT), which is an important tool in natural biodiversity. We performed big data mining and bioinformatics studies on α-, β-, and γ-CA coding genes from the thermophilic microbiome of marine hydrothermal vents. The results showed a reasonable association between thermostable α-, β-, and γ-CAs in the microbial population of the hydrothermal vents. This relationship could be due to HGT. We found evidence of HGT of α- and β-CAs between Cycloclasticus sp., a symbiont of Bathymodiolus heckerae, and an endosymbiont of Riftia pachyptila via Integrons. Conversely, HGT of β-CA genes from the endosymbiont Tevnia jerichonana to the endosymbiont Riftia pachyptila was detected. In addition, Hydrogenovibrio crunogenus SP-41 contains a β-CA gene on genomic islands (GIs). This gene can be transferred by HGT to Hydrogenovibrio sp. MA2-6, a methanotrophic endosymbiont of Bathymodiolus azoricus, and a methanotrophic endosymbiont of Bathymodiolus puteoserpentis. The endosymbiont of R. pachyptila has a γ-CA gene in the genome. If α- and β-CA coding genes have been derived from other microorganisms, such as endosymbionts of T. jerichonana and Cycloclasticus sp. as the endosymbiont of B. heckerae, through HGT, the theory of the necessity of thermostable CA enzymes for survival in the extreme ecosystem of hydrothermal vents is suggested and helps the conservation of microbiome natural diversity in hydrothermal vents. These harsh ecosystems, with their integral players, such as HGT and endosymbionts, significantly impact the enrichment of life on Earth and the carbon cycle in the ocean.},
}
@article {pmid37369847,
year = {2023},
author = {Steenwyk, JL and Li, Y and Zhou, X and Shen, XX and Rokas, A},
title = {Incongruence in the phylogenomics era.},
journal = {Nature reviews. Genetics},
volume = {24},
number = {12},
pages = {834-850},
pmid = {37369847},
issn = {1471-0064},
support = {R01 AI153356/AI/NIAID NIH HHS/United States ; },
mesh = {Phylogeny ; *Biological Evolution ; *Genome ; Evolution, Molecular ; Hybridization, Genetic ; },
abstract = {Genome-scale data and the development of novel statistical phylogenetic approaches have greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its branches. However, incongruence - the inference of conflicting evolutionary histories - remains pervasive in phylogenomic data, hampering our ability to reconstruct and interpret the tree of life. Biological factors, such as incomplete lineage sorting, horizontal gene transfer, hybridization, introgression, recombination and convergent molecular evolution, can lead to gene phylogenies that differ from the species tree. In addition, analytical factors, including stochastic, systematic and treatment errors, can drive incongruence. Here, we review these factors, discuss methodological advances to identify and handle incongruence, and highlight avenues for future research.},
}
@article {pmid37369704,
year = {2023},
author = {Huang, J and Dai, X and Wu, Z and Hu, X and Sun, J and Tang, Y and Zhang, W and Han, P and Zhao, J and Liu, G and Wang, X and Mao, S and Wang, Y and Call, DR and Liu, J and Wang, L},
title = {Conjugative transfer of streptococcal prophages harboring antibiotic resistance and virulence genes.},
journal = {The ISME journal},
volume = {17},
number = {9},
pages = {1467-1481},
pmid = {37369704},
issn = {1751-7370},
mesh = {Animals ; *Prophages/genetics ; Virulence/genetics ; Streptococcus/genetics ; *Anti-Infective Agents ; Drug Resistance, Microbial ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Plasmids ; Conjugation, Genetic ; },
abstract = {Prophages play important roles in the transduction of various functional traits, including virulence factors, but remain debatable in harboring and transmitting antimicrobial resistance genes (ARGs). Herein we characterize a prevalent family of prophages in Streptococcus, designated SMphages, which harbor twenty-five ARGs that collectively confer resistance to ten antimicrobial classes, including vanG-type vancomycin resistance locus and oxazolidinone resistance gene optrA. SMphages integrate into four chromosome attachment sites by utilizing three types of integration modules and undergo excision in response to phage induction. Moreover, we characterize four subtypes of Alp-related surface proteins within SMphages, the lethal effects of which are extensively validated in cell and animal models. SMphages transfer via high-frequency conjugation that is facilitated by integrative and conjugative elements from either donors or recipients. Our findings explain the widespread of SMphages and the rapid dissemination of ARGs observed in members of the Streptococcus genus.},
}
@article {pmid37368881,
year = {2023},
author = {Tanabe, TS and Grosser, M and Hahn, L and Kümpel, C and Hartenfels, H and Vtulkin, E and Flegler, W and Dahl, C},
title = {Identification of a novel lipoic acid biosynthesis pathway reveals the complex evolution of lipoate assembly in prokaryotes.},
journal = {PLoS biology},
volume = {21},
number = {6},
pages = {e3002177},
pmid = {37368881},
issn = {1545-7885},
mesh = {*Thioctic Acid/genetics/metabolism ; Peptide Synthases/genetics/metabolism ; Phylogeny ; Bacterial Proteins/metabolism ; Sulfur ; },
abstract = {Lipoic acid is an essential biomolecule found in all domains of life and is involved in central carbon metabolism and dissimilatory sulfur oxidation. The machineries for lipoate assembly in mitochondria and chloroplasts of higher eukaryotes, as well as in the apicoplasts of some protozoa, are all of prokaryotic origin. Here, we provide experimental evidence for a novel lipoate assembly pathway in bacteria based on a sLpl(AB) lipoate:protein ligase, which attaches octanoate or lipoate to apo-proteins, and 2 radical SAM proteins, LipS1 and LipS2, which work together as lipoyl synthase and insert 2 sulfur atoms. Extensive homology searches combined with genomic context analyses allowed us to precisely distinguish between the new and established pathways and map them on the tree of life. This not only revealed a much wider distribution of lipoate biogenesis systems than expected, in particular, the novel sLpl(AB)-LipS1/S2 pathway, and indicated a highly modular nature of the enzymes involved, with unforeseen combinations, but also provided a new framework for the evolution of lipoate assembly. Our results show that dedicated machineries for both de novo lipoate biogenesis and scavenging from the environment were implemented early in evolution and that their distribution in the 2 prokaryotic domains was shaped by a complex network of horizontal gene transfers, acquisition of additional genes, fusions, and losses. Our large-scale phylogenetic analyses identify the bipartite archaeal LplAB ligase as the ancestor of the bacterial sLpl(AB) proteins, which were obtained by horizontal gene transfer. LipS1/S2 have a more complex evolutionary history with multiple of such events but probably also originated in the domain archaea.},
}
@article {pmid37368681,
year = {2023},
author = {Boss, L and Kędzierska, B},
title = {Bacterial Toxin-Antitoxin Systems' Cross-Interactions-Implications for Practical Use in Medicine and Biotechnology.},
journal = {Toxins},
volume = {15},
number = {6},
pages = {},
pmid = {37368681},
issn = {2072-6651},
mesh = {*Bacterial Toxins/metabolism ; Prospective Studies ; *Toxin-Antitoxin Systems/genetics ; Bacteria/genetics/metabolism ; *Antitoxins/genetics ; Biotechnology ; Bacterial Proteins/genetics ; },
abstract = {Toxin-antitoxin (TA) systems are widely present in bacterial genomes. They consist of stable toxins and unstable antitoxins that are classified into distinct groups based on their structure and biological activity. TA systems are mostly related to mobile genetic elements and can be easily acquired through horizontal gene transfer. The ubiquity of different homologous and non-homologous TA systems within a single bacterial genome raises questions about their potential cross-interactions. Unspecific cross-talk between toxins and antitoxins of non-cognate modules may unbalance the ratio of the interacting partners and cause an increase in the free toxin level, which can be deleterious to the cell. Moreover, TA systems can be involved in broadly understood molecular networks as transcriptional regulators of other genes' expression or modulators of cellular mRNA stability. In nature, multiple copies of highly similar or identical TA systems are rather infrequent and probably represent a transition stage during evolution to complete insulation or decay of one of them. Nevertheless, several types of cross-interactions have been described in the literature to date. This implies a question of the possibility and consequences of the TA system cross-interactions, especially in the context of the practical application of the TA-based biotechnological and medical strategies, in which such TAs will be used outside their natural context, will be artificially introduced and induced in the new hosts. Thus, in this review, we discuss the prospective challenges of system cross-talks in the safety and effectiveness of TA system usage.},
}
@article {pmid37367481,
year = {2023},
author = {Fakhar, AZ and Liu, J and Pajerowska-Mukhtar, KM and Mukhtar, MS},
title = {The Lost and Found: Unraveling the Functions of Orphan Genes.},
journal = {Journal of developmental biology},
volume = {11},
number = {2},
pages = {},
pmid = {37367481},
issn = {2221-3759},
support = {IOS-2038872//National Science Foundation/ ; },
abstract = {Orphan Genes (OGs) are a mysterious class of genes that have recently gained significant attention. Despite lacking a clear evolutionary history, they are found in nearly all living organisms, from bacteria to humans, and they play important roles in diverse biological processes. The discovery of OGs was first made through comparative genomics followed by the identification of unique genes across different species. OGs tend to be more prevalent in species with larger genomes, such as plants and animals, and their evolutionary origins remain unclear but potentially arise from gene duplication, horizontal gene transfer (HGT), or de novo origination. Although their precise function is not well understood, OGs have been implicated in crucial biological processes such as development, metabolism, and stress responses. To better understand their significance, researchers are using a variety of approaches, including transcriptomics, functional genomics, and molecular biology. This review offers a comprehensive overview of the current knowledge of OGs in all domains of life, highlighting the possible role of dark transcriptomics in their evolution. More research is needed to fully comprehend the role of OGs in biology and their impact on various biological processes.},
}
@article {pmid37367332,
year = {2023},
author = {Fallon, AM and Carroll, EM},
title = {Virus-like Particles from Wolbachia-Infected Cells May Include a Gene Transfer Agent.},
journal = {Insects},
volume = {14},
number = {6},
pages = {},
pmid = {37367332},
issn = {2075-4450},
abstract = {Wolbachia are obligate intracellular bacteria that occur in insects and filarial worms. Strains that infect insects have genomes that encode mobile genetic elements, including diverse lambda-like prophages called Phage WO. Phage WO packages an approximately 65 kb viral genome that includes a unique eukaryotic association module, or EAM, that encodes unusually large proteins thought to mediate interactions between the bacterium, its virus, and the eukaryotic host cell. The Wolbachia supergroup B strain, wStri from the planthopper Laodelphax striatellus, produces phage-like particles that can be recovered from persistently infected mosquito cells by ultracentrifugation. Illumina sequencing, assembly, and manual curation of DNA from two independent preparations converged on an identical 15,638 bp sequence that encoded packaging, assembly, and structural proteins. The absence of an EAM and regulatory genes defined for Phage WO from the wasp, Nasonia vitripennis, was consistent with the possibility that the 15,638 bp sequence represents an element related to a gene transfer agent (GTA), characterized by a signature head-tail region encoding structural proteins that package host chromosomal DNA. Future investigation of GTA function will be supported by the improved recovery of physical particles, electron microscopic examination of potential diversity among particles, and rigorous examination of DNA content by methods independent of sequence assembly.},
}
@article {pmid37360531,
year = {2023},
author = {Gaballa, A and Wiedmann, M and Carroll, LM},
title = {More than mcr: canonical plasmid- and transposon-encoded mobilized colistin resistance genes represent a subset of phosphoethanolamine transferases.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1060519},
pmid = {37360531},
issn = {2235-2988},
mesh = {Humans ; *Colistin/pharmacology ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; Transferases/genetics ; *Escherichia coli Proteins/genetics/metabolism ; Microbial Sensitivity Tests ; },
abstract = {Mobilized colistin resistance genes (mcr) may confer resistance to the last-resort antimicrobial colistin and can often be transmitted horizontally. mcr encode phosphoethanolamine transferases (PET), which are closely related to chromosomally encoded, intrinsic lipid modification PET (i-PET; e.g., EptA, EptB, CptA). To gain insight into the evolution of mcr within the context of i-PET, we identified 69,814 MCR-like proteins present across 256 bacterial genera (obtained by querying known MCR family representatives against the National Center for Biotechnology Information [NCBI] non-redundant protein database via protein BLAST). We subsequently identified 125 putative novel mcr-like genes, which were located on the same contig as (i) ≥1 plasmid replicon and (ii) ≥1 additional antimicrobial resistance gene (obtained by querying the PlasmidFinder database and NCBI's National Database of Antibiotic Resistant Organisms, respectively, via nucleotide BLAST). At 80% amino acid identity, these putative novel MCR-like proteins formed 13 clusters, five of which represented putative novel MCR families. Sequence similarity and a maximum likelihood phylogeny of mcr, putative novel mcr-like, and ipet genes indicated that sequence similarity was insufficient to discriminate mcr from ipet genes. A mixed-effect model of evolution (MEME) indicated that site- and branch-specific positive selection played a role in the evolution of alleles within the mcr-2 and mcr-9 families. MEME suggested that positive selection played a role in the diversification of several residues in structurally important regions, including (i) a bridging region that connects the membrane-bound and catalytic periplasmic domains, and (ii) a periplasmic loop juxtaposing the substrate entry tunnel. Moreover, eptA and mcr were localized within different genomic contexts. Canonical eptA genes were typically chromosomally encoded in an operon with a two-component regulatory system or adjacent to a TetR-type regulator. Conversely, mcr were represented by single-gene operons or adjacent to pap2 and dgkA, which encode a PAP2 family lipid A phosphatase and diacylglycerol kinase, respectively. Our data suggest that eptA can give rise to "colistin resistance genes" through various mechanisms, including mobilization, selection, and diversification of genomic context and regulatory pathways. These mechanisms likely altered gene expression levels and enzyme activity, allowing bona fide eptA to evolve to function in colistin resistance.},
}
@article {pmid37360032,
year = {2023},
author = {Fleming, JF and Valero-Gracia, A and Struck, TH},
title = {Identifying and addressing methodological incongruence in phylogenomics: A review.},
journal = {Evolutionary applications},
volume = {16},
number = {6},
pages = {1087-1104},
pmid = {37360032},
issn = {1752-4571},
abstract = {The availability of phylogenetic data has greatly expanded in recent years. As a result, a new era in phylogenetic analysis is dawning-one in which the methods we use to analyse and assess our data are the bottleneck to producing valuable phylogenetic hypotheses, rather than the need to acquire more data. This makes the ability to accurately appraise and evaluate new methods of phylogenetic analysis and phylogenetic artefact identification more important than ever. Incongruence in phylogenetic reconstructions based on different datasets may be due to two major sources: biological and methodological. Biological sources comprise processes like horizontal gene transfer, hybridization and incomplete lineage sorting, while methodological ones contain falsely assigned data or violations of the assumptions of the underlying model. While the former provides interesting insights into the evolutionary history of the investigated groups, the latter should be avoided or minimized as best as possible. However, errors introduced by methodology must first be excluded or minimized to be able to conclude that biological sources are the cause. Fortunately, a variety of useful tools exist to help detect such misassignments and model violations and to apply ameliorating measurements. Still, the number of methods and their theoretical underpinning can be overwhelming and opaque. Here, we present a practical and comprehensive review of recent developments in techniques to detect artefacts arising from model violations and poorly assigned data. The advantages and disadvantages of the different methods to detect such misleading signals in phylogenetic reconstructions are also discussed. As there is no one-size-fits-all solution, this review can serve as a guide in choosing the most appropriate detection methods depending on both the actual dataset and the computational power available to the researcher. Ultimately, this informed selection will have a positive impact on the broader field, allowing us to better understand the evolutionary history of the group of interest.},
}
@article {pmid37358464,
year = {2023},
author = {Binsker, U and Oelgeschläger, K and Neumann, B and Werner, G and Käsbohrer, A and Hammerl, JA},
title = {Genomic Evidence of mcr-1.26 IncX4 Plasmid Transmission between Poultry and Humans.},
journal = {Microbiology spectrum},
volume = {11},
number = {4},
pages = {e0101523},
pmid = {37358464},
issn = {2165-0497},
mesh = {Animals ; Humans ; *Colistin ; Escherichia coli ; Anti-Bacterial Agents/pharmacology ; Poultry ; *Escherichia coli Proteins/genetics ; Plasmids/genetics ; Genomics ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; },
abstract = {Colistin is still commonly used and misused in animal husbandry driving the evolution and dissemination of transmissible plasmid-mediated colistin resistance (mcr). mcr-1.26 is a rare variant and, so far, has only been detected in Escherichia coli obtained from a hospitalized patient in Germany in 2018. Recently, it was also notified in fecal samples from a pigeon in Lebanon. We report on the presence of 16 colistin-resistant, mcr-1.26-carrying extended-spectrum beta-lactamase (ESBL)-producing and commensal E. coli isolated from poultry samples in Germany, of which retail meat was the most common source. Short- and long-read genome sequencing and bioinformatic analyses revealed the location of mcr-1.26 exclusively on IncX4 plasmids. mcr-1.26 was identified on two different IncX4 plasmid types of 33 and 38 kb and was associated with an IS6-like element. Based on the genetic diversity of E. coli isolates, transmission of the mcr-1.26 resistance determinant is mediated by horizontal transfer of IncX4 plasmids, as confirmed by conjugation experiments. Notably, the 33-kb plasmid is highly similar to the plasmid reported for the human sample. Furthermore, we identified the acquisition of an additional beta-lactam resistance linked to a Tn2 transposon on the mcr-1.26 IncX4 plasmids of three isolates, indicating progressive plasmid evolution. Overall, all described mcr-1.26-carrying plasmids contain a highly conserved core genome necessary for colistin resistance development, transmission, replication, and maintenance. Variations in the plasmid sequences are mainly caused by the acquisition of insertion sequences and alteration in intergenic sequences or genes of unknown function. IMPORTANCE Evolutionary events causing the emergence of new resistances/variants are usually rare and challenging to predict. Conversely, common transmission events of widespread resistance determinants are quantifiable and predictable. One such example is the transmissible plasmid-mediated colistin resistance. The main determinant, mcr-1, has been notified in 2016 but has successfully established itself in multiple plasmid backbones in diverse bacterial species across all One Health sectors. So far, 34 variants of mcr-1 are described, of which some can be used for epidemiological tracing-back analysis to identify the origin and transmission dynamics of these genes. Here, we report the presence of the rare mcr-1.26 gene in E. coli isolated from poultry since 2014. Based on the temporal occurrence and high similarity of the plasmids between poultry and human isolates, our study provides first indications for poultry husbandry as the primary source of mcr-1.26 and its transmission between different niches.},
}
@article {pmid37353919,
year = {2023},
author = {Frazão, N and Gordo, I},
title = {Ecotype formation and prophage domestication during gut bacterial evolution.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {45},
number = {8},
pages = {e2300063},
doi = {10.1002/bies.202300063},
pmid = {37353919},
issn = {1521-1878},
mesh = {Animals ; Prophages/genetics ; *Gastrointestinal Microbiome ; Domestication ; Ecotype ; Lysogeny ; *Bacteriophages/genetics ; Bacteria/genetics ; Mammals ; },
abstract = {How much bacterial evolution occurs in our intestines and which factors control it are currently burning questions. The formation of new ecotypes, some of which capable of coexisting for long periods of time, is highly likely in our guts. Horizontal gene transfer driven by temperate phages that can perform lysogeny is also widespread in mammalian intestines. Yet, the roles of mutation and especially lysogeny as key drivers of gut bacterial adaptation remain poorly understood. The mammalian gut contains hundreds of bacterial species, each with many strains and ecotypes, whose abundance varies along the lifetime of a host. A continuous high input of mutations and horizontal gene transfer events mediated by temperate phages drives that diversity. Future experiments to study the interaction between mutations that cause adaptation in microbiomes and lysogenic events with different costs and benefits will be key to understand the dynamic microbiomes of mammals. Also see the video abstract here: https://youtu.be/Zjqsiyb5Pk0.},
}
@article {pmid37350784,
year = {2023},
author = {Fujihara, H and Hirose, J and Suenaga, H},
title = {Evolution of genetic architecture and gene regulation in biphenyl/PCB-degrading bacteria.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1168246},
pmid = {37350784},
issn = {1664-302X},
abstract = {A variety of bacteria in the environment can utilize xenobiotic compounds as a source of carbon and energy. The bacterial strains degrading xenobiotics are suitable models to investigate the adaptation and evolutionary processes of bacteria because they appear to have emerged relatively soon after the release of these compounds into the natural environment. Analyses of bacterial genome sequences indicate that horizontal gene transfer (HGT) is the most important contributor to the bacterial evolution of genetic architecture. Further, host bacteria that can use energy effectively by controlling the expression of organized gene clusters involved in xenobiotic degradation will have a survival advantage in harsh xenobiotic-rich environments. In this review, we summarize the current understanding of evolutionary mechanisms operative in bacteria, with a focus on biphenyl/PCB-degrading bacteria. We then discuss metagenomic approaches that are useful for such investigation.},
}
@article {pmid37348862,
year = {2023},
author = {Moradigaravand, D and Li, L and Dechesne, A and Nesme, J and de la Cruz, R and Ahmad, H and Banzhaf, M and Sørensen, SJ and Smets, BF and Kreft, JU},
title = {Plasmid permissiveness of wastewater microbiomes can be predicted from 16S rRNA sequences by machine learning.},
journal = {Bioinformatics (Oxford, England)},
volume = {39},
number = {7},
pages = {},
pmid = {37348862},
issn = {1367-4811},
support = {MR/P028195/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Wastewater ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Permissiveness ; Plasmids/genetics ; *Microbiota ; Gene Transfer, Horizontal ; },
abstract = {MOTIVATION: Wastewater treatment plants (WWTPs) harbor a dense and diverse microbial community. They constantly receive antimicrobial residues and resistant strains, and therefore provide conditions for horizontal gene transfer (HGT) of antimicrobial resistance (AMR) determinants. This facilitates the transmission of clinically important genes between, e.g. enteric and environmental bacteria, and vice versa. Despite the clinical importance, tools for predicting HGT remain underdeveloped.<br><br>RESULTS: In this study, we examined to which extent water cycle microbial community composition, as inferred by partial 16S rRNA gene sequences, can predict plasmid permissiveness, i.e. the ability of cells to receive a plasmid through conjugation, based on data from standardized filter mating assays using fluorescent bio-reporter plasmids. We leveraged a range of machine learning models for predicting the permissiveness for each taxon in the community, representing the range of hosts a plasmid is able to transfer to, for three broad host-range resistance IncP plasmids (pKJK5, pB10, and RP4). Our results indicate that the predicted permissiveness from the best performing model (random forest) showed a moderate-to-strong average correlation of 0.49 for pB10 [95% confidence interval (CI): 0.44-0.55], 0.43 for pKJK5 (0.95% CI: 0.41-0.49), and 0.53 for RP4 (0.95% CI: 0.48-0.57) with the experimental permissiveness in the unseen test dataset. Predictive phylogenetic signals occurred despite the broad host-range nature of these plasmids. Our results provide a framework that contributes to the assessment of the risk of AMR pollution in wastewater systems.<br><br>The predictive tool is available as an application at https://github.com/DaneshMoradigaravand/PlasmidPerm.},
}
@article {pmid37345922,
year = {2023},
author = {Bosch, DE and Abbasian, R and Parajuli, B and Peterson, SB and Mougous, JD},
title = {Structural disruption of Ntox15 nuclease effector domains by immunity proteins protects against type VI secretion system intoxication in Bacteroidales.},
journal = {mBio},
volume = {14},
number = {4},
pages = {e0103923},
pmid = {37345922},
issn = {2150-7511},
support = {K08 AI159619/AI/NIAID NIH HHS/United States ; P30 GM124169/GM/NIGMS NIH HHS/United States ; R01 AI080609/AI/NIAID NIH HHS/United States ; S10 OD021832/OD/NIH HHS/United States ; },
mesh = {*Type VI Secretion Systems/metabolism/genetics ; *Bacterial Proteins/genetics/metabolism/chemistry/immunology ; Humans ; Gene Transfer, Horizontal ; },
abstract = {Bacteroidales use type VI secretion systems (T6SS) to competitively colonize and persist in the colon. We identify a horizontally transferred T6SS with Ntox15 family nuclease effector (Tde1) that mediates interbacterial antagonism among Bacteroidales, including several derived from a single human donor. Expression of cognate (Tdi1) or orphan immunity proteins in acquired interbacterial defense systems protects against Tde1-dependent attack. We find that immunity protein interaction induces a large effector conformational change in Tde nucleases, disrupting the active site and altering the DNA-binding site. Crystallographic snapshots of isolated Tde1, the Tde1/Tdi1 complex, and homologs from Phocaeicola vulgatus (Tde2/Tdi2) illustrate a conserved mechanism of immunity inserting into the central core of Tde, splitting the nuclease fold into two subdomains. The Tde/Tdi interface and immunity mechanism are distinct from all other polymorphic toxin-immunity interactions of known structure. Bacteroidales abundance has been linked to inflammatory bowel disease activity in prior studies, and we demonstrate that Tde and T6SS structural genes are each enriched in fecal metagenomes from ulcerative colitis subjects. Genetically mobile Tde1-encoding T6SS in Bacteroidales mediate competitive growth and may be involved in inflammatory bowel disease. Broad immunity is conferred by Tdi1 homologs through a fold-disrupting mechanism unique among polymorphic effector-immunity pairs of known structure. IMPORTANCE Bacteroidales are related to inflammatory bowel disease severity and progression. We identify type VI secretion system (T6SS) nuclease effectors (Tde) which are enriched in ulcerative colitis and horizontally transferred on mobile genetic elements. Tde-encoding T6SSs mediate interbacterial competition. Orphan and cognate immunity proteins (Tdi) prevent intoxication by multiple Tde through a new mechanism among polymorphic toxin systems. Tdi inserts into the effector central core, splitting Ntox15 into two subdomains and disrupting the active site. This mechanism may allow for evolutionary diversification of the Tde/Tdi interface as observed in colicin nuclease-immunity interactions, promoting broad neutralization of Tde by orphan Tdi. Tde-dependent T6SS interbacterial antagonism may contribute to Bacteroidales diversity in the context of ulcerative colitis.},
}
@article {pmid37339822,
year = {2023},
author = {Arkhipova, IR and Yushenova, IA and Rodriguez, F},
title = {Shaping eukaryotic epigenetic systems by horizontal gene transfer.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {45},
number = {7},
pages = {e2200232},
pmid = {37339822},
issn = {1521-1878},
support = {R01 GM111917/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Eukaryota/genetics/metabolism ; *Gene Transfer, Horizontal ; DNA Methylation/genetics ; Epigenesis, Genetic ; Methyltransferases/genetics ; },
abstract = {DNA methylation constitutes one of the pillars of epigenetics, relying on covalent bonds for addition and/or removal of chemically distinct marks within the major groove of the double helix. DNA methyltransferases, enzymes which introduce methyl marks, initially evolved in prokaryotes as components of restriction-modification systems protecting host genomes from bacteriophages and other invading foreign DNA. In early eukaryotic evolution, DNA methyltransferases were horizontally transferred from bacteria into eukaryotes several times and independently co-opted into epigenetic regulatory systems, primarily via establishing connections with the chromatin environment. While C5-methylcytosine is the cornerstone of plant and animal epigenetics and has been investigated in much detail, the epigenetic role of other methylated bases is less clear. The recent addition of N4-methylcytosine of bacterial origin as a metazoan DNA modification highlights the prerequisites for foreign gene co-option into the host regulatory networks, and challenges the existing paradigms concerning the origin and evolution of eukaryotic regulatory systems.},
}
@article {pmid37339743,
year = {2023},
author = {Takeuchi, N and Hamada-Zhu, S and Suzuki, H},
title = {Prophages and plasmids can display opposite trends in the types of accessory genes they carry.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {2001},
pages = {20231088},
pmid = {37339743},
issn = {1471-2954},
mesh = {*Prophages/genetics ; Plasmids ; Escherichia coli/genetics ; *Bacteriophages ; Virulence Factors/genetics ; Anti-Bacterial Agents ; },
abstract = {Mobile genetic elements (MGEs), such as phages and plasmids, often possess accessory genes encoding bacterial functions, facilitating bacterial evolution. Are there rules governing the arsenal of accessory genes MGEs carry? If such rules exist, they might be reflected in the types of accessory genes different MGEs carry. To test this hypothesis, we compare prophages and plasmids with respect to the frequencies at which they carry antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in the genomes of 21 pathogenic bacterial species using public databases. Our results indicate that prophages tend to carry VFGs more frequently than ARGs in three species, whereas plasmids tend to carry ARGs more frequently than VFGs in nine species, relative to genomic backgrounds. In Escherichia coli, where this prophage-plasmid disparity is detected, prophage-borne VFGs encode a much narrower range of functions than do plasmid-borne VFGs, typically involved in damaging host cells or modulating host immunity. In the species where the above disparity is not detected, ARGs and VFGs are barely found in prophages and plasmids. These results indicate that MGEs can differentiate in the types of accessory genes they carry depending on their infection strategies, suggesting a rule governing horizontal gene transfer mediated by MGEs.},
}
@article {pmid37337195,
year = {2023},
author = {Zhang, Y and Miao, J and Zhang, N and Wang, X and Li, Z and Richard, OA and Li, B},
title = {The analysis of the function, diversity, and evolution of the Bacillus phage genome.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {170},
pmid = {37337195},
issn = {1471-2180},
mesh = {*Bacillus Phages/genetics ; Genome, Viral ; *Bacteriophages/genetics ; Prophages/genetics ; Mutation ; Evolution, Molecular ; },
abstract = {BACKGROUND: Phages play a pivotal role in the evolution of microbial populations. The interactions between phages and their hosts are complex and may vary in response to host physiology and environmental conditions. Here, we have selected the genomes of some representative Bacillus prophages and lysosomes from the NCBI database for evolutionary analysis. We explored their evolutionary relationships and analyzed the protein information encoded by hundreds of Bacillus phages.<br><br>RESULTS: We obtained the following conclusions: First, Bacillus phages carried some known functional gene fragments and a large number of unknown functional gene fragments, which might have an important impact on Bacillus populations, such as the formation of spores and biofilms and the transmission of virulence factors. Secondly, the Bacillus phage genome showed diversity, with a clear genome boundary between Bacillus prophages and Bacillus lytic phages. Furthermore, genetic mutations, sequence losses, duplications, and host-switching have occurred during the evolution of the Bacillus phage, resulting in low genome similarity between the Bacillus phages. Finally, the lysis module played an important influence on the process of Bacillus phage cross-species infestation.<br><br>CONCLUSIONS: This study systematically described their protein function, diversity, and genome evolution, and the results of this study provide a basis for evolutionary diversity, horizontal gene transfer and co-evolution with the host in Bacillus phages.},
}
@article {pmid37336594,
year = {2023},
author = {Shafiq, M and Bilal, H and Permana, B and Xu, D and Cai, G and Li, X and Zeng, M and Yuan, Y and Jiao, X and Yao, F},
title = {Characterization of antibiotic resistance genes and mobile elements in extended-spectrum β-lactamase-producing Escherichia coli strains isolated from hospitalized patients in Guangdong, China.},
journal = {Journal of applied microbiology},
volume = {134},
number = {7},
pages = {},
doi = {10.1093/jambio/lxad125},
pmid = {37336594},
issn = {1365-2672},
support = {42150410383//National Natural Science Foundation of China/ ; 2020LKSFG03E//Li Ka Shing Foundation Cross-Disciplinary Research/ ; },
mesh = {Humans ; *Escherichia coli ; Anti-Bacterial Agents/pharmacology ; beta-Lactamases/genetics ; *Escherichia coli Infections/epidemiology ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {AIM: This study aimed to investigate the high-resolution phenotypic and genotypic characterization of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli strains isolated from hospitalized patients to explore the resistance genes and mobile genetic elements (MGEs) involved in horizontal dissemination.<br><br>METHODS: Between May and September 2021, a total of 216 ESBL-producing E. coli isolates were recovered from multiple departments. The identification of strains was performed using MALDI-TOF mass spectrometry and PCR, while antibiotic susceptibility testing was carried out using the Vitek 2 COMPACT system to determine resistance patterns, while PCR was used to detect different resistance genes and MGEs. In addition, a conjugation assay was performed to investigate the horizontal gene transfer of resistance genes. Selected isolates underwent whole-genome sequencing (WGS) using the Illumina MiSeq platform.<br><br>RESULTS: A total of 216 out of 409 E. coli isolates recovered from a tertiary hospital were observed to be ESBL-producing, giving a carriage rate of 52.8%, as determined by phenotypic screening. The most frequent sources of ESBL-producing E. coli isolates were urine (129/216, 59.72%) and blood (50/216, 23.14%). The most prevalent ESBL genes identified were blaCTX-M (60.18%), blaTEM (40.27%), and blaSHV (18.05%). Three E. coli isolates were found to carry the genes blaNDM, mcr-1, and fosA3 genes. The most prevalent MGEs were IS26 (95.37%), Int (87.03%), and IncFIB (76.85%). WGS analysis of eight MDR E. coli strains revealed that these isolates belonged to eight different sequence types (STs) and serotypes and were found to harbor multiple plasmid replicons and virulence factors.<br><br>CONCLUSION: This study highlights a high incidence of antibiotic resistance genes and MGEs associated with the dissemination of ESBLs and other resistance genes.},
}
@article {pmid37336333,
year = {2023},
author = {Xia, Y and Zuo, S and Zheng, Y and Yang, W and Tang, X and Ke, X and Zhuo, Q and Yang, X and Li, Y and Liu, H and Fan, B},
title = {Extended one generation reproductive toxicity study and effect on gut flora of genetically modified rice rich in β-carotene in wistar rats.},
journal = {Reproductive toxicology (Elmsford, N.Y.)},
volume = {119},
number = {},
pages = {108424},
doi = {10.1016/j.reprotox.2023.108424},
pmid = {37336333},
issn = {1873-1708},
mesh = {Rats ; Animals ; Rats, Wistar ; *beta Carotene ; Plants, Genetically Modified/genetics/adverse effects ; *Gastrointestinal Microbiome ; Reproduction ; },
abstract = {To evaluate the reproductive toxicity of gene modified rice generated by introducing phytoene synthase (Psy) and bacterial phytoene desaturase (CrtI) from maize and Erwinia uredovora, Wistar rats were allocated into 3 groups and fed with Psy and CrtI gene modified rice mixture diet (GM group), non-gene modified rice mixture diet (non-GM group), and AIN-93 diet (Blank control group) from parental generation (F0) to the offsprings (F1). GM rice, Heijinmi (HJM) and Non-GM rice, Heishuai (HS), were both formulated into diets at ratios of 73.5% and 75.5% according to the AIN93 diet for rodent animals, respectively. Relative to the non-GM group, no biologically relevant differences were observed in GM group rats concerning reproductive performance such as fertility rate, gestation rate, mean duration, hormone level, and reproductive organ pathology. The developmental parameters results were not significantly different from the non-GM group such as body weight, food consumption, developmental neurotoxicity, behavior, hematology, and serum chemistry. In terms of immunotoxicity, the IgG indicators of offspring from the GM group improved in contrast with the non-GM group. Additional gut flora analysis of F0 generation rats resulted as that the treatment elicited an increased gut microflora diversity of F0 rats. And no horizontal gene transfer of Psy and CrtI genes in rats fed a GM rice HJM diet. In conclusion, we found no adverse effects related to GM rice in the extended one-generation reproductive toxicity study, indicating that GM rice is a safe alternative for its counterpart rice regarding reproductive toxicity.},
}
@article {pmid37333098,
year = {2023},
author = {Grodner, B and Shi, H and Farchione, O and Vill, AC and Ntekas, I and Diebold, PJ and Zipfel, WR and Brito, IL and Vlaminck, I},
title = {Spatial Mapping of Mobile Genetic Elements and their Cognate Hosts in Complex Microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37333098},
issn = {2692-8205},
support = {DP2 AI138242/AI/NIAID NIH HHS/United States ; R33 CA235302/CA/NCI NIH HHS/United States ; S10 OD018516/OD/NIH HHS/United States ; },
abstract = {The frequent exchange of mobile genetic elements (MGEs) between bacteria accelerates the spread of functional traits, including antimicrobial resistance, within the human microbiome. Yet, progress in understanding these intricate processes has been hindered by the lack of tools to map the spatial spread of MGEs in complex microbial communities, and to associate MGEs to their bacterial hosts. To overcome this challenge, we present an imaging approach that pairs single molecule DNA Fluorescence In Situ Hybridization (FISH) with multiplexed ribosomal RNA FISH, thereby enabling the simultaneous visualization of both MGEs and host bacterial taxa. We used this methodology to spatially map bacteriophage and antimicrobial resistance (AMR) plasmids in human oral biofilms, and we studied the heterogeneity in their spatial distributions and demonstrated the ability to identify their host taxa. Our data revealed distinct clusters of both AMR plasmids and prophage, coinciding with densely packed regions of host bacteria in the biofilm. These results suggest the existence of specialized niches that maintain MGEs within the community, possibly acting as local hotspots for horizontal gene transfer. The methods introduced here can help advance the study of MGE ecology and address pressing questions regarding antimicrobial resistance and phage therapy.},
}
@article {pmid37332513,
year = {2022},
author = {Morson, N and Molenda, O and Picott, KJ and Richardson, RE and Edwards, EA},
title = {Long-term survival of Dehalococcoides mccartyi strains in mixed cultures under electron acceptor and ammonium limitation.},
journal = {FEMS microbes},
volume = {3},
number = {},
pages = {xtac021},
pmid = {37332513},
issn = {2633-6685},
abstract = {Few strains of Dehalococcoides mccartyi harbour and express the vinyl chloride reductase (VcrA) that catalyzes the dechlorination of vinyl chloride (VC), a carcinogenic soil and groundwater contaminant. The vcrA operon is found on a Genomic Island (GI) and, therefore, believed to participate in horizontal gene transfer (HGT). To try to induce HGT of the vcrA-GI, we blended two enrichment cultures in medium without ammonium while providing VC. We hypothesized that these conditions would select for a mutant strain of D. mccartyi that could both fix nitrogen and respire VC. However, after more than 4 years of incubation, we found no evidence for HGT of the vcrA-GI. Rather, we observed VC-dechlorinating activity attributed to the trichloroethene reductase TceA. Sequencing and protein modelling revealed a mutation in the predicted active site of TceA, which may have influenced substrate specificity. We also identified two nitrogen-fixing D. mccartyi strains in the KB-1 culture. The presence of multiple strains of D. mccartyi with distinct phenotypes is a feature of natural environments and certain enrichment cultures (such as KB-1), and may enhance bioaugmentation success. The fact that multiple distinct strains persist in the culture for decades and that we could not induce HGT of the vcrA-GI suggests that it is not as mobile as predicted, or that mobility is restricted in ways yet to be discovered to specific subclades of Dehalococcoides.},
}
@article {pmid37329912,
year = {2023},
author = {Katsivelou, E and Perruchon, C and Karas, PA and Sarantidou, A and Pappa, E and Katsoula, A and Ligda, P and Sotiraki, S and Martin-Laurent, F and Vasileiadis, S and Karpouzas, DG},
title = {Accelerated dissipation, soil microbial toxicity and dispersal of antimicrobial resistance in soils repeatedly exposed to tiamulin, tilmicosin and sulfamethoxazole.},
journal = {The Science of the total environment},
volume = {893},
number = {},
pages = {164817},
doi = {10.1016/j.scitotenv.2023.164817},
pmid = {37329912},
issn = {1879-1026},
mesh = {*Soil/chemistry ; *Anti-Bacterial Agents/pharmacology ; Sulfamethoxazole/chemistry ; Manure/microbiology ; Soil Microbiology ; Ammonia/pharmacology ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; },
abstract = {The application of manures leads to the contamination of agricultural soils with veterinary antibiotics (VAs). These might exert toxicity on the soil microbiota and threaten environmental quality, and public health. We obtained mechanistic insights about the impact of three VAs, namely, sulfamethoxazole (SMX), tiamulin (TIA) and tilmicosin (TLM), on the abundance of key soil microbial groups, antibiotic resistance genes (ARGs) and class I integron integrases (intl1). In a microcosm study, we repeatedly treated two soils (differing in pH and VA dissipation capacity) with the studied VAs, either directly or via fortified manure. This application scheme resulted in accelerated dissipation of TIA, but not of SMX, and accumulation of TLM. Potential nitrification rates (PNR), and the abundance of ammonia-oxidizing microorganism (AOM) were reduced by SMX and TIA, but not by TLM. VAs strongly impacted the total prokaryotic and AOM communities, whereas manure addition was the main determinant of the fungal and protist communities. SMX stimulated sulfonamide resistance, while manure stimulated ARGs and horizontal gene transfer. Correlations identified opportunistic pathogens like Clostridia, Burkholderia-Caballeronia-Paraburkholderia, and Nocardioides as potential ARG reservoirs in soil. Our results provide unprecedented evidence about the effects of understudied VAs on soil microbiota and highlight risks posed by VA-contaminated manures. ENVIRONMENTAL IMPLICATION: The dispersal of veterinary antibiotics (VAs) through soil manuring enhances antimicrobial resistance (AMR) development and poses a threat to the environment and the public health. We provide insights about the impact of selected VAs on their: (i) microbially-mediated dissipation in soil; (ii) ecotoxicity on the soil microbial communities; (iii) capacity to stimulate AMR. Our results (i) demonstrate the effects of VAs and their application-mode on the bacterial, fungal, and protistan communities, and on the soil ammonia oxidizers; (ii) describe natural attenuation processes against VA dispersal, (iii) depict potential soil microbial AMR reservoirs, essential for the development of risk assessment strategies.},
}
@article {pmid37327521,
year = {2023},
author = {Zhu, S and Yang, B and Wang, Z and Liu, Y},
title = {Augmented dissemination of antibiotic resistance elicited by non-antibiotic factors.},
journal = {Ecotoxicology and environmental safety},
volume = {262},
number = {},
pages = {115124},
doi = {10.1016/j.ecoenv.2023.115124},
pmid = {37327521},
issn = {1090-2414},
abstract = {The emergence and rapid spread of antibiotic resistance seriously compromise the clinical efficacy of current antibiotic therapies, representing a serious public health threat worldwide. Generally, drug-susceptible bacteria can acquire antibiotic resistance through genetic mutation or gene transfer, among which horizontal gene transfer (HGT) plays a dominant role. It is widely acknowledged that the sub-inhibitory concentrations of antibiotics are the key drivers in promoting the transmission of antibiotic resistance. However, accumulating evidence in recent years has shown that in addition to antibiotics, non-antibiotics can also accelerate the horizontal transfer of antibiotic resistance genes (ARGs). Nevertheless, the roles and potential mechanisms of non-antibiotic factors in the transmission of ARGs remain largely underestimated. In this review, we depict the four pathways of HGT and their differences, including conjugation, transformation, transduction and vesiduction. We summarize non-antibiotic factors accounting for the enhanced horizontal transfer of ARGs and their underlying molecular mechanisms. Finally, we discuss the limitations and implications of current studies.},
}
@article {pmid37325804,
year = {2023},
author = {Woods, RJ and Barbosa, C and Koepping, L and Raygoza, JA and Mwangi, M and Read, AF},
title = {The evolution of antibiotic resistance in an incurable and ultimately fatal infection: A retrospective case study.},
journal = {Evolution, medicine, and public health},
volume = {11},
number = {1},
pages = {163-173},
pmid = {37325804},
issn = {2050-6201},
support = {K08 AI119182/AI/NIAID NIH HHS/United States ; },
abstract = {BACKGROUND AND OBJECTIVES: The processes by which pathogens evolve within a host dictate the efficacy of treatment strategies designed to slow antibiotic resistance evolution and influence population-wide resistance levels. The aim of this study is to describe the underlying genetic and phenotypic changes leading to antibiotic resistance within a patient who died as resistance evolved to available antibiotics. We assess whether robust patterns of collateral sensitivity and response to combinations existed that might have been leveraged to improve therapy.<br><br>METHODOLOGY: We used whole-genome sequencing of nine isolates taken from this patient over 279 days of a chronic infection with Enterobacter hormaechei, and systematically measured changes in resistance against five of the most relevant drugs considered for treatment.<br><br>RESULTS: The entirety of the genetic change is consistent with de novo mutations and plasmid loss events, without acquisition of foreign genetic material via horizontal gene transfer. The nine isolates fall into three genetically distinct lineages, with early evolutionary trajectories being supplanted by previously unobserved multi-step evolutionary trajectories. Importantly, although the population evolved resistance to all the antibiotics used to treat the infection, no single isolate was resistant to all antibiotics. Evidence of collateral sensitivity and response to combinations therapy revealed inconsistent patterns across this diversifying population.<br><br>CONCLUSIONS: Translating antibiotic resistance management strategies from theoretical and laboratory data to clinical situations, such as this, will require managing diverse population with unpredictable resistance trajectories.},
}
@article {pmid37323902,
year = {2023},
author = {Nguyen, QH and Le, TTH and Nguyen, ST and Nguyen, KT and Quyen, DV and Hayer, J and Bañuls, AL and Tran, TTT},
title = {Large-scale analysis of putative plasmids in clinical multidrug-resistant Escherichia coli isolates from Vietnamese patients.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1094119},
pmid = {37323902},
issn = {1664-302X},
abstract = {INTRODUCTION: In the past decades, extended-spectrum beta-lactamase (ESBL)-producing and carbapenem-resistant (CR) Escherichia coli isolates have been detected in Vietnamese hospitals. The transfer of antimicrobial resistance (AMR) genes carried on plasmids is mainly responsible for the emergence of multidrug-resistant E. coli strains and the spread of AMR genes through horizontal gene transfer. Therefore, it is important to thoroughly study the characteristics of AMR gene-harboring plasmids in clinical multidrug-resistant bacterial isolates.<br><br>METHODS: The profiles of plasmid assemblies were determined by analyzing previously published whole-genome sequencing data of 751 multidrug-resistant E. coli isolates from Vietnamese hospitals in order to identify the risk of AMR gene horizontal transfer and dissemination.<br><br>RESULTS: The number of putative plasmids in isolates was independent of the sequencing coverage. These putative plasmids originated from various bacterial species, but mostly from the Escherichia genus, particularly E. coli species. Many different AMR genes were detected in plasmid contigs of the studied isolates, and their number was higher in CR isolates than in ESBL-producing isolates. Similarly, the blaKPC-2, blaNDM-5, blaOXA-1, blaOXA-48, and blaOXA-181 &#x3b2;-lactamase genes, associated with resistance to carbapenems, were more frequent in CR strains. Sequence similarity network and genome annotation analyses revealed high conservation of the &#x3b2;-lactamase gene clusters in plasmid contigs that carried the same AMR genes.<br><br>DISCUSSION: Our study provides evidence of horizontal gene transfer in multidrug-resistant E. coli isolates via conjugative plasmids, thus rapidly accelerating the emergence of resistant bacteria. Besides reducing antibiotic misuse, prevention of plasmid transmission also is essential to limit antibiotic resistance.},
}
@article {pmid37321361,
year = {2023},
author = {Zhang, J and Huang, Z and Fu, W and Zhang, C and Zan, T and Nan, P and Li, L and Song, Z and Zhang, W and Yang, J and Wang, Y},
title = {Host shift promotes divergent evolution between closely related holoparasitic species.},
journal = {Molecular phylogenetics and evolution},
volume = {186},
number = {},
pages = {107842},
doi = {10.1016/j.ympev.2023.107842},
pmid = {37321361},
issn = {1095-9513},
mesh = {Humans ; Phylogeny ; *Orobanchaceae/genetics ; Genes, Plant ; *Genome, Plastid ; Repetitive Sequences, Nucleic Acid ; Gene Transfer, Horizontal ; },
abstract = {Distinct hosts have been hypothesized to possess the potential for affecting species differentiation and genome evolution of parasitic organisms. However, what host shift history is experienced by the closely related parasites and whether disparate evolution of their genomes occur remain largely unknown. Here, we screened horizontal gene transfer (HGT) events in a pair of sister species of holoparasitic Boschniakia (Orobanchaceae) having obligate hosts from distinct families to recall the former host-parasite associations and performed a comparative analysis to investigate the difference of their organelle genomes. Except those from the current hosts (Ericaceae and Betulaceae), we identified a number of HGTs from Rosaceae supporting the occurrence of unexpected ancient host shifts. Different hosts transfer functional genes which changed nuclear genomes of this sister species. Likewise, different donors transferred sequences to their mitogenomes, which vary in size due to foreign and repetitive elements rather than other factors found in other parasites. The plastomes are both severely reduced, and the degree of difference in reduction syndrome reaches the intergeneric level. Our findings provide new insights into the genome evolution of parasites adapting to different hosts and extend the mechanism of host shift promoting species differentiation to parasitic plant lineages.},
}
@article {pmid37317293,
year = {2023},
author = {Shelenkov, A and Mikhaylova, Y and Voskanyan, S and Egorova, A and Akimkin, V},
title = {Whole-Genome Sequencing Revealed the Fusion Plasmids Capable of Transmission and Acquisition of Both Antimicrobial Resistance and Hypervirulence Determinants in Multidrug-Resistant Klebsiella pneumoniae Isolates.},
journal = {Microorganisms},
volume = {11},
number = {5},
pages = {},
pmid = {37317293},
issn = {2076-2607},
support = {075-15-2019-1666//the Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {Klebsiella pneumoniae, a member of the Enterobacteriaceae family, has become a dangerous pathogen accountable for a large fraction of the various infectious diseases in both clinical and community settings. In general, the K. pneumoniae population has been divided into the so-called classical (cKp) and hypervirulent (hvKp) lineages. The former, usually developing in hospitals, can rapidly acquire resistance to a wide spectrum of antimicrobial drugs, while the latter is associated with more aggressive but less resistant infections, mostly in healthy humans. However, a growing number of reports in the last decade have confirmed the convergence of these two distinct lineages into superpathogen clones possessing the properties of both, and thus imposing a significant threat to public health worldwide. This process is associated with horizontal gene transfer, in which plasmid conjugation plays a very important role. Therefore, the investigation of plasmid structures and the ways plasmids spread within and between bacterial species will provide benefits in developing prevention measures against these powerful pathogens. In this work, we investigated clinical multidrug-resistant K. pneumoniae isolates using long- and short-read whole-genome sequencing, which allowed us to reveal fusion IncHI1B/IncFIB plasmids in ST512 isolates capable of simultaneously carrying hypervirulence (iucABCD, iutA, prmpA, peg-344) and resistance determinants (armA, blaNDM-1 and others), and to obtain insights into their formation and transmission mechanisms. Comprehensive phenotypic, genotypic and phylogenetic analysis of the isolates, as well as of their plasmid repertoire, was performed. The data obtained will facilitate epidemiological surveillance of high-risk K. pneumoniae clones and the development of prevention strategies against them.},
}
@article {pmid37315610,
year = {2023},
author = {Pires, J and Santos, R and Monteiro, S},
title = {Antibiotic resistance genes in bacteriophages from wastewater treatment plant and hospital wastewaters.},
journal = {The Science of the total environment},
volume = {892},
number = {},
pages = {164708},
doi = {10.1016/j.scitotenv.2023.164708},
pmid = {37315610},
issn = {1879-1026},
mesh = {*Wastewater ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Colistin ; *Bacteriophages/genetics ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Hospitals ; },
abstract = {Antibiotic resistant bacteria (ARB) are a major health risk caused particularly by anthropogenic activities. Acquisition of antibiotic resistances by bacteria is known to have happened before the discovery of antibiotics and can occur through different routes. Bacteriophages are thought to have an important contribution to the dissemination of antibiotic resistance genes (ARGs) in the environment. In this study, seven ARGs (blaTEM, blaSHV, blaCTX-M, blaCMY, mecA, vanA, and mcr-1) were investigated, in the bacteriophage fraction, in raw urban and hospital wastewaters. The genes were quantified in 58 raw wastewater samples collected at five WWTPs (n = 38) and hospitals (n = 20). All genes were detected in the phage DNA fraction, with the bla genes found in higher frequency. On the other hand, mecA and mcr-1 were the least frequently detected genes. Concentrations varied between 10[2] copies/L and 10[6] copies/L. The gene coding for the resistance to colistin (mcr-1), a last-resort antibiotic for the treatment of multidrug-resistant Gram-negative infections, was identified in raw urban and hospital wastewaters with positivity rates of 19 % and 10 %, respectively. ARGs patterns varied between hospital and raw urban wastewaters, and within hospitals and WWTP. This study suggests that phages are reservoirs of ARGs, and that ARGs (with particularly emphasis on resistance to colistin and vancomycin) in the phage fraction are already widely widespread in the environment with potential large implications for public health.},
}
@article {pmid37314210,
year = {2023},
author = {Nguyen, M and Elmore, Z and Ihle, C and Moen, FS and Slater, AD and Turner, BN and Parrello, B and Best, AA and Davis, JJ},
title = {Predicting variable gene content in Escherichia coli using conserved genes.},
journal = {mSystems},
volume = {8},
number = {4},
pages = {e0005823},
pmid = {37314210},
issn = {2379-5077},
support = {75N93019C00076/AI/NIAID NIH HHS/United States ; },
mesh = {Escherichia coli/genetics ; Genome, Bacterial/genetics ; Plasmids ; *Escherichia coli Proteins/genetics ; *Anti-Infective Agents ; },
abstract = {Having the ability to predict the protein-encoding gene content of an incomplete genome or metagenome-assembled genome is important for a variety of bioinformatic tasks. In this study, as a proof of concept, we built machine learning classifiers for predicting variable gene content in Escherichia coli genomes using only the nucleotide k-mers from a set of 100 conserved genes as features. Protein families were used to define orthologs, and a single classifier was built for predicting the presence or absence of each protein family occurring in 10%-90% of all E. coli genomes. The resulting set of 3,259 extreme gradient boosting classifiers had a per-genome average macro F1 score of 0.944 [0.943-0.945, 95% CI]. We show that the F1 scores are stable across multi-locus sequence types and that the trend can be recapitulated by sampling a smaller number of core genes or diverse input genomes. Surprisingly, the presence or absence of poorly annotated proteins, including "hypothetical proteins" was accurately predicted (F1 = 0.902 [0.898-0.906, 95% CI]). Models for proteins with horizontal gene transfer-related functions had slightly lower F1 scores but were still accurate (F1s = 0.895, 0.872, 0.824, and 0.841 for transposon, phage, plasmid, and antimicrobial resistance-related functions, respectively). Finally, using a holdout set of 419 diverse E. coli genomes that were isolated from freshwater environmental sources, we observed an average per-genome F1 score of 0.880 [0.876-0.883, 95% CI], demonstrating the extensibility of the models. Overall, this study provides a framework for predicting variable gene content using a limited amount of input sequence data. IMPORTANCE Having the ability to predict the protein-encoding gene content of a genome is important for assessing genome quality, binning genomes from shotgun metagenomic assemblies, and assessing risk due to the presence of antimicrobial resistance and other virulence genes. In this study, we built a set of binary classifiers for predicting the presence or absence of variable genes occurring in 10%-90% of all publicly available E. coli genomes. Overall, the results show that a large portion of the E. coli variable gene content can be predicted with high accuracy, including genes with functions relating to horizontal gene transfer. This study offers a strategy for predicting gene content using limited input sequence data.},
}
@article {pmid37311294,
year = {2023},
author = {Zhang, Q and Zhou, L and Zhao, Y and Gao, S and Yang, Y and Chen, Q and Li, W and Qi, Q and Dong, Q and Lei, J and Guo, X and Gao, Q and Yang, Y},
title = {Uncovering the virome and its interaction with antibiotic resistome during compost fertilization.},
journal = {Journal of hazardous materials},
volume = {457},
number = {},
pages = {131763},
doi = {10.1016/j.jhazmat.2023.131763},
pmid = {37311294},
issn = {1873-3336},
mesh = {Animals ; Swine ; *Anti-Bacterial Agents/pharmacology ; Virome ; Genes, Bacterial ; *Composting ; Manure/microbiology ; Soil ; Soil Microbiology ; Fertilization ; },
abstract = {Antibiotic resistance is a pressing global health issue, leading to increased illnesses and fatalities. The contribution of viruses to the acquisition, preservation, and dissemination of antibiotic resistance genes (ARGs) is not yet fully understood. By using a high-throughput functional gene-based microarray (GeoChip 5.0), this study examines the prevalence and relative abundance of bacteriophage and eukaryotic viral genes in swine manure, compost, compost-amended agricultural soil, and unamended soil from suburban regions of Beijing, China. Our findings reveal a significantly elevated presence of biomarker viral genes in compost-amended soils compared to unamended soils, suggesting potential health risks associated with compost fertilization. We also observed stronger ecological interactions between ARGs and viral genes in manure and compost than in soils. Network analysis identified arabinose efflux permeases and EmrB/QacA resistance genes, linked to CRISPR encoding sequences, as keystone nodes, indicating possible ARG acquisition via virus infections. Moreover, positive correlations were found between viral genes, antibiotic concentrations, and ARG diversity in manure, compost, and compost-amended soils, highlighting a likely pathway for virus-mediated ARG transfer. In summary, our results indicate that use of compost as a fertilizer in agricultural settings could facilitate the spread of ARGs through viral mechanisms, allowing for time-delayed genetic exchanges over broader temporal and spatial scales than ARGs within bacterial genomes.},
}
@article {pmid37310285,
year = {2023},
author = {Cohen, H and Fridman, CM and Gerlic, M and Salomon, D},
title = {A Vibrio T6SS-Mediated Lethality in an Aquatic Animal Model.},
journal = {Microbiology spectrum},
volume = {11},
number = {4},
pages = {e0109323},
pmid = {37310285},
issn = {2165-0497},
mesh = {Animals ; Humans ; *Inflammasomes ; *Vibrio/genetics ; Eukaryota ; Virulence/genetics ; Phagocytes ; Mammals ; },
abstract = {Bacteria belonging to the genus Vibrio include many known and emerging pathogens. Horizontal gene transfer of pathogenicity islands is a major contributor to the emergence of new pathogenic Vibrio strains. Here, we use the brine shrimp Artemia salina as a model and show that the marine bacterium Vibrio proteolyticus uses a horizontally shared type VI secretion system, T6SS3, to intoxicate a eukaryotic host. Two T6SS3 effectors, which were previously shown to induce inflammasome-mediated pyroptotic cell death in mammalian phagocytic cells, contribute to this toxicity. Furthermore, we find a novel T6SS3 effector that also contributes to the lethality mediated by this system against Artemia salina. Therefore, our results reveal a T6SS that is shared among diverse vibrios and mediates host lethality, indicating that it can lead to the emergence of new pathogenic strains. IMPORTANCE The rise in sea surface temperature has been linked to the spread of bacteria belonging to the genus Vibrio and the human illnesses associated with them. Since vibrios often share virulence traits horizontally, a better understanding of their virulence potential and determinants can prepare us for new emerging pathogens. In this work, we showed that a toxin delivery system found in various vibrios mediates lethality in an aquatic animal. Taken together with previous reports showing that the same system induces inflammasome-mediated cell death in mammalian phagocytic cells, our findings suggest that this delivery system and its associated toxins may contribute to the emergence of pathogenic strains.},
}
@article {pmid37310275,
year = {2023},
author = {Saati-Santamaría, Z},
title = {Global Map of Specialized Metabolites Encoded in Prokaryotic Plasmids.},
journal = {Microbiology spectrum},
volume = {11},
number = {4},
pages = {e0152323},
pmid = {37310275},
issn = {2165-0497},
mesh = {Humans ; *Bacteria/genetics ; Secondary Metabolism/genetics ; Plasmids/genetics ; *Multigene Family ; },
abstract = {Plasmids are the main mobile elements responsible for horizontal gene transfer (HGT) in microorganisms. These replicons extend the metabolic spectrum of their host cells by carrying functional genes. However, it is still unknown to what extent plasmids carry biosynthetic gene clusters (BGCs) related to the production of secondary or specialized metabolites (SMs). Here, we analyzed 9,183 microbial plasmids to unveil their potential to produce SMs, finding a large diversity of cryptic BGCs in a few varieties of prokaryotic host taxa. Some of these plasmids harbored 15 or more BGCs, and many others were exclusively dedicated to mobilizing BGCs. We found an occurrence pattern of BGCs within groups of homologous plasmids shared by a common taxon, mainly in host-associated microbes (e.g., Rhizobiales, Enterobacteriaceae members). Our results add to the knowledge of the ecological functions and potential industrial uses of plasmids and shed light on the dynamics and evolution of SMs in prokaryotes. IMPORTANCE Plasmids are mobile DNA elements that can be shared among microbial cells, and they are useful for bringing to fruition some microbial ecological traits. However, it is not known to what extent plasmids harbor genes related to the production of specialized/secondary metabolites (SMs). In microbes, these metabolites are frequently useful for defense purposes, signaling, etc. In addition, these molecules usually have biotechnological and clinical applications. Here, we analyzed the content, dynamics, and evolution of genes related to the production of SMs in >9,000 microbial plasmids. Our results confirm that some plasmids act as a reservoir of SMs. We also found that some families of biosynthetic gene clusters are exclusively present in some groups of plasmids shared among closely related microbes. Host-associated bacteria (e.g., plant and human microbes) harbor the majority of specialized metabolites encoded in plasmids. These results provide new knowledge about microbial ecological traits and might enable the discovery of novel metabolites.},
}
@article {pmid37307358,
year = {2023},
author = {Marr, RA and Moore, J and Formby, S and Martiniuk, JT and Hamilton, J and Ralli, S and Konwar, K and Rajasundaram, N and Hahn, A and Measday, V},
title = {Whole genome sequencing of Canadian Saccharomyces cerevisiae strains isolated from spontaneous wine fermentations reveals a new Pacific West Coast Wine clade.},
journal = {G3 (Bethesda, Md.)},
volume = {13},
number = {8},
pages = {},
pmid = {37307358},
issn = {2160-1836},
mesh = {*Saccharomyces cerevisiae ; *Wine ; DNA Copy Number Variations ; Fermentation ; Phylogeny ; Canada ; Plant Breeding ; Whole Genome Sequencing ; },
abstract = {Vineyards in wine regions around the world are reservoirs of yeast with oenological potential. Saccharomyces cerevisiae ferments grape sugars to ethanol and generates flavor and aroma compounds in wine. Wineries place a high-value on identifying yeast native to their region to develop a region-specific wine program. Commercial wine strains are genetically very similar due to a population bottleneck and in-breeding compared to the diversity of S. cerevisiae from the wild and other industrial processes. We have isolated and microsatellite-typed hundreds of S. cerevisiae strains from spontaneous fermentations of grapes from the Okanagan Valley wine region in British Columbia, Canada. We chose 75 S. cerevisiae strains, based on our microsatellite clustering data, for whole genome sequencing using Illumina paired-end reads. Phylogenetic analysis shows that British Columbian S. cerevisiae strains cluster into 4 clades: Wine/European, Transpacific Oak, Beer 1/Mixed Origin, and a new clade that we have designated as Pacific West Coast Wine. The Pacific West Coast Wine clade has high nucleotide diversity and shares genomic characteristics with wild North American oak strains but also has gene flow from Wine/European and Ecuadorian clades. We analyzed gene copy number variations to find evidence of domestication and found that strains in the Wine/European and Pacific West Coast Wine clades have gene copy number variation reflective of adaptations to the wine-making environment. The "wine circle/Region B", a cluster of 5 genes acquired by horizontal gene transfer into the genome of commercial wine strains is also present in the majority of the British Columbian strains in the Wine/European clade but in a minority of the Pacific West Coast Wine clade strains. Previous studies have shown that S. cerevisiae strains isolated from Mediterranean Oak trees may be the living ancestors of European wine yeast strains. This study is the first to isolate S. cerevisiae strains with genetic similarity to nonvineyard North American Oak strains from spontaneous wine fermentations.},
}
@article {pmid37302657,
year = {2023},
author = {Wu, T and Mao, H and Hai, D and Cheng, J and Fu, Y and Lin, Y and Jiang, D and Xie, J},
title = {Molecular characterization of a novel fungal alphaflexivirus reveals potential inter-species horizontal gene transfer.},
journal = {Virus research},
volume = {334},
number = {},
pages = {199151},
pmid = {37302657},
issn = {1872-7492},
mesh = {*Flexiviridae/genetics ; Phylogeny ; RNA, Viral/genetics ; Gene Transfer, Horizontal ; RNA-Dependent RNA Polymerase/genetics ; Ascomycota ; *RNA Viruses ; *Fungal Viruses ; Open Reading Frames ; Genome, Viral ; },
abstract = {Sclerotinia sclerotiorum is a notorious phytopathogenic fungus that harbors diverse mycoviruses. A novel positive-sense single-stranded RNA virus, Sclerotinia sclerotiorum alphaflexivirus 2 (SsAFV2), was isolated from the hypovirulent strain 32-9 of S. sclerotiorum, and its complete genome was determined. The SsAFV2 genome contains 7,162 nucleotides (nt), excluding the poly (A) structure, and is composed of four open reading frames (ORF1-4). ORF1 encodes a polyprotein that contains three conserved domains: methyltransferase, helicase, and RNA-dependent RNA polymerase (RdRp). The ORF3 putative encodes coat proteins (CP), with ORF2 and ORF4 encoding hypothetical proteins of unknown functions. Phylogenetic analysis revealed that SsAFV2 clustered with Botrytis virus X (BVX) based on multiple alignments of helicase, RdRp, and CP, but the methyltransferase of SsAFV2 was most closely related to Sclerotinia sclerotiorum alphaflexivirus 1, suggesting that SsAFV2 is a new member of the Botrexvirus genus within the Alphaflexiviridae family, and also revealed the occurrence of potential inter-species horizontal gene transfer events within the Botrexvirus genus during the evolutionary process. Our results contribute to the current knowledge regarding the evolution and divergence of Botrexviruses.},
}
@article {pmid37296404,
year = {2023},
author = {Mehta, RS and Petit, RA and Read, TD and Weissman, DB},
title = {Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes.},
journal = {BMC bioinformatics},
volume = {24},
number = {1},
pages = {243},
pmid = {37296404},
issn = {1471-2105},
support = {R01 AI139188/AI/NIAID NIH HHS/United States ; 214626/WT_/Wellcome Trust/United Kingdom ; AI139188/NH/NIH HHS/United States ; },
mesh = {Humans ; *Staphylococcus aureus/genetics ; Genome, Bacterial ; Virulence/genetics ; *Staphylococcal Infections/genetics/microbiology ; Anti-Bacterial Agents ; },
abstract = {Bacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecting coevolving genes from large datasets of bacterial genomes based on pairwise comparisons of closely related individuals, analogous to a pedigree study in eukaryotic populations. We apply our method to pairs of genes from the Staphylococcus aureus accessory genome of over 75,000 annotated gene families using a database of over 40,000 whole genomes. We find many pairs of genes that appear to be gained or lost in a coordinated manner, as well as pairs where the gain of one gene is associated with the loss of the other. These pairs form networks of rapidly coevolving genes, primarily consisting of genes involved in virulence, mechanisms of horizontal gene transfer, and antibiotic resistance, particularly the SCCmec complex. While we focus on gene gain and loss, our method can also detect genes that tend to acquire substitutions in tandem, or genotype-phenotype or phenotype-phenotype coevolution. Finally, we present the R package DeCoTUR that allows for the computation of our method.},
}
@article {pmid37294009,
year = {2023},
author = {Manoharan-Basil, SS and Gestels, Z and Abdellati, S and Akomoneh, EA and Kenyon, C},
title = {Evidence of horizontal gene transfer within porB in 19 018 whole-genome Neisseria spp. isolates: a global phylogenetic analysis.},
journal = {Microbial genomics},
volume = {9},
number = {6},
pages = {},
pmid = {37294009},
issn = {2057-5858},
mesh = {Humans ; *Neisseria ; Phylogeny ; Gene Transfer, Horizontal ; *Gonorrhea ; Neisseria gonorrhoeae/genetics ; },
abstract = {The PorB porins are the major pore-forming proteins in the genus Neisseria . The trimeric PorB porins consist of 16 highly conserved transmembrane domains that form an amphipathic β-sheet connected by short periplasmic turns and eight extracellular hydrophilic loops. These loops are immunogenic and also play an important role in mediating antimicrobial influx. This study sought to (i) characterize the variations in Neisserial loop 3(355–438 bp) associated with intermediate resistance to penicillin/tetracycline and (ii) evaluate if there was evidence of horizontal gene transfer in any of the loops. We collated an integrated database consisting of 19 018 Neisseria spp. genomes – 17 882 Neisseria gonorrhoeae , 114 Neisseria meningitidis and 1022 commensal Neisseria spp. To identify the porB alleles, a gene-by-gene approach (chewBBACA) was employed. To evaluate the presence of recombination events, the Recombination Detection Programme (RDP4) was used. In total, 3885 porB alleles were detected. Paralogues were identified in 17 Neisseria isolates. Putative recombination was identified in loop regions. Intraspecies recombination among N. gonorrhoeae isolates and interspecies recombination between N. meningitidis and commensal Neisseria spp., and N. gonorrhoeae and N. lactamica were identified. Here, we present a large-scale study of 19 018 Neisseria isolates to describe recombination and variation in the porB gene. Importantly, we found putative recombination in loop regions between the pathogenic and non-pathogenic Neisseria spp. These findings suggest the need for pheno- and genotypic surveillance of antimicrobial susceptibility in commensal Neisseria spp. to prevent the emergence of AMR in the pathogenic Neisseria . This article contains data hosted by Microreact.},
}
@article {pmid37289828,
year = {2023},
author = {Walsh, SK and Imrie, RM and Matuszewska, M and Paterson, GK and Weinert, LA and Hadfield, JD and Buckling, A and Longdon, B},
title = {The host phylogeny determines viral infectivity and replication across Staphylococcus host species.},
journal = {PLoS pathogens},
volume = {19},
number = {6},
pages = {e1011433},
pmid = {37289828},
issn = {1553-7374},
support = {BB/M009122/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; 109385/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Bacteriophages/physiology ; Host Specificity ; Phylogeny ; Polymerase Chain Reaction ; *Staphylococcaceae/classification/virology ; Staphylococcus aureus/virology ; *Staphylococcus Phages/physiology ; Viral Plaque Assay ; Virus Replication ; },
abstract = {Virus host shifts, where a virus transmits to and infects a novel host species, are a major source of emerging infectious disease. Genetic similarity between eukaryotic host species has been shown to be an important determinant of the outcome of virus host shifts, but it is unclear if this is the case for prokaryotes where anti-virus defences can be transmitted by horizontal gene transfer and evolve rapidly. Here, we measure the susceptibility of 64 strains of Staphylococcaceae bacteria (48 strains of Staphylococcus aureus and 16 non-S. aureus species spanning 2 genera) to the bacteriophage ISP, which is currently under investigation for use in phage therapy. Using three methods-plaque assays, optical density (OD) assays, and quantitative (q)PCR-we find that the host phylogeny explains a large proportion of the variation in susceptibility to ISP across the host panel. These patterns were consistent in models of only S. aureus strains and models with a single representative from each Staphylococcaceae species, suggesting that these phylogenetic effects are conserved both within and among host species. We find positive correlations between susceptibility assessed using OD and qPCR and variable correlations between plaque assays and either OD or qPCR, suggesting that plaque assays alone may be inadequate to assess host range. Furthermore, we demonstrate that the phylogenetic relationships between bacterial hosts can generally be used to predict the susceptibility of bacterial strains to phage infection when the susceptibility of closely related hosts is known, although this approach produced large prediction errors in multiple strains where phylogeny was uninformative. Together, our results demonstrate the ability of bacterial host evolutionary relatedness to explain differences in susceptibility to phage infection, with implications for the development of ISP both as a phage therapy treatment and as an experimental system for the study of virus host shifts.},
}
@article {pmid37286020,
year = {2023},
author = {Lapadula, WJ and Juri Ayub, M},
title = {Ribosome inactivating proteins in insects: HGT, gene expression, and functional implications.},
journal = {Gene},
volume = {877},
number = {},
pages = {147547},
doi = {10.1016/j.gene.2023.147547},
pmid = {37286020},
issn = {1879-0038},
mesh = {Animals ; Ribosome Inactivating Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Insecta/genetics ; Protein Biosynthesis ; RNA, Ribosomal ; *Ricin/chemistry/genetics/metabolism ; *Hemiptera/genetics/metabolism ; Plant Proteins/genetics ; },
abstract = {Ribosome-inactivating proteins (RIPs) are RNA N-glycosidases that depurinate an adenine residue in the conserved alpha-sarcin/ricin loop (SRL) of rRNA, inhibiting protein synthesis. Previously, we reported the existence of these toxins in insects, whose presence is restricted to mosquitoes from the Culicinae subfamily (e.g., Aedes aegypti) and whiteflies from the Aleyrodidae family (e.g., Bemisia tabaci). Both groups of genes are derived from two independent horizontal gene transfer (HGT) events and are evolving under purifying selection. Here, we report and characterize the occurrence of a third HGT event in the Sciaroidea superfamily, which supports the recurrent acquisition of RIP genes by insects. Transcriptomic experiments, available in databases, allowed us to describe the temporal and spatial expression profiles for these foreign genes in these organisms. Furthermore, we found that RIP expression is induced after infection with pathogens and provided, for the first time, transcriptomic evidence of parasite SRL depurination. This evidence suggests a possible role of these foreign genes as immune effectors in insects.},
}
@article {pmid37283901,
year = {2023},
author = {Abubaker, KT and Anwar, KA},
title = {Antimicrobial susceptibility and integrons detection among extended-spectrum β-lactamase producing Enterobacteriaceae isolates in patients with urinary tract infection.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15429},
pmid = {37283901},
issn = {2167-8359},
mesh = {Humans ; Escherichia coli/genetics ; Integrons/genetics ; Cross-Sectional Studies ; beta-Lactamases/genetics ; Enterobacteriaceae/genetics ; Anti-Bacterial Agents/pharmacology ; *Urinary Tract Infections/drug therapy ; *Anti-Infective Agents ; },
abstract = {BACKGROUND: Integrons are bacterial mobile genetic components responsible for mediating the antibiotic resistance process by carrying and spreading antimicrobial resistance genes among bacteria through horizontal gene transfer.<br><br>OBJECTIVES: This cross-sectional hospital-based study aimed to find the prevalence of antibiotic resistance patterns and to detect integrons classes (I, II, and III) among bacterial isolates in patients with urinary tract infections (UTI) in Sulaimani, Iraq.<br><br>PATIENTS AND METHODS: Mid-stream urine samples (no. = 400) were collected from patients with UTI at three different Hospitals from Sulaimani, Iraq, between September 2021 to January 2022. Urine samples were cultured on various agar media, and grown bacteria were isolated. Antibiotic susceptibility test (AST) and an extended-spectrum &#x3b2;-lactamase (ESBL) screen were done for isolated bacteria. Then, integrons classes were screened using conventional PCR with gene sequencing and uploaded to the National Center for Biotechnology Information (NCBI).<br><br>RESULTS: The frequency rate of Enterobacteriaceae was 67.03% among positive urine cultures. E. coli (no. = 86) and Klebsiella pneumoniae (no. = 32) isolates were identified. The most sensitive antibiotics were the carbapenem group (85.3%) and nitrofurantoin (NFN) (64.2%), while the most resistant antibiotics were nalidixic acid (NA) and 3[rd] generation cephalosporin. The occurrence rate of ESBL was 56.6% with a predominance of class I integron (54.2%), then class II (15.8%) and no positive record for class III integron were observed.<br><br>CONCLUSION: Most bacterial isolates from patients with UTI produced class I and II integrons genes with favourable ESBL properties.},
}
@article {pmid37283060,
year = {2023},
author = {Yang, L and Mai, G and Hu, Z and Zhou, H and Dai, L and Deng, Z and Ma, Y},
title = {Global transmission of broad-host-range plasmids derived from the human gut microbiome.},
journal = {Nucleic acids research},
volume = {51},
number = {15},
pages = {8005-8019},
pmid = {37283060},
issn = {1362-4962},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; Host Specificity ; Plasmids/genetics ; Bacteria/genetics ; Gene Transfer, Horizontal/genetics ; },
abstract = {Broad-host-range (BHR) plasmids in human gut bacteria are of considerable interest for their ability to mediate horizontal gene transfer (HGT) across large phylogenetic distance. However, the human gut plasmids, especially the BHR plasmids, remain largely unknown. Here, we identified the plasmids in the draft genomes of gut bacterial isolates from Chinese and American donors, resulting in 5372 plasmid-like clusters (PLCs), of which, 820 PLCs (comPLCs) were estimated with > 60% completeness genomes and only 155 (18.9%) were classified to known replicon types (n = 37). We observed that 175 comPLCs had a broad host range across distinct bacterial genera, of which, 71 were detected in at least two human populations of Chinese, American, Spanish, and Danish, and 13 were highly prevalent (>10%) in at least one human population. Haplotype analyses of two widespread PLCs demonstrated their spreading and evolutionary trajectory, suggesting frequent and recent exchanges of the BHR plasmids in environments. In conclusion, we obtained a large collection of plasmid sequences in human gut bacteria and demonstrated that a subset of the BHR plasmids can be transmitted globally, thus facilitating extensive HGT (e.g. antibiotic resistance genes) events. This study highlights the potential implications of the plasmids for global human health.},
}
@article {pmid37280593,
year = {2023},
author = {Guo, X and Hu, X and Li, J and Shao, B and Wang, Y and Wang, L and Li, K and Lin, D and Wang, H and Gao, Z and Jiao, Y and Wen, Y and Ji, H and Ma, C and Ge, S and Jiang, W and Jin, X},
title = {The Sapria himalayana genome provides new insights into the lifestyle of endoparasitic plants.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {134},
pmid = {37280593},
issn = {1741-7007},
mesh = {*Genome, Mitochondrial ; Gene Transfer, Horizontal ; Plants/genetics ; Flowers/genetics ; Phylogeny ; },
abstract = {BACKGROUND: Sapria himalayana (Rafflesiaceae) is an endoparasitic plant characterized by a greatly reduced vegetative body and giant flowers; however, the mechanisms underlying its special lifestyle and greatly altered plant form remain unknown. To illustrate the evolution and adaptation of S. himalayasna, we report its de novo assembled genome and key insights into the molecular basis of its floral development, flowering time, fatty acid biosynthesis, and defense responses.<br><br>RESULTS: The genome of S. himalayana is&#x2009;~&#x2009;1.92&#xa0;Gb with 13,670 protein-coding genes, indicating remarkable gene loss (~&#x2009;54%), especially genes involved in photosynthesis, plant body, nutrients, and defense response. Genes specifying floral organ identity and controlling organ size were identified in S. himalayana and Rafflesia cantleyi, and showed analogous spatiotemporal expression patterns in both plant species. Although the plastid genome had been lost, plastids likely biosynthesize essential fatty acids and amino acids (aromatic amino acids and lysine). A set of credible and functional horizontal gene transfer (HGT) events (involving genes and mRNAs) were identified in the nuclear and mitochondrial genomes of S. himalayana, most of which were under purifying selection. Convergent HGTs in Cuscuta, Orobanchaceae, and S. himalayana were mainly expressed at the parasite-host interface. Together, these results suggest that HGTs act as a bridge between the parasite and host, assisting the parasite in acquiring nutrients from the host.<br><br>CONCLUSIONS: Our results provide new insights into the flower development process and endoparasitic lifestyle of Rafflesiaceae plants. The amount of gene loss in S. himalayana is consistent with the degree of reduction in its body plan. HGT events are common among endoparasites and play an important role in their lifestyle adaptation.},
}
@article {pmid37279941,
year = {2023},
author = {Sheikh, S and Pánek, T and Gahura, O and Týč, J and Záhonová, K and Lukeš, J and Eliáš, M and Hashimi, H},
title = {A Novel Group of Dynamin-Related Proteins Shared by Eukaryotes and Giant Viruses Is Able to Remodel Mitochondria From Within the Matrix.},
journal = {Molecular biology and evolution},
volume = {40},
number = {6},
pages = {},
pmid = {37279941},
issn = {1537-1719},
mesh = {*Giant Viruses/genetics/metabolism ; Phylogeny ; Mitochondrial Proteins/genetics/metabolism ; Mitochondria/genetics/metabolism ; Dynamins/genetics/metabolism ; Saccharomyces cerevisiae/genetics ; },
abstract = {The diverse GTPases of the dynamin superfamily play various roles in the cell, as exemplified by the dynamin-related proteins (DRPs) Mgm1 and Opa1, which remodel the mitochondrial inner membrane in fungi and metazoans, respectively. Via an exhaustive search of genomic and metagenomic databases, we found previously unknown DRP types occurring in diverse eukaryotes and giant viruses (phylum Nucleocytoviricota). One novel DRP clade, termed MidX, combined hitherto uncharacterized proteins from giant viruses and six distantly related eukaryote taxa (Stramenopiles, Telonemia, Picozoa, Amoebozoa, Apusomonadida, and Choanoflagellata). MidX stood out because it was not only predicted to be mitochondria-targeted but also to assume a tertiary structure not observed in other DRPs before. To understand how MidX affects mitochondria, we exogenously expressed MidX from Hyperionvirus in the kinetoplastid Trypanosoma brucei, which lacks Mgm1 or Opa1 orthologs. MidX massively affected mitochondrial morphology from inside the matrix, where it closely associates with the inner membrane. This unprecedented mode of action contrasts to those of Mgm1 and Opa1, which mediate inner membrane remodeling in the intermembrane space. We speculate that MidX was acquired in Nucleocytoviricota evolution by horizontal gene transfer from eukaryotes and is used by giant viruses to remodel host mitochondria during infection. MidX's unique structure may be an adaptation for reshaping mitochondria from the inside. Finally, Mgm1 forms a sister group to MidX and not Opa1 in our phylogenetic analysis, throwing into question the long-presumed homology of these DRPs with similar roles in sister lineages.},
}
@article {pmid37279818,
year = {2023},
author = {Wang, X and Zhang, L and Gu, J and Feng, Y and He, K and Jiang, H},
title = {Effects of soil solarization combined with manure-amended on soil ARGs and microbial communities during summer fallow.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {333},
number = {},
pages = {121950},
doi = {10.1016/j.envpol.2023.121950},
pmid = {37279818},
issn = {1873-6424},
mesh = {*Anti-Bacterial Agents/analysis ; Manure/analysis ; Genes, Bacterial ; Soil ; Drug Resistance, Microbial/genetics ; *Microbiota ; Soil Microbiology ; },
abstract = {Soil solarization (SS) is a technique for managing pathogens and weeds, which involves covering with transparent plastic to increase soil temperature during summer fallow (SF). However, SS also alters the diversity of bacterial communities. Therefore, during SF, various organic modifiers are used in combination with SS to improve its efficacy. Organic amendments may contain antibiotic resistance genes (ARGs). Greenhouse vegetable production (GVP) soils are vital to ensure food security and ecological balance. However, comprehensive study on the effects of SS combined with different types of manure on ARGs in GVP soils during SF remains unclear. Therefore, this study employed high-throughput qPCR to explore the effects of different organic amendments combined with SS on the abundance changes of ARGs and mobile genetic elements (MGEs) in GVP soils during SF. The abundance and diversity of ARGs and MGEs in GVP soils with different manure fertilization and SS decreased during SF. Horizontal gene transfer via MGEs (especially integrases 45.80%) induced by changes in environmental factors (NO3[-]-N 14.7% and NH4[+]-N) was the main factor responsible for the changes in ARGs. Proteobacteria (14.3%) and Firmicutes were the main potential hosts of ARGs. Network analysis suggested that Ornithinimicrobium, Idiomarina and Corynebacterium had positive correlations with aminoglycosides, MLSB, and tetracycline resistance genes. These results provide new insights to understand the fate of ARGs in the GVP soils by manure-amended combined with SS during SF, which may help to reduce the spread of ARGs.},
}
@article {pmid37278656,
year = {2023},
author = {Huo, W and Price, VJ and Sharifi, A and Zhang, MQ and Palmer, KL},
title = {Enterococcus faecalis Strains with Compromised CRISPR-Cas Defense Emerge under Antibiotic Selection for a CRISPR-Targeted Plasmid.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {6},
pages = {e0012423},
pmid = {37278656},
issn = {1098-5336},
support = {R01 AI116610/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *CRISPR-Cas Systems ; *Anti-Bacterial Agents/pharmacology ; Enterococcus faecalis/genetics ; Plasmids/genetics ; Gastrointestinal Tract ; },
abstract = {Enterococcus faecalis is a Gram-positive bacterium that natively colonizes the human gastrointestinal tract and opportunistically causes life-threatening infections. Multidrug-resistant (MDR) E. faecalis strains have emerged that are replete with mobile genetic elements (MGEs). Non-MDR E. faecalis strains frequently possess CRISPR-Cas systems, which reduce the frequency of MGE acquisition. We demonstrated in previous studies that E. faecalis populations can transiently maintain both a functional CRISPR-Cas system and a CRISPR-Cas target. In this study, we used serial passage and deep sequencing to analyze these populations. In the presence of antibiotic selection for the plasmid, mutants with compromised CRISPR-Cas defense and enhanced ability to acquire a second antibiotic resistance plasmid emerged. Conversely, in the absence of selection, the plasmid was lost from wild-type E. faecalis populations but not E. faecalis populations that lacked the cas9 gene. Our results indicate that E. faecalis CRISPR-Cas can become compromised under antibiotic selection, generating populations with enhanced abilities to undergo horizontal gene transfer. IMPORTANCE Enterococcus faecalis is a leading cause of hospital-acquired infections and disseminator of antibiotic resistance plasmids among Gram-positive bacteria. We have previously shown that E. faecalis strains with an active CRISPR-Cas system can prevent plasmid acquisition and thus limit the transmission of antibiotic resistance determinants. However, CRISPR-Cas is not a perfect barrier. In this study, we observed populations of E. faecalis with transient coexistence of CRISPR-Cas and one of its plasmid targets. Our experimental data demonstrate that antibiotic selection results in compromised E. faecalis CRISPR-Cas function, thereby facilitating the acquisition of additional resistance plasmids by E. faecalis.},
}
@article {pmid37278068,
year = {2023},
author = {Guinet, B and Lepetit, D and Charlat, S and Buhl, PN and Notton, DG and Cruaud, A and Rasplus, JY and Stigenberg, J and de Vienne, DM and Boussau, B and Varaldi, J},
title = {Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {37278068},
issn = {2050-084X},
mesh = {Animals ; Female ; Biological Evolution ; DNA ; Domestication ; Genome, Viral ; *Viruses/genetics ; *Wasps/genetics ; },
abstract = {The accidental endogenization of viral elements within eukaryotic genomes can occasionally provide significant evolutionary benefits, giving rise to their long-term retention, that is, to viral domestication. For instance, in some endoparasitoid wasps (whose immature stages develop inside their hosts), the membrane-fusion property of double-stranded DNA viruses have been repeatedly domesticated following ancestral endogenizations. The endogenized genes provide female wasps with a delivery tool to inject virulence factors that are essential to the developmental success of their offspring. Because all known cases of viral domestication involve endoparasitic wasps, we hypothesized that this lifestyle, relying on a close interaction between individuals, may have promoted the endogenization and domestication of viruses. By analyzing the composition of 124 Hymenoptera genomes, spread over the diversity of this clade and including free-living, ecto, and endoparasitoid species, we tested this hypothesis. Our analysis first revealed that double-stranded DNA viruses, in comparison with other viral genomic structures (ssDNA, dsRNA, ssRNA), are more often endogenized and domesticated (that is, retained by selection) than expected from their estimated abundance in insect viral communities. Second, our analysis indicates that the rate at which dsDNA viruses are endogenized is higher in endoparasitoids than in ectoparasitoids or free-living hymenopterans, which also translates into more frequent events of domestication. Hence, these results are consistent with the hypothesis that the endoparasitoid lifestyle has facilitated the endogenization of dsDNA viruses, in turn, increasing the opportunities of domestications that now play a central role in the biology of many endoparasitoid lineages.},
}
@article {pmid37272817,
year = {2023},
author = {Castellanos, A and Restrepo, L and Bajaña, L and Betancourt, I and Bayot, B and Reyes, A},
title = {Genomic and Evolutionary Features of Nine AHPND Positive Vibrio parahaemolyticus Strains Isolated from South American Shrimp Farms.},
journal = {Microbiology spectrum},
volume = {11},
number = {4},
pages = {e0485122},
pmid = {37272817},
issn = {2165-0497},
mesh = {Humans ; *Vibrio parahaemolyticus/genetics ; Plasmids/genetics ; *Toxins, Biological ; Genomics ; Aquaculture ; Necrosis ; },
abstract = {Vibrio parahaemolyticus is a bacterial pathogen that becomes lethal to Penaeus shrimps when acquiring the pVA1-type plasmid carrying the PirAB[vp] genes, causing acute hepatopancreatic necrosis disease (AHPND). This disease causes significant losses across the world, with outbreaks reported in Southeast Asia, Mexico, and South America. Virulence level and mortality differences have been reported in isolates from different locations, and whether this phenomenon is caused by plasmid-related elements or genomic-related elements from the bacteria remains unclear. Here, nine genomes of South American AHPND-causing V. parahaemolyticus (VPAHPND) isolates were assembled and analyzed using a comparative genomics approach at (i) whole-genome, (ii) secretion system, and (iii) plasmid level, and then included for a phylogenomic analysis with another 86 strains. Two main results were obtained from our analyses. First, all isolates contained pVA1-type plasmids harboring the toxin coding genes, and with high similarity with the prototypical sequence of Mexican-like origin, while phylogenomic analysis showed some level of heterogeneity with discrete clusters and wide diversity compared to other available genomes. Second, although a high genomic similarity was observed, variation in virulence genes and clusters was observed, which might be relevant in the expression of the disease. Overall, our results suggest that South American pathogenic isolates are derived from various genetic lineages which appear to have acquired the plasmid through horizontal gene transfer. Furthermore, pathogenicity seems to be a multifactorial trait where the degree of virulence could be altered by the presence or variations of several virulence factors. IMPORTANCE AHPND have caused losses of over $2.6 billion to the aquaculture industry around the world due to its high mortality rate in shrimp farming. The most common etiological agent is V. parahaemolyticus strains possessing the pVA1-type plasmid carrying the PirAB[vp] toxin. Nevertheless, complete understanding of the role of genetic elements and their impact in the virulence of this pathogen remains unclear. In this work, we analyzed nine South American AHPND-causing V. parahaemolyticus isolates at a genomic level, and assessed their evolutionary relationship with other 86 strains. We found that all our isolates were highly similar and possessed the Mexican-type plasmid, but their genomic content did not cluster with other Mexican strains, but instead were spread across all isolates. These results suggest that South American VPAHPND have different genetic backgrounds, and probably proceed from diverse geographical locations, and acquire the pVA1-type plasmid via horizontal gene transfer at different times.},
}
@article {pmid37271423,
year = {2023},
author = {Feyereisen, R and Urban, JM and Nelson, DR},
title = {Aliens in the CYPome of the black fungus gnat, Bradysia coprophila.},
journal = {Insect biochemistry and molecular biology},
volume = {159},
number = {},
pages = {103965},
doi = {10.1016/j.ibmb.2023.103965},
pmid = {37271423},
issn = {1879-0240},
mesh = {Animals ; *Diptera/genetics ; Insecta ; *Insecticides ; Genome ; Fungi ; },
abstract = {The diverse cytochrome P450 enzymes of insects play essential physiological roles and also play important roles in the metabolism of environmental chemicals such as insecticides. We manually curated the complement of P450 (CYP) genes, or CYPome, of the black fungus gnat, Bradysia (Sciara) coprophila (Diptera, Sciaroidea), a species with a variable number of chromosomes. This CYPome carries two types of "alien" P450 genes. The first type of alien P450s was found among the 163 CYP genes of the core genome (autosomes and X). They consist of 28 sequences resulting from horizontal gene transfer, with closest sequences not found in insects, but in other arthropods, often Collembola. These genes are not contaminants, because they are expressed genes with introns, found in synteny with regular dipteran genes, also found in B. odoriphaga and B. hygida. Two such "alien" genes are representatives of CYP clans not otherwise found in insects, a CYP53 sequence related to fungal CYP53 genes, and a CYP19-like sequence similar to some collembolan sequences but of unclear origin. The second type of alien P450s are represented by 99 sequences from germline-restricted chromosomes (GRC). While most are P450 pseudogenes, 33 are apparently intact, with half being more closely related to P450s from Cecidomyiidae than from Sciaridae, thus supporting the hypothesis of a cross-family hybridization origin of the GRC.},
}
@article {pmid37270585,
year = {2023},
author = {Liu, S and Zeng, J and Yu, H and Wang, C and Yang, Y and Wang, J and He, Z and Yan, Q},
title = {Antimony efflux underpins phosphorus cycling and resistance of phosphate-solubilizing bacteria in mining soils.},
journal = {The ISME journal},
volume = {17},
number = {8},
pages = {1278-1289},
pmid = {37270585},
issn = {1751-7370},
mesh = {Antimony/analysis/chemistry ; Soil/chemistry ; Phosphates/analysis ; Phosphorus/analysis ; Phylogeny ; Environmental Monitoring ; *Soil Pollutants/analysis ; *Metals, Heavy/analysis ; Bacteria/genetics ; *Microbiota ; China ; Soil Microbiology ; },
abstract = {Microorganisms play crucial roles in phosphorus (P) turnover and P bioavailability increases in heavy metal-contaminated soils. However, microbially driven P-cycling processes and mechanisms of their resistance to heavy metal contaminants remain poorly understood. Here, we examined the possible survival strategies of P-cycling microorganisms in horizontal and vertical soil samples from the world's largest antimony (Sb) mining site, which is located in Xikuangshan, China. We found that total soil Sb and pH were the primary factors affecting bacterial community diversity, structure and P-cycling traits. Bacteria with the gcd gene, encoding an enzyme responsible for gluconic acid production, largely correlated with inorganic phosphate (Pi) solubilization and significantly enhanced soil P bioavailability. Among the 106 nearly complete bacterial metagenome-assembled genomes (MAGs) recovered, 60.4% carried the gcd gene. Pi transportation systems encoded by pit or pstSCAB were widely present in gcd-harboring bacteria, and 43.8% of the gcd-harboring bacteria also carried the acr3 gene encoding an Sb efflux pump. Phylogenetic and potential horizontal gene transfer (HGT) analyses of acr3 indicated that Sb efflux could be a dominant resistance mechanism, and two gcd-harboring MAGs appeared to acquire acr3 through HGT. The results indicated that Sb efflux could enhance P cycling and heavy metal resistance in Pi-solubilizing bacteria in mining soils. This study provides novel strategies for managing and remediating heavy metal-contaminated ecosystems.},
}
@article {pmid37270161,
year = {2023},
author = {Sharma, HK and Gupta, P and Nagpal, D and Mukherjee, M and Parmar, VS and Lather, V},
title = {Virtual screening and antimicrobial evaluation for identification of natural compounds as the prospective inhibitors of antibacterial drug resistance targets in Staphylococcus aureus.},
journal = {Fitoterapia},
volume = {168},
number = {},
pages = {105554},
doi = {10.1016/j.fitote.2023.105554},
pmid = {37270161},
issn = {1873-6971},
mesh = {Staphylococcus aureus ; *Methicillin-Resistant Staphylococcus aureus ; Thymol ; Eugenol/metabolism ; *Curcumin/metabolism ; Quercetin/pharmacology/metabolism ; *Berberine/metabolism ; Molecular Structure ; Anti-Bacterial Agents/pharmacology/chemistry ; Drug Resistance, Bacterial ; Microbial Sensitivity Tests ; },
abstract = {Infectious diseases have remained a burgeoning cause of death and disability since long. Staphylococcus aureus (S. aureus) is a severe bacterial pathogen causing nosocomial and community infections. It exhibits widespread resistance to antibiotics posing a significant threat to their efficacy. For combating this challenge, different strategies may include modifying existing antibiotics, developing new antibacterial agents, and combining treatments with resistance mechanism inhibitors. Resistance in S. aureus occurs through horizontal gene transfer or chromosomal mutations. Acquisition mechanisms involve enzymatic modification, efflux, target bypass, and drug displacement. Mutations can impact drug targets, activate efflux pumps, or alter cell wall composition to impede drug access. Overcoming S. aureus resistance requires innovative approaches to preserve antibiotic effectiveness. The present study involves the virtual screening of phytochemicals of diverse chemical classes from Zinc database against the antibiotic resistant targets of S. aureus like β-Lactamase, Penicillin Binding Protein 2a (PBP2a), Dihydrofolate reductase (DHFR), DNA gyrase, Multidrug ABC transporter SAV1866, Undecaprenyl diphosphate synthase (UPPS), etc. Thymol, eugenol, gallic acid, l-ascorbic acid, curcumin, berberine and quercetin were identified as potential molecules based on their docking score, binding interactions. These molecules were further analyzed for the ADMET and drug likeness properties using pkCSM, SwissADME and Qikprop tools. Further in vitro evaluation of these molecules against antibiotic-resistant strains of S. aureus, both alone and in combination with antibiotics revealed significant findings. Curcumin demonstrated the lowest MIC values (31.25-62.5 μg/ml) when tested individually. Thymol, berberine, and quercetin displayed MIC values within the range of 125-250 μg/ml, while eugenol and gallic acid exhibited MIC values ranging from 500 to 1000 μg/ml. Notably, thymol exhibited potent synergy with all four antibiotics against clinical isolates of S. aureus, with Fractional inhibitory concentration index (FICI) values consistently below 0.5, highlighting its exceptional antibacterial activity, especially in combination with amoxicillin.},
}
@article {pmid37270129,
year = {2023},
author = {Xu, Y and Liu, Q and Meng, G and Dong, C},
title = {Horizontal gene transfer of Cccyt contributes to virulence of mycoparasite Calcarisporium cordycipiticola by interacting with a host heat shock protein.},
journal = {International journal of biological macromolecules},
volume = {242},
number = {Pt 4},
pages = {124927},
doi = {10.1016/j.ijbiomac.2023.124927},
pmid = {37270129},
issn = {1879-0003},
mesh = {Phylogeny ; Hypocreales ; Virulence/genetics ; *Gene Transfer, Horizontal ; *Heat-Shock Proteins/genetics ; },
abstract = {Horizontal gene transfer (HGT) is an important driving force for virulence evolution of pathogens, however, functions of these transferred genes are still not fully investigated. Here, an HGT effector, CcCYT was reported to contribute to virulence of a mycoparasite, Calcarisporium cordycipiticola to the host Cordyceps militaris, an important mushroom. Cccyt was predicted to be horizontally transferred from Actinobacteria ancestor by phylogenetic, synteny, GC content and codon usage pattern analyses. The transcript of Cccyt was sharply up-regulated at the early stage of infecting C. militaris. This effector was localized to the cell wall and contributed to the virulence of C. cordycipiticola without affecting its morphology, mycelial growth, conidiation, and resistance to abiotic stress. CcCYT can firstly bind the septa, and finally cytoplasm of the deformed hyphal cells of C. militaris. Pull-down assay coupled mass spectrometry revealed that proteins with which CcCYT interacted were related to protein process, folding and degradation. GST-Pull down assay confirmed that C. cordycipiticola effector CcCYT can interact with host protein CmHSP90 to inhibit the immune response of host. The results provided functional evidence that HGT is an important driving force for the virulence evolution and will be helpful for revealing the interaction between mycoparasite and mushroom host.},
}
@article {pmid37269713,
year = {2023},
author = {Dai, X and Zhao, J and Sun, J and Chen, L and Han, P and Wang, X and Huang, J and Wang, L},
title = {ICESpsuAH0906, a novel optrA-carrying element conferring resistance to phenicols and oxazolidinones from Streptococcus parasuis, is transferable to Streptococcus suis.},
journal = {Veterinary microbiology},
volume = {283},
number = {},
pages = {109795},
doi = {10.1016/j.vetmic.2023.109795},
pmid = {37269713},
issn = {1873-2542},
mesh = {*Oxazolidinones ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Animals ; *Streptococcus suis ; Streptococcus ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; },
abstract = {Streptococcus parasuis is a potential opportunistic zoonotic pathogen which is a close relative to Streptococcus suis, which exhibit extensive genetic exchange. The occurrence and dissemination of oxazolidinone resistance poses a severe threat to public health. However, such knowledge about the optrA gene in S. parasuis is limited. Herein, we characterized an optrA-positive multi-resistant S. parasuis isolate AH0906, in which the capsular polysaccharide locus exhibited a hybrid structure of S. suis serotype 11 and S. parasuis serotype 26. The optrA and erm(B) genes were co-located on a novel ICE of the ICESsuYZDH1 family, designated ICESpsuAH0906. IS1216E-optrA-carrying translocatable unit could be formed when excised from ICESpsuAH0906. ICESpsuAH0906 was found to be transferable from isolate AH0906 to Streptococcus suis P1/7RF at a relative high frequency of ∼ 10[-5]. Nonconservative integrations of ICESpsuAH0906 into the primary site SSU0877 and secondary site SSU1797 with 2-/4-nt imperfect direct repeats in recipient P1/7RF were observed. Upon transfer, the transconjugant displayed elevated MICs of the corresponding antimicrobial agents and performed a weak fitness cost when compared with the recipient strain. To our knowledge, it is the first description of the transfer of optrA in S. prarasuis and the first report of interspecies transfer of ICE with triplet serine integrases (of the ICESsuYZDH1 family). Considering the high transmission frequency of the ICEs and the extensive genetic exchange potential of S. parasuis with other streptococci, attention should be paid to the dissemination of the optrA gene from S. parasuis to clinically more important bacterial pathogens.},
}
@article {pmid37268165,
year = {2024},
author = {Kameswaran, S and Gujjala, S and Zhang, S and Kondeti, S and Mahalingam, S and Bangeppagari, M and Bellemkonda, R},
title = {Quenching and quorum sensing in bacterial bio-films.},
journal = {Research in microbiology},
volume = {175},
number = {3},
pages = {104085},
doi = {10.1016/j.resmic.2023.104085},
pmid = {37268165},
issn = {1769-7123},
mesh = {*Quorum Sensing/genetics ; *Bacteria/genetics ; Biofilms ; Lactones ; },
abstract = {Quorum sensing (QS) is the ability of bacteria to monitor their population density and adjust gene expression accordingly. QS-regulated processes include host-microbe interactions, horizontal gene transfer, and multicellular behaviours (such as the growth and development of biofilm). The creation, transfer, and perception of bacterial chemicals known as autoinducers or QS signals are necessary for QS signalling (e.g. N-acylhomoserine lactones). Quorum quenching (QQ), another name for the disruption of QS signalling, comprises a wide range of events and mechanisms that are described and analysed in this study. In order to better comprehend the targets of the QQ phenomena that organisms have naturally developed and are currently being actively researched from practical perspectives, we first surveyed the diversity of QS-signals and QS-associated responses. Next, the mechanisms, molecular players, and targets related to QS interference are discussed, with a focus on natural QQ enzymes and compounds that function as QS inhibitors. To illustrate the processes and biological functions of QS inhibition in microbe-microbe and host-microbe interactions, a few QQ paradigms are described in detail. Finally, certain QQ techniques are offered as potential instruments in a variety of industries, including agriculture, medical, aquaculture, crop production, and anti-biofouling areas.},
}
@article {pmid37267763,
year = {2023},
author = {Sun, S and Wang, Q and Wang, N and Yang, S and Qi, H},
title = {High-risk antibiotics positively correlated with antibiotic resistance genes in five typical urban wastewater.},
journal = {Journal of environmental management},
volume = {342},
number = {},
pages = {118296},
doi = {10.1016/j.jenvman.2023.118296},
pmid = {37267763},
issn = {1095-8630},
mesh = {Humans ; *Wastewater ; *Anti-Bacterial Agents/pharmacology/analysis ; Genes, Bacterial ; Ecosystem ; Drug Resistance, Microbial/genetics ; Pharmaceutical Preparations ; },
abstract = {Antibiotic resistance genes (ARGs) and antibiotic amount increased within close proximity to human dominated ecosystems. However, few studies assessed the distribution of antibiotics and ARGs in multiple ecosystems especially the different urban wastewater. In this study, the spatial distribution of ARGs and antibiotics across the urban wastewater included domestic, livestock, hospital, pharmaceutical wastewater, influent of the wastewater treatment plant (WWTP) in Northeast China. The q-PCR results showed that ARGs were most abundant in community wastewater and followed by WWTP influent, livestock wastewater, pharmaceutical wastewater and hospital wastewater. The ARG composition differed among the five ecotypes with qnrS was the dominant ARG subtypes in WWTP influent and community wastewater, while sul2 dominant in livestock, hospital, pharmaceutical wastewater. The concentration of antibiotics was closely related to the antibiotic usage and consumption data. In addition to the high concentration of azithromycin at all sampling points, more than half of the antibiotics in livestock wastewater were veterinary antibiotics. However, antibiotics that closely related to humankind such as roxithromycin and sulfamethoxazole accounted for a higher proportion in hospital wastewater (13.6%) and domestic sewage (33.6%), respectively. The ambiguous correlation between ARGs and their corresponding antibiotics was detected. However, antibiotics that exhibited high ecotoxic effects were closely and positively correlated with ARGs and the class 1 integrons (intI1), which indicated that high ecotoxic compounds might affect antimicrobial resistance of bacteria by mediating horizontal gene transfer of ARGs. The coupling mechanism between the ecological risk of antibiotics and bacterial resistance needed to be further studied, and thereby provided a new insight to study the impact of environmental pollutants on ARGs in various ecotypes.},
}
@article {pmid37267681,
year = {2023},
author = {Carlsen, L and Büttner, H and Christner, M and Cordts, L and Franke, G and Hoffmann, A and Knobling, B and Lütgehetmann, M and Nakel, J and Werner, T and Knobloch, JK},
title = {Long time persistence and evolution of carbapenemase-producing Enterobacterales in the wastewater of a tertiary care hospital in Germany.},
journal = {Journal of infection and public health},
volume = {16},
number = {8},
pages = {1142-1148},
doi = {10.1016/j.jiph.2023.05.029},
pmid = {37267681},
issn = {1876-035X},
mesh = {Humans ; *Wastewater ; *Escherichia coli ; Tertiary Care Centers ; Bacterial Proteins/genetics ; beta-Lactamases/genetics ; Klebsiella pneumoniae/genetics ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; },
abstract = {BACKGROUND: Worldwide observations revealed increased frequencies of multi-resistant Enterobacterales and resistance genes in hospital wastewater compared to any other type of wastewater. Despite the description of clonal lineages possibly adapted to hospital wastewater, little is known about long term persistence as well as evolution of these lineages.<br><br>METHODS: In this study, wastewater isolates of different Enterobacterales species from a tertiary care hospital were investigated with 2.5 years distance. Whole Genome Sequencing (WGS) and resistance gene identification were performed for E. coli, C. freundii, S. marcescens, K. pneumoniae, K. oxytoca, and E. cloacae isolates (n&#xa0;=&#xa0;59), isolated in 2022 and compared with strains isolated from the same wastewater pipeline in 2019 (n&#xa0;=&#xa0;240).<br><br>RESULTS: Individual clonal lineages with highly related isolates could be identified in all species identified more than once in 2022 that appear to persist in the wastewater drainage. A common motif of all persistent clonal lineages was the carriage of mobile genetic elements encoding carbapenemase genes with hints for horizontal gene transfer in persistent clones in this environment observed over the 2.5-year period. Multiple plasmid replicons could be detected in both years. In 2022 isolates blaVIM-1 replaced blaOXA-48 as the most common carbapenemase gene compared to 2019. Interestingly, despite a similar abundance of carbapenemase genes (>80% of all isolates) at both time points genes encoding extended spectrum &#x3b2;-lactamases decreased over time.<br><br>CONCLUSIONS: This data indicates that hospital wastewater continuously releases genes encoding carbapenemases to the urban wastewater system. The evolution of the resident clones as well as the reasons for the selection advantage in this specific ecological niche needs to be further investigated in the future.},
}
@article {pmid37263036,
year = {2023},
author = {Wu, C and Zhang, G and Zhang, K and Sun, J and Cui, Z and Guo, Y and Liu, H and Xu, W},
title = {Strong variation in sedimental antibiotic resistomes among urban rivers, estuaries and coastal oceans: Evidence from a river-connected coastal water ecosystem in northern China.},
journal = {Journal of environmental management},
volume = {342},
number = {},
pages = {118132},
doi = {10.1016/j.jenvman.2023.118132},
pmid = {37263036},
issn = {1095-8630},
mesh = {*Anti-Bacterial Agents/analysis ; *Estuaries ; Rivers/microbiology ; Genes, Bacterial ; Ecosystem ; Bacteria/genetics ; Oceans and Seas ; China ; Water ; },
abstract = {Sediment is thought to be a vital reservoir to spread antibiotic resistance genes (ARGs) among various natural environments. However, the spatial distribution patterns of the sedimental antibiotic resistomes around the Bohai Bay region, a river-connected coastal water ecosystem, are still poorly understood. The present study conducted a comprehensive investigation of ARGs among urban rivers (UR), estuaries (ES) and Bohai Bay (BHB) by metagenomic sequencing. Overall, a total of 169 unique ARGs conferring resistance to 15 antimicrobial classes were detected across all sediment samples. The Kruskal-Wallis test showed that the diversity and abundance of ARGs in the UR were all significantly higher than those in the ES and BHB (p < 0.05 and p < 0.01), revealing the distance dilution of the sedimental resistomes from the river to the ocean. Multidrug resistance genes contained most of the ARG subtypes, whereas rifamycin resistance genes were the most abundant ARGs in this region. Our study demonstrated that most antimicrobial resistomes were highly accumulated in urban river sediments, whereas beta-lactamase resistance genes (mainly PNGM-1) dramatically increased away from the estuary to the open ocean. The relative abundance of mobile genetic elements (MGEs) also gradually decreased from rivers to the coastal ocean, whereas the difference in pathogenic bacteria was not significant in the three classifications. Among MGEs, plasmids were recognized as the most important carriers to support the horizontal gene transfer of ARGs within and between species. According to co-occurrence networks, pathogenic Proteobacteria, Actinobacteria, and Bacteroidetes were recognized as potential and important hosts of ARGs. Heavy metals, pH and moisture content were all recognized as the vital environmental factors influencing the distribution of ARGs in sediment samples. Overall, the present study may help to understand the distribution patterns of ARGs at a watershed scale, and help to make effective policies to control the emergence, spread and evolution of different ARG subtypes in different habitats.},
}
@article {pmid37261234,
year = {2023},
author = {Fatima, S and Ishaq, Z and Irfan, M and AlAsmari, AF and Achakzai, JK and Zaheer, T and Ali, A and Akbar, A},
title = {Whole-genome sequencing of multidrug resistance Salmonella Typhi clinical strains isolated from Balochistan, Pakistan.},
journal = {Frontiers in public health},
volume = {11},
number = {},
pages = {1151805},
pmid = {37261234},
issn = {2296-2565},
mesh = {Humans ; *Salmonella typhi/genetics ; Multilocus Sequence Typing ; Pakistan ; *Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Whole Genome Sequencing ; Drug Resistance, Multiple ; },
abstract = {INTRODUCTION: Salmonella enterica serovar Typhi (S. Typhi) is a major cause of morbidity and mortality in developing countries, contributing significantly to the global disease burden.<br><br>METHODS: In this study, S. Typhi strains were isolated from 100 patients exhibiting symptoms of typhoid fever at a tertiary care hospital in Pakistan. Antimicrobial testing of all isolates was performed to determine the sensitivity and resistance pattern. Three MDR strains, namely QS194, QS430, and QS468, were subjected to whole genome sequencing for genomic characterization.<br><br>RESULTS AND DISCUSSION: MLST analysis showed that QS194, belonged to ST19, which is commonly associated with Salmonella enterica serovar typhimurium. In contrast, QS430 and QS468, belonged to ST1, a sequence type frequently associated with S. Typhi. PlasmidFinder identified the presence of IncFIB(S) and IncFII(S) plasmids in QS194, while IncQ1 was found in QS468. No plasmid was detected in QS430. CARD-based analysis showed that the strains were largely resistant to a variety of antibiotics and disinfecting agents/antiseptics, including fluoroquinolones, cephalosporins, monobactams, cephamycins, penams, phenicols, tetracyclines, rifamycins, aminoglycosides, etc. The S. Typhi strains possessed various virulence factors, such as Vi antigen, Agf/Csg, Bcf, Fim, Pef, etc. The sequencing data indicated that the strains had antibiotic resistance determinants and shared common virulence factors. Pangenome analysis of the selected S. Typhi strains identified 13,237 genes, with 3,611 being core genes, 2,093 shell genes, and 7,533 cloud genes. Genome-based typing and horizontal gene transfer analysis revealed that the strains had different evolutionary origins and may have adapted to distinct environments or host organisms. These findings provide important insights into the genetic characteristics of S. Typhi strains and their potential association with various ecological niches and host organisms.},
}
@article {pmid37258869,
year = {2023},
author = {Abdelrazik, E and El-Hadidi, M},
title = {Tracking Antibiotic Resistance from the Environment to Human Health.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2649},
number = {},
pages = {289-301},
pmid = {37258869},
issn = {1940-6029},
mesh = {Humans ; *Bacteria/genetics ; Drug Resistance, Microbial/genetics ; *Anti-Bacterial Agents/pharmacology ; Genome, Bacterial ; Metagenome ; Genes, Bacterial ; Metagenomics ; },
abstract = {Antimicrobial resistance (AMR) is one of the threats to our world according to the World Health Organization (WHO). Resistance is an evolutionary dynamic process where host-associated microbes have to adapt to their stressful environments. AMR could be classified according to the mechanism of resistance or the biome where resistance takes place. Antibiotics are one of the stresses that lead to resistance through antibiotic resistance genes (ARGs). The resistome could be defined as the collection of all ARGs in an organism's genome or metagenome. Currently, there is a growing body of evidence supporting that the environment is the largest source of ARGs, but to what extent the environment does contribute to the antimicrobial resistance evolution is a matter of investigation. Monitoring the ARGs transfer route from the environment to humans and vice versa is a nature-to-nature feedback loop where you cannot set an accurate starting point of the evolutionary event. Thus, tracking resistome evolution and transfer to and from different biomes is crucial for the surveillance and prediction of the next resistance outbreak.Herein, we review the overlap between clinical and environmental resistomes and the available databases and computational analysis tools for resistome analysis through ARGs detection and characterization in bacterial genomes and metagenomes. Till this moment, there is no tool that can predict the resistance evolution and dynamics in a distinct biome. But, hopefully, by understanding the complicated relationship between the environmental and clinical resistome, we could develop tools that track the feedback loop from nature to nature in terms of evolution, mobilization, and transfer of ARGs.},
}
@article {pmid37257204,
year = {2023},
author = {Chen, P and Yu, K and He, Y},
title = {The dynamics and transmission of antibiotic resistance associated with plant microbiomes.},
journal = {Environment international},
volume = {176},
number = {},
pages = {107986},
doi = {10.1016/j.envint.2023.107986},
pmid = {37257204},
issn = {1873-6750},
mesh = {Humans ; *Bacteria/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; *Microbiota ; Soil ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; },
abstract = {Antibiotic resistance genes (ARGs) have been widely found and studied in soil and water environments. However, the propagation of ARGs in plant microbiomes has attracted insufficient attention. Plant microbiomes, especially the rhizosphere microorganisms, are closely connected with water, soil, and air, which allows ARGs to spread widely in ecosystems and pose a threat to human health after entering the human body with bacteria. Therefore, it is necessary to deeply understand and explore the dynamics and the transmission of ARGs in rhizosphere microorganisms and endophytes of plants. In this review, the transmission and influencing factors of ARGs in the microorganisms associated with plants, especially the influence of root exudates on plant microbiomes, are analyzed. Notably, the role of intrinsic genes of plants in determining root exudates and their potential effects on ARGs are proposed and analyzed. The important role of phyllosphere microorganisms and endophytes in the transmission of ARGs and co-resistance of antibiotics and other substances are also emphasized. The proliferation and transmission of ARGs associated with plant microbiomes addressed in this review is conducive to revealing the fate of ARGs in plant microorganisms and alleviating ARG pollution.},
}
@article {pmid37256324,
year = {2023},
author = {Oliveira, GS and Lentz, SA and Wink, PL and Martins, AF},
title = {Molecular typing of mcr-1 Escherichia coli isolates from pigs and farm environment based on fumC and fimH alleles.},
journal = {Future microbiology},
volume = {18},
number = {},
pages = {481-488},
doi = {10.2217/fmb-2022-0173},
pmid = {37256324},
issn = {1746-0921},
mesh = {Animals ; Swine ; Escherichia coli ; Farms ; *Escherichia coli Infections/veterinary/genetics ; Alleles ; Phylogeny ; *Escherichia coli Proteins/genetics ; Multilocus Sequence Typing ; Anti-Bacterial Agents/pharmacology ; Colistin/pharmacology ; Microbial Sensitivity Tests ; Adhesins, Escherichia coli/genetics ; Fimbriae Proteins/genetics ; },
abstract = {Background: The dissemination of polymyxin resistance represents a significant threat to public health. Materials &amp; methods: Sequence-based typing was performed by 53 mcr-1 Escherichia coli isolates using fumC/fimH (CH) genes to characterize clones spreading from pig farming. Furthermore, 12 isolates had their whole genome sequenced for phylogenetic study. Results: The isolates were classified into 22 distinct CH types, and two novel CH types (CH41-1578 and CH4-1579) and one sequence type (ST12652) was also described. According to phylogenetic study, both multilocus sequence typing and CH methods grouped the isolates similarly. Conclusion: Our findings suggest that the dissemination of the mcr-1 gene in pig farming has occurred mainly by horizontal gene transfer, and CH typing proved to be a good tool to characterize E. coli clones.},
}
@article {pmid37254648,
year = {2023},
author = {Rana, R and Jaiswal, G and Bansal, K and Patil, PB},
title = {Comparative genomics reveals the emergence of copper resistance in a non-pigmented Xanthomonas pathogen of grapevine.},
journal = {Environmental microbiology reports},
volume = {15},
number = {6},
pages = {716-726},
pmid = {37254648},
issn = {1758-2229},
support = {OLP0191-20//CSIR - Institute of Microbial Technology/ ; },
mesh = {*Copper/pharmacology ; *Xanthomonas/genetics ; Genomics ; Gene Transfer, Horizontal ; Plant Diseases/microbiology ; },
abstract = {Xanthomonas citri pv. viticola (Xcv) is the causal agent of bacterial canker in grapevine. The pathogen is restricted to India, where it was first reported in the 1970s, and Brazil. In the present study, we report the first complete genome sequence of Xcv LMG965, which is a reference pathotype strain. We also report genome sequences of additional isolates from India and comparative genome-based studies of isolates from Brazil. Apart from revealing the monophyletic origin of the pathovar, we could also confirm a common frameshift mutation in a gene that is part of the Xanthomonadin pigment biosynthetic gene cluster in all the isolates. The comparative study also revealed multiple intrinsic copper resistance-related genes in Brazilian isolates, suggesting intense selection, possibly because of heavy and indiscriminate usage of copper as an antimicrobial agent in the orchards. There is also the association of a Tn3-like transposase in the vicinity of the copper resistance genes, indicating a potential for rapid diversification through horizontal gene transfer events. The findings, along with genomic resources, will allow for systematic genetic and functional studies of Xcv.},
}
@article {pmid37252660,
year = {2023},
author = {Tokuda, R and Iwabuchi, N and Kitazawa, Y and Nijo, T and Suzuki, M and Maejima, K and Oshima, K and Namba, S and Yamaji, Y},
title = {Potential mobile units drive the horizontal transfer of phytoplasma effector phyllogen genes.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1132432},
pmid = {37252660},
issn = {1664-8021},
abstract = {Phytoplasmas are obligate intracellular plant pathogenic bacteria that can induce phyllody, which is a type of abnormal floral organ development. Phytoplasmas possess phyllogens, which are effector proteins that cause phyllody in plants. Phylogenetic comparisons of phyllogen and 16S rRNA genes have suggested that phyllogen genes undergo horizontal transfer between phytoplasma species and strains. However, the mechanisms and evolutionary implications of this horizontal gene transfer are unclear. Here, we analyzed synteny in phyllogen flanking genomic regions from 17 phytoplasma strains that were related to six 'Candidatus' species, including three strains newly sequenced in this study. Many of the phyllogens were flanked by multicopy genes within potential mobile units (PMUs), which are putative transposable elements found in phytoplasmas. The multicopy genes exhibited two distinct patterns of synteny that correlated with the linked phyllogens. The low level of sequence identities and partial truncations found among these phyllogen flanking genes indicate that the PMU sequences are deteriorating, whereas the highly conserved sequences and functions (e.g., inducing phyllody) of the phyllogens suggest that the latter are important for phytoplasma fitness. Furthermore, although their phyllogens were similar, PMUs in strains related to 'Ca. P. asteris' were often located in different regions of the genome. These findings strongly indicate that PMUs drive the horizontal transfer of phyllogens among phytoplasma species and strains. These insights improve our understanding of how symptom-determinant genes have been shared among phytoplasmas.},
}
@article {pmid37251586,
year = {2023},
author = {Scott, TW and West, SA and Dewar, AE and Wild, G},
title = {Is cooperation favored by horizontal gene transfer?.},
journal = {Evolution letters},
volume = {7},
number = {3},
pages = {113-120},
pmid = {37251586},
issn = {2056-3744},
support = {834164/ERC_/European Research Council/International ; },
abstract = {It has been hypothesized that horizontal gene transfer on plasmids can facilitate the evolution of cooperation, by allowing genes to jump between bacteria, and hence increase genetic relatedness at the cooperative loci. However, we show theoretically that horizontal gene transfer only appreciably increases relatedness when plasmids are rare, where there are many plasmid-free cells available to infect (many opportunities for horizontal gene transfer). In contrast, when plasmids are common, there are few opportunities for horizontal gene transfer, meaning relatedness is not appreciably increased, and so cooperation is not favored. Plasmids, therefore, evolve to be rare and cooperative, or common and noncooperative, meaning plasmid frequency and cooperativeness are never simultaneously high. The overall level of plasmid-mediated cooperation, given by the product of plasmid frequency and cooperativeness, is therefore consistently negligible or low.},
}
@article {pmid37250807,
year = {2023},
author = {Mwakyoma, AA and Kidenya, BR and Minja, CA and Mushi, MF and Sandeman, A and Sabiti, W and Holden, MTG and Mshana, SE},
title = {Comparison of Horizontal blaCTX-M Gene Transfer via Conjugation among Extended Spectrum β-Lactamases Producing Escherichia coli Isolates from Patients with Urinary Tract Infection, Their Animals, and Environment.},
journal = {Archives of molecular biology and genetics},
volume = {2},
number = {1},
pages = {1-8},
pmid = {37250807},
issn = {2831-6754},
support = {MR/S004785/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {BACKGROUND: The dissemination of the extended spectrum β-lactamases (ESBL) producing E. coli poses a significant public health problem. Understanding the efficiency and frequency of horizontal gene transfer via conjugation of ESBL producing E. coli is imperative towards devising prevention and control measures. This study compared the frequencies and efficiencies of horizontal blaCTX-M gene transfer via conjugation among Escherichia coli isolates from urine and gastrointestinal tract (GIT) of patients with urinary tract infection (UTI), their animals and environment.<br><br>METHODS: Horizontal blaCTX-M gene transfer via conjugation by a broth mating experiment was performed using 50 confirmed ESBL producing E. coli isolates as donors and Escherichia coli J53 (F[-], met, pro, Az[r]), as the recipient. The transconjugants were detected and their frequencies and efficiencies of conjugation were measured and compared between ESBL producing E. coli isolates multi-sourced from urine, GIT, animals and environment. Antimicrobial susceptibility testing of all resulting transconjugants was performed. DNA was extracted from all transconjugants to confirm the presence and the acquisition of blaCTX-M gene.<br><br>RESULTS: Out of 50 ESBL producing E. coli isolates harboring blaCTX-M gene, 37 (74.0%) successfully exercised horizontal gene transfer through conjugation. All transconjugants were confirmed phenotypically and genotypically by PCR. Of note, all of the isolates from environment 100.0% (7/7) performed conjugation, exhibiting the highest transfer efficiency, followed by isolates from urine and animals, with the conjugation transfer efficiency of 77.8% (14/18) and 76.1% (10/13), respectively. The isolates from the environment conjugated with a significant more efficiency than those from the GIT [Two-sample test of proportions; p-value = 0.0119]. The overall conjugation transfer frequencies ranged from 0.4 &#xd7; 10[-14] - 5.5 &#xd7; 10[-11] per donor cells with the highest median conjugation transfer frequency observed among isolates from animal (3.23 &#xd7; 10[-12] [IQR: 0.70 &#xd7; 10[-12] - 7.22 &#xd7; 10[-12]]) followed by that of isolates from the environment (1.60 &#xd7; 10[-12] [IQR: 0.30 &#xd7; 10[-12] - 5.0 &#xd7; 10[-12]]).<br><br>CONCLUSION: ESBL producing E. coli from human, animals and environment exercises horizontal blaCTX-M gene transfer efficiently with the highest occurrence among isolates from the environment and animals. The antimicrobial resistance control and prevention strategies should be widened up to explore strategies to prevent horizontal AMR gene transfer.},
}
@article {pmid37246713,
year = {2023},
author = {Jowsey, WJ and Morris, CRP and Hall, DA and Sullivan, JT and Fagerlund, RD and Eto, KY and Solomon, PD and Mackay, JP and Bond, CS and Ramsay, JP and Ronson, CW},
title = {DUF2285 is a novel helix-turn-helix domain variant that orchestrates both activation and antiactivation of conjugative element transfer in proteobacteria.},
journal = {Nucleic acids research},
volume = {51},
number = {13},
pages = {6841-6856},
pmid = {37246713},
issn = {1362-4962},
mesh = {Quorum Sensing/genetics ; Gene Transfer, Horizontal ; Transcriptional Activation ; Bacterial Proteins/genetics/metabolism ; Transcription Factors/metabolism ; *Conjugation, Genetic ; *Proteobacteria/genetics ; Mesorhizobium ; },
abstract = {Horizontal gene transfer is tightly regulated in bacteria. Often only a fraction of cells become donors even when regulation of horizontal transfer is coordinated at the cell population level by quorum sensing. Here, we reveal the widespread 'domain of unknown function' DUF2285 represents an 'extended-turn' variant of the helix-turn-helix domain that participates in both transcriptional activation and antiactivation to initiate or inhibit horizontal gene transfer. Transfer of the integrative and conjugative element ICEMlSymR7A is controlled by the DUF2285-containing transcriptional activator FseA. One side of the DUF2285 domain of FseA has a positively charged surface which is required for DNA binding, while the opposite side makes critical interdomain contacts with the N-terminal FseA DUF6499 domain. The QseM protein is an antiactivator of FseA and is composed of a DUF2285 domain with a negative surface charge. While QseM lacks the DUF6499 domain, it can bind the FseA DUF6499 domain and prevent transcriptional activation by FseA. DUF2285-domain proteins are encoded on mobile elements throughout the proteobacteria, suggesting regulation of gene transfer by DUF2285 domains is a widespread phenomenon. These findings provide a striking example of how antagonistic domain paralogues have evolved to provide robust molecular control over the initiation of horizontal gene transfer.},
}
@article {pmid37246198,
year = {2023},
author = {Shafique, MS and Guo, W and Chen, X and Zhao, K and Liu, Y and Wang, C and Ji, Z},
title = {Genome resource of Xanthomonas oryzae pv. oryzae Chinese strain NE-8 causing bacterial blight of rice.},
journal = {Functional &amp; integrative genomics},
volume = {23},
number = {2},
pages = {189},
pmid = {37246198},
issn = {1438-7948},
support = {2019SLJ020378//China Scholarship council/ ; Y2022QC01//Central Public-interest Scientific Institution Basal Research Fund/ ; Y2022QC01//Central Public-interest Scientific Institution Basal Research Fund/ ; B21HJ0218//Hainan Yazhou-Bay Seed Laboratory/ ; B21HJ0218//Hainan Yazhou-Bay Seed Laboratory/ ; },
mesh = {Bacterial Proteins/genetics ; *Oryza/genetics/microbiology ; Plant Diseases/genetics/microbiology ; *Xanthomonas/genetics ; },
}
@article {pmid37243281,
year = {2023},
author = {Arnau, V and Díaz-Villanueva, W and Mifsut Benet, J and Villasante, P and Beamud, B and Mompó, P and Sanjuan, R and González-Candelas, F and Domingo-Calap, P and Džunková, M},
title = {Inference of the Life Cycle of Environmental Phages from Genomic Signature Distances to Their Hosts.},
journal = {Viruses},
volume = {15},
number = {5},
pages = {},
pmid = {37243281},
issn = {1999-4915},
mesh = {*Bacteriophages/genetics ; Lysogeny ; Genomics ; Genome, Viral ; Bacteria/genetics ; Oligonucleotides ; },
abstract = {The environmental impact of uncultured phages is shaped by their preferred life cycle (lytic or lysogenic). However, our ability to predict it is very limited. We aimed to discriminate between lytic and lysogenic phages by comparing the similarity of their genomic signatures to those of their hosts, reflecting their co-evolution. We tested two approaches: (1) similarities of tetramer relative frequencies, (2) alignment-free comparisons based on exact k = 14 oligonucleotide matches. First, we explored 5126 reference bacterial host strains and 284 associated phages and found an approximate threshold for distinguishing lysogenic and lytic phages using both oligonucleotide-based methods. The analysis of 6482 plasmids revealed the potential for horizontal gene transfer between different host genera and, in some cases, distant bacterial taxa. Subsequently, we experimentally analyzed combinations of 138 Klebsiella pneumoniae strains and their 41 phages and found that the phages with the largest number of interactions with these strains in the laboratory had the shortest genomic distances to K. pneumoniae. We then applied our methods to 24 single-cells from a hot spring biofilm containing 41 uncultured phage-host pairs, and the results were compatible with the lysogenic life cycle of phages detected in this environment. In conclusion, oligonucleotide-based genome analysis methods can be used for predictions of (1) life cycles of environmental phages, (2) phages with the broadest host range in culture collections, and (3) potential horizontal gene transfer by plasmids.},
}
@article {pmid37239594,
year = {2023},
author = {Tuvo, B and Scarpaci, M and Bracaloni, S and Esposito, E and Costa, AL and Ioppolo, M and Casini, B},
title = {Microplastics and Antibiotic Resistance: The Magnitude of the Problem and the Emerging Role of Hospital Wastewater.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {10},
pages = {},
pmid = {37239594},
issn = {1660-4601},
mesh = {Humans ; *Microplastics ; *Wastewater ; Plastics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Hospitals ; },
abstract = {The role of microplastics (MPs) in the spread of antibiotic resistance genes (ARGs) is increasingly attracting global research attention due to their unique ecological and environmental effects. The ubiquitous use of plastics and their release into the environment by anthropic/industrial activities are the main sources for MP contamination, especially of water bodies. Because of their physical and chemical characteristics, MPs represent an ideal substrate for microbial colonization and formation of biofilm, where horizontal gene transfer is facilitated. In addition, the widespread and often injudicious use of antibiotics in various human activities leads to their release into the environment, mainly through wastewater. For these reasons, wastewater treatment plants, in particular hospital plants, are considered hotspots for the selection of ARGs and their diffusion in the environment. As a result, the interaction of MPs with drug-resistant bacteria and ARGs make them vectors for the transport and spread of ARGs and harmful microorganisms. Microplastic-associated antimicrobial resistance is an emerging threat to the environment and consequently for human health. More studies are required to better understand the interaction of these pollutants with the environment as well as to identify effective management systems to reduce the related risk.},
}
@article {pmid37239483,
year = {2023},
author = {Alim, NTB and Koppenhöfer, S and Lang, AS and Beatty, JT},
title = {Extracellular Polysaccharide Receptor and Receptor-Binding Proteins of the Rhodobacter capsulatus Bacteriophage-like Gene Transfer Agent RcGTA.},
journal = {Genes},
volume = {14},
number = {5},
pages = {},
pmid = {37239483},
issn = {2073-4425},
mesh = {Carrier Proteins/metabolism ; Bacterial Proteins/genetics/metabolism ; *Rhodobacter capsulatus/genetics/metabolism ; *Bacteriophages/genetics ; Polysaccharides ; },
abstract = {A variety of prokaryotes produce a bacteriophage-like gene transfer agent (GTA), and the alphaproteobacterial Rhodobacter capsulatus RcGTA is a model GTA. Some environmental isolates of R. capsulatus lack the ability to acquire genes transferred by the RcGTA (recipient capability). In this work, we investigated the reason why R. capsulatus strain 37b4 lacks recipient capability. The RcGTA head spike fiber and tail fiber proteins have been proposed to bind extracellular oligosaccharide receptors, and strain 37b4 lacks a capsular polysaccharide (CPS). The reason why strain 37b4 lacks a CPS was unknown, as was whether the provision of a CPS to 37b4 would result in recipient capability. To address these questions, we sequenced and annotated the strain 37b4 genome and used BLAST interrogations of this genome sequence to search for homologs of genes known to be needed for R. capsulatus recipient capability. We also created a cosmid-borne genome library from a wild-type strain, mobilized the library into 37b4, and used the cosmid-complemented strain 37b4 to identify genes needed for a gain of function, allowing for the acquisition of RcGTA-borne genes. The relative presence of CPS around a wild-type strain, 37b4, and cosmid-complemented 37b4 cells was visualized using light microscopy of stained cells. Fluorescently tagged head spike fiber and tail fiber proteins of the RcGTA particle were created and used to measure the relative binding to wild-type and 37b4 cells. We found that strain 37b4 lacks recipient capability because of an inability to bind RcGTA; the reason it is incapable of binding is that it lacks CPS, and the absence of CPS is due to the absence of genes previously shown to be needed for CPS production in another strain. In addition to the head spike fiber, we found that the tail fiber protein also binds to the CPS.},
}
@article {pmid37239397,
year = {2023},
author = {Dey, S and Gaur, M and Sykes, EME and Prusty, M and Elangovan, S and Dixit, S and Pati, S and Kumar, A and Subudhi, E},
title = {Unravelling the Evolutionary Dynamics of High-Risk Klebsiella pneumoniae ST147 Clones: Insights from Comparative Pangenome Analysis.},
journal = {Genes},
volume = {14},
number = {5},
pages = {},
pmid = {37239397},
issn = {2073-4425},
mesh = {Humans ; *beta-Lactamases/genetics ; Klebsiella pneumoniae/genetics ; Phylogeny ; Bayes Theorem ; *Klebsiella Infections/epidemiology/genetics/drug therapy ; },
abstract = {BACKGROUND: The high prevalence and rapid emergence of antibiotic resistance in high-risk Klebsiella pneumoniae (KP) ST147 clones is a global health concern and warrants molecular surveillance.<br><br>METHODS: A pangenome analysis was performed using publicly available ST147 complete genomes. The characteristics and evolutionary relationships among ST147 members were investigated through a Bayesian phylogenetic analysis.<br><br>RESULTS: The large number of accessory genes in the pangenome indicates genome plasticity and openness. Seventy-two antibiotic resistance genes were found to be linked with antibiotic inactivation, efflux, and target alteration. The exclusive detection of the blaOXA-232 gene within the ColKp3 plasmid of KP_SDL79 suggests its acquisition through horizontal gene transfer. The association of seventy-six virulence genes with the acrAB efflux pump, T6SS system and type I secretion system describes its pathogenicity. The presence of Tn6170, a putative Tn7-like transposon in KP_SDL79 with an insertion at the flanking region of the tnsB gene, establishes its transmission ability. The Bayesian phylogenetic analysis estimates ST147's initial divergence in 1951 and the most recent common ancestor for the entire KP population in 1621.<br><br>CONCLUSIONS: Present study highlights the genetic diversity and evolutionary dynamics of high-risk clones of K. pneumoniae. Further inter-clonal diversity studies will help us understand its outbreak more precisely and pave the way for therapeutic interventions.},
}
@article {pmid37237011,
year = {2023},
author = {Negeri, AA and Mamo, H and Gahlot, DK and Gurung, JM and Seyoum, ET and Francis, MS},
title = {Characterization of plasmids carrying blaCTX-M genes among extra-intestinal Escherichia coli clinical isolates in Ethiopia.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {8595},
pmid = {37237011},
issn = {2045-2322},
mesh = {Humans ; Anti-Bacterial Agents ; beta-Lactamases/genetics ; *Escherichia coli/genetics ; *Escherichia coli Infections/epidemiology ; Ethiopia/epidemiology ; *Plasmids/genetics ; },
abstract = {CTX-Ms are encoded by blaCTX-M genes and are widely distributed extended-spectrum β-lactamases (ESBLs). They are the most important antimicrobial resistance (AMR) mechanism to β-lactam antibiotics in the Enterobacteriaceae. However, the role of transmissible AMR plasmids in the dissemination of blaCTX-M genes has scarcely been studied in Africa where the burden of AMR is high and rapidly spreading. In this study, AMR plasmid transmissibility, replicon types and addiction systems were analysed in CTX-M-producing Escherichia coli clinical isolates in Ethiopia with a goal to provide molecular insight into mechanisms underlying such high prevalence and rapid dissemination. Of 100 CTX-Ms-producing isolates obtained from urine (84), pus (10) and blood (6) from four geographically distinct healthcare settings, 75% carried transmissible plasmids encoding for CTX-Ms, with CTX-M-15 being predominant (n = 51). Single IncF plasmids with the combination of F-FIA-FIB (n = 17) carried the bulk of blaCTX-M-15 genes. In addition, IncF plasmids were associated with multiple addiction systems, ISEcp1 and various resistance phenotypes for non-cephalosporin antibiotics. Moreover, IncF plasmid carriage is associated with the international pandemic E. coli ST131 lineage. Furthermore, several CTX-M encoding plasmids were associated with serum survival of the strains, but less so with biofilm formation. Hence, both horizontal gene transfer and clonal expansion may contribute to the rapid and widespread distribution of blaCTX-M genes among E. coli populations in Ethiopian clinical settings. This information is relevant for local epidemiology and surveillance, but also for global understanding of the successful dissemination of AMR gene carrying plasmids.},
}
@article {pmid37236960,
year = {2023},
author = {Wang, WJ and Yu, LM and Shao, MY and Jia, YT and Liu, LQ and Ma, XH and Zheng, Y and Liu, YF and Zhang, YZ and Luo, XX and Li, FM and Zheng, H},
title = {Research review on the pollution of antibiotic resistance genes in livestock and poultry farming environments.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {34},
number = {5},
pages = {1415-1429},
doi = {10.13287/j.1001-9332.202305.032},
pmid = {37236960},
issn = {1001-9332},
mesh = {Animals ; Humans ; *Poultry/genetics ; *Anti-Bacterial Agents/pharmacology ; Livestock/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Agriculture ; },
abstract = {Increasingly serious pollution of antibiotic resistance genes (ARGs) caused by the abuse of antibiotics in livestock and poultry industry has raised worldwide concerns. ARGs could spread among various farming environmental media through adsorption, desorption, migration, and also could transfer into human gut microbiome by hori-zontal gene transfer (HGT), posing potential threats to public health. However, the comprehensive review on the pollution patterns, environmental behaviors, and control techniques of ARGs in livestock and poultry environments in view of One Health is still inadequate, resulting in the difficulties in effectively assessing ARGs transmission risk and developing the efficient control strategies. Here, we analyzed the pollution characteristics of typical ARGs in various countries, regions, livestock species, and environmental media, reviewed the critical environmental fate and influencing factors, control strategies, and the shortcomings of current researches about ARGs in the livestock and poultry farming industry combined with One Health philosophy. In particular, we addressed the importance and urgency of identifying the distribution characteristics and environmental process mechanisms of ARGs, and developing green and efficient ARG control means in livestock farming environments. We further proposed gaps and prospects for the future research. It would provide theoretical basis for the research on health risk assessment and technology exploitation of alleviating ARG pollution in livestock farming environment.},
}
@article {pmid37236388,
year = {2023},
author = {Song, D and Tang, X and Tariq, A and Pan, K and Li, D},
title = {Regional distribution and migration potential of antibiotic resistance genes in croplands of Qinghai Tibet Plateau.},
journal = {Environmental research},
volume = {231},
number = {Pt 2},
pages = {116233},
doi = {10.1016/j.envres.2023.116233},
pmid = {37236388},
issn = {1096-0953},
mesh = {Tibet ; Anti-Bacterial Agents/pharmacology ; Ecosystem ; *Soil Pollutants/analysis ; *Metals, Heavy/analysis ; Soil/chemistry ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Soil Microbiology ; Crops, Agricultural ; },
abstract = {Agricultural activities have recently disturbed the ecosystem of the Qinghai-Tibet Plateau and the shift of antibiotic resistance genes (ARGs) in the different types of farmlands is not well understood, so more comprehensive ecological barrier management measures cannot be provided for the region. This research was performed to exploring ARG pollution in cropland soil on the Qinghai-Tibet Plateau to obtain information on the geographical and climatic factors shaping the ARG distribution. Based on high-throughput quantitative PCR (HT-qPCR) analysis, the ARG abundance in farmland ranged from 5.66 × 10[5] to 6.22 × 10[7] copies per gram of soil higher than previous research at soil and wetland in Qinghai-Tibet plateau, and it was higher in wheat and barley soils than in corn soil. The distribution of ARGs exhibited regional features as ARG abundance was adversely affected by mean annual precipitation and temperature with lower temperature and less rainfall at high altitude. According to network analysis and structural equation modeling (SEM), mobile genetic elements (MGEs) and heavy metals are the key drivers of ARG dissemination on the Qinghai-Tibet Plateau as they show negative relationship with ARGs, and selection copressure from heavy metals in cropland soil increases the horizontal gene transfer (HGT) potential of ARGs through synergistic selection effects, each contribution to the ARGs was 19% and 29% respectively. This research suggests the need to focus on controlling heavy metals and MGEs to constrain the dissemination of ARGs, as arable soil is already slightly contaminated by heavy metals.},
}
@article {pmid37232518,
year = {2023},
author = {Burch, CL and Romanchuk, A and Kelly, M and Wu, Y and Jones, CD},
title = {Empirical Evidence That Complexity Limits Horizontal Gene Transfer.},
journal = {Genome biology and evolution},
volume = {15},
number = {6},
pages = {},
pmid = {37232518},
issn = {1759-6653},
mesh = {*Gene Transfer, Horizontal ; *Evolution, Molecular ; Genome, Bacterial ; Bacteria/genetics ; Prokaryotic Cells ; Escherichia coli/genetics ; },
abstract = {Horizontal gene transfer (HGT) is a major contributor to bacterial genome evolution, generating phenotypic diversity, driving the expansion of protein families, and facilitating the evolution of new phenotypes, new metabolic pathways, and new species. Comparative studies of gene gain in bacteria suggest that the frequency with which individual genes successfully undergo HGT varies considerably and may be associated with the number of protein-protein interactions in which the gene participates, that is, its connectivity. Two nonexclusive hypotheses have emerged to explain why transferability should decrease with connectivity: the complexity hypothesis (Jain R, Rivera MC, Lake JA. 1999. Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci U S A. 96:3801-3806.) and the balance hypothesis (Papp B, Pál C, Hurst LD. 2003. Dosage sensitivity and the evolution of gene families in yeast. Nature 424:194-197.). These hypotheses predict that the functional costs of HGT arise from a failure of divergent homologs to make normal protein-protein interactions or from gene misexpression, respectively. Here we describe genome-wide assessments of these hypotheses in which we used 74 existing prokaryotic whole genome shotgun libraries to estimate rates of horizontal transfer of genes from taxonomically diverse prokaryotic donors into Escherichia coli. We show that 1) transferability declines as connectivity increases, 2) transferability declines as the divergence between donor and recipient orthologs increases, and that 3) the magnitude of this negative effect of divergence on transferability increases with connectivity. These effects are particularly robust among the translational proteins, which span the widest range of connectivities. Whereas the complexity hypothesis explains all three of these observations, the balance hypothesis explains only the first one.},
}
@article {pmid37227565,
year = {2023},
author = {Chettri, U and Nongkhlaw, M and Joshi, SR},
title = {Molecular Evidence for Occurrence of Heavy Metal and Antibiotic Resistance Genes Among Predominant Metal Tolerant Pseudomonas sp. and Serratia sp. Prevalent in the Teesta River.},
journal = {Current microbiology},
volume = {80},
number = {7},
pages = {226},
pmid = {37227565},
issn = {1432-0991},
support = {SR/FST/ LSI-666/2016(C)//Department of Science and Technology India/ ; F.4-7/2016/DRS-1 (SAP-II)//University Grants Commission India/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology/metabolism ; Pseudomonas/genetics/metabolism ; Rivers ; Ecosystem ; Phylogeny ; *Metals, Heavy/pharmacology/metabolism ; Drug Resistance, Microbial ; Bacteria/genetics ; },
abstract = {Riverine ecosystems polluted by pharmaceutical and metal industries are potential incubators of bacteria with dual resistance to heavy metals and antibiotics. The processes of co-resistance and cross resistance that empower bacteria to negotiate these challenges, strongly endorse dangers of antibiotic resistance generated by metal stress. Therefore, investigation into the molecular evidence of heavy metal and antibiotic resistance genes was the prime focus of this study. The selected Pseudomonas and Serratia species isolates evinced by their minimum inhibitory concentration and multiple antibiotic resistance (MAR) index showed significant heavy metal tolerance and multi-antibiotic resistance capability, respectively. Consequently, isolates with higher tolerance for the most toxic metal cadmium evinced high MAR index value (0.53 for Pseudomonas sp., and 0.46 for Serratia sp.) in the present investigation. Metal tolerance genes belonging to PIB-type and resistance nodulation division family of proteins were evident in these isolates. The antibiotic resistance genes like mexB, mexF and mexY occurred in Pseudomonas isolates while sdeB genes were present in Serratia isolates. Phylogenetic incongruency and GC composition analysis of PIB-type genes suggested that some of these isolates had acquired resistance through horizontal gene transfer (HGT). Therefore, the Teesta River has become a reservoir for resistant gene exchange or movement via selective pressure exerted by metals and antibiotics. The resultant adaptive mechanisms and altered phenotypes are potential tools to track metal tolerant strains with clinically significant antibiotic resistance traits.},
}
@article {pmid37227251,
year = {2023},
author = {Tonkin-Hill, G and Corander, J and Parkhill, J},
title = {Challenges in prokaryote pangenomics.},
journal = {Microbial genomics},
volume = {9},
number = {5},
pages = {},
pmid = {37227251},
issn = {2057-5858},
mesh = {Phylogeny ; *Evolution, Molecular ; *Prokaryotic Cells ; Bacteria/genetics ; Gene Transfer, Horizontal ; },
abstract = {Horizontal gene transfer (HGT) and the resulting patterns of gene gain and loss are a fundamental part of bacterial evolution. Investigating these patterns can help us to understand the role of selection in the evolution of bacterial pangenomes and how bacteria adapt to a new niche. Predicting the presence or absence of genes can be a highly error-prone process that can confound efforts to understand the dynamics of horizontal gene transfer. This review discusses both the challenges in accurately constructing a pangenome and the potential consequences errors can have on downstream analyses. We hope that by summarizing these issues researchers will be able to avoid potential pitfalls, leading to improved bacterial pangenome analyses.},
}
@article {pmid37221009,
year = {2023},
author = {Shaferman, M and Gencel, M and Alon, N and Alasad, K and Rotblat, B and Serohijos, AWR and Alfonta, L and Bershtein, S},
title = {The Fitness Effects of Codon Composition of the Horizontally Transferred Antibiotic Resistance Genes Intensify at Sub-lethal Antibiotic Levels.},
journal = {Molecular biology and evolution},
volume = {40},
number = {6},
pages = {},
pmid = {37221009},
issn = {1537-1719},
mesh = {*Anti-Bacterial Agents/pharmacology ; Codon ; RNA, Messenger ; Drug Resistance, Microbial/genetics ; *Trimethoprim/pharmacology ; },
abstract = {The rampant variability in codon bias existing between bacterial genomes is expected to interfere with horizontal gene transfer (HGT), a phenomenon that drives bacterial adaptation. However, delineating the constraints imposed by codon bias on functional integration of the transferred genes is complicated by multiple genomic and functional barriers controlling HGT, and by the dependence of the evolutionary outcomes of HGT on the host's environment. Here, we designed an experimental system in which codon composition of the transferred genes is the only variable triggering fitness change of the host. We replaced Escherichia coli's chromosomal folA gene encoding dihydrofolate reductase, an essential enzyme that constitutes a target for trimethoprim, with combinatorial libraries of synonymous codons of folA genes from trimethoprim-sensitive Listeria grayi and trimethoprim-resistant Neisseria sicca. The resulting populations underwent selection at a range of trimethoprim concentrations, and the ensuing changes in variant frequencies were used to infer the fitness effects of the individual combinations of codons. We found that when HGT causes overstabilization of the 5'-end mRNA, the fitness contribution of mRNA folding stability dominates over that of codon optimality. The 5'-end overstabilization can also lead to mRNA accumulation outside of the polysome, thus preventing the decay of the foreign transcripts despite the codon composition-driven reduction in translation efficiency. Importantly, the fitness effects of mRNA stability or codon optimality become apparent only at sub-lethal levels of trimethoprim individually tailored for each library, emphasizing the central role of the host's environment in shaping the codon bias compatibility of horizontally transferred genes.},
}
@article {pmid37219457,
year = {2023},
author = {Murthy, AC and Aleksanyan, N and Morton, GM and Toyoda, HC and Kalashyan, M and Chen, S and Ragucci, AE and Broulidakis, MP and Swerdlow, KJ and Bui, MNN and Muccioli, M and Berkmen, MB},
title = {Characterization of ConE, the VirB4 Homolog of the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis.},
journal = {Journal of bacteriology},
volume = {205},
number = {6},
pages = {e0003323},
pmid = {37219457},
issn = {1098-5530},
mesh = {*Bacillus subtilis/genetics/metabolism ; *Conjugation, Genetic ; DNA, Bacterial/genetics/metabolism ; DNA Transposable Elements ; Bacterial Proteins/genetics/metabolism ; Adenosine Triphosphatases/genetics/metabolism ; Gene Transfer, Horizontal ; },
abstract = {Conjugation is a major form of horizontal gene transfer, contributing to bacterial evolution and the acquisition of new traits. During conjugation, a donor cell transfers DNA to a recipient through a specialized DNA translocation channel classified as a type IV secretion system (T4SS). Here, we focused on the T4SS of ICEBs1, an integrative and conjugative element in Bacillus subtilis. ConE, encoded by ICEBs1, is a member of the VirB4 family of ATPases, the most conserved component of T4SSs. ConE is required for conjugation and localizes to the cell membrane, predominantly at the cell poles. In addition to Walker A and B boxes, VirB4 homologs have conserved ATPase motifs C, D, and E. Here, we created alanine substitutions in five conserved residues within or near ATPase motifs in ConE. Mutations in all five residues drastically decreased conjugation frequency but did not affect ConE protein levels or localization, indicating that an intact ATPase domain is critical for DNA transfer. Purified ConE is largely monomeric with some oligomers and lacks enzymatic activity, suggesting that ATP hydrolysis may be regulated or require special solution conditions. Finally, we investigated which ICEBs1 T4SS components interact with ConE using a bacterial two-hybrid assay. ConE interacts with itself, ConB, and ConQ, but these interactions are not required to stabilize ConE protein levels and largely do not depend on conserved residues within the ATPase motifs of ConE. The structure-function characterization of ConE provides more insight into this conserved component shared by all T4SSs. IMPORTANCE Conjugation is a major form of horizontal gene transfer and involves the transfer of DNA from one bacterium to another through the conjugation machinery. Conjugation contributes to bacterial evolution by disseminating genes involved in antibiotic resistance, metabolism, and virulence. Here, we characterized ConE, a protein component of the conjugation machinery of the conjugative element ICEBs1 of the bacterium Bacillus subtilis. We found that mutations in the conserved ATPase motifs of ConE disrupt mating but do not alter ConE localization, self-interaction, or levels. We also explored which conjugation proteins ConE interacts with and whether these interactions contribute to stabilizing ConE. Our work contributes to the understanding of the conjugative machinery of Gram-positive bacteria.},
}
@article {pmid37218693,
year = {2023},
author = {Bejenari, M and Sondergaard, TE and Sørensen, JL},
title = {6-MSA, a secondary metabolite distribution hub with multiple fungal destinations.},
journal = {Journal of applied microbiology},
volume = {134},
number = {6},
pages = {},
doi = {10.1093/jambio/lxad107},
pmid = {37218693},
issn = {1365-2672},
support = {NNF20OC0064343//Novo Nordisk Foundation/ ; },
mesh = {Humans ; *Patulin ; Multigene Family ; Bacteria/genetics ; Polyketide Synthases/genetics ; },
abstract = {6-methylsalicylic acid (6-MSA) is a small, simple polyketide produced by a broad spectrum of fungal species. Since fungi obtained the ability to synthesize 6-MSA from bacteria through a horizontal gene transfer event, it has developed into a multipurpose metabolic hub from where numerous complex compounds are produced. The most relevant metabolite from a human perspective is the small lactone patulin as it is one of the most potent mycotoxins. Other important end products derived from 6-MSA include the small quinone epoxide terreic acid and the prenylated yanuthones. The most advanced modification of 6-MSA is observed in the aculin biosynthetic pathway, which is mediated by a non-ribosomal peptide synthase and a terpene cyclase. In this short review, we summarize for the first time all the possible pathways that takes their onset from 6-MSA and provide a synopsis of the responsible gene clusters and derive the resulting biosynthetic pathways.},
}
@article {pmid37217185,
year = {2023},
author = {Maruyama, M and Kagamoto, T and Matsumoto, Y and Onuma, R and Miyagishima, SY and Tanifuji, G and Nakazawa, M and Kashiyama, Y},
title = {Horizontally Acquired Nitrate Reductase Realized Kleptoplastic Photoautotrophy of Rapaza viridis.},
journal = {Plant &amp; cell physiology},
volume = {64},
number = {9},
pages = {1082-1090},
doi = {10.1093/pcp/pcad044},
pmid = {37217185},
issn = {1471-9053},
support = {18H03743 21H02273 21H02554 21K19240 21K19303//Japan Society for the Promotion of Science/ ; },
mesh = {Nitrate Reductase/genetics/metabolism ; *Nitrates/metabolism ; Phylogeny ; *Ammonium Compounds ; Nitrogen/metabolism ; },
abstract = {While photoautotrophic organisms utilize inorganic nitrogen as the nitrogen source, heterotrophic organisms utilize organic nitrogen and thus do not generally have an inorganic nitrogen assimilation pathway. Here, we focused on the nitrogen metabolism of Rapaza viridis, a unicellular eukaryote exhibiting kleptoplasty. Although belonging to the lineage of essentially heterotrophic flagellates, R. viridis exploits the photosynthetic products of the kleptoplasts and was therefore suspected to potentially utilize inorganic nitrogen. From the transcriptome data of R. viridis, we identified gene RvNaRL, which had sequence similarity to genes encoding nitrate reductases in plants. Phylogenetic analysis revealed that RvNaRL was acquired by a horizontal gene transfer event. To verify the function of the protein product RvNaRL, we established RNAi-mediated knock-down and CRISPR-Cas9-mediated knock-out experiments for the first time in R. viridis and applied them to this gene. The RvNaRL knock-down and knock-out cells exhibited significant growth only when ammonium was supplied. However, in contrast to the wild-type cells, no substantial growth was observed when nitrate was supplied. Such arrested growth in the absence of ammonium was attributed to impaired amino acid synthesis due to the deficiency of nitrogen supply from the nitrate assimilation pathway; this in turn resulted in the accumulation of excess photosynthetic products in the form of cytosolic polysaccharide grains, as observed. These results indicate that RvNaRL is certainly involved in nitrate assimilation by R. viridis. Thus, we inferred that R. viridis achieved its advanced kleptoplasty for photoautotrophy, owing to the acquisition of nitrate assimilation via horizontal gene transfer.},
}
@article {pmid37215039,
year = {2023},
author = {Giengkam, S and Kullapanich, C and Wongsantichon, J and Adcox, HE and Gillespie, JJ and Salje, J},
title = {Orientia tsutsugamushi: analysis of the mobilome of a highly fragmented and repetitive genome reveals ongoing lateral gene transfer in an obligate intracellular bacterium.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37215039},
issn = {2692-8205},
support = {/WT_/Wellcome Trust/United Kingdom ; R21 AI156762/AI/NIAID NIH HHS/United States ; R21 AI166832/AI/NIAID NIH HHS/United States ; },
abstract = {The rickettsial human pathogen Orientia tsutsugamushi (Ot) is an obligate intracellular Gram-negative bacterium with one of the most highly fragmented and repetitive genomes of any organism. Around 50% of its ~2.3 Mb genome is comprised of repetitive DNA that is derived from the highly proliferated Rickettsiales amplified genetic element (RAGE). RAGE is an integrative and conjugative element (ICE) that is present in a single Ot genome in up to 92 copies, most of which are partially or heavily degraded. In this report, we analysed RAGEs in eight fully sequenced Ot genomes and manually curated and reannotated all RAGE-associated genes, including those encoding DNA mobilisation proteins, P-type (vir) and F-type (tra) type IV secretion system (T4SS) components, Ankyrin repeat- and tetratricopeptide repeat-containing effectors, and other piggybacking cargo. Originally, the heavily degraded Ot RAGEs led to speculation that they are remnants of historical ICEs that are no longer active. Our analysis, however, identified two Ot genomes harbouring one or more intact RAGEs with complete F-T4SS genes essential for mediating ICE DNA transfer. As similar ICEs have been identified in unrelated rickettsial species, we assert that RAGEs play an ongoing role in lateral gene transfer within the Rickettsiales. Remarkably, we also identified in several Ot genomes remnants of prophages with no similarity to other rickettsial prophages. Together these findings indicate that, despite their obligate intracellular lifestyle and host range restricted to mites, rodents and humans, Ot genomes are highly dynamic and shaped through ongoing invasions by mobile genetic elements and viruses.},
}
@article {pmid37213501,
year = {2023},
author = {Huang, Y and Jiang, P and Liang, Z and Chen, R and Yue, Z and Xie, X and Guan, C and Fang, X},
title = {Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1145315},
pmid = {37213501},
issn = {1664-302X},
abstract = {Human gut microbiota is associated with human health and disease, and is known to have the second-largest genome in the human body. The microbiota genome is important for their functions and metabolites; however, accurate genomic access to the microbiota of the human gut is hindered due to the difficulty of cultivating and the shortcomings of sequencing technology. Therefore, we applied the stLFR library construction method to assemble the microbiota genomes and demonstrated that assembly property outperformed standard metagenome sequencing. Using the assembled genomes as references, SNP, INDEL, and HGT gene analyses were performed. The results demonstrated significant differences in the number of SNPs and INDELs among different individuals. The individual displayed a unique species variation spectrum, and the similarity of strains within individuals decreased over time. In addition, the coverage depth analysis of the stLFR method shows that a sequencing depth of 60X is sufficient for SNP calling. HGT analysis revealed that the genes involved in replication, recombination and repair, mobilome prophages, and transposons were the most transferred genes among different bacterial species in individuals. A preliminary framework for human gut microbiome studies was established using the stLFR library construction method.},
}
@article {pmid37213168,
year = {2023},
author = {Youngblom, MA and Shockey, AC and Callaghan, MM and Dillard, JP and Pepperell, CS},
title = {The Gonococcal Genetic Island defines distinct sub-populations of Neisseria gonorrhoeae.},
journal = {Microbial genomics},
volume = {9},
number = {5},
pages = {},
pmid = {37213168},
issn = {2057-5858},
support = {R01 AI047958/AI/NIAID NIH HHS/United States ; R01 AI113287/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Neisseria gonorrhoeae/genetics ; DNA ; *Gonorrhea ; Type IV Secretion Systems/genetics ; Genomics ; },
abstract = {The incidence of gonorrhoea is increasing at an alarming pace, and therapeutic options continue to narrow as a result of worsening drug resistance. Neisseria gonorrhoeae is naturally competent, allowing the organism to adapt rapidly to selection pressures including antibiotics. A sub-population of N. gonorrhoeae carries the Gonococcal Genetic Island (GGI), which encodes a type IV secretion system (T4SS) that secretes chromosomal DNA. Previous research has shown that the GGI increases transformation efficiency in vitro, but the extent to which it contributes to horizontal gene transfer (HGT) during infection is unknown. Here we analysed genomic data from clinical isolates of N. gonorrhoeae to better characterize GGI+ and GGI- sub-populations and to delineate patterns of variation at the locus itself. We found the element segregating at an intermediate frequency (61%), and it appears to act as a mobile genetic element with examples of gain, loss, exchange and intra-locus recombination within our sample. We further found evidence suggesting that GGI+ and GGI- sub-populations preferentially inhabit distinct niches with different opportunities for HGT. Previously, GGI+ isolates were reported to be associated with more severe clinical infections, and our results suggest this could be related to metal-ion trafficking and biofilm formation. The co-segregation of GGI+ and GGI- isolates despite mobility of the element suggests that both niches inhabited by N. gonorrhoeae remain important to its overall persistence as has been demonstrated previously for cervical- and urethral-adapted sub-populations. These data emphasize the complex population structure of N. gonorrhoeae and its capacity to adapt to diverse niches.},
}
@article {pmid37213139,
year = {2023},
author = {C Silva-de-Jesus, A and Rossi, CC and Pereira-Ribeiro, PM and Guaraldi, AL and Giambiagi-deMarval, M},
title = {Unusual carriage of virulence genes sasX/sesI/shsA by nosocomial Staphylococcus haemolyticus from Brazil.},
journal = {Future microbiology},
volume = {18},
number = {},
pages = {407-414},
doi = {10.2217/fmb-2022-0225},
pmid = {37213139},
issn = {1746-0921},
support = {23038.002486/2018-26//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 001463/2019, 010.00128/2016, 101056/2018, 200.895/2021, 201.071/2020, 211.554/2019, E-26/010.000172/2016//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 305940/2018-0, PIBICUFRJ-CNPq 2020//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Humans ; Staphylococcus haemolyticus/genetics ; Virulence/genetics ; Brazil/epidemiology ; *Cross Infection/epidemiology ; *Staphylococcal Infections/epidemiology ; Staphylococcus epidermidis/genetics ; Hospitals ; Anti-Bacterial Agents ; },
abstract = {Background: Staphylococcus haemolyticus is an emerging threat in the nosocomial environment but only some virulence factors are known. Materials &amp; methods: The frequency of the sasX gene (or orthologues sesI/shsA), encoding an invasiveness-related surface-associated protein, in S. haemolyticus was detected in different hospitals in Rio de Janeiro. Results: 9.4% of strains were sasX/sesI/shsA-positive, some were in the context of the ΦSPβ-like prophage and devoid of CRISPR systems, indicating potential transferability of their virulence genes. Gene sequencing evidenced that Brazilian S. haemolyticus harbored sesI, instead of the usual sasX, while S. epidermidis had sasX instead of sesI, suggesting horizontal acquisition. Conclusion: The contexts of Brazilian sasX/sesI/shsA favor transfer, which is alarming given the difficulty in treating infections caused by S. haemolyticus.},
}
@article {pmid37210032,
year = {2023},
author = {Yin, Y and Lou, T and Song, W and Wang, C and Wang, J},
title = {Production of medium chain fatty acids from antibiotic fermentation residuals pretreated by ionizing radiation: Elimination of antibiotic resistance genes.},
journal = {Bioresource technology},
volume = {382},
number = {},
pages = {129180},
doi = {10.1016/j.biortech.2023.129180},
pmid = {37210032},
issn = {1873-2976},
mesh = {*Anti-Bacterial Agents/pharmacology/metabolism ; Fermentation ; *Genes, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Radiation, Ionizing ; },
abstract = {The propagation of antibiotic resistance genes (ARGs) restricts the application of antibiotic fermentation residues (AFRs). This study investigated medium chain fatty acids (MCFA) production from AFRs, focusing on the effect of ionizing radiation pretreatment on the fates of ARGs. The results indicated that ionizing radiation pretreatment not only stimulated the MCFA production, but also inhibited the proliferation of ARGs. Radiation at 10-50 kGy decreased ARGs abundances by 0.6-21.1% at the end of fermentation process. Mobile genetic elements (MGEs) exhibited higher resistance to ionizing radiation, radiation over 30 kGy was required to suppress the proliferation of MGEs. Radiation at 50 kGy achieved an adequate inhibition to MGEs, and the degradation efficiency was 17.8-74.5% for different kinds of MGEs. This work suggested that ionizing radiation pretreatment could be a good option to ensure the safer application of AFRs by eliminating the ARGs and preventing the horizontal gene transfer of ARGs.},
}
@article {pmid37209559,
year = {2023},
author = {Yuan, B and Zhang, Y and Zhang, Z and Lin, Z and Ma, Y and Sun, Y},
title = {Fluorescent tag reveals the potential mechanism of how indigenous soil bacteria affect the transfer of the wild fecal antibiotic resistance plasmid pKANJ7 in different habitat soils.},
journal = {Journal of hazardous materials},
volume = {455},
number = {},
pages = {131659},
doi = {10.1016/j.jhazmat.2023.131659},
pmid = {37209559},
issn = {1873-3336},
mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Drug Resistance, Microbial/genetics ; Ecosystem ; Genes, Bacterial ; Manure/microbiology ; Plasmids/genetics ; *Soil/chemistry ; *Soil Microbiology ; },
abstract = {Plasmids have increasingly become a point of concern since they act as a vital medium for the dissemination of antibiotic resistance genes (ARGs). Although indigenous soil bacteria are critical hosts for these plasmids, the mechanisms driving the transfer of antibiotic resistance plasmids (ARPs) have not been well researched. In this study, we tracked and visualized the colonization of the wild fecal antibiotic resistance plasmid pKANJ7 in indigenous bacteria of different habitat soils (unfertilized soil (UFS), chemical fertilized soil (CFS), and manure fertilized soil (MFS)). The results showed that plasmid pKANJ7 mainly transferred to the dominant genera in the soil and genera that were highly related to the donor. More importantly, plasmid pKANJ7 also transferred to intermediate hosts which aid in the survival and persistence of these plasmids in soil. Nitrogen levels also raised the plasmid transfer rate (14th day: UFS: 0.09%, CFS: 1.21%, MFS: 4.57%). Lastly, our structural equation model (SEM) showed that dominant bacteria shifts caused by nitrogen and loam were the major driver shaping the difference in the transfer of plasmid pKANJ7. Overall, our findings enhance the mechanistic understanding of indigenous soil bacteria's role in plasmid transfer and inform potential methods to prevent the transmission of plasmid-borne resistance in the environment.},
}
@article {pmid37204585,
year = {2023},
author = {Lü, W and Ren, H and Ding, W and Li, H and Yao, X and Jiang, X},
title = {Rapid shifts in pond sediment microbiota in response to high ambient temperature in a water-sediment microcosm.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {29},
pages = {74358-74371},
doi = {10.1007/s11356-023-26823-7},
pmid = {37204585},
issn = {1614-7499},
support = {2017ZX07206//Major Science and Technology Program for Water Pollution Control and Treatment of China/ ; 41977322//National Natural Science Foundation of China/ ; 41907335//National Natural Science Foundation of China/ ; },
mesh = {*Ecosystem ; Temperature ; Ponds ; Hot Temperature ; *Microbiota ; Bacteria ; Climate Change ; Soil Microbiology ; },
abstract = {Unlike the extensive research on the response of soil microorganisms to high ambient temperature (HTA), the response of sediment microorganisms to HTA remains unclear. Understanding the response of sediment microorganisms to HTA is important to forecast their impacts on ecosystems and climate warming under projected climate change scenarios. Against the background of climate warming and frequent high ambient temperatures in summer, we conducted a laboratory incubation experiment to clarify the unique assembly characteristics of pond sediment bacterial communities at different temperatures (4, 10, 15, 25, 30 and 35 °C). The results showed that the structure and function of the microbial community in pond sediments at 35 °C were different from those under other temperatures; the microbial community structure at 35 °C had the most large modules and an average module size. Temperature and dissolved oxygen influenced the microbial community network modularity. The CO2 emission rates of pond sediments at 35 °C were significantly higher than those at other temperatures. At 35 °C, heterogeneous selection was the most important assembly process. Additionally, warming altered the microbial network structure and ecosystem functioning but not the microbial diversity or community composition, which may be related to horizontal gene transfer. Revealing the rapid response of pond sediment microorganisms to HTA is important for identifying their role in nutrient cycling and assessing the ecological impacts of climate warming and high ambient temperatures on inland water sediments.},
}
@article {pmid37201375,
year = {2023},
author = {Huang, DQ and Wu, Q and Yang, JH and Jiang, Y and Li, ZY and Fan, NS and Jin, RC},
title = {Deciphering endogenous and exogenous regulations of anammox consortia in responding to lincomycin by multiomics: quorum sensing and CRISPR system.},
journal = {Water research},
volume = {239},
number = {},
pages = {120061},
doi = {10.1016/j.watres.2023.120061},
pmid = {37201375},
issn = {1879-2448},
mesh = {Animals ; Humans ; *Quorum Sensing ; *CRISPR-Cas Systems ; Lincomycin/pharmacology ; Multiomics ; Anaerobic Ammonia Oxidation ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The widespread use of antibiotics has created an antibiotic resistance genes (ARGs)-enriched environment, which causes high risks on human and animal health. Although antibiotics can be partially adsorbed and degraded in wastewater treatment processes, striving for a complete understanding of the microbial adaptive mechanism to antibiotic stress remains urgent. Combined with metagenomics and metabolomics, this study revealed that anammox consortia could adapt to lincomycin by spontaneously changing the preference for metabolite utilization and establishing interactions with eukaryotes, such as Ascomycota and Basidiomycota. Specifically, quorum sensing (QS) based microbial regulation and the ARGs transfer mediated by clustered regularly interspaced short palindromic repeats (CRISPR) system and global regulatory genes were the principal adaptive strategies. Western blotting results validated that Cas9 and TrfA were mainly responsible for the alteration of ARGs transfer pathway. These findings highlight the potential adaptative mechanism of microbes to antibiotic stress and fill gaps in horizontal gene transfer pathways in the anammox process, further facilitating the ARGs control through molecular and synthetic biology techniques.},
}
@article {pmid37196739,
year = {2023},
author = {Zhang, W and Yu, C and Yin, S and Chang, X and Chen, K and Xing, Y and Yang, Y},
title = {Transmission and retention of antibiotic resistance genes (ARGs) in chicken and sheep manure composting.},
journal = {Bioresource technology},
volume = {382},
number = {},
pages = {129190},
doi = {10.1016/j.biortech.2023.129190},
pmid = {37196739},
issn = {1873-2976},
mesh = {Animals ; Sheep/genetics ; *Composting ; Chickens/genetics ; Genes, Bacterial/genetics ; Manure/microbiology ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; },
abstract = {Transmission of ARGs during composting with different feedstocks (i.e., sheep manure (SM), chicken manure (CM) and mixed manure (MM, SM:CM = 3:1 ratio) was studied by metagenomic sequencing. 53 subtypes of ARGs for 22 types of antibiotics were identified as commonly present in these compost mixes; among them, CM had higher abundance of ARGs, 1.69 times than that in SM, while the whole elimination rate of CM, MM and SM were 55.2%, 54.7% and 42.9%, respectively. More than 50 subtypes of ARGs (with 8.6%, 11.4% and 20.9% abundance in the initial stage in CM, MM and SM composting) were "diehard" ARGs, and their abundance grew significantly to 56.5%, 63.2% and 69.9% at the mature stage. These "diehard" ARGs were transferred from initial hosts of pathogenic and/or probiotic bacteria to final hosts of thermophilic bacteria, by horizontal gene transfer (HGT) via mobile gene elements (MGEs), and became rooted in composting products.},
}
@article {pmid37191574,
year = {2023},
author = {Zhu, Q and Gao, S and Xiao, B and He, Z and Hu, S},
title = {Plasmer: an Accurate and Sensitive Bacterial Plasmid Prediction Tool Based on Machine Learning of Shared k-mers and Genomic Features.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0464522},
pmid = {37191574},
issn = {2165-0497},
mesh = {*Genomics/methods ; Plasmids/genetics ; *Genome, Bacterial ; Machine Learning ; },
abstract = {Identification of plasmids in bacterial genomes is critical for many factors, including horizontal gene transfer, antibiotic resistance genes, host-microbe interactions, cloning vectors, and industrial production. There are several in silico methods to predict plasmid sequences in assembled genomes. However, existing methods have evident shortcomings, such as unbalance in sensitivity and specificity, dependency on species-specific models, and performance reduction in sequences shorter than 10 kb, which has limited their scope of applicability. In this work, we proposed Plasmer, a novel plasmid predictor based on machine-learning of shared k-mers and genomic features. Unlike existing k-mer or genomic-feature based methods, Plasmer employs the random forest algorithm to make predictions using the percent of shared k-mers with plasmid and chromosome databases combined with other genomic features, including alignment E value and replicon distribution scores (RDS). Plasmer can predict on multiple species and has achieved an average the area under the curve (AUC) of 0.996 with accuracy of 98.4%. Compared to existing methods, tests of both sliding sequences and simulated and de novo assemblies have consistently shown that Plasmer has outperforming accuracy and stable performance across long and short contigs above 500 bp, demonstrating its applicability for fragmented assemblies. Plasmer also has excellent and balanced performance on both sensitivity and specificity (both >0.95 above 500 bp) with the highest F1-score, which has eliminated the bias on sensitivity or specificity that was common in existing methods. Plasmer also provides taxonomy classification to help identify the origin of plasmids. IMPORTANCE In this study, we proposed a novel plasmid prediction tool named Plasmer. Technically, unlike existing k-mer or genomic features-based methods, Plasmer is the first tool to combine the advantages of the percent of shared k-mers and the alignment score of genomic features. This has given Plasmer (i) evident improvement in performance compared to other methods, with the best F1-score and accuracy on sliding sequences, simulated contigs, and de novo assemblies; (ii) applicability for contigs above 500 bp with highest accuracy, enabling plasmid prediction in fragmented short-read assemblies; (iii) excellent and balanced performance between sensitivity and specificity (both >0.95 above 500 bp) with the highest F1-score, which eliminated the bias on sensitivity or specificity that commonly existed in other methods; and (iv) no dependency of species-specific training models. We believe that Plasmer provides a more reliable alternative for plasmid prediction in bacterial genome assemblies.},
}
@article {pmid37187278,
year = {2023},
author = {Zhou, Q and Zhang, J and Fang, Q and Zhang, M and Wang, X and Zhang, D and Pan, X},
title = {Microplastic biodegradability dependent responses of plastisphere antibiotic resistance to simulated freshwater-seawater shift in onshore marine aquaculture zones.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {331},
number = {Pt 2},
pages = {121828},
doi = {10.1016/j.envpol.2023.121828},
pmid = {37187278},
issn = {1873-6424},
mesh = {*Microplastics ; *Anti-Bacterial Agents/pharmacology ; Plastics/pharmacology ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Fresh Water/microbiology ; Seawater/microbiology ; Aquaculture ; Water ; },
abstract = {MPs carrying ARGs can travel between freshwater and seawater due to intensive land-sea interaction in onshore marine aquaculture zones (OMAZ). However, the response of ARGs in plastisphere with different biodegradability to freshwater-seawater shift is still unknown. In this study, ARG dynamics and associated microbiota on biodegradable poly (butyleneadipate-co-terephthalate) (PBAT) and non-biodegradable polyethylene terephthalate (PET) MPs were investigated through a simulated freshwater-seawater shift. The results exhibited that freshwater-seawater shift significantly influenced ARG abundance in plastisphere. The relative abundance of most studied ARGs decreased rapidly in plastisphere after they entered seawater from freshwater but increased on PBAT after MPs entered freshwater from seawater. Besides, the high relative abundance of multi-drug resistance (MDR) genes occurred in plastisphere, and the co-change between most ARGs and mobile genetic elements indicated the role of horizontal gene transfer on ARG regulation. Proteobacteria was dominant phylum in plastisphere and the dominant genera, such as Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Afipia, Gemmobacter and Enhydrobacter, were significantly associated with qnrS, tet and MDR genes in plastisphere. Moreover, after MPs entered new water environment, the ARGs and microbiota genera in plastisphere changed significantly and tended to converge with those in receiving water. These results indicated that MP biodegradability and freshwater-seawater interaction influenced potential hosts and distributions of ARGs, of which biodegradable PBAT posed a high risk in ARG dissemination. This study would be helpful for understanding the impact of biodegradable MP pollution on spread of antibiotic resistance in OMAZ.},
}
@article {pmid37185344,
year = {2023},
author = {Riccardi, C and Koper, P and Innocenti, G and diCenzo, GC and Fondi, M and Mengoni, A and Perrin, E},
title = {Independent origins and evolution of the secondary replicons of the class Gammaproteobacteria.},
journal = {Microbial genomics},
volume = {9},
number = {5},
pages = {},
pmid = {37185344},
issn = {2057-5858},
mesh = {Genome, Bacterial ; Plasmids/genetics ; Replicon/genetics ; *Sinorhizobium meliloti/genetics ; *Gammaproteobacteria/genetics ; },
abstract = {Multipartite genomes, consisting of more than one replicon, have been found in approximately 10 % of bacteria, many of which belong to the phylum Proteobacteria. Many aspects of their origin and evolution, and the possible advantages related to this type of genome structure, remain to be elucidated. Here, we performed a systematic analysis of the presence and distribution of multipartite genomes in the class Gammaproteobacteria, which includes several genera with diverse lifestyles. Within this class, multipartite genomes are mainly found in the order Alteromonadales (mostly in the genus Pseudoalteromonas) and in the family Vibrionaceae. Our data suggest that the emergence of secondary replicons in Gammaproteobacteria is rare and that they derive from plasmids. Despite their multiple origins, we highlighted the presence of evolutionary trends such as the inverse proportionality of the genome to chromosome size ratio, which appears to be a general feature of bacteria with multipartite genomes irrespective of taxonomic group. We also highlighted some functional trends. The core gene set of the secondary replicons is extremely small, probably limited to essential genes or genes that favour their maintenance in the genome, while the other genes are less conserved. This hypothesis agrees with the idea that the primary advantage of secondary replicons could be to facilitate gene acquisition through horizontal gene transfer, resulting in replicons enriched in genes associated with adaptation to different ecological niches. Indeed, secondary replicons are enriched both in genes that could promote adaptation to harsh environments, such as those involved in antibiotic, biocide and metal resistance, and in functional categories related to the exploitation of environmental resources (e.g. carbohydrates), which can complement chromosomal functions.},
}
@article {pmid37178001,
year = {2023},
author = {Vesel, N and Iseli, C and Guex, N and Lemopoulos, A and Blokesch, M},
title = {DNA modifications impact natural transformation of Acinetobacter baumannii.},
journal = {Nucleic acids research},
volume = {51},
number = {11},
pages = {5661-5677},
pmid = {37178001},
issn = {1362-4962},
mesh = {*Acinetobacter baumannii/genetics ; DNA, Bacterial ; DNA Methylation ; *Drug Resistance, Bacterial ; DNA Restriction-Modification Enzymes ; },
abstract = {Acinetobacter baumannii is a dangerous nosocomial pathogen, especially due to its ability to rapidly acquire new genetic traits, including antibiotic resistance genes (ARG). In A. baumannii, natural competence for transformation, one of the primary modes of horizontal gene transfer (HGT), is thought to contribute to ARG acquisition and has therefore been intensively studied. However, knowledge regarding the potential role of epigenetic DNA modification(s) on this process remains lacking. Here, we demonstrate that the methylome pattern of diverse A. baumannii strains differs substantially and that these epigenetic marks influence the fate of transforming DNA. Specifically, we describe a methylome-dependent phenomenon that impacts intra- and inter-species DNA exchange by the competent A. baumannii strain A118. We go on to identify and characterize an A118-specific restriction-modification (RM) system that impairs transformation when the incoming DNA lacks a specific methylation signature. Collectively, our work contributes towards a more holistic understanding of HGT in this organism and may also aid future endeavors towards tackling the spread of novel ARGs. In particular, our results suggest that DNA exchanges between bacteria that share similar epigenomes are favored and could therefore guide future research into identifying the reservoir(s) of dangerous genetic traits for this multi-drug resistant pathogen.},
}
@article {pmid37177929,
year = {2023},
author = {Lu, JW and Xu, CY and Hu, C and Liu, SR and Li, F},
title = {[Occurrence Characteristics of Microplastics and Metal Elements in the Surface Water of Huangpu River and Their Associations with Metal Resistance Genes].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {44},
number = {5},
pages = {2551-2561},
doi = {10.13227/j.hjkx.202206267},
pmid = {37177929},
issn = {0250-3301},
mesh = {*Microplastics ; Genes, Bacterial ; Plastics ; Rivers ; Water ; Metals ; *Mercury ; Anti-Bacterial Agents ; },
abstract = {Urban rivers have been regarded as the "hotspots" for microplastic (MPs) and metal contamination as they play important roles in pollution migration. However, as important sinks and sources of resistance genes, there has been little to no research investigating the associations between MPs, metal contaminations, and metal resistance genes (MRGs). Ten water samples were collected from the Huangpu River in situ; along with metal elements, MPs characteristics analyzed. Metal resistance genes and mobile genetic elements (MGEs) in waters and MPs were detected using metagenomic technology. As a result, the highest metal concentration was that of Sb in surface water (3.16±0.419) μg·L[-1]. The average abundance of MPs was (1.78±0.84) n·L[-1], and the peak levels located in industrial and densely populated areas, which was significantly higher than those in agricultural and low population density areas. Fibrous, small-size (<0.5 mm), and transparent polyethylene terephthalate (PET) were the largest contributors of MPs. Eighteen MRGs were detected in all the samples. The relative abundance of MRGs in water was 1.68±0.21. The most dominant MRGs subtypes were merR and ruvB, which are subtypes resistant to mercury and Multi_metals. Correlation analysis showed that chromium and nickel in waters were significantly positively associated with MRG-Cr, MRG-Ni, and Multi_metals resistance genes. For MPs particles, the relative abundance of MRGs was 1.63±0.53. The most dominant MRGs subtypes were merT-P and copB, which also belong to mercury-resistant and Multi_metals. The Multi_metals resistance gene, ctpC, cueA, czrA, kmtR, etc., had significant positive associations with Ni, Cr, and Sb in waters. Compared with water samples, MPs selectively enriched merT-P, copB, ziaA, sodA, and dmeF. Additionally, the co-occurrence patterns of MRGs and MGEs were explored based on network analysis. In water samples, the transposases (tnpA_1 and tnpA_2), integrase (qacEdelta), and insertion sequence (IS91) were the major contributors of the horizontal gene transfer (HGT) of specific MRGs. Multiple subtypes resistant to copper and Multi_metals resistance genes on MPs were positively associated with IncFIC(FII), Rep7, rep7, and rep13, which were subtypes of plasmids. The presence of MPs exerted a significant impact on HGT of specific MRGs mediated by plasmids.},
}
@article {pmid37173437,
year = {2023},
author = {Feng, SY and Hauck, Y and Morgene, F and Mohammedi, R and Mirouze, N},
title = {The complex regulation of competence in Staphylococcus aureus under microaerobic conditions.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {512},
pmid = {37173437},
issn = {2399-3642},
mesh = {Humans ; *Staphylococcus aureus/genetics ; *Gene Expression Profiling ; },
abstract = {To perform natural transformation, one of the three main Horizontal Gene Transfer mechanisms, bacteria need to enter a physiological differentiated state called genetic competence. Interestingly, new bacteria displaying such aptitude are often discovered, and one of the latest is the human pathogen Staphylococcus aureus.Here, we show an optimized protocol, based on planktonic cells cultures, leading to a large percentage of the population activating the development of competence and a significant improvement of S. aureus natural transformation efficiencies. Taking advantage of these conditions, we perform transcriptomics analyses to characterize the regulon of each central competence regulator. SigH and ComK1 are both found essential for activating natural transformation genes but also important for activation or repression of peripheral functions. Even though ComK2 is not found important for the control of transformation genes, its regulon shows an important overlap with that of SigH and ComK1. Finally, we propose that microaerobic conditions, sensed by the SrrAB two-component system, are key to activate competence in S. aureus.},
}
@article {pmid37173063,
year = {2023},
author = {Ayllón, MA and Vainio, EJ},
title = {Mycoviruses as a part of the global virome: Diversity, evolutionary links and lifestyle.},
journal = {Advances in virus research},
volume = {115},
number = {},
pages = {1-86},
doi = {10.1016/bs.aivir.2023.02.002},
pmid = {37173063},
issn = {1557-8399},
mesh = {*Fungal Viruses/genetics ; Phylogeny ; Virome ; *Viruses/genetics ; RNA, Double-Stranded ; *RNA Viruses/genetics ; RNA, Viral/genetics ; Genome, Viral ; },
abstract = {Knowledge of mycovirus diversity, evolution, horizontal gene transfer and shared ancestry with viruses infecting distantly related hosts, such as plants and arthropods, has increased vastly during the last few years due to advances in the high throughput sequencing methodologies. This also has enabled the discovery of novel mycoviruses with previously unknown genome types, mainly new positive and negative single-stranded RNA mycoviruses ((+) ssRNA and (-) ssRNA) and single-stranded DNA mycoviruses (ssDNA), and has increased our knowledge of double-stranded RNA mycoviruses (dsRNA), which in the past were thought to be the most common viruses infecting fungi. Fungi and oomycetes (Stramenopila) share similar lifestyles and also have similar viromes. Hypothesis about the origin and cross-kingdom transmission events of viruses have been raised and are supported by phylogenetic analysis and by the discovery of natural exchange of viruses between different hosts during virus-fungus coinfection in planta. In this review we make a compilation of the current information on the genome organization, diversity and taxonomy of mycoviruses, discussing their possible origins. Our focus is in recent findings suggesting the expansion of the host range of many viral taxa previously considered to be exclusively fungal, but we also address factors affecting virus transmissibility and coexistence in single fungal or oomycete isolates, as well as the development of synthetic mycoviruses and their use in investigating mycovirus replication cycles and pathogenicity.},
}
@article {pmid37172383,
year = {2023},
author = {Liu, YJ and Li, ZH and He, YT and Yuan, L and Sheng, GP},
title = {Antibiotic resistomes in face-mask biofilm along an urban river: Multiple drivers and co-occurrence with human opportunistic pathogens.},
journal = {Journal of hazardous materials},
volume = {455},
number = {},
pages = {131587},
pmid = {37172383},
issn = {1873-3336},
mesh = {Humans ; *Genes, Bacterial ; Masks ; Rivers ; Anti-Bacterial Agents/pharmacology/analysis ; Pandemics ; *COVID-19 ; Water ; Biofilms ; },
abstract = {Discarded face masks from the global COVID-19 pandemic have contributed significantly to plastic pollution in surface water, whereas their potential as a reservoir for aquatic pollutants is not well understood. Herein, we conducted a field experiment along a human-impacted urban river, investigating the variations of antibiotic resistance genes (ARGs), pathogens, and water-borne contaminants in commonly-used face masks. Results showed that high-biomass biofilms formed on face masks selectively enriched more ARGs than stone biofilm (0.08-0.22 vs 0.07-0.15 copies/16 S rRNA gene copies) from bulk water, which mainly due to unique microbial communities, enhanced horizontal gene transfer, and selective pressure of accumulated contaminants based on redundancy analysis and variation partitioning analysis. Several human opportunistic pathogens (e.g., Acinetobacter, Escherichia-Shigella, Bacillus, and Klebsiella), which are considered potential ARG carriers, were also greatly concentrated in face-mask biofilms, imposing a potential threat to aquatic ecological environment and human health. Moreover, wastewater treatment plant effluents, as an important source of pollutants to urban rivers, further aggravated the abundances of ARGs and opportunistic pathogens in face-mask biofilms. Our findings demonstrated that discarded face masks provide a hotspot for the proliferation and spread of ARGs and pathogens in urban water, highlighting the urgent requirement for implementing stricter regulations in face mask disposal.},
}
@article {pmid37172034,
year = {2023},
author = {Green, VE and Klancher, CA and Yamamoto, S and Dalia, AB},
title = {The molecular mechanism for carbon catabolite repression of the chitin response in Vibrio cholerae.},
journal = {PLoS genetics},
volume = {19},
number = {5},
pages = {e1010767},
pmid = {37172034},
issn = {1553-7404},
support = {R35 GM128674/GM/NIGMS NIH HHS/United States ; R01 GM130874/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Vibrio cholerae/genetics/metabolism ; Chitin/genetics/metabolism ; *Catabolite Repression/genetics ; Oligosaccharides/genetics/metabolism ; Gene Expression Regulation, Bacterial ; },
abstract = {Vibrio cholerae is a facultative pathogen that primarily occupies marine environments. In this niche, V. cholerae commonly interacts with the chitinous shells of crustacean zooplankton. As a chitinolytic microbe, V. cholerae degrades insoluble chitin into soluble oligosaccharides. Chitin oligosaccharides serve as both a nutrient source and an environmental cue that induces a strong transcriptional response in V. cholerae. Namely, these oligosaccharides induce the chitin sensor, ChiS, to activate the genes required for chitin utilization and horizontal gene transfer by natural transformation. Thus, interactions with chitin impact the survival of V. cholerae in marine environments. Chitin is a complex carbon source for V. cholerae to degrade and consume, and the presence of more energetically favorable carbon sources can inhibit chitin utilization. This phenomenon, known as carbon catabolite repression (CCR), is mediated by the glucose-specific Enzyme IIA (EIIAGlc) of the phosphoenolpyruvate-dependent phosphotransferase system (PTS). In the presence of glucose, EIIAGlc becomes dephosphorylated, which inhibits ChiS transcriptional activity by an unknown mechanism. Here, we show that dephosphorylated EIIAGlc interacts with ChiS. We also isolate ChiS suppressor mutants that evade EIIAGlc-dependent repression and demonstrate that these alleles no longer interact with EIIAGlc. These findings suggest that EIIAGlc must interact with ChiS to exert its repressive effect. Importantly, the ChiS suppressor mutations we isolated also relieve repression of chitin utilization and natural transformation by EIIAGlc, suggesting that CCR of these behaviors is primarily regulated through ChiS. Together, our results reveal how nutrient conditions impact the fitness of an important human pathogen in its environmental reservoir.},
}
@article {pmid37168121,
year = {2023},
author = {Tao, S and Zhou, D and Chen, H and Li, N and Zheng, L and Fang, Y and Xu, Y and Jiang, Q and Liang, W},
title = {Analysis of genetic structure and function of clustered regularly interspaced short palindromic repeats loci in 110 Enterococcus strains.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1177841},
pmid = {37168121},
issn = {1664-302X},
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) are an adaptive immune system involved in specific defenses against the invasion of foreign mobile genetic elements, such as plasmids and phages. This study aims to analyze the gene structure and to explore the function of the CRISPR system in the Enterococcus genome, especially with regard to drug resistance. The whole genome information of 110 enterococci was downloaded from the NCBI database to analyze the distribution and the structure of the CRISPR-Cas system including the Cas gene, repeat sequences, and spacer sequence of the CRISPR-Cas system by bioinformatics methods, and to find drug resistance-related genes and analyze the relationship between them and the CRISPR-Cas system. Multilocus sequence typing (MLST) of enterococci was performed against the reference MLST database. Information on the drug resistance of Enterococcus was retrieved from the CARD database, and its relationship to the presence or absence of CRISPR was statistically analyzed. Among the 110 Enterococcus strains, 39 strains (35.45%) contained a complete CRISPR-Cas system, 87 CRISPR arrays were identified, and 62 strains contained Cas gene clusters. The CRISPR system in the Enterococcus genome was mainly type II-A (59.68%), followed by type II-C (33.87%). The phylogenetic analysis of the cas1 gene sequence was basically consistent with the typing of the CRISPR-Cas system. Of the 74 strains included in the study for MLST typing, only 19 (25.68%) were related to CRISPR-Cas typing, while the majority of the strains (74.32%) of MLST typing were associated with the untyped CRISPR system. Additionally, the CRISPR-Cas system may only be related to the carrying rate of some drug-resistant genes and the drug-resistant phenotype. In conclusion, the distribution of the enterococcus CRISPR-Cas system varies greatly among different species and the presence of CRISPR loci reduces the horizontal transfer of some drug resistance genes.},
}
@article {pmid37167868,
year = {2023},
author = {Cai, P and Chen, Q and Du, W and Yang, S and Li, J and Cai, H and Zhao, X and Sun, W and Xu, N and Wang, J},
title = {Deciphering the dynamics of metal and antibiotic resistome profiles under different metal(loid) contamination levels.},
journal = {Journal of hazardous materials},
volume = {455},
number = {},
pages = {131567},
doi = {10.1016/j.jhazmat.2023.131567},
pmid = {37167868},
issn = {1873-3336},
mesh = {*Genes, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Metals ; Drug Resistance, Microbial/genetics ; Sewage ; },
abstract = {Metal(loid) contaminations pose considerable threats to ecological security and public health, yet little is known about the dynamics of metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) under different metal(loid) contamination levels. Here, we provided a systematic investigation of MRGs and ARGs in three zones (Zones I, II, and III) with different metal(loid) contamination levels across an abandoned sewage reservoir. More diverse MRGs and ARGs were detected from the high-contaminated Zone I and the moderate-contaminated Zone II, while the abundant MGEs (mobile genetic elements) potentially enhanced the horizontal gene transfer potential and the resistome diversity in Zone I. Particularly, resistome hosts represented by Thiobacillus, Ramlibacter, and Dyella were prevalent in Zone II, promoting the vertical gene transfer of MRGs and ARGs. The highest health risk of ARGs was predicted for Zone I (about 7.58% and 0.48% of ARGs classified into Rank I and Rank II, respectively), followed by Zone II (2.11% and 0%) and Zone III (0% and 0%). However, the ARGs co-occurring with MRGs might exhibit low proportions and low health risks (all were Rank IV) in the three zones. Overall, these findings uncovered the dynamic responses of resistomes and their hosts to different metal(loid) contamination levels, contributing to formulating accurate management and bioremediation countermeasures for various metal(loid) contaminated environments.},
}
@article {pmid37166501,
year = {2023},
author = {Weber, M and Göpfert, B and von Wezyk, S and Savin-Hoffmeyer, M and Lipski, A},
title = {Correlation between Bacterial Cell Density and Abundance of Antibiotic Resistance on Milking Machine Surfaces Assessed by Cultivation and Direct qPCR Methods.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1676-1685},
pmid = {37166501},
issn = {1432-184X},
support = {41.2015.02//Ministry for Environment, Agriculture, Conservation and Consumer Protection of the State of North Rhine-Westphalia/ ; },
mesh = {Animals ; Cattle ; Female ; RNA, Ribosomal, 16S/genetics ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics ; Tetracycline ; Cloxacillin ; Drug Resistance, Microbial/genetics ; Cell Count ; Genes, Bacterial ; },
abstract = {The relative abundance of antibiotic-resistant bacteria and antibiotic-resistance genes was surveyed for different parts of a milking machine. A cultivation approach based on swab samples showed a highly diverse microbiota, harboring resistances against cloxacillin, ampicillin, penicillin, and tetracycline. This approach demonstrated a substantial cloxacillin resistance of numerous taxa within milking machine microbiota coming along with regular use of cloxacillin for dry-off therapy of dairy cows. For the less abundant tetracycline-resistant bacteria we found a positive correlation between microbial cell density and relative abundance of tetracycline-resistant microorganisms (R[2] = 0.73). This indicated an accelerated dispersion of resistant cells for sampling locations with high cell density. However, the direct quantification of the tetM gene from the swap samples by qPCR showed the reverse relation to bacterial density if normalized against the abundance of 16S rRNA genes (R[2] = 0.88). The abundance of 16S rRNA genes was analyzed by qPCR combined with a propidium monoazide treatment, which eliminates 16S rRNA gene signals in negative controls.},
}
@article {pmid37164096,
year = {2023},
author = {Gao, Y and Luo, W and Zhang, H and Chen, Y and Li, Z and Wei, G and Chen, W},
title = {Enrichment of antibiotic resistance genes in roots is related to specific bacterial hosts and soil properties in two soil-plant systems.},
journal = {The Science of the total environment},
volume = {886},
number = {},
pages = {163933},
doi = {10.1016/j.scitotenv.2023.163933},
pmid = {37164096},
issn = {1879-1026},
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Soil/chemistry ; RNA, Ribosomal, 16S ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Soil Microbiology ; Endophytes ; },
abstract = {Soil microorganisms carrying antibiotic resistance genes (ARGs) can colonize plants as endophytes, posing a huge risk to human health. However, the distribution and transmission patterns of ARGs in different soil-plant systems are unclear. Here, we investigated the distribution of ARGs and the microbial communities in the soil-wheat and soil-cucumber systems by quantitative PCR (qPCR) and 16S rRNA gene sequencing. The results showed that the relative abundances of seven ARGs and intI1 in roots were higher than those of other samples in both soil-plant systems. Pseudomonas, Enterobacteriaceae, Rhizobiales and Gammaproteobacteria were dominant potential bacterial hosts of endophytic ARGs, with enrichment patterns similar to that of ARGs in roots. In addition, more ARGs were significantly positively correlated with intI1 in roots, indicating that ARGs may be more prone to horizontal gene transfer (HGT). Variation partitioning analysis (VPA) and structural equation models (SEM) revealed that the variations of ARGs were mainly directly affected by the HGT of intI1 and indirectly affected by soil properties in roots. These results demonstrated that root could have a strong proliferative effect on ARGs entering host plant endophytes. Overall, our findings enhanced the understanding distribution patterns of ARGs in different soil-plant systems, and provided an effective basis for developing measures to minimize the spread of ARGs.},
}
@article {pmid37158891,
year = {2023},
author = {Tapia, SM and Macías, LG and Pérez-Torrado, R and Daroqui, N and Manzanares, P and Querol, A and Barrio, E},
title = {A novel aminotransferase gene and its regulator acquired in Saccharomyces by a horizontal gene transfer event.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {102},
pmid = {37158891},
issn = {1741-7007},
mesh = {*Transaminases ; *Saccharomyces/genetics ; Gene Transfer, Horizontal ; Phylogeny ; Saccharomyces cerevisiae ; Amino Acids ; Aminoisobutyric Acids ; },
abstract = {BACKGROUND: Horizontal gene transfer (HGT) is an evolutionary mechanism of adaptive importance, which has been deeply studied in wine S. cerevisiae strains, where those acquired genes conferred improved traits related to both transport and metabolism of the nutrients present in the grape must. However, little is known about HGT events that occurred in wild Saccharomyces yeasts and how they determine their phenotypes.<br><br>RESULTS: Through a comparative genomic approach among Saccharomyces species, we detected a subtelomeric segment present in the S. uvarum, S. kudriavzevii, and S. eubayanus species, belonging to the first species to diverge in the Saccharomyces genus, but absent in the other Saccharomyces species. The segment contains three genes, two of which were characterized, named DGD1 and DGD2. DGD1 encodes dialkylglicine decarboxylase, whose specific substrate is the non-proteinogenic amino acid 2-aminoisobutyric acid (AIB), a rare amino acid present in some antimicrobial peptides of fungal origin. DGD2 encodes putative zinc finger transcription factor, which is essential to induce the AIB-dependent expression of DGD1. Phylogenetic analysis showed that DGD1 and DGD2 are closely related to two adjacent genes present in Zygosaccharomyces.<br><br>CONCLUSIONS: The presented results show evidence of an early HGT event conferring new traits to the ancestor of the Saccharomyces genus that could be lost in the evolutionary more recent Saccharomyces species, perhaps due to loss of function during the colonization of new habitats.},
}
@article {pmid37156983,
year = {2023},
author = {Calderón-Franco, D and van Loosdrecht, MCM and Abeel, T and Weissbrodt, DG},
title = {Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing.},
journal = {Antonie van Leeuwenhoek},
volume = {116},
number = {7},
pages = {667-685},
pmid = {37156983},
issn = {1572-9699},
support = {15812//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
mesh = {*Wastewater ; Anti-Bacterial Agents/therapeutic use ; Plasmids/genetics ; DNA ; *Microbiota ; Gene Transfer, Horizontal ; Conjugation, Genetic ; },
abstract = {The transformation of environmental microorganisms by extracellular DNA is an overlooked mechanism of horizontal gene transfer and evolution. It initiates the acquisition of exogenous genes and propagates antimicrobial resistance alongside vertical and conjugative transfers. We combined mixed-culture biotechnology and Hi-C sequencing to elucidate the transformation of wastewater microorganisms with a synthetic plasmid encoding GFP and kanamycin resistance genes, in the mixed culture of chemostats exposed to kanamycin at concentrations representing wastewater, gut and polluted environments (0.01-2.5-50-100 mg L[-1]). We found that the phylogenetically distant Gram-negative Runella (102 Hi-C links), Bosea (35), Gemmobacter (33) and Zoogloea (24) spp., and Gram-positive Microbacterium sp. (90) were transformed by the foreign plasmid, under high antibiotic exposure (50 mg L[-1]). In addition, the antibiotic pressure shifted the origin of aminoglycoside resistance genes from genomic DNA to mobile genetic elements on plasmids accumulating in microorganisms. These results reveal the power of Hi-C sequencing to catch and surveil the transfer of xenogenetic elements inside microbiomes.},
}
@article {pmid37156401,
year = {2023},
author = {Gartzonika, K and Politi, L and Mavroidi, A and Tsantes, AG and Spanakis, N and Priavali, E and Vrioni, G and Tsakris, A},
title = {High prevalence of clonally related ST182 NDM-1-producing Enterobacter cloacae complex clinical isolates in Greece.},
journal = {International journal of antimicrobial agents},
volume = {62},
number = {1},
pages = {106837},
doi = {10.1016/j.ijantimicag.2023.106837},
pmid = {37156401},
issn = {1872-7913},
mesh = {Humans ; Multilocus Sequence Typing ; *Enterobacter cloacae/genetics ; Greece/epidemiology ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Prevalence ; Phylogeny ; Retrospective Studies ; beta-Lactamases/genetics ; Carbapenems/pharmacology ; Plasmids/genetics ; Escherichia coli/genetics ; Microbial Sensitivity Tests ; },
abstract = {NDM-type metallo-β-lactamase (MBL)-producing Enterobacterales remain uncommon in the European region, especially among species other than Klebsiella pneumoniae and Escherichia coli. The aim of this study was to describe epidemiological and molecular characteristics of a widespread NDM-1-producing Enterobacter cloacae complex outbreak in Greece. Over a 6-year period (March 2016-March 2022), a retrospective study was conducted in a tertiary care Greek hospital. Ninety single-patient carbapenem-non-susceptible E. cloacae complex clinical isolates were recovered consecutively. The isolates were subjected to further investigation, including antimicrobial susceptibility testing and combined disc tests for carbapenemase production, polymerase chain reaction and sequencing for resistance genes, molecular fingerprinting by pulsed-field gel electrophoresis (PFGE), plasmid profiling, replicon typing, conjugation experiments, genotyping by multi-locus sequence typing (MLST), whole-genome sequencing and phylogenetic analysis. Phenotypic and molecular testing confirmed the presence of blaNDM-1 in 47 (52.2%) of the E. cloacae complex isolates. MLST analysis clustered all but four of the NDM-1 producers into a single MLST sequence type (ST182), whereas single isolates belonged to different sequence types (ST190, ST269, ST443 and ST743). PFGE analysis revealed that ST182 isolates were clustered into a single clonal type, with three subtypes, which differed from the clonal types detected among the remaining carbapenem non-susceptible E. cloacae complex isolates identified during the study period. All ST182 blaNDM-1-carrying isolates also harboured the blaACT-16 AmpC gene, while the blaESBL, blaOXA-1 and blaTEM-1 genes were detected in most cases. In all clonal isolates, the blaNDM-1 gene was located on an IncA/C-type plasmid, and flanked upstream by an ISAba125 element and downstream by bleMBL. Conjugation experiments failed to produce carbapenem-resistant transconjugants, indicating a low dynamic for horizontal gene transfer. Application of enforced infection control measures led to the absence of new NDM-positive cases for periods of time during the survey. This study represents the largest clonal outbreak of NDM-producing E. cloacae complex in Europe.},
}
@article {pmid37156383,
year = {2023},
author = {Tyrrell, C and Do, TT and Leigh, RJ and Burgess, CM and Brennan, FP and Walsh, F},
title = {Differential impact of swine, bovine and poultry manure on the microbiome and resistome of agricultural grassland.},
journal = {The Science of the total environment},
volume = {886},
number = {},
pages = {163926},
doi = {10.1016/j.scitotenv.2023.163926},
pmid = {37156383},
issn = {1879-1026},
mesh = {Animals ; Cattle ; Swine ; *Genes, Bacterial ; Manure/analysis ; Poultry ; RNA, Ribosomal, 16S/genetics ; Grassland ; Drug Resistance, Microbial/genetics ; Soil Microbiology ; Agriculture ; *Microbiota ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology/analysis ; Soil ; Real-Time Polymerase Chain Reaction ; Poaceae ; },
abstract = {Land spreading of animal manure is an essential process in agriculture. Despite the importance of grassland in global food security the potential of the grass phyllosphere as a reservoir of antimicrobial resistance (AMR) is unknown. Additionally, the comparative risk associated with different manure sources is unclear. Due to the One Health nature of AMR there is an urgent need to fully understand the risk associated with AMR at the agriculture - environmental nexus. We performed a grassland field study to assess and compare the relative and temporal impact of bovine, swine and poultry manure application on the grass phyllosphere and soil microbiome and resistome over a period of four months, using 16S rRNA amplicon sequencing and high-throughput quantitative PCR (HT-qPCR). The soil and grass phyllosphere contained a diverse range of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). Manure treatment was found to introduce ARGs belonging to clinically important antimicrobial classes, such as aminoglycoside and sulphonamide into grass and soil. Temporal analysis of ARGs and MGEs associated with manure treatment indicated ARGs patterns were similar across the different manure types in the manure treated soil and grass phyllosphere. Manure treatment resulted in the enrichment in members of the indigenous microbiota and the introduction of manure associated bacteria, with this impact extending past the recommended six-week exclusion period. However, these bacteria were in low relative abundance and manure treatment was not found to significantly impact the overall composition of the microbiome or resistome. This provides evidence that the current guidelines facilitate reduction of biological risk to livestock. Additionally, in soil and grass samples MGEs correlated with ARGs from clinically important antimicrobial classes, indicating the key role MGEs play in horizontal gene transfer in agricultural grassland. These results demonstrate the role of the grass phyllosphere as an under-studied sink of AMR.},
}
@article {pmid37155884,
year = {2023},
author = {Kinsella, CM and van der Hoek, L},
title = {Vertebrate-tropism of a cressdnavirus lineage implicated by poxvirus gene capture.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {20},
pages = {e2303844120},
pmid = {37155884},
issn = {1091-6490},
mesh = {Animals ; Phylogeny ; *Poxviridae/genetics ; *Avipoxvirus/genetics ; Birds ; Tropism ; },
abstract = {Among cressdnaviruses, only the family Circoviridae is recognized to infect vertebrates, while many others have unknown hosts. Detection of virus-to-host horizontal gene transfer is useful for solving such virus-host relationships. Here, we extend this utility to an unusual case of virus-to-virus horizontal transfer, showing multiple ancient captures of cressdnavirus Rep genes by avipoxviruses-large dsDNA pathogens of birds and other saurians. As gene transfers must have occurred during virus coinfections, saurian hosts were implied for the cressdnavirus donor lineage. Surprisingly, phylogenetic analysis revealed that donors were not members of the vertebrate-infecting Circoviridae, instead belonging to a previously unclassified family that we name Draupnirviridae. While draupnirviruses still circulate today, we show that those in the genus Krikovirus infected saurian vertebrates at least 114 Mya, leaving endogenous viral elements inside snake, lizard, and turtle genomes throughout the Cretaceous Period. Endogenous krikovirus elements in some insect genomes and frequent detection in mosquitoes imply that spillover to vertebrates was arthropod mediated, while ancestral draupnirviruses likely infected protists before their emergence in animals. A modern krikovirus sampled from an avipoxvirus-induced lesion shows that their interaction with poxviruses is ongoing. Captured Rep genes in poxvirus genomes often have inactivated catalytic motifs, yet near-total presence across the Avipoxvirus genus, and evidence of both expression and purifying selection on them suggests currently unknown functions.},
}
@article {pmid37155541,
year = {2023},
author = {Jiang, Y and Zhao, L and Li, JD and Sun, J and Miao, R and Shao, B and Wu, P},
title = {The universality of eAREs in animal feces suggesting that eAREs function possibly in horizontal gene transfer.},
journal = {Journal of advanced veterinary and animal research},
volume = {10},
number = {1},
pages = {103-112},
pmid = {37155541},
issn = {2311-7710},
abstract = {OBJECTIVES: This study aimed to pinpoint the universality of extracellular antimicrobial resistance elements (eAREs) and compare the contents of eAREs with those of intracellular AREs (iAREs) in animal feces, thus laying a foundation for the further analysis of the horizontal transfer of antimicrobial resistance genes (ARGs) in the animal guts.<br><br>MATERIALS AND METHODS: Extracellular DNAs were isolated from the fecal samples of Pavo cristatus (n = 18), Ursus thibetanus (n = 2), two breeds of broilers (n = 21 and 11, respectively), and from the contents of rabbit intestines (n = 5). eAREs were detected by PCR technology. iAREs in P. cristatus and broiler feces were also detected and compared with the corresponding eAREs. In addition, some gene cassettes of class 1 integrons were sequenced and analyzed.<br><br>RESULTS: The results showed that eAREs exist in animal feces and intestinal contents. In this study, different eAREs were detected from animal feces and intestinal contents, and tetA, tetB, sul1, sul2, class 1 integron, and IncFIB presented the highest detection rates. The detection rates of certain eAREs were significantly higher than those of parallel iAREs. The integral cassettes with intact structures were found in eAREs, and the cassettes carried ARGs.<br><br>CONCLUSIONS: The presented study here sheds light on the presence of eAREs in animal feces or guts, and eAREs may play an important role in the horizontal gene transfer of ARGs.},
}
@article {pmid37154532,
year = {2023},
author = {Cai, L},
title = {Rethinking convergence in plant parasitism through the lens of molecular and population genetic processes.},
journal = {American journal of botany},
volume = {110},
number = {5},
pages = {e16174},
doi = {10.1002/ajb2.16174},
pmid = {37154532},
issn = {1537-2197},
mesh = {Phylogeny ; *Plants/genetics ; *Photosynthesis/genetics ; Genome, Plant ; Evolution, Molecular ; },
abstract = {The autotrophic lifestyle of photosynthetic plants has profoundly shaped their body plan, physiology, and gene repertoire. Shifts to parasitism and heterotrophy have evolved at least 12 times in more than 4000 species, and this transition has consequently left major evolutionary footprints among these parasitic lineages. Features that are otherwise rare at the molecular level and beyond have evolved repetitively, including reduced vegetative bodies, carrion-mimicking during reproduction, and the incorporation of alien genetic material. Here, I propose an integrated conceptual model, referred to as the funnel model, to define the general evolutionary trajectory of parasitic plants and provide a mechanistic explanation for their convergent evolution. This model connects our empirical understanding of gene regulatory networks in flowering plants with classical theories of molecular and population genetics. It emphasizes that the cascading effects brought about by the loss of photosynthesis may be a major force constraining the physiological capacity of parasitic plants and shaping their genomic landscapes. Here I review recent studies on the anatomy, physiology, and genetics of parasitic plants that lend support to this photosynthesis-centered funnel model. Focusing on nonphotosynthetic holoparasites, I elucidate how they may inevitably reach an evolutionary terminal status (i.e., extinction) and highlight the utility of a general, explicitly described and falsifiable model for future studies of parasitic plants.},
}
@article {pmid37152757,
year = {2023},
author = {Nie, Z and Tang, K and Wang, W and Wang, P and Guo, Y and Wang, Y and Kao, SJ and Yin, J and Wang, X},
title = {Comparative genomic insights into habitat adaptation of coral-associated Prosthecochloris.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1138751},
pmid = {37152757},
issn = {1664-302X},
abstract = {Green sulfur bacteria (GSB) are a distinct group of anoxygenic phototrophic bacteria that are found in many ecological niches. Prosthecochloris, a marine representative genus of GSB, was found to be dominant in some coral skeletons. However, how coral-associated Prosthecochloris (CAP) adapts to diurnal changing microenvironments in coral skeletons is still poorly understood. In this study, three Prosthecochloris genomes were obtained through enrichment culture from the skeleton of the stony coral Galaxea fascicularis. These divergent three genomes belonged to Prosthecochloris marina and two genomes were circular. Comparative genomic analysis showed that between the CAP and non-CAP clades, CAP genomes possess specialized metabolic capacities (CO oxidation, CO2 hydration and sulfur oxidation), gas vesicles (vertical migration in coral skeletons), and cbb 3-type cytochrome c oxidases (oxygen tolerance and gene regulation) to adapt to the microenvironments of coral skeletons. Within the CAP clade, variable polysaccharide synthesis gene clusters and phage defense systems may endow bacteria with differential cell surface structures and phage susceptibility, driving strain-level evolution. Furthermore, mobile genetic elements (MGEs) or evidence of horizontal gene transfer (HGT) were found in most of the genomic loci containing the above genes, suggesting that MGEs play an important role in the evolutionary diversification between CAP and non-CAP strains and within CAP clade strains. Our results provide insight into the adaptive strategy and population evolution of endolithic Prosthecochloris strains in coral skeletons.},
}
@article {pmid37149187,
year = {2023},
author = {Li, LG and Zhang, T},
title = {Plasmid-mediated antibiotic resistance gene transfer under environmental stresses: Insights from laboratory-based studies.},
journal = {The Science of the total environment},
volume = {887},
number = {},
pages = {163870},
doi = {10.1016/j.scitotenv.2023.163870},
pmid = {37149187},
issn = {1879-1026},
mesh = {Phylogeny ; *Plastics ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Environmental Pollutants ; Plasmids ; Gene Transfer, Horizontal ; Pharmaceutical Preparations ; },
abstract = {Although clinical settings play a major role in the current global dissemination of antibiotic resistance, once antibiotic resistance bacteria and genes are released into the environment, their fate will be subject to complex ecological processes. One of the processes prevalent in microbial communities - horizontal gene transfer - can largely facilitate the dissemination of antibiotic resistance genes (ARGs) across phylogenetic and ecological boundaries. Especially, plasmid transfer has aroused increasing concern as it has been proved a significant role in promoting ARG dissemination. As a multi-step process, plasmid transfer can be influenced by various factors, among which those stresses caused by environmental pollutants are important elements affecting the plasmid mediated ARG transfer in the environment. In fact, diverse traditional and emerging pollutants are continuously entering the environment nowadays, as evidenced by the global occurrence of pollutants like metals and pharmaceuticals in aquatic and terrestrial systems. It is therefore imperative to understand to what extent and in which way the plasmid mediated ARG dissemination can be influenced by these stresses. Over the past decades, numerous research endeavours have been made to understand the plasmid mediated ARG transfer under various environmental relevant pressures. In this review, progress and challenges of studies on environmental stress regulating plasmid mediated ARG dissemination will be discussed, with specific focus on emerging pollutants like antibiotics and non-antibiotic pharmaceuticals, metals and their nanoparticles, disinfectants and disinfection by-products, as well as the emerging particulate matter like microplastics. Despite the previous efforts, we are still lacking insights into the in situ plasmid transfer under environmental stresses, which can be addressed by future studies considering environmental relevant pollution status and multi-species microbial communities. We believe that future development of standardized high-throughput screening platforms will assist in rapidly identifying which pollutants enhance plasmid transfer and also which ones may block such gene transfer processes.},
}
@article {pmid37148762,
year = {2023},
author = {Jiang, H and Zhang, L and Wang, X and Gu, J and Song, Z and Wei, S and Guo, H and Xu, L and Qian, X},
title = {Reductions in abundances of intracellular and extracellular antibiotic resistance genes by SiO2 nanoparticles during composting driven by mobile genetic elements.},
journal = {Journal of environmental management},
volume = {341},
number = {},
pages = {118071},
doi = {10.1016/j.jenvman.2023.118071},
pmid = {37148762},
issn = {1095-8630},
mesh = {Animals ; Swine ; Genes, Bacterial ; Silicon Dioxide ; *Composting ; Anti-Bacterial Agents/pharmacology ; Manure/microbiology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Livestock ; *Nanoparticles ; Interspersed Repetitive Sequences ; },
abstract = {Applying exogenous additives during the aerobic composting of livestock manure is effective for slowing down the spread of antibiotic resistance genes (ARGs) in the environment. Nanomaterials have received much attention because only low amounts need to be added and they have a high capacity for adsorbing pollutants. Intracellular ARGs (i-ARGs) and extracellular ARGs (e-ARGs) comprise the resistome in livestock manure but the effects of nanomaterials on the fates of these different fractions during composting are still unclear. Thus, we investigated the effects of adding SiO2 nanoparticles (SiO2NPs) at four levels (0 (CK), 0.5 (L), 1 (M), and 2 g/kg (H)) on i-ARGs, e-ARGs, and the bacterial community during composting. The results showed that i-ARGs represented the main fraction of ARGs during aerobic composting of swine manure, and their abundance was lowest under M. Compared with CK, M increased the removal rates of i-ARGs and e-ARGs by 17.9% and 100%, respectively. SiO2NPs enhanced the competition between ARGs hosts and non-hosts. M optimized the bacterial community by reducing the abundances of co-hosts (Clostridium_sensu_stricto_1, Terrisporobacter, and Turicibacter) of i-ARGs and e-ARGs (by 96.0% and 99.3%, respectively) and killing 49.9% of antibiotic-resistant bacteria. Horizontal gene transfer dominated by mobile genetic elements (MGEs) played a key role in the changes in the abundances of ARGs. i-intI1 and e-Tn916/1545 were key MGEs related closely to ARGs, and the maximum decreases of 52.8% and 100%, respectively, occurred under M, which mainly explained the decreased abundances of i-ARGs and e-ARGs. Our findings provide new insights into the distribution and main drivers of i-ARGs and e-ARGs, as well as demonstrating the possibility of adding 1 g/kg SiO2NPs to reduce the propagation of ARGs.},
}
@article {pmid37146969,
year = {2023},
author = {Takada, H and Katoh, T and Sakanaka, M and Odamaki, T and Katayama, T},
title = {GH20 and GH84 β-N-acetylglucosaminidases with different linkage specificities underpin mucin O-glycan breakdown capability of Bifidobacterium bifidum.},
journal = {The Journal of biological chemistry},
volume = {299},
number = {6},
pages = {104781},
pmid = {37146969},
issn = {1083-351X},
mesh = {Animals ; *Acetylglucosaminidase/chemistry/metabolism ; *Bacterial Proteins/metabolism ; *Bifidobacterium bifidum/classification/enzymology/genetics ; *Mucins/metabolism ; Phylogeny ; Swine ; },
abstract = {Intestinal mucous layers mediate symbiosis and dysbiosis of host-microbe interactions. These interactions are influenced by the mucin O-glycan degrading ability of several gut microbes. The identities and prevalence of many glycoside hydrolases (GHs) involved in microbial mucin O-glycan breakdown have been previously reported; however, the exact mechanisms and extent to which these GHs are dedicated to mucin O-glycan degradation pathways warrant further research. Here, using Bifidobacterium bifidum as a model mucinolytic bacterium, we revealed that two β-N-acetylglucosaminidases belonging to the GH20 (BbhI) and GH84 (BbhIV) families play important roles in mucin O-glycan degradation. Using substrate specificity analysis of natural oligosaccharides and O-glycomic analysis of porcine gastric mucin (PGM) incubated with purified enzymes or B. bifidum carrying bbhI and/or bbhIV mutations, we showed that BbhI and BbhIV are highly specific for β-(1→3)- and β-(1→6)-GlcNAc linkages of mucin core structures, respectively. Interestingly, we found that efficient hydrolysis of the β-(1→3)-linkage by BbhI of the mucin core 4 structure [GlcNAcβ1-3(GlcNAcβ1-6)GalNAcα-O-Thr] required prior removal of the β-(1→6)-GlcNAc linkage by BbhIV. Consistent with this, inactivation of bbhIV markedly decreased the ability of B. bifidum to release GlcNAc from PGM. When combined with a bbhI mutation, we observed that the growth of the strain on PGM was reduced. Finally, phylogenetic analysis suggests that GH84 members may have gained diversified functions through microbe-microbe and host-microbe horizontal gene transfer events. Taken together, these data strongly suggest the involvement of GH84 family members in host glycan breakdown.},
}
@article {pmid37144438,
year = {2023},
author = {Hu, X and Xu, Y and Liu, S and Gudda, FO and Ling, W and Qin, C and Gao, Y},
title = {Graphene Quantum Dots Nonmonotonically Influence the Horizontal Transfer of Extracellular Antibiotic Resistance Genes via Bacterial Transformation.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {19},
number = {37},
pages = {e2301177},
doi = {10.1002/smll.202301177},
pmid = {37144438},
issn = {1613-6829},
mesh = {Humans ; Anti-Bacterial Agents/pharmacology ; *Graphite/pharmacology ; *Quantum Dots ; Transformation, Bacterial ; Drug Resistance, Microbial/genetics ; Escherichia coli/genetics ; },
abstract = {Graphene quantum dots (GQDs) coexist with antibiotic resistance genes (ARGs) in the environment. Whether GQDs influence ARG spread needs investigation, since the resulting development of multidrug-resistant pathogens would threaten human health. This study investigates the effect of GQDs on the horizontal transfer of extracellular ARGs (i.e., transformation, a pivotal way that ARGs spread) mediated by plasmids into competent Escherichia coli cells. GQDs enhance ARG transfer at lower concentrations, which are close to their environmental residual concentrations. However, with further increases in concentration (closer to working concentrations needed for wastewater remediation), the effects of enhancement weaken or even become inhibitory. At lower concentrations, GQDs promote the gene expression related to pore-forming outer membrane proteins and the generation of intracellular reactive oxygen species, thus inducing pore formation and enhancing membrane permeability. GQDs may also act as carriers to transport ARGs into cells. These factors result in enhanced ARG transfer. At higher concentrations, GQD aggregation occurs, and aggregates attach to the cell surface, reducing the effective contact area of recipients for external plasmids. GQDs also form large agglomerates with plasmids and thus hindering ARG entrance. This study could promote the understanding of the GQD-caused ecological risks and benefit their safe application.},
}
@article {pmid37143068,
year = {2023},
author = {Valach, M and Moreira, S and Petitjean, C and Benz, C and Butenko, A and Flegontova, O and Nenarokova, A and Prokopchuk, G and Batstone, T and Lapébie, P and Lemogo, L and Sarrasin, M and Stretenowich, P and Tripathi, P and Yazaki, E and Nara, T and Henrissat, B and Lang, BF and Gray, MW and Williams, TA and Lukeš, J and Burger, G},
title = {Recent expansion of metabolic versatility in Diplonema papillatum, the model species of a highly speciose group of marine eukaryotes.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {99},
pmid = {37143068},
issn = {1741-7007},
support = {BB/R016437/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Humans ; *Eukaryota/genetics ; Meiotic Prophase I ; Euglenozoa/genetics ; *Kinetoplastida/genetics ; Multigene Family ; Phylogeny ; },
abstract = {BACKGROUND: Diplonemid flagellates are among the most abundant and species-rich of known marine microeukaryotes, colonizing all habitats, depths, and geographic regions of the world ocean. However, little is known about their genomes, biology, and ecological role.<br><br>RESULTS: We present the first nuclear genome sequence from a diplonemid, the type species Diplonema papillatum. The&#x2009;~&#x2009;280-Mb genome assembly contains about 32,000 protein-coding genes, likely co-transcribed in groups of up to 100. Gene clusters are separated by long repetitive regions that include numerous transposable elements, which also reside within introns. Analysis of gene-family evolution reveals that the last common diplonemid ancestor underwent considerable metabolic expansion. D. papillatum-specific gains of carbohydrate-degradation capability were apparently acquired via horizontal gene transfer. The predicted breakdown of polysaccharides including pectin and xylan is at odds with reports of peptides being the predominant carbon source of this organism. Secretome analysis together with feeding experiments suggest that D. papillatum is predatory, able to degrade cell walls of live microeukaryotes, macroalgae, and water plants, not only for protoplast feeding but also for metabolizing cell-wall carbohydrates as an energy source. The analysis of environmental barcode samples shows that D. papillatum is confined to temperate coastal waters, presumably acting in bioremediation of eutrophication.<br><br>CONCLUSIONS: Nuclear genome information will allow systematic functional and cell-biology studies in D. papillatum. It will also serve as a reference for the highly diverse diplonemids and provide a point of comparison for studying gene complement evolution in the sister group of Kinetoplastida, including human-pathogenic taxa.},
}
@article {pmid37138596,
year = {2023},
author = {Zhao, Y and Wei, HM and Yuan, JL and Xu, L and Sun, JQ},
title = {A comprehensive genomic analysis provides insights on the high environmental adaptability of Acinetobacter strains.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1177951},
pmid = {37138596},
issn = {1664-302X},
abstract = {Acinetobacter is ubiquitous, and it has a high species diversity and a complex evolutionary pattern. To elucidate the mechanism of its high ability to adapt to various environment, 312 genomes of Acinetobacter strains were analyzed using the phylogenomic and comparative genomics methods. It was revealed that the Acinetobacter genus has an open pan-genome and strong genome plasticity. The pan-genome consists of 47,500 genes, with 818 shared by all the genomes of Acinetobacter, while 22,291 are unique genes. Although Acinetobacter strains do not have a complete glycolytic pathway to directly utilize glucose as carbon source, most of them harbored the n-alkane-degrading genes alkB/alkM (97.1% of tested strains) and almA (96.7% of tested strains), which were responsible for medium-and long-chain n-alkane terminal oxidation reaction, respectively. Most Acinetobacter strains also have catA (93.3% of tested strains) and benAB (92.0% of tested strains) genes that can degrade the aromatic compounds catechol and benzoic acid, respectively. These abilities enable the Acinetobacter strains to easily obtain carbon and energy sources from their environment for survival. The Acinetobacter strains can manage osmotic pressure by accumulating potassium and compatible solutes, including betaine, mannitol, trehalose, glutamic acid, and proline. They respond to oxidative stress by synthesizing superoxide dismutase, catalase, disulfide isomerase, and methionine sulfoxide reductase that repair the damage caused by reactive oxygen species. In addition, most Acinetobacter strains contain many efflux pump genes and resistance genes to manage antibiotic stress and can synthesize a variety of secondary metabolites, including arylpolyene, β-lactone and siderophores among others, to adapt to their environment. These genes enable Acinetobacter strains to survive extreme stresses. The genome of each Acinetobacter strain contained different numbers of prophages (0-12) and genomic islands (GIs) (6-70), and genes related to antibiotic resistance were found in the GIs. The phylogenetic analysis revealed that the alkM and almA genes have a similar evolutionary position with the core genome, indicating that they may have been acquired by vertical gene transfer from their ancestor, while catA, benA, benB and the antibiotic resistance genes could have been acquired by horizontal gene transfer from the other organisms.},
}
@article {pmid37137974,
year = {2023},
author = {Ikhimiukor, OO and Souza, SSR and Marcovici, MM and Nye, GJ and Gibson, R and Andam, CP},
title = {Leaky barriers to gene sharing between locally co-existing coagulase-negative Staphylococcus species.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {482},
pmid = {37137974},
issn = {2399-3642},
support = {R35 GM142924/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Coagulase/genetics ; Staphylococcus/genetics ; Plasmids ; *Bacteriophages ; },
abstract = {Coagulase-negative Staphylococcus (CoNS) are opportunistic pathogens implicated in many human and animal infections. The evolutionary history of CoNS remains obscure because of the historical lack of recognition for their clinical importance and poor taxonomic sampling. Here, we sequenced the genomes of 191 CoNS isolates representing 15 species sampled from diseased animals diagnosed in a veterinary diagnostic laboratory. We found that CoNS are important reservoirs of diverse phages, plasmids and mobilizable genes encoding antimicrobial resistance, heavy metal resistance, and virulence. Frequent exchange of DNA between certain donor-recipient partners suggests that specific lineages act as hubs of gene sharing. We also detected frequent recombination between CoNS regardless of their animal host species, indicating that ecological barriers to horizontal gene transfer can be surmounted in co-circulating lineages. Our findings reveal frequent but structured patterns of transfer that exist within and between CoNS species, which are driven by their overlapping ecology and geographical proximity.},
}
@article {pmid37133439,
year = {2023},
author = {Tran, NN and Morrisette, T and Jorgensen, SCJ and Orench-Benvenutti, JM and Kebriaei, R},
title = {Current therapies and challenges for the treatment of Staphylococcus aureus biofilm-related infections.},
journal = {Pharmacotherapy},
volume = {43},
number = {8},
pages = {816-832},
doi = {10.1002/phar.2806},
pmid = {37133439},
issn = {1875-9114},
mesh = {Humans ; Staphylococcus aureus ; Biofilms ; *Staphylococcal Infections/drug therapy ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Community-Acquired Infections/drug therapy ; *Methicillin-Resistant Staphylococcus aureus/physiology ; Microbial Sensitivity Tests ; },
abstract = {Staphylococcus aureus is a major cause of nosocomial and community-acquired infections and contributes to significant increase in morbidity and mortality especially when associated with medical devices and in biofilm form. Biofilm structure provides a pathway for the enrichment of resistant and persistent phenotypes of S. aureus leading to relapse and recurrence of infection. Minimal diffusion of antibiotics inside biofilm structure leads to heterogeneity and distinct physiological activity. Additionally, horizontal gene transfer between cells in proximity adds to the challenges associated with eradication of biofilms. This narrative review focuses on biofilm-associated infections caused by S. aureus, the impact of environmental conditions on biofilm formation, interactions inside biofilm communities, and the clinical challenges that they present. Conclusively, potential solutions, novel treatment strategies, combination therapies, and reported alternatives are discussed.},
}
@article {pmid37126651,
year = {2023},
author = {Akmal, M and Akatsuka, M and Nishiki, I and Yoshida, T},
title = {Resistance and genomic characterization of a plasmid pkh2101 harbouring erm(B) isolated from emerging fish pathogen Lactococcus garvieae serotype II in Japan.},
journal = {Journal of fish diseases},
volume = {46},
number = {8},
pages = {841-848},
doi = {10.1111/jfd.13793},
pmid = {37126651},
issn = {1365-2761},
support = {21H02287//Grants-in-Aid for Scientific Research from JSPS KAKENHI/ ; },
mesh = {Animals ; Japan ; Serogroup ; *Fish Diseases ; Plasmids/genetics ; Lactococcus/genetics ; Erythromycin ; Genomics ; },
abstract = {The emergence of antibiotic-resistant pathogenic strains of Lactococcus garvieae serotype II isolated from fish in Japan has become a growing concern in recent years. The data on drug susceptibility and its associated resistance mechanism are limited. Therefore, the present study was conducted to determine the minimum inhibitory concentrations (MICs) of chemotherapeutic agents against 98 pathogenic strains of emerging Lactococcus garvieae serotype II isolated from fish from six different prefectures in Japan from 2018 to 2021. The tested strains were resistant to erythromycin, lincomycin and tiamulin. PCR amplification revealed the presence of erm(B) in all erythromycin-resistant strains, while a conjugation experiment confirmed that these strains carried erm(B) that could be transferred to recipient Enterococcus faecalis OG1RF with frequencies from 10[-4] to 10[-6] per donor cells. Nucleotide sequencing of the representative isolated plasmid pkh2101 from an erythromycin-resistant strain showed that it was a 26,850 bp molecule with an average GC content of 33.49%, comprising 31 CDSs, 13 of which remained without any functional annotation. Comparative genomic analysis suggested that pkh2101 shared the highest similarity (97.57% identity) with the plasmid pAMbeta1, which was previously isolated clinically from Enterococcus faecalis DS-5. This study provides potential evidence that the plasmid harbouring erm(B) could be a source of antibiotic resistance transmission in emerging L. garvieae infection in aquaculture.},
}
@article {pmid37125932,
year = {2023},
author = {Quan, J and Hu, H and Zhang, H and Meng, Y and Liao, W and Zhou, J and Han, X and Shi, Q and Zhao, D and Wang, Q and Jiang, Y and Yu, Y},
title = {Investigating Possible Interspecies Communication of Plasmids Associated with Transfer of Third-Generation Cephalosporin, Quinolone, and Colistin Resistance Between Simultaneously Isolated Escherichia Coli and Klebsiella Pneumoniae.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0355422},
pmid = {37125932},
issn = {2165-0497},
mesh = {Humans ; Escherichia coli/metabolism ; Colistin ; Klebsiella pneumoniae/metabolism ; Anti-Bacterial Agents/pharmacology ; *Quinolones ; *Coinfection ; Plasmids/genetics ; *Escherichia coli Proteins/genetics ; Cephalosporins/pharmacology ; Communication ; *Cross Infection ; Microbial Sensitivity Tests ; beta-Lactamases/genetics ; Drug Resistance, Bacterial/genetics ; *Klebsiella Infections ; },
abstract = {The coinfection process producing multiple species of pathogens provides a specific ecological niche for the exchange of genetic materials between pathogens, in which plasmids play a vital role in horizontal gene transfer, especially for drug resistance, but the underlying transfer pathway remains unclear. Interspecies communication of the plasmids associated with the transfer of third-generation cephalosporins, quinolones, and colistin resistance has been observed in simultaneously isolated Escherichia coli and Klebsiella pneumoniae from abdominal drainage following surgery. The MICs of antimicrobial agents were determined by the broth microdilution method. The complete chromosome and plasmid sequences were obtained by combining Illumina paired-end short reads and MinION long reads. S1-PFGE, southern blot analysis and conjugation assay confirmed the transferability of the mcr-1-harboring plasmid. Both the E. coli isolate EC15255 and K. pneumoniae isolate KP15255 from the same specimen presented multidrug resistance. Each of them harbored one chromosome and three plasmids, and two plasmids and their mediated resistance could be transferred to the recipient by conjugation. Comparison of their genome sequences suggested that several genetic communication events occurred between species, especially among their plasmids, such as whole-plasmid transfer, insertion, deletion, amplification, or inversion. Exchange of plasmids or the genetic elements they harbor plays a critical role in antimicrobial resistance gene transmission and poses a substantial threat to nosocomial infection control, necessitating the continued surveillance of multidrug resistant pathogens, especially during coinfection. IMPORTANCE The genome sequence of bacterial pathogens commonly provides a detailed clue of genetic communication among clones or even distinct species. The intestinal microecological environment is a representative ecological niche for genetic communication. However, it is still difficult to describe the details of horizontal gene transfer or other genetic events within them because the evidence in the genome sequence is incomplete and limited. In this study, the simultaneously isolated Escherichia coli and Klebsiella pneumoniae from a coinfection process provided an excellent example for observation of interspecies communication between the two genomes and the plasmids they harbor. A complete genome sequence acquired by combining the Illumina and MinION sequencing platforms facilitated the understanding of genetic communication events, such as whole-plasmid transfer, insertion, deletion, amplification, or inversion, which contribute to antimicrobial resistance gene transmission and are a substantial threat to nosocomial infection control.},
}
@article {pmid37125466,
year = {2023},
author = {Castanheira, M and Mendes, RE and Gales, AC},
title = {Global Epidemiology and Mechanisms of Resistance of Acinetobacter baumannii-calcoaceticus Complex.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {76},
number = {Suppl 2},
pages = {S166-S178},
pmid = {37125466},
issn = {1537-6591},
mesh = {Humans ; *Acinetobacter baumannii/genetics ; Anti-Bacterial Agents/pharmacology ; *Acinetobacter calcoaceticus/genetics ; *Acinetobacter Infections/epidemiology ; *Acinetobacter ; *Bacteremia/epidemiology ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {Acinetobacter baumannii-calcoaceticus complex is the most commonly identified species in the genus Acinetobacter and it accounts for a large percentage of nosocomial infections, including bacteremia, pneumonia, and infections of the skin and urinary tract. A few key clones of A. baumannii-calcoaceticus are currently responsible for the dissemination of these organisms worldwide. Unfortunately, multidrug resistance is a common trait among these clones due to their unrivalled adaptive nature. A. baumannii-calcoaceticus isolates can accumulate resistance traits by a plethora of mechanisms, including horizontal gene transfer, natural transformation, acquisition of mutations, and mobilization of genetic elements that modulate expression of intrinsic and acquired genes.},
}
@article {pmid37121291,
year = {2023},
author = {Kosterlitz, O and Huisman, JS},
title = {Guidelines for the estimation and reporting of plasmid conjugation rates.},
journal = {Plasmid},
volume = {126},
number = {},
pages = {102685},
doi = {10.1016/j.plasmid.2023.102685},
pmid = {37121291},
issn = {1095-9890},
mesh = {*Bacteria/genetics ; *Conjugation, Genetic/genetics ; *Gene Transfer, Horizontal/genetics ; *Plasmids/genetics ; Terminology as Topic ; *Research Design ; },
abstract = {Conjugation is a central characteristic of plasmid biology and an important mechanism of horizontal gene transfer in bacteria. However, there is little consensus on how to accurately estimate and report plasmid conjugation rates, in part due to the wide range of available methods. Given the similarity between approaches, we propose general reporting guidelines for plasmid conjugation experiments. These constitute best practices based on recent literature about plasmid conjugation and methods to measure conjugation rates. In addition to the general guidelines, we discuss common theoretical assumptions underlying existing methods to estimate conjugation rates and provide recommendations on how to avoid violating these assumptions. We hope this will aid the implementation and evaluation of conjugation rate measurements, and initiate a broader discussion regarding the practice of quantifying plasmid conjugation rates.},
}
@article {pmid37120693,
year = {2023},
author = {Kuppa Baskaran, DK and Umale, S and Zhou, Z and Raman, K and Anantharaman, K},
title = {Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {42},
pmid = {37120693},
issn = {2730-6151},
abstract = {Deep-sea hydrothermal vents are abundant on the ocean floor and play important roles in ocean biogeochemistry. In vent ecosystems such as hydrothermal plumes, microorganisms rely on reduced chemicals and gases in hydrothermal fluids to fuel primary production and form diverse and complex microbial communities. However, microbial interactions that drive these complex microbiomes remain poorly understood. Here, we use microbiomes from the Guaymas Basin hydrothermal system in the Pacific Ocean to shed more light on the key species in these communities and their interactions. We built metabolic models from metagenomically assembled genomes (MAGs) and infer possible metabolic exchanges and horizontal gene transfer (HGT) events within the community. We highlight possible archaea-archaea and archaea-bacteria interactions and their contributions to the robustness of the community. Cellobiose, D-Mannose 1-phosphate, O2, CO2, and H2S were among the most exchanged metabolites. These interactions enhanced the metabolic capabilities of the community by exchange of metabolites that cannot be produced by any other community member. Archaea from the DPANN group stood out as key microbes, benefiting significantly as acceptors in the community. Overall, our study provides key insights into the microbial interactions that drive community structure and organisation in complex hydrothermal plume microbiomes.},
}
@article {pmid37120212,
year = {2023},
author = {Ammoun, I and Kothe, CI and Mohellibi, N and Beal, C and Yaacoub, R and Renault, P},
title = {Lebanese fermented goat milk products: From tradition to meta-omics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {168},
number = {},
pages = {112762},
doi = {10.1016/j.foodres.2023.112762},
pmid = {37120212},
issn = {1873-7145},
mesh = {Female ; Animals ; *Cultured Milk Products ; Ecosystem ; *Kefir ; *Lactococcus lactis ; Goats ; },
abstract = {Ambriss, Serdaleh and Labneh El Darff are traditional Lebanese products made from fermented goat's milk. A questionnaire completed by 50 producers of these products showed that they are prepared by periodic percolation either by milk or by Laban in amphora or goat skins during the lactation season. Production is carried out on a small scale and in a limited number of production units, often by elderly people, resulting in a real risk of disappearance of these products and loss of the corresponding microbial resources. In this study, 34 samples from 18 producers were characterized by culture-dependent and -independent analyses. The results obtained from these two methods were radically different, the latter revealing in Ambriss and Serdaleh the co-dominance of Lactobacillus kefiranofaciens, a fastidious-growing species, and Lactococcus lactis in a viable but not culturable state. Overall, their composition is reminiscent of kefir grains. Phylogenomic and functional analyses of the genomes of the key species Lb. kefiranofaciens have revealed differences from those found in kefir, particularly in their polysaccharide genes, which may explain the absence of grains. However, Labneh El Darff displayed a dominance of Lactobacillus delbrueckii, probably due to the addition of Laban. In addition, the study identified several zoonotic pathogens, including Streptococcus parasuis, which dominated in one sample. Metagenome-Assembled Genome (MAG) analysis indicated that this pathogen acquired lactose utilization genes through horizontal gene transfer. The contamination of the herd with Mycoplasmopsis agalactiae in the Chouf region was also revealed by MAG analysis of the Serdaleh samples. Antibiotic resistance genes were detected in most of the samples, particularly in the Serdaleh ones, where the dominant L. lactis strains possessed a plasmid with a multi-resistance island. Finally, this study paves the way for further analyses to shed light on the resilience of these ecosystems established in amphora or in goatskins and to improve hygiene practices for milk production.},
}
@article {pmid37120023,
year = {2023},
author = {Adomako, MO and Yu, FH},
title = {Potential effects of micro- and nanoplastics on phyllosphere microorganisms and their evolutionary and ecological responses.},
journal = {The Science of the total environment},
volume = {884},
number = {},
pages = {163760},
doi = {10.1016/j.scitotenv.2023.163760},
pmid = {37120023},
issn = {1879-1026},
mesh = {*Microplastics ; Plastics ; Environmental Pollution ; *Microbiota ; Soil ; Plants ; },
abstract = {Plastic pollution is among the most urgent environmental and social challenges of the 21st century, and their influxes in the environment have altered critical growth drivers in all biomes, attracting global concerns. In particular, the consequences of microplastics on plants and their associated soil microorganisms have gained a large audience. On the contrary, how microplastics and nanoplastics (M/NPs) may influence the plant-associated microorganisms in the phyllosphere (i.e., the aboveground portion of plants) is nearly unknown. We, therefore, summarize evidence that may potentially connect M/NPs, plants, and phyllosphere microorganisms based on studies on other analogous contaminants such as heavy metals, pesticides, and nanoparticles. We show seven pathways that may link M/NPs into the phyllosphere environment, and provide a conceptual framework explaining the direct and indirect (soil legacy) effects of M/NPs on phyllosphere microbial communities. We also discuss the adaptive evolutionary and ecological responses, such as acquiring novel resistance genes via horizontal gene transfer and microbial degradation of plastics of the phyllosphere microbial communities, to M/NPs-induced threats. Finally, we highlight the global consequences (e.g., disruption of ecosystem biogeochemical cycling and impaired host-pathogen defense chemistry that can lead to reduced agricultural productivity) of altered plant-microbiome interactions in the phyllosphere in the context of a predicted surge of plastic production and conclude with pending questions for future research priorities. In conclusion, M/NPs are very likely to produce significant effects on phyllosphere microorganisms and mediate their evolutionary and ecological responses.},
}
@article {pmid37119017,
year = {2023},
author = {Shin, NR and Okamura, Y and Kirsch, R and Pauchet, Y},
title = {Genome sequencing provides insights into the evolution of gene families encoding plant cell wall-degrading enzymes in longhorned beetles.},
journal = {Insect molecular biology},
volume = {32},
number = {5},
pages = {469-483},
doi = {10.1111/imb.12844},
pmid = {37119017},
issn = {1365-2583},
mesh = {Animals ; *Coleoptera/genetics ; Larva/genetics ; Base Sequence ; Genome ; Cell Wall/metabolism ; },
abstract = {With more than 36,000 species, the longhorned beetles (family Cerambycidae) are a mega-diverse lineage of mostly xylophagous insects, all of which are represented by the sole sequenced genome of the Asian longhorned beetle (Anoplophora glabripennis; Lamiinae). Their successful radiation has been linked to their ability to degrade plant cell wall components using a range of so-called plant cell wall-degrading enzymes (PCWDEs). Our previous analysis of larval gut transcriptomes demonstrated that cerambycid beetles horizontally acquired genes encoding PCWDEs from various microbial donors; these genes evolved through multiple duplication events to form gene families. To gain further insights into the evolution of these gene families during the Cerambycidae radiation, we assembled draft genomes for four beetle species belonging to three subfamilies using long-read nanopore sequencing. All the PCWDE-encoding genes we annotated from the corresponding larval gut transcriptomes were present in these draft genomes. We confirmed that the newly discovered horizontally acquired glycoside hydrolase family 7 (GH7), subfamily 26 of GH43 (GH43_26), and GH53 (all of which are absent from the A. glabripennis genome) were indeed encoded by these beetles' genome. Most of the PCWDE-encoding genes of bacterial origin gained introns after their transfer into the beetle genome. Altogether, we show that draft genome assemblies generated from nanopore long-reads offer meaningful information to the study of the evolution of gene families in insects. We anticipate that our data will support studies aiming to better understand the biology of the Cerambycidae and other beetles in general.},
}
@article {pmid37116631,
year = {2023},
author = {Garcillán-Barcia, MP and Redondo-Salvo, S and de la Cruz, F},
title = {Plasmid classifications.},
journal = {Plasmid},
volume = {126},
number = {},
pages = {102684},
doi = {10.1016/j.plasmid.2023.102684},
pmid = {37116631},
issn = {1095-9890},
mesh = {Plasmids/genetics ; *Bacteria/genetics ; *Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; },
abstract = {Plasmids are universally present in bacteria and play key roles in the dissemination of genes such as antibiotic resistance determinants. Major concepts in Plasmid Biology derive from the efforts to classify plasmids. Here, we review the main plasmid classification systems, starting by phenotype-based methods, such as fertility inhibition and incompatibility, followed by schemes based on a single gene (replicon type and MOB class), and finishing with recently developed approaches that use genetic distances between whole plasmid sequences. A comparison of the latter highlights significant differences between them. We further discuss the need for an operational definition of plasmid species that reveals their biological features, akin to plasmid taxonomic units (PTUs).},
}
@article {pmid37115189,
year = {2023},
author = {Salamzade, R and Cheong, JZA and Sandstrom, S and Swaney, MH and Stubbendieck, RM and Starr, NL and Currie, CR and Singh, AM and Kalan, LR},
title = {Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC.},
journal = {Microbial genomics},
volume = {9},
number = {4},
pages = {},
pmid = {37115189},
issn = {2057-5858},
support = {R35 GM137828/GM/NIGMS NIH HHS/United States ; U19 AI142720/AI/NIAID NIH HHS/United States ; },
mesh = {*Microbiota/genetics ; Metagenome ; Biological Evolution ; },
abstract = {Bacterial secondary metabolites, synthesized by enzymes encoded in biosynthetic gene clusters (BGCs), can underlie microbiome homeostasis and serve as commercialized products, which have historically been mined from a select group of taxa. While evolutionary approaches have proven beneficial for prioritizing BGCs for experimental characterization efforts to uncover new natural products, dedicated bioinformatics tools designed for comparative and evolutionary analysis of BGCs within focal taxa are limited. We thus developed lineage specific analysis of BGCs (lsaBGC; https://github.com/Kalan-Lab/lsaBGC) to aid exploration of microdiversity and evolutionary trends across homologous groupings of BGCs, gene cluster families (GCFs), in any bacterial taxa of interest. lsaBGC enables rapid and direct identification of GCFs in genomes, calculates evolutionary statistics and conservation for BGC genes, and builds a framework to allow for base resolution mining of novel variants through metagenomic exploration. Through application of the suite to four genera commonly found in skin microbiomes, we uncover new insights into the evolution and diversity of their BGCs. We show that the BGC of the virulence-associated carotenoid staphyloxanthin in Staphylococcus aureus is ubiquitous across the genus Staphylococcus . While one GCF encoding the biosynthesis of staphyloxanthin showcases evidence for plasmid-mediated horizontal gene transfer (HGT) between species, another GCF appears to be transmitted vertically amongst a sub-clade of skin-associated Staphylococcus . Further, the latter GCF, which is well conserved in S. aureus , has been lost in most Staphylococcus epidermidis , which is the most common Staphylococcus species on human skin and is also regarded as a commensal. We also identify thousands of novel single-nucleotide variants (SNVs) within BGCs from the Corynebacterium tuberculostearicum sp. complex, a narrow, multi-species clade that features the most prevalent Corynebacterium in healthy skin microbiomes. Although novel SNVs were approximately 10 times as likely to correspond to synonymous changes when located in the top five percentile of conserved sites, lsaBGC identified SNVs that defied this trend and are predicted to underlie amino acid changes within functionally key enzymatic domains. Ultimately, beyond supporting evolutionary investigations of BGCs, lsaBGC also provides important functionalities to aid efforts for the discovery or directed modification of natural products.},
}
@article {pmid37110299,
year = {2023},
author = {Qi, Q and Kamruzzaman, M and Iredell, JR},
title = {A Streamlined Approach for Fluorescence Labelling of Low-Copy-Number Plasmids for Determination of Conjugation Frequency by Flow Cytometry.},
journal = {Microorganisms},
volume = {11},
number = {4},
pages = {},
pmid = {37110299},
issn = {2076-2607},
support = {G1145914//National Health and Medical Research Council/ ; },
abstract = {Bacterial conjugation plays a major role in the dissemination of antibiotic resistance and virulence traits through horizontal transfer of plasmids. Robust measurement of conjugation frequency of plasmids between bacterial strains and species is therefore important for understanding the transfer dynamics and epidemiology of conjugative plasmids. In this study, we present a streamlined experimental approach for fluorescence labelling of low-copy-number conjugative plasmids that allows plasmid transfer frequency during filter mating to be measured by flow cytometry. A blue fluorescent protein gene is inserted into a conjugative plasmid of interest using a simple homologous recombineering procedure. A small non-conjugative plasmid, which carries a red fluorescent protein gene with a toxin-antitoxin system that functions as a plasmid stability module, is used to label the recipient bacterial strain. This offers the dual advantage of circumventing chromosomal modifications of recipient strains and ensuring that the red fluorescent protein gene-bearing plasmid can be stably maintained in recipient cells in an antibiotic-free environment during conjugation. A strong constitutive promoter allows the two fluorescent protein genes to be strongly and constitutively expressed from the plasmids, thus allowing flow cytometers to clearly distinguish between donor, recipient, and transconjugant populations in a conjugation mix for monitoring conjugation frequencies more precisely over time.},
}
@article {pmid37110264,
year = {2023},
author = {Vittorakis, E and Vică, ML and Zervaki, CO and Vittorakis, E and Maraki, S and Mavromanolaki, VE and Schürger, ME and Neculicioiu, VS and Papadomanolaki, E and Sinanis, T and Giannoulaki, G and Xydaki, E and Kastanakis, SG and Junie, LM},
title = {Examining the Prevalence and Antibiotic Susceptibility of S. aureus Strains in Hospitals: An Analysis of the pvl Gene and Its Co-Occurrence with Other Virulence Factors.},
journal = {Microorganisms},
volume = {11},
number = {4},
pages = {},
pmid = {37110264},
issn = {2076-2607},
abstract = {S. aureus is a pathogenic bacterium that causesinfections. Its virulence is due to surface components, proteins, virulence genes, SCCmec, pvl, agr, and SEs, which are low molecular weight superantigens. SEs are usually encoded by mobile genetic elements, and horizontal gene transfer accounts for their widespread presence in S. aureus. This study analyzed the prevalence of MRSA and MSSA strains of S. aureus in two hospitals in Greece between 2020-2022 and their susceptibility to antibiotics. Specimens collected were tested using the VITEK 2 system and the PCR technique to detect SCCmec types, agr types, pvl genes, and sem and seg genes. Antibiotics from various classes were also tested. This study examined the prevalence and resistance of S. aureus strains in hospitals. It found a high prevalence of MRSA and that the MRSA strains were more resistant to antibiotics. The study also identified the genotypes of the S. aureus isolates and the associated antibiotic resistances. This highlights the need for continued surveillance and effective strategies to combat the spread of MRSA in hospitals. This study examined the prevalence of the pvl gene and its co-occurrence with other genes in S. aureus strains, as well as their antibiotic susceptibility. The results showed that 19.15% of the isolates were pvl-positive and 80.85% were pvl-negative. The pvl gene co-existed with other genes, such as the agr and enterotoxin genes. The results could inform treatment strategies for S. aureus infections.},
}
@article {pmid37110261,
year = {2023},
author = {Karnachuk, OV and Beletsky, AV and Rakitin, AL and Ikkert, OP and Avakyan, MR and Zyusman, VS and Napilov, A and Mardanov, AV and Ravin, NV},
title = {Antibiotic-Resistant Desulfovibrio Produces H2S from Supplements for Animal Farming.},
journal = {Microorganisms},
volume = {11},
number = {4},
pages = {},
pmid = {37110261},
issn = {2076-2607},
support = {Agreement &#x2116; 075-15-2021-1401, 03 November 2021//Ministry of Science and Higher Education of the Russian Fed-eration/ ; },
abstract = {Sulphate-reducing bacteria, primarily Desulfovibrio, are responsible for the active generation of H2S in swine production waste. The model species for sulphate reduction studies, Desulfovibrio vulgaris strain L2, was previously isolated from swine manure characterized by high rates of dissimilatory sulphate reduction. The source of electron acceptors in low-sulphate swine waste for the high rate of H2S formation remains uncertain. Here, we demonstrate the ability of the L2 strain to use common animal farming supplements including L-lysine-sulphate, gypsum and gypsum plasterboards as electron acceptors for H2S production. Genome sequencing of strain L2 revealed the presence of two megaplasmids and predicted resistance to various antimicrobials and mercury, which was confirmed in physiological experiments. Most of antibiotic resistance genes (ARG) are carried by two class 1 integrons located on the chromosome and on the plasmid pDsulf-L2-2. These ARGs, predicted to confer resistance to beta-lactams, aminoglycosides, lincosamides, sulphonamides, chloramphenicol and tetracycline, were probably laterally acquired from various Gammaproteobacteria and Firmicutes. Resistance to mercury is likely enabled by two mer operons also located on the chromosome and on pDsulf-L2-2 and acquired via horizontal gene transfer. The second megaplasmid, pDsulf-L2-1, encoded nitrogenase, catalase and type III secretion system suggesting close contact of the strain with intestinal cells in the swine gut. The location of ARGs on mobile elements allows us to consider D. vulgaris strain L2 as a possible vector transferring antimicrobials resistance determinants between the gut microbiote and microbial communities in environmental biotopes.},
}
@article {pmid37107701,
year = {2023},
author = {Wu, L and Fan, P and Zhou, J and Li, Y and Xu, Z and Lin, Y and Wang, Y and Song, J and Yao, H},
title = {Gene Losses and Homology of the Chloroplast Genomes of Taxillus and Phacellaria Species.},
journal = {Genes},
volume = {14},
number = {4},
pages = {},
pmid = {37107701},
issn = {2073-4425},
mesh = {*Loranthaceae/genetics ; Phylogeny ; *Genome, Chloroplast ; Base Sequence ; },
abstract = {Research on the chloroplast genome of parasitic plants is limited. In particular, the homology between the chloroplast genomes of parasitic and hyperparasitic plants has not been reported yet. In this study, three chloroplast genomes of Taxillus (Taxillus chinensis, Taxillus delavayi, and Taxillus thibetensis) and one chloroplast genome of Phacellaria (Phacellaria rigidula) were sequenced and analyzed, among which T. chinensis is the host of P. rigidula. The chloroplast genomes of the four species were 119,941-138,492 bp in length. Compared with the chloroplast genome of the autotrophic plant Nicotiana tabacum, all of the ndh genes, three ribosomal protein genes, three tRNA genes and the infA gene were lost in the three Taxillus species. Meanwhile, in P. rigidula, the trnV-UAC gene and the ycf15 gene were lost, and only one ndh gene (ndhB) existed. The results of homology analysis showed that the homology between P. rigidula and its host T. chinensis was low, indicating that P. rigidula grows on its host T. chinensis but they do not share the chloroplast genome. In addition, horizontal gene transfer was not found between P. rigidula and its host T. chinensis. Several candidate highly variable regions in the chloroplast genomes of Taxillus and Phacellaria species were selected for species identification study. Phylogenetic analysis revealed that the species of Taxillus and Scurrula were closely related and supported that Scurrula and Taxillus should be treated as congeneric, while species in Phacellaria had a close relationship with that in Viscum.},
}
@article {pmid37104544,
year = {2023},
author = {Brual, T and Effantin, G and Baltenneck, J and Attaiech, L and Grosbois, C and Royer, M and Cigna, J and Faure, D and Hugouvieux-Cotte-Pattat, N and Gueguen, E},
title = {A natural single nucleotide mutation in the small regulatory RNA ArcZ of Dickeya solani switches off the antimicrobial activities against yeast and bacteria.},
journal = {PLoS genetics},
volume = {19},
number = {4},
pages = {e1010725},
pmid = {37104544},
issn = {1553-7404},
mesh = {*Multigene Family/genetics ; *Point Mutation ; Genomics ; RNA, Bacterial/genetics/metabolism ; Polyketide Synthases/genetics ; *Antimicrobial Peptides/genetics/pharmacology ; Bacteria/drug effects ; Ascomycota/drug effects ; Dickeya/genetics/metabolism ; Gene Expression Regulation, Bacterial/genetics ; },
abstract = {The necrotrophic plant pathogenic bacterium Dickeya solani emerged in the potato agrosystem in Europe. All isolated strains of D. solani contain several large polyketide synthase/non-ribosomal peptide synthetase (PKS/NRPS) gene clusters. Analogy with genes described in other bacteria suggests that the clusters ooc and zms are involved in the production of secondary metabolites of the oocydin and zeamine families, respectively. A third cluster named sol was recently shown to produce an antifungal molecule. In this study, we constructed mutants impaired in each of the three secondary metabolite clusters sol, ooc, and zms to compare first the phenotype of the D. solani wild-type strain D s0432-1 with its associated mutants. We demonstrated the antimicrobial functions of these three PKS/NRPS clusters against bacteria, yeasts or fungi. The cluster sol, conserved in several other Dickeya species, produces a secondary metabolite inhibiting yeasts. Phenotyping and comparative genomics of different D. solani wild-type isolates revealed that the small regulatory RNA ArcZ plays a major role in the control of the clusters sol and zms. A single-point mutation, conserved in some Dickeya wild-type strains, including the D. solani type strain IPO 2222, impairs the ArcZ function by affecting its processing into an active form.},
}
@article {pmid37102089,
year = {2023},
author = {Shao, M and Liu, L and Liu, B and Zheng, H and Meng, W and Liu, Y and Zhang, X and Ma, X and Sun, C and Luo, X and Li, F and Xing, B},
title = {Hormetic Effect of Pyroligneous Acids on Conjugative Transfer of Plasmid-mediated Multi-antibiotic Resistance Genes within Bacterial Genus.},
journal = {ACS environmental Au},
volume = {3},
number = {2},
pages = {105-120},
pmid = {37102089},
issn = {2694-2518},
abstract = {Spread of antibiotic resistance genes (ARGs) by conjugation poses great challenges to public health. Application of pyroligneous acids (PA) as soil amendments has been evidenced as a practical strategy to remediate pollution of ARGs in soils. However, little is known about PA effects on horizontal gene transfer (HGT) of ARGs by conjugation. This study investigated the effects of a woody waste-derived PA prepared at 450°C and its three distillation components (F1, F2, and F3) at different temperatures (98, 130, and 220°C) on conjugative transfer of plasmid RP4 within Escherichia coli. PA at relatively high amount (40-100 μL) in a 30-mL mating system inhibited conjugation by 74-85%, following an order of PA > F3 ≈ F2 ≈ F1, proving the hypothesis that PA amendments may mitigate soil ARG pollution by inhibiting HGT. The bacteriostasis caused by antibacterial components of PA, including acids, phenols, and alcohols, as well as its acidity (pH 2.81) contributed to the inhibited conjugation. However, a relatively low amount (10-20 μL) of PA in the same mating system enhanced ARG transfer by 26-47%, following an order of PA > F3 ≈ F2 > F1. The opposite effect at low amount is mainly attributed to the increased intracellular reactive oxygen species production, enhanced cell membrane permeability, increased extracellular polymeric substance contents, and reduced cell surface charge. Our findings highlight the hormesis (low-amount promotion and high-amount inhibition) of PA amendments on ARG conjugation and provide evidence for selecting an appropriate amount of PA amendment to control the dissemination of soil ARGs. Moreover, the promoted conjugation also triggers questions regarding the potential risks of soil amendments (e.g., PA) in the spread of ARGs via HGT.},
}
@article {pmid37099912,
year = {2023},
author = {Sun, X and Kong, T and Huang, D and Chen, Z and Kolton, M and Yang, J and Huang, Y and Cao, Y and Gao, P and Yang, N and Li, B and Liu, H and Sun, W},
title = {Arsenic (As) oxidation by core endosphere microbiome mediates As speciation in Pteris vittata roots.},
journal = {Journal of hazardous materials},
volume = {454},
number = {},
pages = {131458},
doi = {10.1016/j.jhazmat.2023.131458},
pmid = {37099912},
issn = {1873-3336},
mesh = {*Arsenic/metabolism ; *Pteris/metabolism ; Plant Roots/metabolism ; Oxidation-Reduction ; Oxidoreductases/metabolism ; Biodegradation, Environmental ; *Soil Pollutants/metabolism ; },
abstract = {Pteris vittata is an arsenic(As)-hyperaccumulator that may be employed in phytoremediation of As-contaminated soils. P. vittata-associated microbiome are adapted to elevated As and may be important for host survival under stresses. Although P. vittata root endophytes could be critical for As biotransformation in planta, their compositions and metabolisms remain elusive. The current study aims to characterize the root endophytic community composition and As-metabolizing potentials in P. vittata. High As(III) oxidase gene abundances and rapid As(III) oxidation activity indicated that As(III) oxidation was the dominant microbial As-biotransformation processes compared to As reduction and methylization in P. vittata roots. Members of Rhizobiales were the core microbiome and the dominant As(III) oxidizers in P. vittata roots. Acquasition of As-metabolising genes, including both As(III) oxidase and As(V) detoxification reductase genes, through horizontal gene transfer was identified in a Saccharimonadaceae genomic assembly, which was another abundant population residing in P. vittata roots. Acquisition of these genes might improve the fitness of Saccharimonadaceae population to elevated As concentrations in P. vittata. Diverse plant growth promoting traits were encoded by the core root microbiome populations Rhizobiales. We propose that microbial As(III) oxidation and plant growth promotion are critical traits for P. vittata survival in hostile As-contaiminated sites.},
}
@article {pmid37098416,
year = {2023},
author = {Gong, H and Huang, X and Zhu, W and Chen, J and Huang, Y and Zhao, Z and Weng, J and Che, Y and Wang, J and Wang, X},
title = {Pan-genome analysis of the Burkholderia gladioli PV. Cocovenenans reveal the extent of variation in the toxigenic gene cluster.},
journal = {Food microbiology},
volume = {113},
number = {},
pages = {104249},
doi = {10.1016/j.fm.2023.104249},
pmid = {37098416},
issn = {1095-9998},
mesh = {Humans ; *Burkholderia gladioli/genetics ; Bongkrekic Acid/analysis ; Multigene Family ; *Foodborne Diseases/microbiology ; },
abstract = {Burkholderia gladioli has been reported as the pathogen responsible for cases of foodborne illness in many countries. The poisonous bongkrekic acid (BA) produced by B. gladioli was linked to a gene cluster absent in non-pathogenic strains. The whole genome sequence of eight bacteria strains, which were screened from the collected 175 raw food and environmental samples, were assembled and analyzed to detect a significant association of 19 protein-coding genes with the pathogenic status. Except for the common BA synthesis-related gene, several other genes, including the toxin-antitoxin genes, were also absent in the non-pathogenic strains. The bacteria strains with the BA gene cluster were found to form a single cluster in the analysis of all B. gladioli genome assemblies for the variants in the gene cluster. Divergence of this cluster was detected in the analysis for both the flanking sequences and those of the whole genome level, which indicates its complex origin. Genome recombination was found to cause a precise sequence deletion in the gene cluster region, which was found to be predominant in the non-pathogenic strains indicating the possible effect of horizontal gene transfer. Our study provided new information and resources for understanding the evolution and divergence of the B. gladioli species.},
}
@article {pmid37098287,
year = {2023},
author = {Nõlvak, H and Truu, M and Tiirik, K and Devarajan, AK and Peeb, A and Truu, J},
title = {The effect of synthetic silver nanoparticles on the antibiotic resistome and the removal efficiency of antibiotic resistance genes in a hybrid filter system treating municipal wastewater.},
journal = {Water research},
volume = {237},
number = {},
pages = {119986},
doi = {10.1016/j.watres.2023.119986},
pmid = {37098287},
issn = {1879-2448},
mesh = {*Wastewater ; Anti-Bacterial Agents/pharmacology/analysis ; Silver/analysis ; *Metal Nanoparticles ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Integrases/genetics ; Waste Disposal, Fluid/methods ; },
abstract = {Engineered nanoparticles, including silver nanoparticles (AgNPs), are released into the environment mainly through wastewater treatment systems. Knowledge of the impact of AgNPs on the abundance and removal efficiency of antibiotic resistance genes (ARGs) in wastewater treatment facilities, including constructed wetlands (CWs), is essential in the context of public health. This study evaluated the effect of increased (100-fold) collargol (protein-coated AgNPs) and ionic Ag[+] in municipal wastewater on the structure, abundance, and removal efficiency of the antibiotic resistome, integron-integrase genes, and pathogens in a hybrid CW using quantitative PCR and metagenomic approaches. The abundance of ARGs in wastewater and the removal efficiency of ARGs in the hybrid system were significantly affected by higher Ag concentrations, especially with collargol treatment, resulting in an elevated ARG discharge of system effluent into the environment. The accumulated Ag in the filters had a more profound effect on the absolute and relative abundance of ARGs in the treated water than the Ag content in the water. This study recorded significantly enhanced relative abundance values for tetracycline (tetA, tetC, tetQ), sulfonamide (sul1, sul2), and aminoglycoside (aadA) resistance genes, which are frequently found on mobile genetic elements in collargol- and, to a lesser extent, AgNO3-treated subsystems. Elevated plasmid and integron-integrase gene levels, especially intI1, in response to collargol presence indicated the substantial role of AgNPs in promoting horizontal gene transfer in the treatment system. The pathogenic segment of the prokaryotic community was similar to a typical sewage community, and strong correlations between pathogen and ARG proportions were recorded in vertical subsurface flow filters. Furthermore, the proportion of Salmonella enterica was positively related to the Ag content in these filter effluents. The effect of AgNPs on the nature and characteristics of prominent resistance genes carried by mobile genetic elements in CWs requires further investigation.},
}
@article {pmid37097444,
year = {2023},
author = {Bibi, S and Weis, K and Kaur, A and Bhandari, R and Goss, E and Jones, JB and Potnis, N},
title = {A Brief Evaluation of a Copper Resistance Mobile Genetic Island in the Bacterial Leaf Spot Pathogen Xanthomonas euvesicatoria pv. perforans.},
journal = {Phytopathology},
volume = {113},
number = {8},
pages = {1394-1398},
doi = {10.1094/PHYTO-02-23-0077-SC},
pmid = {37097444},
issn = {0031-949X},
abstract = {Due to the continuous use of copper containing bactericides without effective alternative bactericides, copper resistance has become more prevalent in plant pathogens, including Xanthomonas euvesicatoria pv. perforans (formerly Xanthomonas perforans), a predominant cause of bacterial leaf spot disease of tomato and pepper in the Southeastern United States. Previously, reports of copper resistance have been associated with a large conjugative plasmid. However, we have characterized a copper resistance genomic island located within the chromosome of multiple X. euvesicatoria pv. perforans strains. The island is distinct from a previously described chromosomally encoded copper resistance island in X. vesicatoria strain XVP26. Computational analysis revealed the genomic island to contain multiple genes associated with genetic mobility, including both phage-related genes and transposase. Among copper-tolerant strains of X. euvesicatoria pv. perforans isolated from Florida, the majority of strains were found to have the copper resistance chromosomally encoded rather than plasmid borne. Our results suggest that this copper resistance island may have two modes of horizontal gene transfer and that chromosomally encoded copper resistance genes may provide a fitness advantage over plasmid-borne resistance.},
}
@article {pmid37097343,
year = {2023},
author = {Francis, A and Steel, M},
title = {Labellable Phylogenetic Networks.},
journal = {Bulletin of mathematical biology},
volume = {85},
number = {6},
pages = {46},
pmid = {37097343},
issn = {1522-9602},
mesh = {Phylogeny ; *Evolution, Molecular ; *Models, Biological ; Models, Genetic ; Mathematical Concepts ; Algorithms ; },
abstract = {Phylogenetic networks are mathematical representations of evolutionary history that are able to capture both tree-like evolutionary processes (speciations) and non-tree-like 'reticulate' processes such as hybridization or horizontal gene transfer. The additional complexity that comes with this capacity, however, makes networks harder to infer from data, and more complicated to work with as mathematical objects. In this paper, we define a new, large class of phylogenetic networks, that we call labellable, and show that they are in bijection with the set of 'expanding covers' of finite sets. This correspondence is a generalisation of the encoding of phylogenetic forests by partitions of finite sets. Labellable networks can be characterised by a simple combinatorial condition, and we describe the relationship between this large class and other commonly studied classes. Furthermore, we show that all phylogenetic networks have a quotient network that is labellable.},
}
@article {pmid37095096,
year = {2023},
author = {Ahmad, M and Prensky, H and Balestrieri, J and ElNaggar, S and Gomez-Simmonds, A and Uhlemann, AC and Traxler, B and Singh, A and Lopatkin, AJ},
title = {Tradeoff between lag time and growth rate drives the plasmid acquisition cost.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {2343},
pmid = {37095096},
issn = {2041-1723},
support = {R15 GM143694/GM/NIGMS NIH HHS/United States ; R35 GM148351/GM/NIGMS NIH HHS/United States ; R01 AI150152/AI/NIAID NIH HHS/United States ; },
mesh = {Plasmids ; *Bacteria/genetics ; *Gene Transfer, Horizontal ; },
abstract = {Conjugative plasmids drive genetic diversity and evolution in microbial populations. Despite their prevalence, plasmids can impose long-term fitness costs on their hosts, altering population structure, growth dynamics, and evolutionary outcomes. In addition to long-term fitness costs, acquiring a new plasmid introduces an immediate, short-term perturbation to the cell. However, due to the transient nature of this plasmid acquisition cost, a quantitative understanding of its physiological manifestations, overall magnitudes, and population-level implications, remains unclear. To address this, here we track growth of single colonies immediately following plasmid acquisition. We find that plasmid acquisition costs are primarily driven by changes in lag time, rather than growth rate, for nearly 60 conditions covering diverse plasmids, selection environments, and clinical strains/species. Surprisingly, for a costly plasmid, clones exhibiting longer lag times also achieve faster recovery growth rates, suggesting an evolutionary tradeoff. Modeling and experiments demonstrate that this tradeoff leads to counterintuitive ecological dynamics, whereby intermediate-cost plasmids outcompete both their low and high-cost counterparts. These results suggest that, unlike fitness costs, plasmid acquisition dynamics are not uniformly driven by minimizing growth disadvantages. Moreover, a lag/growth tradeoff has clear implications in predicting the ecological outcomes and intervention strategies of bacteria undergoing conjugation.},
}
@article {pmid37094448,
year = {2023},
author = {Zhu, S and Yang, B and Jia, Y and Yu, F and Wang, Z and Liu, Y},
title = {Comprehensive analysis of disinfectants on the horizontal transfer of antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {453},
number = {},
pages = {131428},
doi = {10.1016/j.jhazmat.2023.131428},
pmid = {37094448},
issn = {1873-3336},
mesh = {Humans ; Anti-Bacterial Agents/pharmacology ; *Disinfectants/pharmacology ; Genes, Bacterial ; Pandemics ; *COVID-19 ; Drug Resistance, Microbial/genetics ; Guanidines ; Gene Transfer, Horizontal ; Plasmids/genetics ; },
abstract = {The propagation of antimicrobial resistance (AMR) is constantly paralyzing our healthcare systems. In addition to the pressure of antibiotic selection, the roles of non-antibiotic compounds in disseminating antibiotic resistance genes (ARGs) are a matter of great concerns. This study aimed to explore the impact of different disinfectants on the horizontal transfer of ARGs and their underlying mechanisms. First, the effects of different kinds of disinfectants on the conjugative transfer of RP4-7 plasmid were evaluated. Results showed that quaternary ammonium salt, organic halogen, alcohol and guanidine disinfectants significantly facilitated the conjugative transfer. Conversely, heavy-metals, peroxides and phenols otherwise displayed an inhibitory effect. Furthermore, we deciphered the mechanism by which guanidine disinfectants promoted conjugation, which includes increased cell membrane permeability, over-production of ROS, enhanced SOS response, and altered expression of conjugative transfer-related genes. More critically, we also revealed that guanidine disinfectants promoted bacterial energy metabolism by enhancing the activity of electron transport chain (ETC) and proton force motive (PMF), thus promoting ATP synthesis and flagellum motility. Overall, our findings reveal the promotive effects of disinfectants on the transmission of ARGs and highlight the potential risks caused by the massive use of guanidine disinfectants, especially during the COVID-19 pandemic.},
}
@article {pmid37093956,
year = {2023},
author = {Baumdicker, F and Kupczok, A},
title = {Tackling the Pangenome Dilemma Requires the Concerted Analysis of Multiple Population Genetic Processes.},
journal = {Genome biology and evolution},
volume = {15},
number = {5},
pages = {},
pmid = {37093956},
issn = {1759-6653},
mesh = {Humans ; *Prokaryotic Cells ; *Gene Transfer, Horizontal ; Computer Simulation ; Mutation ; },
abstract = {The pangenome is the set of all genes present in a prokaryotic population. Most pangenomes contain many accessory genes of low and intermediate frequencies. Different population genetics processes contribute to the shape of these pangenomes, namely selection and fitness-independent processes such as gene transfer, gene loss, and migration. However, their relative importance is unknown and highly debated. Here, we argue that the debate around prokaryotic pangenomes arose due to the imprecise application of population genetics models. Most importantly, two different processes of horizontal gene transfer act on prokaryotic populations, which are frequently confused, despite their fundamentally different behavior. Genes acquired from distantly related organisms (termed here acquiring gene transfer) are most comparable to mutation in nucleotide sequences. In contrast, gene gain within the population (termed here spreading gene transfer) has an effect on gene frequencies that is identical to the effect of positive selection on single genes. We thus show that selection and fitness-independent population genetic processes affecting pangenomes are indistinguishable at the level of single gene dynamics. Nevertheless, population genetics processes are fundamentally different when considering the joint distribution of all accessory genes across individuals of a population. We propose that, to understand to which degree the different processes shaped pangenome diversity, the development of comprehensive models and simulation tools is mandatory. Furthermore, we need to identify summary statistics and measurable features that can distinguish between the processes, where considering the joint distribution of accessory genes across individuals of a population will be particularly relevant.},
}
@article {pmid37092000,
year = {2023},
author = {Han, Z and Xu, S and Gao, T},
title = {Unexpected complex horizontal gene transfer in teleost fish.},
journal = {Current zoology},
volume = {69},
number = {2},
pages = {222-223},
pmid = {37092000},
issn = {1674-5507},
}
@article {pmid37091576,
year = {2022},
author = {Varner, PM and Allemann, MN and Michener, JK and Gunsch, CK},
title = {The effect of bacterial growth strategies on plasmid transfer and naphthalene degradation for bioremediation.},
journal = {Environmental technology &amp; innovation},
volume = {28},
number = {},
pages = {},
pmid = {37091576},
issn = {2352-1864},
support = {P42 ES010356/ES/NIEHS NIH HHS/United States ; },
abstract = {Mobilizable plasmids are extra-chromosomal, circular DNA that have contributed to the rapid evolution of bacterial genomes and have been used in environmental, biotechnological, and medicinal applications. Degradative plasmids with genetic capabilities to degrade organic contaminants, such as polycyclic aromatic hydrocarbons (PAHs), have the potential to be useful for more environmentally friendly and cost-effective remediation technologies compared to existing physical remediation methods. Genetic bioaugmentation, the addition of catabolic genes into well-adapted communities via plasmid transfer (conjugation), is being explored as a remediation approach that is sustainable and long-lasting. Here, we explored the effect of the ecological growth strategies of plasmid donors and recipients on conjugation and naphthalene degradation of two PAH-degrading plasmids, pNL1 and NAH7. Overall, both pNL1 and NAH7 showed conjugation preferences towards a slow-growing ecological growth strategy, except when NAH7 was in a mixed synthetic community. These conjugation preferences were partially described by a combination of growth strategy, GC content, and phylogenetic relatedness. Further, removal of naphthalene via plasmid-mediated degradation was consistently higher in a community consisting of recipients with a slow-growing ecological growth strategy compared to a mixed community or a community consisting of fast-growing ecological growth strategy. Understanding plasmid conjugation and degradative preferences has the capacity to influence future remediation technology design and has broad implications in biomedical, environmental, and health fields.},
}
@article {pmid37087920,
year = {2023},
author = {Zheng, CW and Luo, YH and Long, X and Gu, H and Cheng, J and Zhang, L and Lai, YJS and Rittmann, BE},
title = {The structure of biodegradable surfactants shaped the microbial community, antimicrobial resistance, and potential for horizontal gene transfer.},
journal = {Water research},
volume = {236},
number = {},
pages = {119944},
doi = {10.1016/j.watres.2023.119944},
pmid = {37087920},
issn = {1879-2448},
mesh = {*Surface-Active Agents/chemistry ; Anti-Bacterial Agents ; Cetrimonium/chemistry ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; *Anti-Infective Agents ; Quaternary Ammonium Compounds/chemistry ; },
abstract = {While most household surfactants are biodegradable in aerobic conditions, their biodegradability may obscure their environmental risks. The presence of surfactants in a biological treatment process can lead to the proliferation of antimicrobial-resistance genes (ARG) in the biomass. Surfactants can be cationic, anionic, or zwitterionic, and these different classes may have different effects on the proliferation ARG. Cationic hexadecyltrimethyl-ammonium (CTAB), anionic sodium dodecyl sulfate (SDS), and zwitterionic 3-(decyldimethylammonio)-propanesulfonate inner salt (DAPS) were used to represent the three classes of surfactants in domestic household clean-up products. This study focused on the removal of these surfactants by the O2-based Membrane Biofilm Reactor (O2-MBfR) for hotspot scenarios (∼1 mM) and how the three classes of surfactants affected the microbial community's structure and ARG. Given sufficient O2 delivery, the MBfR provided at least 98% surfactant removal. The presence and biodegradation for each surfactant uniquely shaped the biofilms' microbial communities and the presence of ARG. CTAB had by far the strongest impact and the higher ARG abundance. In particular, Pseudomonas and Stenotrophomonas, the two main genera in the biofilm treating CTAB, were highly correlated to the abundance of ARG for efflux pumps and antibiotic inactivation. CTAB also led to more functional genes relevant to the Type-IV secretion system and protection against oxidative stress, which also could encourage horizontal gene transfer. Our findings highlight that the biodegradation of quaternary ammonium surfactants, while beneficial, can pose public health concerns from its ability to promote the proliferation of ARG.},
}
@article {pmid37083586,
year = {2023},
author = {Maphosa, S and Moleleki, LN and Motaung, TE},
title = {Bacterial secretion system functions: evidence of interactions and downstream implications.},
journal = {Microbiology (Reading, England)},
volume = {169},
number = {4},
pages = {},
pmid = {37083586},
issn = {1465-2080},
mesh = {*Bacterial Secretion Systems/genetics ; *Gram-Negative Bacteria/genetics ; Virulence ; Bacteria/genetics ; Virulence Factors ; Bacterial Proteins/genetics ; },
abstract = {Unprecedented insights into the biology and functions of bacteria have been and continue to be gained through studying bacterial secretion systems in isolation. This method, however, results in our understanding of the systems being primarily based on the idea that they operate independently, ignoring the subtleties of downstream interconnections. Gram-negative bacteria are naturally able to adapt to and navigate their frequently varied and dynamic surroundings, mostly because of the covert connections between secretion systems. Therefore, to comprehend some of the linked downstream repercussions for organisms that follow this discourse, it is vital to have mechanistic insights into how the intersecretion system functions in bacterial rivalry, virulence, and survival, among other things. To that purpose, this paper discusses a few key instances of molecular antagonistic and interdependent relationships between bacterial secretion systems and their produced functional products.},
}
@article {pmid37083356,
year = {2023},
author = {Wu, J and Zhou, JH and Liu, DF and Wu, J and He, RL and Cheng, ZH and Li, HH and Li, WW},
title = {Phthalates Promote Dissemination of Antibiotic Resistance Genes: An Overlooked Environmental Risk.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {17},
pages = {6876-6887},
doi = {10.1021/acs.est.2c09491},
pmid = {37083356},
issn = {1520-5851},
mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Bacteria/genetics ; Genes, Bacterial ; Plastics ; Gene Transfer, Horizontal ; },
abstract = {Plastics-microorganism interactions have aroused growing environmental and ecological concerns. However, previous studies concentrated mainly on the direct interactions and paid little attention to the ecotoxicology effects of phthalates (PAEs), a common plastic additive that is continuously released and accumulates in the environment. Here, we provide insights into the impacts of PAEs on the dissemination of antibiotic resistance genes (ARGs) among environmental microorganisms. Dimethyl phthalate (DMP, a model PAE) at environmentally relevant concentrations (2-50 μg/L) significantly boosted the plasmid-mediated conjugation transfer of ARGs among intrageneric, intergeneric, and wastewater microbiota by up to 3.82, 4.96, and 4.77 times, respectively. The experimental and molecular dynamics simulation results unveil a strong interaction between the DMP molecules and phosphatidylcholine bilayer of the cell membrane, which lowers the membrane lipid fluidity and increases the membrane permeability to favor transfer of ARGs. In addition, the increased reactive oxygen species generation and conjugation-associated gene overexpression under DMP stress also contribute to the increased gene transfer. This study provides fundamental knowledge of the PAE-bacteria interactions to broaden our understanding of the environmental and ecological risks of plastics, especially in niches with colonized microbes, and to guide the control of ARG environmental spreading.},
}
@article {pmid37079454,
year = {2023},
author = {Gulliver, EL and Adams, V and Marcelino, VR and Gould, J and Rutten, EL and Powell, DR and Young, RB and D'Adamo, GL and Hemphill, J and Solari, SM and Revitt-Mills, SA and Munn, S and Jirapanjawat, T and Greening, C and Boer, JC and Flanagan, KL and Kaldhusdal, M and Plebanski, M and Gibney, KB and Moore, RJ and Rood, JI and Forster, SC},
title = {Extensive genome analysis identifies novel plasmid families in Clostridium perfringens.},
journal = {Microbial genomics},
volume = {9},
number = {4},
pages = {},
pmid = {37079454},
issn = {2057-5858},
mesh = {Humans ; *Clostridium perfringens ; *Bacterial Toxins/genetics ; Phylogeny ; Base Composition ; Sequence Analysis, DNA ; RNA, Ribosomal, 16S ; Plasmids/genetics ; },
abstract = {Globally, the anaerobic bacterium Clostridium perfringens causes severe disease in a wide array of hosts; however, C. perfringens strains are also carried asymptomatically. Accessory genes are responsible for much of the observed phenotypic variation and virulence within this species, with toxins frequently encoded on conjugative plasmids and many isolates carrying up to 10 plasmids. Despite this unusual biology, current genomic analyses have largely excluded isolates from healthy hosts or environmental sources. Accessory genomes, including plasmids, also have often been excluded from broader scale phylogenetic investigations. Here we interrogate a comprehensive collection of 464 C. perfringens genomes and identify the first putative non-conjugative enterotoxin (CPE)-encoding plasmids and a putative novel conjugative locus (Bcp) with sequence similarity to a locus reported from Clostridium botulinum. We sequenced and archived 102 new C. perfringens genomes, including those from rarely sequenced toxinotype B, C, D and E isolates. Long-read sequencing of 11 C. perfringens strains representing all toxinotypes (A-G) identified 55 plasmids from nine distinct plasmid groups. Interrogation of the 464 genomes in this collection identified 1045 plasmid-like contigs from the nine plasmid families, with a wide distribution across the C. perfringens isolates. Plasmids and plasmid diversity play an essential role in C. perfringens pathogenicity and broader biology. We have expanded the C. perfringens genome collection to include temporal, spatial and phenotypically diverse isolates including those carried asymptomatically in the gastrointestinal microbiome. This analysis has resulted in the identification of novel C. perfringens plasmids whilst providing a comprehensive understanding of species diversity.},
}
@article {pmid37078595,
year = {2023},
author = {Botelho, J},
title = {Defense systems are pervasive across chromosomally integrated mobile genetic elements and are inversely correlated to virulence and antimicrobial resistance.},
journal = {Nucleic acids research},
volume = {51},
number = {9},
pages = {4385-4397},
pmid = {37078595},
issn = {1362-4962},
mesh = {*Anti-Bacterial Agents ; *Conjugation, Genetic ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Virulence/genetics ; *Bacteria/genetics ; *Archaea/genetics ; },
abstract = {Mobile genetic elements (MGEs) are key promoters of microbial evolution. These elements can be located extrachromosomally or integrated into the chromosome. Well-known examples of chromosomally integrated MGEs (ciMGEs) are integrative and conjugative/mobilizable elements (ICEs and IMEs), and most studies to date have focused on the biological mechanisms that shape their lifestyle. It is crucial to profile the diversity and understand their distribution across the microbial community, as the number of genome sequences increases exponentially. Herein, I scanned a collection of >20 000 bacterial and archaeal non-redundant genomes and found over 13 000 ciMGEs across multiple phyla, representing a massive increase in the number of ciMGEs available in public databases (<1000). Although ICEs are the most important ciMGEs for the accretion of defense systems, virulence, and antimicrobial resistance (AMR) genes, IMEs outnumbered ICEs. Moreover, defense systems, AMR, and virulence genes were negatively correlated in both ICEs and IMEs. Multiple ciMGEs form heterogeneous communities and challenge inter-phylum barriers. Finally, I observed that the functional landscape of ICEs was populated by uncharacterized proteins. Altogether, this study provides a comprehensive catalog of nucleotide sequences and associated metadata for ciMGEs from 34 phyla across the bacterial and archaeal domains.},
}
@article {pmid37072776,
year = {2023},
author = {Hernández, M and Roy, S and Keevil, CW and Dumont, MG},
title = {Identification of diverse antibiotic resistant bacteria in agricultural soil with H2[18]O stable isotope probing combined with high-throughput sequencing.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {34},
pmid = {37072776},
issn = {2524-6372},
support = {NE/N02026X/1//Natural Environment Research Council/ ; NE/N02026X/1//Natural Environment Research Council/ ; },
abstract = {BACKGROUND: We aimed to identify bacteria able to grow in the presence of several antibiotics including the ultra-broad-spectrum antibiotic meropenem in a British agricultural soil by combining DNA stable isotope probing (SIP) with high throughput sequencing. Soil was incubated with cefotaxime, meropenem, ciprofloxacin and trimethoprim in [18]O-water. Metagenomes and the V4 region of the 16S rRNA gene from the labelled "heavy" and the unlabelled "light" SIP fractions were sequenced.<br><br>RESULTS: An increase of the 16S rRNA copy numbers in the "heavy" fractions of the treatments with [18]O-water compared with their controls was detected. The treatments resulted in differences in the community composition of bacteria. Members of the phyla Acidobacteriota (formally Acidobacteria) were highly abundant after two days of incubation with antibiotics. Pseudomonadota (formally Proteobacteria) including Stenotrophomonas were prominent after four days of incubation. Furthermore, a metagenome-assembled genome (MAG-1) from the genus Stenotrophomonas (90.7% complete) was retrieved from the heavy fraction. Finally, 11 antimicrobial resistance genes (ARGs) were identified in the unbinned-assembled heavy fractions, and 10 ARGs were identified in MAG-1. In comparison, only two ARGs from the unbinned-assembled light fractions were identified.<br><br>CONCLUSIONS: The results indicate that both non-pathogenic soil-dwelling bacteria as well as potential clinical pathogens are present in this agricultural soil and several ARGs were identified from the labelled communities, but it is still unclear if horizontal gene transfer between these groups can occur.},
}
@article {pmid37072330,
year = {2023},
author = {Fokina, AS and Karyagina, AS and Rusinov, IS and Moshensky, DM and Spirin, SA and Alexeevski, AV},
title = {Evolution of Restriction-Modification Systems Consisting of One Restriction Endonuclease and Two DNA Methyltransferases.},
journal = {Biochemistry. Biokhimiia},
volume = {88},
number = {2},
pages = {253-261},
doi = {10.1134/S0006297923020086},
pmid = {37072330},
issn = {1608-3040},
mesh = {DNA Restriction Enzymes/genetics ; *DNA Restriction-Modification Enzymes/genetics ; Phylogeny ; *Methyltransferases/genetics ; DNA ; },
abstract = {Some restriction-modification systems contain two DNA methyltransferases. In the present work, we have classified such systems according to the families of catalytic domains present in the restriction endonucleases and both DNA methyltransferases. Evolution of the restriction-modification systems containing an endonuclease with a NOV_C family domain and two DNA methyltransferases, both with DNA_methylase family domains, was investigated in detail. Phylogenetic tree of DNA methyltransferases from the systems of this class consists of two clades of the same size. Two DNA methyltransferases of each restriction-modification system of this class belong to the different clades. This indicates independent evolution of the two methyltransferases. We detected multiple cross-species horizontal transfers of the systems as a whole, as well as the cases of gene transfer between the systems.},
}
@article {pmid37070987,
year = {2023},
author = {Dai, X and Sun, J and Zhu, B and Lv, M and Chen, L and Chen, L and Wang, X and Huang, J and Wang, L},
title = {Various Mobile Genetic Elements Involved in the Dissemination of the Phenicol-Oxazolidinone Resistance Gene optrA in the Zoonotic Pathogen Streptococcus suis: a Nonignorable Risk to Public Health.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0487522},
pmid = {37070987},
issn = {2165-0497},
mesh = {Humans ; *Oxazolidinones ; *Streptococcus suis/genetics ; Public Health ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences ; },
abstract = {The rapid increase of phenicol-oxazolidinone (PhO) resistance in Streptococcus suis due to transferable resistance gene optrA is a matter of concern. However, genetic mechanisms for the dissemination of the optrA gene remain to be discovered. Here, we selected 33 optrA-positive S. suis isolates for whole-genome sequencing and analysis. The IS1216E element was present in 85% of the optrA-carrying contigs despite genetic variation observed in the flanking region. IS1216E-optrA-carrying segments could be inserted into larger mobile genetic elements (MGEs), including integrative and conjugative elements, plasmids, prophages, and antibiotic resistance-associated genomic islands. IS1216E-mediated circularization occurred to form the IS1216E-optrA-carrying translocatable units, suggesting a crucial role of IS1216E in optrA spreading. Three optrA-carrying MGEs (ICESsuAKJ47_SSU1797, plasmid pSH0918, and prophage ΦSsuFJSM5_rum) were successfully transferred via conjugation at different transfer frequencies. Interestingly, two types of transconjugants were observed due to the multilocus integration of ICESsuAKJ47 into an alternative SSU1943 attachment site along with the primary SSU1797 attachment site (type 1) or into the single SSU1797 attachment site (type 2). In addition, conjugative transfer of an optrA-carrying plasmid and prophage in streptococci was validated for the first time. Considering the abundance of MGEs in S. suis and the mobility of IS1216E-optrA-carrying translocatable units, attention should be paid to the potential risks to public health from the emergence and spread of PhO-resistant S. suis. IMPORTANCE Antimicrobial resistance to phenicols and oxazolidinones by the dissemination of the optrA gene leads to treatment failure in both veterinary and human medicine. However, information about the profile of these MGEs (mobilome) that carry optrA and their transferability in streptococci was limited, especially for the zoonotic pathogen S. suis. This study showed that the optrA-carrying mobilome in S. suis includes integrative and conjugative elements (ICEs), plasmids, prophages, and antibiotic resistance-associated genomic islands. IS1216E-mediated formation of optrA-carrying translocatable units played important roles in optrA spreading between types of MGEs, and conjugative transfer of various optrA-carrying MGEs (ICEs, plasmids, and prophages) further facilitated the transfer of optrA across strains, highlighting a nonignorable risk to public health of optrA dissemination to other streptococci and even to bacteria of other genera.},
}
@article {pmid37070984,
year = {2023},
author = {Wu, HY and Wei, ZL and Shi, DY and Li, HB and Li, XM and Yang, D and Zhou, SQ and Peng, XX and Yang, ZW and Yin, J and Chen, TJ and Li, JW and Jin, M},
title = {Simulated Gastric Acid Promotes the Horizontal Transfer of Multidrug Resistance Genes across Bacteria in the Gastrointestinal Tract at Elevated pH Levels.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0482022},
pmid = {37070984},
issn = {2165-0497},
mesh = {Humans ; *Genes, MDR ; Reactive Oxygen Species ; *Angiotensin Receptor Antagonists/pharmacology ; Gastric Acid ; Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Intestines ; Hydrogen-Ion Concentration ; Gene Transfer, Horizontal ; Genes, Bacterial ; Plasmids ; },
abstract = {The assessment of factors that can promote the transmission of antibiotic resistance genes (ARGs) across bacteria in the gastrointestinal tract is in great demand to understand the occurrence of infections related to antibiotic-resistant bacteria (ARB) in humans. However, whether acid-resistant enteric bacteria can promote ARG transmission in gastric fluid under high-pH conditions remains unknown. This study assessed the effects of simulated gastric fluid (SGF) at different pH levels on the RP4 plasmid-mediated conjugative transfer of ARGs. Moreover, transcriptomic analysis, measurement of reactive oxygen species (ROS) levels, assessment of cell membrane permeability, and real-time quantitative assessment of the expression of key genes were performed to identify the underlying mechanisms. The frequency of conjugative transfer was the highest in SGF at pH 4.5. Antidepressant consumption and certain dietary factors further negatively impacted this situation, with 5.66-fold and 4.26-fold increases in the conjugative transfer frequency being noted upon the addition of sertraline and 10% glucose, respectively, compared with that in the control group without any additives. The induction of ROS generation, the activation of cellular antioxidant systems, increases in cell membrane permeability, and the promotion of adhesive pilus formation were factors potentially contributing to the increased transfer frequency. These findings indicate that conjugative transfer could be enhanced under certain circumstances in SGF at elevated pH levels, thereby facilitating ARG transmission in the gastrointestinal tract. IMPORTANCE The low pH of gastric acid kills unwanted microorganisms, in turn affecting their inhabitation in the intestine. Hence, studies on the factors that influence antibiotic resistance gene (ARG) propagation in the gastrointestinal tract and on the underlying mechanisms are limited. In this study, we constructed a conjugative transfer model in the presence of simulated gastric fluid (SGF) and found that SGF could promote the dissemination of ARGs under high-pH conditions. Furthermore, antidepressant consumption and certain dietary factors could negatively impact this situation. Transcriptomic analysis and a reactive oxygen species assay revealed the overproduction of reactive oxygen species as a potential mechanism by which SGF could promote conjugative transfer. This finding can help provide a comprehensive understanding of the bloom of antibiotic-resistant bacteria in the body and create awareness regarding the risk of ARG transmission due to certain diseases or an improper diet and the subsequent decrease in gastric acid levels.},
}
@article {pmid37071810,
year = {2023},
author = {Paulat, NS and Storer, JM and Moreno-Santillán, DD and Osmanski, AB and Sullivan, KAM and Grimshaw, JR and Korstian, J and Halsey, M and Garcia, CJ and Crookshanks, C and Roberts, J and Smit, AFA and Hubley, R and Rosen, J and Teeling, EC and Vernes, SC and Myers, E and Pippel, M and Brown, T and Hiller, M and , and Rojas, D and Dávalos, LM and Lindblad-Toh, K and Karlsson, EK and Ray, DA},
title = {Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia.},
journal = {Molecular biology and evolution},
volume = {40},
number = {5},
pages = {},
pmid = {37071810},
issn = {1537-1719},
support = {MR/T021985/1/MRC_/Medical Research Council/United Kingdom ; R01 HG002939/HG/NHGRI NIH HHS/United States ; R01 HG008742/HG/NHGRI NIH HHS/United States ; U24 HG010136/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; *DNA Transposable Elements/genetics ; *Chiroptera/genetics ; Gene Transfer, Horizontal ; Evolution, Molecular ; Mammals/genetics ; Phylogeny ; },
abstract = {Horizontal transfer of transposable elements (TEs) is an important mechanism contributing to genetic diversity and innovation. Bats (order Chiroptera) have repeatedly been shown to experience horizontal transfer of TEs at what appears to be a high rate compared with other mammals. We investigated the occurrence of horizontally transferred (HT) DNA transposons involving bats. We found over 200 putative HT elements within bats; 16 transposons were shared across distantly related mammalian clades, and 2 other elements were shared with a fish and two lizard species. Our results indicate that bats are a hotspot for horizontal transfer of DNA transposons. These events broadly coincide with the diversification of several bat clades, supporting the hypothesis that DNA transposon invasions have contributed to genetic diversification of bats.},
}
@article {pmid37065212,
year = {2023},
author = {Wang, H and Cheng, H and Huang, B and Hu, X and Chen, Y and Zheng, L and Yang, L and Deng, J and Wang, Q},
title = {Characterization of resistance genes and plasmids from sick children caused by Salmonella enterica resistance to azithromycin in Shenzhen, China.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1116172},
pmid = {37065212},
issn = {2235-2988},
mesh = {Humans ; Child ; Azithromycin/pharmacology ; *Salmonella enterica/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Salmonella Infections/microbiology ; Salmonella/genetics ; Plasmids/genetics ; Microbial Sensitivity Tests ; Chloramphenicol/pharmacology ; Drug Resistance, Multiple, Bacterial ; },
abstract = {INTRODUCTION: Samonella is 1 of 4 key global causes of diarrhoeal diseases, sometimes it can be serious, especially for yong children. Due to the extensive resistance of salmonella serotypes to conventional first-line drugs, macrolides (such as azithromycin) have been designated as the most important antibiotics for the treatment of salmonella. Antimicrobial resistance is a major public health problem in the world, and the mechanism of azithromycin resistance is rarely studied.<br><br>METHODS: This study determined the azithromycin resistance and plasmids of Salmonella enterica isolates from children attending the Shenzhen Children's Hospital. The susceptibility of ampicillin (AMP), ciprofloxacin (CIP), ceftriaxone (CRO), sulfamethoxazole (SMZ), chloramphenicol (CL), and azithromycin (AZM) were detected and the genes and plasmids from azithromycin-resistant Salmonella were detected by Illumina hi-seq and Nanopore MinIone whole genome sequencing (WGS) using a map-based method, and the genomic background of these factors was evaluated using various bioinformatics tools.<br><br>RESULTS: In total, 15 strains of nontyphoid Salmonella strains that were isolated (including S. typhimurium, S.London, S. Goldcoast, and S.Stanley) demonstrated resistance to azithromycin (minimum inhibitory concentration,MIC from 32 to >256 &#xb5;g/mL), and the resistance rate was 3.08% (15/487). The sensitivity test to other antibiotics demonstrated 100% resistance to AMP, and the resistance to SMZ and CL was 86.7% and 80.0%, respectively. Through WGS analysis, all isolates were positive for a plasmid-encoded mphA gene. Plasmid incompatibility typing identified five IncFIB(K), five IncHI2/HI2A/Q1, two IncC, one IncHI2/HI2A/N, one IncR, one IncFII and one IncHI2/HI2A plasmids. Sequence analyses of plasmids revealed extensive homology to various plasmids or transposons in regions involved in plasmid replication/maintenance functions and/or in antibiotic resistance gene clusters.<br><br>CONCLUSION: mphA is the main gene involved in azithromycin, a macrolide, and resistance to Salmonella. It is usually located on plasmids and easily spreads, hence posing a great threat to the current treatment of Salmonella infection. The plasmid sequence similarities suggest that the plasmids acquired resistance genes from a variety of enterica bacteria and underscore the importance of a further understanding of horizontal gene transfer among enterica bacteria.},
}
@article {pmid37062264,
year = {2023},
author = {Jin, C and Cao, J and Zhang, K and Zhang, X and Cao, Z and Zou, W},
title = {Promotion effects and mechanisms of molybdenum disulfide on the propagation of antibiotic resistance genes in soil.},
journal = {Ecotoxicology and environmental safety},
volume = {256},
number = {},
pages = {114913},
doi = {10.1016/j.ecoenv.2023.114913},
pmid = {37062264},
issn = {1090-2414},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Molybdenum/pharmacology ; Genes, Bacterial ; Soil ; Gene Transfer, Horizontal ; Drug Resistance, Microbial/genetics ; Escherichia coli ; Plasmids ; },
abstract = {The rapid development of nanotechnology has aroused considerable attentions toward understanding the effects of engineered nanomaterials (ENMs) on the propagation of antibiotic resistance. Molybdenum disulfide (MoS2) is an extensively used ENM and poses potential risks associated with environmental exposure; nevertheless, the role of MoS2 toward antibiotic resistance genes (ARGs) transfer remains largely unknown. Herein, it was discovered that MoS2 nanosheets accelerated the horizontal transfer of RP4 plasmid across Escherichia coli in a dose-dependent manner (0.5-10 mg/L), with the maximum transfer frequency 2.07-fold higher than that of the control. Integration of physiological, transcriptomics, and metabolomics analyses demonstrated that SOS response in bacteria was activated by MoS2 due to the elevation of oxidative damage, accompanied by cell membrane permeabilization. MoS2 promoted bacterial adhesion and intercellular contact via stimulating the secretion of extracellular polysaccharides. The ATP levels were maximally increased by 305.7 % upon exposure to MoS2, and the expression of plasmid transfer genes was up-regulated, contributing to the accelerated plasmid conjugation and increased ARG abundance in soil. Our findings highlight the roles of emerging ENMs (e.g., MoS2) in ARGs dissemination, which is significant for the safe applications and risk management of ENMs under the development scenarios of nanotechnology.},
}
@article {pmid37061654,
year = {2023},
author = {Elbehery, AHA and Beason, E and Siam, R},
title = {Metagenomic profiling of antibiotic resistance genes in Red Sea brine pools.},
journal = {Archives of microbiology},
volume = {205},
number = {5},
pages = {195},
pmid = {37061654},
issn = {1432-072X},
support = {Faculty (Research) Support Grant//The American University in Cairo/ ; },
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Indian Ocean ; *Drug Resistance, Bacterial/genetics ; Macrolides ; Genes, Bacterial ; },
abstract = {Antibiotic resistance (AR) is an alarming global health concern, causing an annual death rate of more than 35,000 deaths in the US. AR is a natural phenomenon, reported in several pristine environments. In this study, we report AR in pristine Red Sea deep brine pools. Antimicrobial resistance genes (ARGs) were detected for several drug classes with tetracycline and macrolide resistance being the most abundant. As expected, ARGs abundance increased in accordance with the level of human impact with pristine Red Sea samples having the lowest mean ARG level followed by estuary samples, while activated sludge samples showed a significantly higher ARG level. ARG hierarchical clustering grouped drug classes for which resistance was detected in Atlantis II Deep brine pool independent of the rest of the samples. ARG abundance was significantly lower in the Discovery Deep brine pool. A correlation between integrons and ARGs abundance in brine pristine samples could be detected, while insertion sequences and plasmids showed a correlation with ARGs abundance in human-impacted samples not seen in brine pristine samples. This suggests different roles of distinct mobile genetic elements (MGEs) in ARG distribution in pristine versus human-impacted sites. Additionally, we showed the presence of mobile antibiotic resistance genes in the Atlantis II brine pool as evidenced by the co-existence of integrases and plasmid replication proteins on the same contigs harboring predicted multidrug-resistant efflux pumps. This study addresses the role of non-pathogenic environmental bacteria as a silent reservoir for ARGs, and the possible horizontal gene transfer mechanism mediating ARG acquisition.},
}
@article {pmid37061183,
year = {2023},
author = {Gilbert, C and Maumus, F},
title = {Sidestepping Darwin: horizontal gene transfer from plants to insects.},
journal = {Current opinion in insect science},
volume = {57},
number = {},
pages = {101035},
doi = {10.1016/j.cois.2023.101035},
pmid = {37061183},
issn = {2214-5753},
mesh = {Animals ; *Gene Transfer, Horizontal ; Insecta/genetics ; *Hemiptera/genetics ; Plants/genetics ; Bacteria ; },
abstract = {Horizontal transfer of genetic material (HT) is the passage of DNA between organisms by means other than reproduction. Increasing numbers of HT are reported in insects, with bacteria, fungi, plants, and insects acting as the main sources of these transfers. Here, we provide a detailed account of plant-to-insect HT events. At least 14 insect species belonging to 6 orders are known to have received plant genetic material through HT. One of them, the whitefly Bemisia tabaci (Middle East Asia Minor 1), concentrates most of these transfers, with no less than 28 HT events yielding 55 plant-derived genes in this species. Several plant-to-insect HT events reported so far involve gene families known to play a role in plant-parasite interactions. We highlight methodological approaches that may further help characterize these transfers. We argue that plant-to-insect HT is likely more frequent than currently appreciated and that in-depth studies of these transfers will shed new light on plant-insect interactions.},
}
@article {pmid37055994,
year = {2023},
author = {Li, B and Jeon, MK and Li, X and Yan, T},
title = {Differential impacts of salinity on antibiotic resistance genes during cattle manure stockpiling are linked to mobility potentials revealed by metagenomic sequencing.},
journal = {Journal of hazardous materials},
volume = {445},
number = {},
pages = {130590},
doi = {10.1016/j.jhazmat.2022.130590},
pmid = {37055994},
issn = {1873-3336},
mesh = {Cattle ; Animals ; *Anti-Bacterial Agents/pharmacology ; *Manure/analysis ; Genes, Bacterial ; Salinity ; Drug Resistance, Microbial/genetics ; },
abstract = {Livestock manure is an important source of antibiotic resistance genes (ARGs), and its salinity level can change during stockpiling. To understand how the salinity changes affect the fate of ARGs, cattle manure was adjusted of salinity and stockpiled in laboratory microcosms at low (0.3% salt), moderate (3.0%) and high salinity levels (10.0%) for 44 days. Amongst the five ARGs (tetO, blaTEM, sul1, tetM, and ermB) and the first-class integrase (intI1) monitored by qPCR, the relative abundance of tetO and blaTEM exhibited no clear trend in response to salinity levels, while that of sul1, tetM, ermB and intI1 showed clear downward trends over time at the lower salinity levels (0.3% and 3%) but not at the high salinity level (10%). Metagenomic contig construction of cattle manure samples revealed that sul1, tetM and ermB genes were more likely to associate with mobile genetic elements (MGEs) than tetO and blaTEM, suggesting that their slower decay at higher salinity levels was either caused by horizontal gene transfer or co-selection of ARGs and osmotic stress resistant determinants. Further analysis of metagenomic contigs showed that osmotic stress resistance can also be located on MGEs or in conjunction with ARGs.},
}
@article {pmid37054673,
year = {2023},
author = {Moura de Sousa, J and Lourenço, M and Gordo, I},
title = {Horizontal gene transfer among host-associated microbes.},
journal = {Cell host &amp; microbe},
volume = {31},
number = {4},
pages = {513-527},
doi = {10.1016/j.chom.2023.03.017},
pmid = {37054673},
issn = {1934-6069},
mesh = {*Gene Transfer, Horizontal ; Bacteria/genetics ; Biological Evolution ; *Microbiota/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Horizontal gene transfer is an important evolutionary force, facilitating bacterial diversity. It is thought to be pervasive in host-associated microbiomes, where bacterial densities are high and mobile elements are frequent. These genetic exchanges are also key for the rapid dissemination of antibiotic resistance. Here, we review recent studies that have greatly extended our knowledge of the mechanisms underlying horizontal gene transfer, the ecological complexities of a network of interactions involving bacteria and their mobile elements, and the effect of host physiology on the rates of genetic exchanges. Furthermore, we discuss other, fundamental challenges in detecting and quantifying genetic exchanges in vivo, and how studies have contributed to start overcoming these challenges. We highlight the importance of integrating novel computational approaches and theoretical models with experimental methods where multiple strains and transfer elements are studied, both in vivo and in controlled conditions that mimic the intricacies of host-associated environments.},
}
@article {pmid37052605,
year = {2023},
author = {Calder, A and Snyder, LAS},
title = {Diversity of the type VI secretion systems in the Neisseria spp.},
journal = {Microbial genomics},
volume = {9},
number = {4},
pages = {},
pmid = {37052605},
issn = {2057-5858},
mesh = {Humans ; *Type VI Secretion Systems/genetics ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Complete Type VI Secretion Systems were identified in the genome sequence data of Neisseria subflava isolates sourced from throat swabs of human volunteers. The previous report was the first to describe two complete Type VI Secretion Systems in these isolates, both of which were distinct in terms of their gene organization and sequence homology. Since publication of the first report, Type VI Secretion System subtypes have been identified in Neisseria spp. The characteristics of each type in N. subflava are further investigated here and in the context of the other Neisseria spp., including identification of the lineages containing the different types and subtypes. Type VI Secretion Systems use VgrG for delivery of toxin effector proteins; several copies of vgrG and associated effector / immunity pairs are present in Neisseria spp. Based on sequence similarity between strains and species, these core Type VI Secretion System genes, vgrG, and effector / immunity genes may diversify via horizontal gene transfer, an instrument for gene acquisition and repair in Neisseria spp.},
}
@article {pmid37052502,
year = {2023},
author = {Tang, B and Yang, A and Liu, P and Wang, Z and Jian, Z and Chen, X and Yan, Q and Liang, X and Liu, W},
title = {Outer Membrane Vesicles Transmitting blaNDM-1 Mediate the Emergence of Carbapenem-Resistant Hypervirulent Klebsiella pneumoniae.},
journal = {Antimicrobial agents and chemotherapy},
volume = {67},
number = {5},
pages = {e0144422},
pmid = {37052502},
issn = {1098-6596},
mesh = {Humans ; Klebsiella pneumoniae ; Meropenem/pharmacology ; *Klebsiella Infections/drug therapy ; Carbapenems/pharmacology ; Anti-Bacterial Agents/pharmacology ; *Carbapenem-Resistant Enterobacteriaceae ; },
abstract = {Dissemination of hypervirulent and carbapenem-resistant Klebsiella pneumoniae (CRKP) has been reported worldwide, posing a serious threat to antimicrobial therapy and public health. Outer membrane vesicles (OMVs) act as vectors for the horizontal transfer of virulence and resistance genes. However, K. pneumoniae OMVs that transfer carbapenem resistance genes into hypervirulent K. pneumoniae (hvKP) have been insufficiently investigated. Therefore, this study investigates the transmission of the blaNDM-1 gene encoding resistance via OMVs released from CRKP and the potential mechanism responsible for the carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) emergence. OMVs were isolated via ultracentrifugation from CRKP with or without meropenem selective pressure. OMVs were then used to transform classical K. pneumoniae (ckp) ATCC 10031, extended-spectrum β-lactamase (ESBL)-producing K. pneumoniae ATCC 700603, and hvKP NTUH-K2044. Our results showed that meropenem treatment resulted in changes in the number and diameter of OMVs secreted by CRKP. OMVs derived from CRKP mediated the transfer of blaNDM-1 to ckp and hvKP, thereby increasing the carbapenem MIC of transformants. Further experiments confirmed that NTUH-K2044 transformants exhibited hypervirulence. Our study demonstrates, for the first time, that OMVs derived from CRKP can carry blaNDM-1 and deliver resistance genes to other K. pneumoniae strains, even hvKP. The transfer of carbapenem genes into hypervirulent strains may promote the emergence and dissemination of CR-hvKP. This study elucidates a new mechanism underlying the formation of CR-hvKP.},
}
@article {pmid37047476,
year = {2023},
author = {Msaddak, A and Mars, M and Quiñones, MA and Lucas, MM and Pueyo, JJ},
title = {Lupin, a Unique Legume That Is Nodulated by Multiple Microsymbionts: The Role of Horizontal Gene Transfer.},
journal = {International journal of molecular sciences},
volume = {24},
number = {7},
pages = {},
pmid = {37047476},
issn = {1422-0067},
support = {//Ministry of High Education and Scientific Research, Tunisia/ ; AGL2017-88381-R//Agencia Estatal de Investigaci&#xf3;n, AEI, Spain/ ; PID2021-125371OB-I00//Agencia Estatal de Investigaci&#xf3;n, AEI, Spain/ ; COOPB20610//Spanish National Research Council/ ; },
mesh = {*Fabaceae/genetics/microbiology ; *Lupinus/genetics/microbiology ; Root Nodules, Plant/microbiology ; Phylogeny ; Gene Transfer, Horizontal ; Health Promotion ; DNA, Bacterial/genetics ; Vegetables/genetics ; *Rhizobium/genetics ; *Bradyrhizobium/genetics ; Symbiosis/genetics ; Sequence Analysis, DNA ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Lupin is a high-protein legume crop that grows in a wide range of edaphoclimatic conditions where other crops are not viable. Its unique seed nutrient profile can promote health benefits, and it has been proposed as a phytoremediation plant. Most rhizobia nodulating Lupinus species belong to the genus Bradyrhizobium, comprising strains that are phylogenetically related to B. cytisi, B. hipponenese, B. rifense, B. iriomotense/B. stylosanthis, B. diazoefficiens, B. japonicum, B. canariense/B. lupini, and B. retamae/B. valentinum. Lupins are also nodulated by fast-growing bacteria within the genera Microvirga, Ochrobactrum, Devosia, Phyllobacterium, Agrobacterium, Rhizobium, and Neorhizobium. Phylogenetic analyses of the nod and nif genes, involved in microbial colonization and symbiotic nitrogen fixation, respectively, suggest that fast-growing lupin-nodulating bacteria have acquired their symbiotic genes from rhizobial genera other than Bradyrhizobium. Horizontal transfer represents a key mechanism allowing lupin to form symbioses with bacteria that were previously considered as non-symbiotic or unable to nodulate lupin, which might favor lupin's adaptation to specific habitats. The characterization of yet-unstudied Lupinus species, including microsymbiont whole genome analyses, will most likely expand and modify the current lupin microsymbiont taxonomy, and provide additional knowledge that might help to further increase lupin's adaptability to marginal soils and climates.},
}
@article {pmid37043515,
year = {2023},
author = {Novelo, M and Dutra, HL and Metz, HC and Jones, MJ and Sigle, LT and Frentiu, FD and Allen, SL and Chenoweth, SF and McGraw, EA},
title = {Dengue and chikungunya virus loads in the mosquito Aedes aegypti are determined by distinct genetic architectures.},
journal = {PLoS pathogens},
volume = {19},
number = {4},
pages = {e1011307},
pmid = {37043515},
issn = {1553-7374},
support = {R01 AI143758/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; *Chikungunya virus/physiology ; *Aedes ; Mosquito Vectors ; *Chikungunya Fever ; *Dengue ; },
abstract = {Aedes aegypti is the primary vector of the arboviruses dengue (DENV) and chikungunya (CHIKV). These viruses exhibit key differences in their vector interactions, the latter moving more quicky through the mosquito and triggering fewer standard antiviral pathways. As the global footprint of CHIKV continues to expand, we seek to better understand the mosquito's natural response to CHIKV-both to compare it to DENV:vector coevolutionary history and to identify potential targets in the mosquito for genetic modification. We used a modified full-sibling design to estimate the contribution of mosquito genetic variation to viral loads of both DENV and CHIKV. Heritabilities were significant, but higher for DENV (40%) than CHIKV (18%). Interestingly, there was no genetic correlation between DENV and CHIKV loads between siblings. These data suggest Ae. aegypti mosquitoes respond to the two viruses using distinct genetic mechanisms. We also examined genome-wide patterns of gene expression between High and Low CHIKV families representing the phenotypic extremes of viral load. Using RNAseq, we identified only two loci that consistently differentiated High and Low families: a long non-coding RNA that has been identified in mosquito screens post-infection and a distant member of a family of Salivary Gland Specific (SGS) genes. Interestingly, the latter gene is also associated with horizontal gene transfer between mosquitoes and the endosymbiotic bacterium Wolbachia. This work is the first to link the SGS gene to a mosquito phenotype. Understanding the molecular details of how this gene contributes to viral control in mosquitoes may, therefore, also shed light on its role in Wolbachia.},
}
@article {pmid37037946,
year = {2023},
author = {Yang, P and Zhu, X and Ning, K},
title = {Microbiome-based enrichment pattern mining has enabled a deeper understanding of the biome-species-function relationship.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {391},
pmid = {37037946},
issn = {2399-3642},
mesh = {*Copper ; Biological Evolution ; *Microbiota/genetics ; Soil ; Metagenome ; },
abstract = {Microbes live in diverse habitats (i.e. biomes), yet their species and genes were biome-specific, forming enrichment patterns. These enrichment patterns have mirrored the biome-species-function relationship, which is shaped by ecological and evolutionary principles. However, a grand picture of these enrichment patterns, as well as the roles of external and internal factors in driving these enrichment patterns, remain largely unexamined. In this work, we have examined the enrichment patterns based on 1705 microbiome samples from four representative biomes (Engineered, Gut, Freshwater, and Soil). Moreover, an "enrichment sphere" model was constructed to elucidate the regulatory principles behind these patterns. The driving factors for this model were revealed based on two case studies: (1) The copper-resistance genes were enriched in Soil biomes, owing to the copper contamination and horizontal gene transfer. (2) The flagellum-related genes were enriched in the Freshwater biome, due to high fluidity and vertical gene accumulation. Furthermore, this enrichment sphere model has valuable applications, such as in biome identification for metagenome samples, and in guiding 3D structure modeling of proteins. In summary, the enrichment sphere model aims towards creating a bluebook of the biome-species-function relationships and be applied in many fields.},
}
@article {pmid37037312,
year = {2023},
author = {Wang, H and Min, C and Xia, F and Xia, Y and Tang, M and Li, J and Hu, Y and Zou, M},
title = {Metagenomic analysis reveals the short-term influences on conjugation of blaNDM-1 and microbiome in hospital wastewater by silver nanoparticles at environmental-related concentration.},
journal = {Environmental research},
volume = {228},
number = {},
pages = {115866},
doi = {10.1016/j.envres.2023.115866},
pmid = {37037312},
issn = {1096-0953},
mesh = {Wastewater ; Silver ; Metagenome ; *Metal Nanoparticles ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Microbiota ; Hospitals ; },
abstract = {Hospital wastewater contains large amounts of antibiotic-resistant bacteria and serves as an important reservoir for horizontal gene transfer (HGT). However, the response of the microbiome in hospital wastewater to silver remains unclear. In this study, the short-term impacts of silver on the microbiome in hospital wastewater were investigated by metagenome next-generation sequencing. The influence of silver on the conjugation of plasmid carrying blaNDM-1 was further examined. Our results showed that in hospital wastewater, high abundances of antibiotic resistance genes (ARGs) were detected. The distribution tendencies of certain ARG types on chromosomes or plasmids were different. Clinically important ARGs were identified in phage-like contigs, indicating potential transmission via transduction. Pseudomonadales, Enterobacterales, and Bacteroidales were the major ARG hosts. Mobile genetic elements were mainly detected in plasmids and associated with various types of ARGs. The binning approach identified 29 bins that were assigned to three phyla. Various ARGs and virulence factors were identified in 14 and 11 bins, respectively. MetaCHIP identified 49 HGT events. The transferred genes were annotated as ARGs, mobile genetic elements, and functional genes, and they mainly originated from donors belonging to Bacteroides and Pseudomonadales. In addition, 20 nm AgNPs reduced microbial diversity and enhanced the relative abundance of Acinetobacter. The changes induced by 20 nm AgNPs included increases in the abundances of ARGs and genes involved lipid metabolism pathway. Conjugation experiments showed that Ag[+] and 20 nm AgNPs caused 2.38-, 3.31-, 4.72-, and 4.57-fold and 1.46-, 1.61-, 3.86-, and 2.16-fold increases in conjugation frequencies of plasmid with blaNDM-1 at 0.1, 1, 10, and 100 μg/L, respectively. Our findings provide insight into the response of the microbiome in hospital wastewater to silver, emphasize the adaptation capability of Acinetobacter inhabiting hospitals against adverse environments, and highlight the promotion of silver for antibiotic resistance.},
}
@article {pmid37036996,
year = {2023},
author = {Kalluraya, CA and Weitzel, AJ and Tsu, BV and Daugherty, MD},
title = {Bacterial origin of a key innovation in the evolution of the vertebrate eye.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {16},
pages = {e2214815120},
pmid = {37036996},
issn = {1091-6490},
support = {R35 GM133633/GM/NIGMS NIH HHS/United States ; T32 GM007240/GM/NIGMS NIH HHS/United States ; 1021386//Burroughs Wellcome Fund (BWF)/ ; 00032011//Pew Charitable Trusts (Pew)/ ; },
mesh = {Animals ; *Genes, Bacterial ; *Vertebrates/metabolism ; Eye Proteins/genetics ; Retinoids/metabolism ; Invertebrates/genetics ; Vision, Ocular/genetics ; },
abstract = {The vertebrate eye was described by Charles Darwin as one of the greatest potential challenges to a theory of natural selection by stepwise evolutionary processes. While numerous evolutionary transitions that led to the vertebrate eye have been explained, some aspects appear to be vertebrate specific with no obvious metazoan precursor. One critical difference between vertebrate and invertebrate vision hinges on interphotoreceptor retinoid-binding protein (IRBP, also known as retinol-binding protein, RBP3), which enables the physical separation and specialization of cells in the vertebrate visual cycle by promoting retinoid shuttling between cell types. While IRBP has been functionally described, its evolutionary origin has remained elusive. Here, we show that IRBP arose via acquisition of novel genetic material from bacteria by interdomain horizontal gene transfer (iHGT). We demonstrate that a gene encoding a bacterial peptidase was acquired prior to the radiation of extant vertebrates >500 Mya and underwent subsequent domain duplication and neofunctionalization to give rise to vertebrate IRBP. Our phylogenomic analyses on >900 high-quality genomes across the tree of life provided the resolution to distinguish contamination in genome assemblies from true instances of horizontal acquisition of IRBP and led us to discover additional independent transfers of the same bacterial peptidase gene family into distinct eukaryotic lineages. Importantly, this work illustrates the evolutionary basis of a key transition that led to the vertebrate visual cycle and highlights the striking impact that acquisition of bacterial genes has had on vertebrate evolution.},
}
@article {pmid37036995,
year = {2023},
author = {Verster, KI and Cinege, G and Lipinszki, Z and Magyar, LB and Kurucz, &#xc9; and Tarnopol, RL and Ábrahám, E and Darula, Z and Karageorgi, M and Tamsil, JA and Akalu, SM and Andó, I and Whiteman, NK},
title = {Evolution of insect innate immunity through domestication of bacterial toxins.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {16},
pages = {e2218334120},
pmid = {37036995},
issn = {1091-6490},
support = {R35 GM119816/GM/NIGMS NIH HHS/United States ; T32 GM132022/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Domestication ; *Bacterial Toxins/metabolism ; Drosophila/genetics/metabolism ; Gene Transfer, Horizontal ; *Wasps/metabolism ; Immunity, Innate/genetics ; },
abstract = {Toxin cargo genes are often horizontally transferred by phages between bacterial species and are known to play an important role in the evolution of bacterial pathogenesis. Here, we show how these same genes have been horizontally transferred from phage or bacteria to animals and have resulted in novel adaptations. We discovered that two widespread bacterial genes encoding toxins of animal cells, cytolethal distending toxin subunit B (cdtB) and apoptosis-inducing protein of 56 kDa (aip56), were captured by insect genomes through horizontal gene transfer from bacteria or phages. To study the function of these genes in insects, we focused on Drosophila ananassae as a model. In the D. ananassae subgroup species, cdtB and aip56 are present as singular (cdtB) or fused copies (cdtB::aip56) on the second chromosome. We found that cdtB and aip56 genes and encoded proteins were expressed by immune cells, some proteins were localized to the wasp embryo's serosa, and their expression increased following parasitoid wasp infection. Species of the ananassae subgroup are highly resistant to parasitoid wasps, and we observed that D. ananassae lines carrying null mutations in cdtB and aip56 toxin genes were more susceptible to parasitoids than the wild type. We conclude that toxin cargo genes were captured by these insects millions of years ago and integrated as novel modules into their innate immune system. These modules now represent components of a heretofore undescribed defense response and are important for resistance to parasitoid wasps. Phage or bacterially derived eukaryotic toxin genes serve as macromutations that can spur the instantaneous evolution of novelty in animals.},
}
@article {pmid37036347,
year = {2023},
author = {Lewis, AM and Willard, DJ and H Manesh, MJ and Sivabalasarma, S and Albers, SV and Kelly, RM},
title = {Stay or Go: Sulfolobales Biofilm Dispersal Is Dependent on a Bifunctional VapB Antitoxin.},
journal = {mBio},
volume = {14},
number = {2},
pages = {e0005323},
pmid = {37036347},
issn = {2150-7511},
support = {T32 GM133366/GM/NIGMS NIH HHS/United States ; 2T32GM008776/NH/NIH HHS/United States ; },
mesh = {*Antitoxins/metabolism ; Bacterial Proteins/metabolism ; *Bacterial Toxins/metabolism ; Sulfolobales ; Biofilms ; },
abstract = {A type II VapB14 antitoxin regulates biofilm dispersal in the archaeal thermoacidophile Sulfolobus acidocaldarius through traditional toxin neutralization but also through noncanonical transcriptional regulation. Type II VapC toxins are ribonucleases that are neutralized by their proteinaceous cognate type II VapB antitoxin. VapB antitoxins have a flexible tail at their C terminus that covers the toxin's active site, neutralizing its activity. VapB antitoxins also have a DNA-binding domain at their N terminus that allows them to autorepress not only their own promoters but also distal targets. VapB14 antitoxin gene deletion in S. acidocaldarius stunted biofilm and planktonic growth and increased motility structures (archaella). Conversely, planktonic cells were devoid of archaella in the ΔvapC14 cognate toxin mutant. VapB14 is highly conserved at both the nucleotide and amino acid levels across the Sulfolobales, extremely unusual for type II antitoxins, which are typically acquired through horizontal gene transfer. Furthermore, homologs of VapB14 are found across the Crenarchaeota, in some Euryarchaeota, and even bacteria. S. acidocaldarius vapB14 and its homolog in the thermoacidophile Metallosphaera sedula (Msed_0871) were both upregulated in biofilm cells, supporting the role of the antitoxin in biofilm regulation. In several Sulfolobales species, including M. sedula, homologs of vapB14 and vapC14 are not colocalized. Strikingly, Sulfuracidifex tepidarius has an unpaired VapB14 homolog and lacks a cognate VapC14, illustrating the toxin-independent conservation of the VapB14 antitoxin. The findings here suggest that a stand-alone VapB-type antitoxin was the product of selective evolutionary pressure to influence biofilm formation in these archaea, a vital microbial community behavior. IMPORTANCE Biofilms allow microbes to resist a multitude of stresses and stay proximate to vital nutrients. The mechanisms of entering and leaving a biofilm are highly regulated to ensure microbial survival, but are not yet well described in archaea. Here, a VapBC type II toxin-antitoxin system in the thermoacidophilic archaeon Sulfolobus acidocaldarius was shown to control biofilm dispersal through a multifaceted regulation of the archaeal motility structure, the archaellum. The VapC14 toxin degrades an RNA that causes an increase in archaella and swimming. The VapB14 antitoxin decreases archaella and biofilm dispersal by binding the VapC14 toxin and neutralizing its activity, while also repressing the archaellum genes. VapB14-like antitoxins are highly conserved across the Sulfolobales and respond similarly to biofilm growth. In fact, VapB14-like antitoxins are also found in other archaea, and even in bacteria, indicating an evolutionary pressure to maintain this protein and its role in biofilm formation.},
}
@article {pmid37036197,
year = {2023},
author = {Mota-Bravo, L and Camps, M and Muñoz-Gutiérrez, I and Tatarenkov, A and Warner, C and Suarez, I and Cortés-Cortés, G},
title = {Detection of Horizontal Gene Transfer Mediated by Natural Conjugative Plasmids in E. coli.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {193},
pages = {},
doi = {10.3791/64523},
pmid = {37036197},
issn = {1940-087X},
mesh = {*Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Conjugation, Genetic ; Plasmids/genetics ; Anti-Bacterial Agents ; },
abstract = {Conjugation represents one of the main mechanisms facilitating horizontal gene transfer in Gram-negative bacteria. This work describes methods for the study of the mobilization of naturally occurring conjugative plasmids, using two naturally-occurring plasmids as an example. These protocols rely on the differential presence of selectable markers in donor, recipient, and conjugative plasmid. Specifically, the methods described include 1) the identification of natural conjugative plasmids, 2) the quantification of conjugation rates in solid culture, and 3) the diagnostic detection of the antibiotic resistance genes and plasmid replicon types in transconjugant recipients by polymerase chain reaction (PCR). The protocols described here have been developed in the context of studying the evolutionary ecology of horizontal gene transfer, to screen for the presence of conjugative plasmids carrying antibiotic-resistance genes in bacteria found in the environment. The efficient transfer of conjugative plasmids observed in these experiments in culture highlights the biological relevance of conjugation as a mechanism promoting horizontal gene transfer in general and the spread of antibiotic resistance in particular.},
}
@article {pmid37033775,
year = {2023},
author = {Alborzi, A and Hosseini, M and Bahrami, S and Ghorbanpoor, M and Tabandeh, M},
title = {Evaluation of hematological changes, oxidant/antioxidant status and immuno-logical responses in sheep and goats naturally infected with Linguatula serrata.},
journal = {Veterinary research forum : an international quarterly journal},
volume = {14},
number = {3},
pages = {161-167},
pmid = {37033775},
issn = {2008-8140},
abstract = {Linguatula serrata is a worldwide zoonotic food-borne parasite. The parasite is responsible for linguatulosis and poses a concern to human and animal health in endemic regions. This study investigated the hematological changes, oxidant/antioxidant status and immunological responses in goats and sheep naturally infected with L. serrata. Hematological changes, antioxidant enzymes and malondialdehyde (MDA) levels were measured. The level of inter-leukin-2 (IL-2), IL-4, IL-5, IL-10, and tumor necrosis factor alpha (TNF-α) mRNA expression was investigated in lymph nodes. According to the hemogram results, eosinophils were significantly increased in the infected goats and sheep, and Horizontal Gene Transfer (HGT), hematocrit (HCT), and mean corpuscular hemoglobin concentration (MCHC) were significantly decreased. The levels of MDA and the activity of glutathione peroxidase (GPx) were significantly higher in infected animals than in non-infected animals. However, the activity of superoxide dismutase (SOD) and catalase (CAT) was significantly lower in infected animals than in non-infected animals. A comparison of the cytokine mRNA expression in lymph nodes from infected and non-infected animals showed higher cytokine expression in the infected animals. Infection with L. serrata caused microcytic hypochromic and normocytic hypochromic anemia in goats and sheep. The inconsistent results of immunological changes were found in infected goats and sheep. In both animals, oxidative stress occurred and led to an increase in lipid peroxidation. L. serrata created a cytokine microenvironment biased towards the type 2 immune responses.},
}
@article {pmid37030228,
year = {2023},
author = {Chen, J and Xia, H and Huang, K and Li, J and Xie, J},
title = {Earthworms restructure the distribution of extracellular antibiotics resistance genes of sludge by modifying the structure of extracellular polymeric substances during vermicomposting.},
journal = {Journal of hazardous materials},
volume = {452},
number = {},
pages = {131315},
doi = {10.1016/j.jhazmat.2023.131315},
pmid = {37030228},
issn = {1873-3336},
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Sewage/chemistry ; Extracellular Polymeric Substance Matrix ; *Oligochaeta/genetics ; Genes, Bacterial ; },
abstract = {The role of earthworms in reducing the antibiotic resistance genes (ARGs) in sludge vermicompost remains unclear. The structure of extracellular polymeric substance (EPS) of sludge may be associated with the horizontal gene transfer behavior of ARGs in the vermicomposting of sludge. Therefore, this study aimed to investigate the effects of earthworms on the structural characteristics of EPS associated with the fate of ARGs in EPS during the vermicomposting of sludge. The results showed vermicomposting could diminish the abundance of ARGs and mobile genetic elements (MGEs) in the EPS of sludge by 47.93 % and 7.75 %, compared to the control, respectively. Relative to the control, vermicomposting also led to the reduction of MGEs abundances in the soluble EPS of 40.04 %, lightly bound EPS of 43.53 %, and tightly bound EPS of 70.49 %, respectively. The total abundances of certain ARGs dramatically diminished 95.37 % in tightly bound EPS of sludge during vermicomposting. In vermicomposting, the main influencing factor of ARGs distribution was the proteins in LB-EPS, accounting for 48.5 % of the variation. This study suggests that the earthworms lower the total abundances of ARGs by regulating the microbial community and modifying the microbial metabolic pathways associated with ARGs and MGEs in the EPS of sludge.},
}
@article {pmid37023995,
year = {2023},
author = {Botts, RT and Page, DM and Bravo, JA and Brown, ML and Castilleja, CC and Guzman, VL and Hall, S and Henderson, JD and Kenney, SM and Lensink, ME and Paternoster, MV and Pyle, SL and Ustick, L and Walters-Laird, CJ and Top, EM and Cummings, DE},
title = {Polluted wetlands contain multidrug-resistance plasmids encoding CTX-M-type extended-spectrum β-lactamases.},
journal = {Plasmid},
volume = {126},
number = {},
pages = {102682},
pmid = {37023995},
issn = {1095-9890},
support = {R15 GM102995/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Plasmids/genetics ; *Escherichia coli/genetics ; Wetlands ; Anti-Bacterial Agents/pharmacology ; Cefotaxime/pharmacology ; Virulence Factors ; beta-Lactamases/genetics ; *Escherichia coli Infections ; Microbial Sensitivity Tests ; },
abstract = {While most detailed analyses of antibiotic resistance plasmids focus on those found in clinical isolates, less is known about the vast environmental reservoir of mobile genetic elements and the resistance and virulence factors they encode. We selectively isolated three strains of cefotaxime-resistant Escherichia coli from a wastewater-impacted coastal wetland. The cefotaxime-resistant phenotype was transmissible to a lab strain of E. coli after one hour, with frequencies as high as 10[-3] transconjugants per recipient. Two of the plasmids also transferred cefotaxime resistance to Pseudomonas putida, but these were unable to back-transfer this resistance from P. putida to E. coli. In addition to the cephalosporins, E. coli transconjugants inherited resistance to at least seven distinct classes of antibiotics. Complete nucleotide sequences revealed large IncF-type plasmids with globally distributed replicon sequence types F31:A4:B1 and F18:B1:C4 carrying diverse antibiotic resistance and virulence genes. The plasmids encoded extended-spectrum β-lactamases blaCTX-M-15 or blaCTX-M-55, each associated with the insertion sequence ISEc9, although in different local arrangements. Despite similar resistance profiles, the plasmids shared only one resistance gene in common, the aminoglycoside acetyltransferase aac(3)-IIe. Plasmid accessory cargo also included virulence factors involved in iron acquisition and defense against host immunity. Despite their sequence similarities, several large-scale recombination events were detected, including rearrangements and inversions. In conclusion, selection with a single antibiotic, cefotaxime, yielded conjugative plasmids conferring multiple resistance and virulence factors. Clearly, efforts to limit the spread of antibiotic resistance and virulence among bacteria must include a greater understanding of mobile elements in the natural and human-impacted environments.},
}
@article {pmid37023132,
year = {2023},
author = {Urquhart, AS and Vogan, AA and Gardiner, DM and Idnurm, A},
title = {Starships are active eukaryotic transposable elements mobilized by a new family of tyrosine recombinases.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {15},
pages = {e2214521120},
pmid = {37023132},
issn = {1091-6490},
mesh = {*DNA Transposable Elements/genetics ; *Eukaryota/genetics ; Gene Transfer, Horizontal ; Recombinases/genetics ; Tyrosine/genetics ; Evolution, Molecular ; },
abstract = {Transposable elements in eukaryotic organisms have historically been considered "selfish," at best conferring indirect benefits to their host organisms. The Starships are a recently discovered feature in fungal genomes that are, in some cases, predicted to confer beneficial traits to their hosts and also have hallmarks of being transposable elements. Here, we provide experimental evidence that Starships are indeed autonomous transposons, using the model Paecilomyces variotii, and identify the HhpA "Captain" tyrosine recombinase as essential for their mobilization into genomic sites with a specific target site consensus sequence. Furthermore, we identify multiple recent horizontal gene transfers of Starships, implying that they jump between species. Fungal genomes have mechanisms to defend against mobile elements, which are frequently detrimental to the host. We discover that Starships are also vulnerable to repeat-induced point mutation defense, thereby having implications on the evolutionary stability of such elements.},
}
@article {pmid37022443,
year = {2023},
author = {Stentz, R and Cheema, J and Philo, M and Carding, SR},
title = {A Possible Aquatic Origin of the Thiaminase TenA of the Human Gut Symbiont Bacteroides thetaiotaomicron.},
journal = {Journal of molecular evolution},
volume = {91},
number = {4},
pages = {482-491},
pmid = {37022443},
issn = {1432-1432},
support = {BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG1860/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Humans ; Animals ; *Bacteroides thetaiotaomicron/metabolism ; Phylogeny ; Australia ; Thiamine/metabolism ; },
abstract = {TenA thiamin-degrading enzymes are commonly found in prokaryotes, plants, fungi and algae and are involved in the thiamin salvage pathway. The gut symbiont Bacteroides thetaiotaomicron (Bt) produces a TenA protein (BtTenA) which is packaged into its extracellular vesicles. An alignment of BtTenA protein sequence with proteins from different databases using the basic local alignment search tool (BLAST) and the generation of a phylogenetic tree revealed that BtTenA is related to TenA-like proteins not only found in a small number of intestinal bacterial species but also in some aquatic bacteria, aquatic invertebrates, and freshwater fish. This is, to our knowledge, the first report describing the presence of TenA-encoding genes in the genome of members of the animal kingdom. By searching metagenomic databases of diverse host-associated microbial communities, we found that BtTenA homologues were mostly represented in biofilms present on the surface of macroalgae found in Australian coral reefs. We also confirmed the ability of a recombinant BtTenA to degrade thiamin. Our study shows that BttenA-like genes which encode a novel sub-class of TenA proteins are sparingly distributed across two kingdoms of life, a feature of accessory genes known for their ability to spread between species through horizontal gene transfer.},
}
@article {pmid37022212,
year = {2023},
author = {Tóth, AG and Judge, MF and Nagy, S&#xc1; and Papp, M and Solymosi, N},
title = {A survey on antimicrobial resistance genes of frequently used probiotic bacteria, 1901 to 2022.},
journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin},
volume = {28},
number = {14},
pages = {},
pmid = {37022212},
issn = {1560-7917},
mesh = {*Gram-Positive Bacteria/drug effects/genetics ; *Drug Resistance, Bacterial/genetics ; Probiotics ; Bifidobacterium animalis/drug effects/genetics ; Lactobacillales/drug effects/genetics ; Genome, Bacterial ; *Genes, Bacterial ; },
abstract = {BackgroundAntimicrobial resistance (AMR) is caused by AMR determinants, mainly genes (ARGs) in the bacterial genome. Bacteriophages, integrative mobile genetic elements (iMGEs) or plasmids can allow ARGs to be exchanged among bacteria by horizontal gene transfer (HGT). Bacteria, including bacteria with ARGs, can be found in food. Thus, it is conceivable that in the gastrointestinal tract, bacteria from the gut flora could take up ARGs from food.AimThe study objective was to gain insight into the ARG set carried by commonly used probiotic bacteria that may enter the human body with non-fermented foods, fermented foods, or probiotic dietary supplements (FFPs) and to assess ARG mobility.MethodsNext generation sequencing whole genome data from 579 isolates of 12 commonly employed probiotic bacterial species were collected from a public repository. Using bioinformatical tools, ARGs were analysed and linkage with mobile genetic elements assessed.ResultsResistance genes were found in eight bacterial species. The ratios of ARG positive/negative samples per species were: Bifidobacterium animalis (65/0), Lactiplantibacillus plantarum (18/194), Lactobacillus delbrueckii (1/40), Lactobacillus helveticus (2/64), Lactococcus lactis (74/5), Leucoconstoc mesenteroides (4/8), Levilactobacillus brevis (1/46), Streptococcus thermophilus (4/19). In 66% (112/169) of the ARG-positive samples, at least one ARG could be linked to plasmids or iMGEs. No bacteriophage-linked ARGs were found.ConclusionThe finding of potentially mobile ARGs in probiotic strains for human consumption raises awareness of a possibility of ARG HGT in the gastrointestinal tract. In addition to existing recommendations, screening FFP bacterial strains for ARG content and mobility characteristics might be considered.},
}
@article {pmid37020720,
year = {2023},
author = {Liu, Q and Yang, LL and Xin, YH},
title = {Diversity of the genus Cryobacterium and proposal of 19 novel species isolated from glaciers.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1115168},
pmid = {37020720},
issn = {1664-302X},
abstract = {The bacterial genus Cryobacterium includes at present 14 species that live in cryospheric environments. In this study, we analyzed 101 genomes of Cryobacterium with pure cultures obtained from GenBank. They could be classified into 44 species based on average nucleotide identity (ANI) analysis, showing the diversity of Cryobacterium. Among these, 19 strains in our laboratory were isolated from the glacier samples in China. The pairwise ANI values of these 19 strains and known species were <95%, indicating that they represented 19 novel species. The comparative genomic analysis showed significant differences in gene content between the two groups with a maximum growth temperature (T max) of ≤ 20°C and a T max of >20°C. A comprehensive and robust phylogenetic tree, including 14 known species and 19 novel species, was constructed and showed five phylogenetic branches based on 265 concatenated single-copy gene sequences. The T max parameter had a strong phylogenetic signal, indicating that the temperature adaptation of Cryobacterium was largely through vertical transfer rather than horizontal gene transfer and was affected by selection. Furthermore, using polyphasic taxonomy combined with phylogenomic analysis, we proposed 19 novel species of the genus Cryobacterium by the following 19 names: Cryobacterium serini sp. nov., Cryobacterium lactosi sp. nov., Cryobacterium gelidum sp. nov., Cryobacterium suzukii sp. nov., Cryobacterium fucosi sp. nov., Cryobacterium frigoriphilum sp. nov., Cryobacterium cryoconiti sp. nov., Cryobacterium lyxosi sp. nov., Cryobacterium sinapicolor sp. nov., Cryobacterium sandaracinum sp. nov., Cryobacterium cheniae sp. nov., Cryobacterium shii sp. nov., Cryobacterium glucosi sp. nov., Cryobacterium algoritolerans sp. nov., Cryobacterium mannosilyticum sp. nov., Cryobacterium adonitolivorans sp. nov., Cryobacterium algoricola sp. nov., Cryobacterium tagatosivorans sp. nov., and Cryobacterium glaciale sp. nov. Overall, the taxonomy and genomic analysis can improve our knowledge of phenotypic diversity, genetic diversity, and evolutionary characteristics of Cryobacterium.},
}
@article {pmid37019751,
year = {2023},
author = {Dart, E and Ahlgren, NA},
title = {New tRNA-targeting transposons that hijack phage and vesicles.},
journal = {Trends in genetics : TIG},
volume = {39},
number = {6},
pages = {433-435},
doi = {10.1016/j.tig.2023.03.004},
pmid = {37019751},
issn = {0168-9525},
mesh = {*Bacteriophages/genetics ; Gene Transfer, Horizontal/genetics ; *Cyanobacteria/genetics ; RNA, Transfer/genetics ; Genomic Islands ; },
abstract = {Genomic islands are hotspots for horizontal gene transfer (HGT) in bacteria, but, for Prochlorococcus, an abundant marine cyanobacterium, how these islands form has puzzled scientists. With the discovery of tycheposons, a new family of transposons, Hackl et al. provide evidence for elegant new mechanisms of gene rearrangement and transfer among Prochlorococcus and bacteria more broadly.},
}
@article {pmid37018030,
year = {2023},
author = {Jerez, SA and Plaza, N and Bravo, V and Urrutia, IM and Blondel, CJ},
title = {Vibrio type III secretion system 2 is not restricted to the Vibrionaceae and encodes differentially distributed repertoires of effector proteins.},
journal = {Microbial genomics},
volume = {9},
number = {4},
pages = {},
pmid = {37018030},
issn = {2057-5858},
mesh = {Humans ; Type III Secretion Systems ; *Vibrionaceae ; Phylogeny ; *Vibrio Infections/microbiology ; *Vibrio parahaemolyticus/genetics ; },
abstract = {Vibrio parahaemolyticus is the leading cause of seafood-borne gastroenteritis worldwide. A distinctive feature of the O3:K6 pandemic clone, and its derivatives, is the presence of a second, phylogenetically distinct, type III secretion system (T3SS2) encoded within the genomic island VPaI-7. The T3SS2 allows the delivery of effector proteins directly into the cytosol of infected eukaryotic cells to subvert key host-cell processes, critical for V. parahaemolyticus to colonize and cause disease. Furthermore, the T3SS2 also increases the environmental fitness of V. parahaemolyticus in its interaction with bacterivorous protists; hence, it has been proposed that it contributed to the global oceanic spread of the pandemic clone. Several reports have identified T3SS2-related genes in Vibrio and non-Vibrio species, suggesting that the T3SS2 gene cluster is not restricted to the Vibrionaceae and can mobilize through horizontal gene transfer events. In this work, we performed a large-scale genomic analysis to determine the phylogenetic distribution of the T3SS2 gene cluster and its repertoire of effector proteins. We identified putative T3SS2 gene clusters in 1130 bacterial genomes from 8 bacterial genera, 5 bacterial families and 47 bacterial species. A hierarchical clustering analysis allowed us to define six T3SS2 subgroups (I-VI) with different repertoires of effector proteins, redefining the concepts of T3SS2 core and accessory effector proteins. Finally, we identified a subset of the T3SS2 gene clusters (subgroup VI) that lacks most T3SS2 effector proteins described to date and provided a list of 10 novel effector candidates for this subgroup through bioinformatic analysis. Collectively, our findings indicate that the T3SS2 extends beyond the family Vibrionaceae and suggest that different effector protein repertories could have a differential impact on the pathogenic potential and environmental fitness of each bacterium that has acquired the Vibrio T3SS2 gene cluster.},
}
@article {pmid37017542,
year = {2023},
author = {Joglekar, P and Ferrell, BD and Jarvis, T and Haramoto, K and Place, N and Dums, JT and Polson, SW and Wommack, KE and Fuhrmann, JJ},
title = {Spontaneously Produced Lysogenic Phages Are an Important Component of the Soybean Bradyrhizobium Mobilome.},
journal = {mBio},
volume = {14},
number = {2},
pages = {e0029523},
pmid = {37017542},
issn = {2150-7511},
support = {P20 GM139760/GM/NIGMS NIH HHS/United States ; P20 GM103446/GM/NIGMS NIH HHS/United States ; },
mesh = {Glycine max ; *Bacteriophages/genetics ; *Bradyrhizobium/genetics ; Base Sequence ; Phylogeny ; Symbiosis ; },
abstract = {The ability of Bradyrhizobium spp. to nodulate and fix atmospheric nitrogen in soybean root nodules is critical to meeting humanity's nutritional needs. The intricacies of soybean bradyrhizobia-plant interactions have been studied extensively; however, bradyrhizobial ecology as influenced by phages has received somewhat less attention, even though these interactions may significantly impact soybean yield. In batch culture, four soybean bradyrhizobia strains, Bradyrhizobium japonicum S06B (S06B-Bj), B. japonicum S10J (S10J-Bj), Bradyrhizobium diazoefficiens USDA 122 (USDA 122-Bd), and Bradyrhizobium elkanii USDA 76[T] (USDA 76-Be), spontaneously (without apparent exogenous chemical or physical induction) produced tailed phages throughout the growth cycle; for three strains, phage concentrations exceeded cell numbers by ~3-fold after 48 h of incubation. Phage terminase large-subunit protein phylogeny revealed possible differences in phage packaging and replication mechanisms. Bioinformatic analyses predicted multiple prophage regions within each soybean bradyrhizobia genome, preventing accurate identification of spontaneously produced prophage (SPP) genomes. A DNA sequencing and mapping approach accurately delineated the boundaries of four SPP genomes within three of the soybean bradyrhizobia chromosomes and suggested that the SPPs were capable of transduction. In addition to the phages, S06B-Bj and USDA 76-Be contained three to four times more insertion sequences (IS) and large, conjugable, broad host range plasmids, both of which are known drivers of horizontal gene transfer (HGT) in soybean bradyrhizobia. These factors indicate that SPP along with IS and plasmids participate in HGT, drive bradyrhizobia evolution, and play an outsized role in bradyrhizobia ecology. IMPORTANCE Previous studies have shown that IS and plasmids mediate HGT of symbiotic nodulation (nod) genes in soybean bradyrhizobia; however, these events require close cell-to-cell contact, which could be limited in soil environments. Bacteriophage-assisted gene transduction through spontaneously produced prophages provides a stable means of HGT not limited by the constraints of proximal cell-to-cell contact. These phage-mediated HGT events may shape soybean bradyrhizobia population ecology, with concomitant impacts on soybean agriculture.},
}
@article {pmid37017538,
year = {2023},
author = {Jonsdottir, I and Given, C and Penttinen, R and Jalasvuori, M},
title = {Preceding Host History of Conjugative Resistance Plasmids Affects Intra- and Interspecific Transfer Potential from Biofilm.},
journal = {mSphere},
volume = {8},
number = {3},
pages = {e0010723},
pmid = {37017538},
issn = {2379-5042},
support = {322204//Academy of Finland (AKA)/ ; 347531//Academy of Finland (AKA)/ ; },
mesh = {Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics ; Bacteria/genetics ; beta-Lactams ; Klebsiella pneumoniae/genetics ; },
abstract = {Conjugative plasmids can confer antimicrobial resistance (AMR) to their host bacterium. The plasmids disperse even between distantly related host species, rescuing the host from otherwise detrimental effects of antibiotics. Little is known about the role of these plasmids in the spread of AMR during antibiotic treatment. One unstudied question is whether the past evolutionary history of a plasmid in a particular species creates host specificity in its rescue potential or if interspecific coevolution can improve interspecific rescues. To study this, we coevolved the plasmid RP4 under three different host settings; solely Escherichia coli or Klebsiella pneumoniae, or alternating between both of them. The ability of evolved plasmids in bacterial biofilm to rescue susceptible planktonic host bacteria of either the same or different species during beta-lactam treatment was tested. The interspecific coevolution seemed to decrease rescue potential for the RP4 plasmid, while the K. pneumoniae evolved plasmid became more host specific. Large deletion in the region encoding the mating pair formation (Tra2) apparatus was detected in the plasmids evolved with K. pneumoniae. This adaptation resulted in the exapted evolution of resistance against a plasmid-dependent bacteriophage PRD1. Further, previous studies have suggested that mutations in this region completely abolish the plasmid's ability to conjugate; however, our study shows it is not essential for conjugation but rather affects the host-specific conjugation efficiency. Overall, the results suggest that previous evolutionary history can result in the separation of host-specific plasmid lineages that may be further amplified by unselected exaptations such as phage resistance. IMPORTANCE Antimicrobial resistance (AMR) is a major global public health threat which can rapidly spread in microbial communities via conjugative plasmids. Here, we advance with evolutionary rescue via conjugation in a more natural setting, namely, biofilm, and incorporate a broad-host range plasmid RP4 to test whether intra- and interspecific host histories affect its transfer potential. Escherichia coli and Klebsiella pneumoniae hosts were seen to elicit different evolutionary influences on the RP4 plasmid, leading to clear differences in the rescue potential and underlining the significant role of the plasmid-host interactions in the spread of AMR. We also contradicted previous reports that established certain conjugal transfer genes of RP4 as essential. This work enhances the understanding of how plasmid host range evolve in different host settings and further, the potential effects it may have on the horizontal spread of AMR in complex environments such as biofilms.},
}
@article {pmid37014461,
year = {2023},
author = {Talat, A and Miranda, C and Poeta, P and Khan, AU},
title = {Farm to table: colistin resistance hitchhiking through food.},
journal = {Archives of microbiology},
volume = {205},
number = {5},
pages = {167},
pmid = {37014461},
issn = {1432-072X},
support = {BT/PR40148/BTIS/137/20/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {Animals ; Humans ; *Colistin/pharmacology ; Farms ; Chickens/microbiology ; Escherichia coli/genetics ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Poultry/microbiology ; *Escherichia coli Proteins/genetics ; Plasmids ; Microbial Sensitivity Tests ; },
abstract = {Colistin is a high priority, last-resort antibiotic recklessly used in livestock and poultry farms. It is used as an antibiotic for treating multi-drug resistant Gram-negative bacterial infections as well as a growth promoter in poultry and animal farms. The sub-therapeutic doses of colistin exert a selection pressure on bacteria leading to the emergence of colistin resistance in the environment. Colistin resistance gene, mcr are mostly plasmid-mediated, amplifying the horizontal gene transfer. Food products such as chicken, meat, pork etc. disseminate colistin resistance to humans through zoonotic transfer. The antimicrobial residues used in livestock and poultry often leaches to soil and water through faeces. This review highlights the recent status of colistin use in food-producing animals, its association with colistin resistance adversely affecting public health. The underlying mechanism of colistin resistance has been explored. The prohibition of over-the-counter colistin sales and as growth promoters for animals and broilers has exhibited effective stewardship of colistin resistance in several countries.},
}
@article {pmid37009500,
year = {2023},
author = {Nodari, CS and Opazo-Capurro, A and Castillo-Ramirez, S and Mattioni Marchetti, V},
title = {Editorial: Mobile genetic elements as dissemination drivers of multidrug-resistant Gram-negative bacteria.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1180510},
pmid = {37009500},
issn = {2235-2988},
mesh = {*Drug Resistance, Multiple, Bacterial/genetics ; *Drug Resistance, Bacterial/genetics ; Gram-Negative Bacteria/genetics ; Interspersed Repetitive Sequences ; },
}
@article {pmid37007505,
year = {2023},
author = {Apari, P and Földvári, G},
title = {Domestication and microbiome succession may drive pathogen spillover.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1102337},
pmid = {37007505},
issn = {1664-302X},
abstract = {Emerging infectious diseases have posed growing medical, social and economic threats to humanity. The biological background of pathogen spillover or host switch, however, still has to be clarified. Disease ecology finds pathogen spillovers frequently but struggles to explain at the molecular level. Contrarily, molecular biological traits of host-pathogen relationships with specific molecular binding mechanisms predict few spillovers. Here we aim to provide a synthetic explanation by arguing that domestication, horizontal gene transfer even between superkingdoms as well as gradual exchange of microbiome (microbiome succession) are essential in the whole scenario. We present a new perspective at the molecular level which can explain the observations of frequent pathogen spillover events at the ecological level. This proposed rationale is described in detail, along with supporting evidence from the peer-reviewed literature and suggestions for testing hypothesis validity. We also highlight the importance of systematic monitoring of virulence genes across taxonomical categories and in the whole biosphere as it helps prevent future epidemics and pandemics. We conclude that that the processes of domestication, horizontal gene transfer and microbial succession might be important mechanisms behind the many spillover events driven and accelerated by climate change, biodiversity loss and globalization.},
}
@article {pmid37004306,
year = {2023},
author = {Deng, X and Yuan, J and Chen, L and Chen, H and Wei, C and Nielsen, PH and Wuertz, S and Qiu, G},
title = {CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter.},
journal = {Water research},
volume = {235},
number = {},
pages = {119906},
doi = {10.1016/j.watres.2023.119906},
pmid = {37004306},
issn = {1879-2448},
mesh = {Prophages/genetics ; CRISPR-Cas Systems ; *Bacteriophages/genetics ; Phylogeny ; Wastewater ; *Betaproteobacteria ; },
abstract = {Candidatus Accumulibacter plays a major role in enhanced biological phosphorus removal (EBPR) from wastewater. Although bacteriophages have been shown to represent fatal threats to Ca. Accumulibacter organisms and thus interfere with the stability of the EBPR process, little is known about the ability of different Ca. Accumulibacter strains to resist phage infections. We conducted a systematic analysis of the occurrence and characteristics of clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) systems and prophages in Ca. Accumulibacter lineage members (43 in total, including 10 newly recovered genomes). Results indicate that 28 Ca. Accumulibacter genomes encode CRISPR-Cas systems. They were likely acquired via horizontal gene transfer, conveying a distinct adaptivity to phage predation to different Ca. Accumulibacter members. Major differences in the number of spacers show the unique phage resistance of these members. A comparison of the spacers in closely related Ca. Accumulibacter members from distinct geographical locations indicates that habitat isolation may have resulted in the acquisition of resistance to different phages by different Ca. Accumulibacter. Long-term operation of three laboratory-scale EBPR bioreactors revealed high relative abundances of Ca. Accumulibacter with CRISPSR-Cas systems. Their specific resistance to phages in these reactors was indicated by spacer analysis. Metatranscriptomic analyses showed the activation of the CRISPR-Cas system under both anaerobic and aerobic conditions. Additionally, 133 prophage regions were identified in 43 Ca. Accumulibacter genomes. Twenty-seven of them (in 19 genomes) were potentially active. Major differences in the occurrence of CRISPR-Cas systems and prophages in Ca. Accumulibacter will lead to distinct responses to phage predation. This study represents the first systematic analysis of CRISPR-Cas systems and prophages in the Ca. Accumulibacter lineage, providing new perspectives on the potential impacts of phages on Ca. Accumulibacter and EBPR systems.},
}
@article {pmid37002975,
year = {2023},
author = {Stockdale, SR and Hill, C},
title = {Incorporating plasmid biology and metagenomics into a holistic model of the human gut microbiome.},
journal = {Current opinion in microbiology},
volume = {73},
number = {},
pages = {102307},
doi = {10.1016/j.mib.2023.102307},
pmid = {37002975},
issn = {1879-0364},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Plasmids/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Metagenomics ; },
abstract = {The human gut microbiome is often described as the collection of bacteria, archaea, fungi, protists, and viruses associated with an individual, with no acknowledgement of the plasmid constituents. However, like viruses, plasmids are autonomous intracellular replicating entities that can influence the genotype and phenotype of their host and mediate trans-kingdom interactions. Plasmids are frequently noted as vehicles for horizontal gene transfer and for spreading antibiotic resistance, yet their multifaceted contribution to mutualistic and antagonistic interactions within the human microbiome and impact on human health is overlooked. In this review, we highlight the importance of plasmids and their biological properties as overlooked components of microbiomes. Subsequent human microbiome studies should include dedicated analyses of plasmids, particularly as a holistic understanding of human-microbial interactions is required before effective and safe interventions can be implemented to improve human well-being.},
}
@article {pmid37001724,
year = {2023},
author = {Boiten, KE and Kuijper, EJ and Schuele, L and van Prehn, J and Bode, LGM and Maat, I and van Asten, SAV and Notermans, DW and Rossen, JWA and Veloo, ACM},
title = {Characterization of mobile genetic elements in multidrug-resistant Bacteroides fragilis isolates from different hospitals in the Netherlands.},
journal = {Anaerobe},
volume = {81},
number = {},
pages = {102722},
doi = {10.1016/j.anaerobe.2023.102722},
pmid = {37001724},
issn = {1095-8274},
mesh = {Humans ; Bacteroides fragilis/genetics ; Genes, Bacterial ; Netherlands ; *Bacterial Infections ; Interspersed Repetitive Sequences ; Anti-Bacterial Agents/pharmacology ; *Bacteroides Infections/epidemiology/microbiology ; Microbial Sensitivity Tests ; },
abstract = {OBJECTIVES: Five human clinical multidrug-resistant (MDR) Bacteroides fragilis isolates, including resistance to meropenem and metronidazole, were recovered at different hospitals in the Netherlands between 2014 and 2020 and sent to the anaerobic reference laboratory for full characterization.<br><br>METHODS: Isolates were recovered from a variety of clinical specimens from patients with unrelated backgrounds. Long- and short-read sequencing was performed, followed by a hybrid assembly to study the presence of mobile genetic elements (MGEs) and antimicrobial resistance genes (ARGs).<br><br>RESULTS: A cfxA gene was present on a transposon (Tn) similar to Tn4555 in two isolates. In two isolates a novel Tn was present with the cfxA gene. Four isolates harbored a nimE gene, located on a pBFS01_2 plasmid. One isolate contained a novel plasmid carrying a nimA gene with IS1168. The tetQ gene was present on novel conjugative transposons (CTns) belonging to the CTnDOT family. Two isolates harbored a novel plasmid with tetQ. Other ARGs in these isolates, but not on an MGE, were: cfiA, ermF, mef(EN2), and sul2. ARGs harboured differed between isolates and corresponded with the observed phenotypic resistance.<br><br>CONCLUSIONS: Novel CTns, Tns, and plasmids were encountered in the five MDR B.&#xa0;fragilis isolates, complementing our knowledge on MDR and horizontal gene transfer in anaerobic bacteria.},
}
@article {pmid36996986,
year = {2023},
author = {Cheng, Y and Wang, X and Zhao, L and Zhang, X and Kong, Q and Li, H and You, X and Li, Y},
title = {Wheat straw pyrochar more efficiently decreased enantioselective uptake of dinotefuran by lettuce and dissemination of antibiotic resistance genes than hydrochar in an agricultural soil.},
journal = {The Science of the total environment},
volume = {880},
number = {},
pages = {163088},
doi = {10.1016/j.scitotenv.2023.163088},
pmid = {36996986},
issn = {1879-1026},
mesh = {Humans ; *Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; Lactuca ; Triticum ; Ecosystem ; Stereoisomerism ; Drug Resistance, Microbial/genetics ; *Pesticides ; Bacteria/genetics ; Soil Microbiology ; Genes, Bacterial ; },
abstract = {Remediation of soils pollution caused by dinotefuran, a chiral pesticide, is indispensable for ensuring human food security. In comparison with pyrochar, the effect of hydrochar on enantioselective fate of dinotefuran, and antibiotic resistance genes (ARGs) profiles in the contaminated soils remain poorly understood. Therefore, wheat straw hydrochar (SHC) and pyrochar (SPC) were prepared at 220 and 500 °C, respectively, to investigate their effects and underlying mechanisms on enantioselective fate of dinotefuran enantiomers and metabolites, and soil ARG abundance in soil-plant ecosystems using a 30-day pot experiment planted with lettuce. SPC showed a greater reduction effect on the accumulation of R- and S-dinotefuran and metabolites in lettuce shoots than SHC. This was mainly resulted from the lowered soil bioavailability of R- and S-dinotefuran due to adsorption/immobilization by chars, together with the char-enhanced pesticide-degrading bacteria resulted from increased soil pH and organic matter content. Both SPC and SHC efficiently reduced ARG levels in soils, owing to lowered abundance of ARG-carrying bacteria and declined horizontal gene transfer induced by decreased dinotefuran bioavailability. The above results provide new insights for optimizing char-based sustainable technologies to mitigate pollution of dinotefuran and spread of ARGs in agroecosystems.},
}
@article {pmid36996977,
year = {2023},
author = {Zhang, C and Wang, C and Zhao, X and Hakizimana, I},
title = {Effect of resistance difference on distribution of antibiotics in bacterial cell and conjugative gene transfer risks during electrochemical flow through reaction.},
journal = {The Science of the total environment},
volume = {878},
number = {},
pages = {163142},
doi = {10.1016/j.scitotenv.2023.163142},
pmid = {36996977},
issn = {1879-1026},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics ; Genes, Bacterial ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Plasmids ; },
abstract = {The occurrences and spread of antibiotic resistance (AR) mediated by horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) in aquatic environment have been aggravated because of the abuse of antibiotics. While the pressure of different antibiotics is known to induce the spread of AR in bacteria, whether distribution of different antibiotics in cell structure could affect HGT risks is not clear. Here, a significant difference between the distribution of tetracycline hydrochloride (Tet) and sulfamethoxazole (Sul) in cell structure during electrochemical flow through reaction (EFTR) process was firstly reported. Meanwhile, EFTR treatment possessed excellent disinfection performance and consequently controlled the HGT risks. The intracellular Tet (iTet) was discharged through efflux pumps to increase the content of extracellular Tet (eTet) due to the resistance of donor E. coli DH5α under the selective pressure of Tet, declining the damage of donor and plasmid RP4. The HGT frequency was 8.18-fold increase compared with that by EFTR treatment alone. While the secretion of intracellular Sul (iSul) was inhibited by blocking the formation of efflux pumps to inactivate the donor under the Sul pressure, and the total content of iSul and adsorbed Sul (aSul) to be 1.36-fold higher than that of eSul. Therefore, the reactive oxygen species (ROS) generation and cell membrane permeability were improved to release ARGs, and •OH attacked plasmid RP4 in the EFTR process, inhibiting the HGT risks. This study advances the awareness of the interaction between distribution of different antibiotics in cell structure and the HGT risks in the EFTR process.},
}
@article {pmid36995244,
year = {2023},
author = {Herviou, P and Balvay, A and Bellet, D and Bobet, S and Maudet, C and Staub, J and Alric, M and Leblond-Bourget, N and Delorme, C and Rabot, S and Denis, S and Payot, S},
title = {Transfer of the Integrative and Conjugative Element ICESt3 of Streptococcus thermophilus in Physiological Conditions Mimicking the Human Digestive Ecosystem.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0466722},
pmid = {36995244},
issn = {2165-0497},
mesh = {Animals ; Mice ; Humans ; *Streptococcus thermophilus/genetics ; Conjugation, Genetic ; Gastrointestinal Tract ; Gene Transfer, Horizontal ; *Microbiota ; },
abstract = {Metagenome analyses of the human microbiome suggest that horizontal gene transfer (HGT) is frequent in these rich and complex microbial communities. However, so far, only a few HGT studies have been conducted in vivo. In this work, three different systems mimicking the physiological conditions encountered in the human digestive tract were tested, including (i) the TNO gastro-Intestinal tract Model 1 (TIM-1) system (for the upper part of the intestine), (ii) the ARtificial COLon (ARCOL) system (to mimic the colon), and (iii) a mouse model. To increase the likelihood of transfer by conjugation of the integrative and conjugative element studied in the artificial digestive systems, bacteria were entrapped in alginate, agar, and chitosan beads before being placed in the different gut compartments. The number of transconjugants detected decreased, while the complexity of the ecosystem increased (many clones in TIM-1 but only one clone in ARCOL). No clone was obtained in a natural digestive environment (germfree mouse model). In the human gut, the richness and diversity of the bacterial community would offer more opportunities for HGT events to occur. In addition, several factors (SOS-inducing agents, microbiota-derived factors) that potentially increase in vivo HGT efficiency were not tested here. Even if HGT events are rare, expansion of the transconjugant clones can happen if ecological success is fostered by selecting conditions or by events that destabilize the microbial community. IMPORTANCE The human gut microbiota plays a key role in maintaining normal host physiology and health, but its homeostasis is fragile. During their transit in the gastrointestinal tract, bacteria conveyed by food can exchange genes with resident bacteria. New traits acquired by HGT (e.g., new catabolic properties, bacteriocins, antibiotic resistance) can impact the gut microbial composition and metabolic potential. We showed here that TIM-1, a system mimicking the upper digestive tract, is a useful tool to evaluate HGT events in conditions closer to the physiological ones. Another important fact pointed out in this work is that Enterococcus faecalis is a good candidate for foreign gene acquisition. Due to its high ability to colonize the gut and acquire mobile genetic elements, this commensal bacterium could serve as an intermediate for HGT in the human gut.},
}
@article {pmid36995224,
year = {2023},
author = {Piscon, B and Pia Esposito, E and Fichtman, B and Samburski, G and Efremushkin, L and Amselem, S and Harel, A and Rahav, G and Zarrilli, R and Gal-Mor, O},
title = {The Effect of Outer Space and Other Environmental Cues on Bacterial Conjugation.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0368822},
pmid = {36995224},
issn = {2165-0497},
mesh = {*Conjugation, Genetic ; *Cues ; Plasmids ; Bacteria/genetics ; Gene Transfer, Horizontal ; },
abstract = {Bacterial conjugation is one of the most abundant horizontal gene transfer (HGT) mechanisms, playing a fundamental role in prokaryote evolution. A better understanding of bacterial conjugation and its cross talk with the environment is needed for a more complete understanding of HGT mechanisms and to fight the dissemination of malicious genes between bacteria. Here, we studied the effect of outer space, microgravity, and additional key environmental cues on transfer (tra) gene expression and conjugation efficiency, using the under studied broad-host range plasmid pN3, as a model. High resolution scanning electron microscopy revealed the morphology of the pN3 conjugative pili and mating pair formation during conjugation. Using a nanosatellite carrying a miniaturized lab, we studied pN3 conjugation in outer space, and used qRT-PCR, Western blotting and mating assays to determine the effect of ground physicochemical parameters on tra gene expression and conjugation. We showed for the first time that bacterial conjugation can occur in outer space and on the ground, under microgravity-simulated conditions. Furthermore, we demonstrated that microgravity, liquid media, elevated temperature, nutrient depletion, high osmolarity and low oxygen significantly reduce pN3 conjugation. Interestingly, under some of these conditions we observed an inverse correlation between tra gene transcription and conjugation frequency and found that induction of at least traK and traL can negatively affect pN3 conjugation frequency in a dose-dependent manner. Collectively, these results uncover pN3 regulation by various environmental cues and highlight the diversity of conjugation systems and the different ways in which they may be regulated in response to abiotic signals. IMPORTANCE Bacterial conjugation is a highly ubiquitous and promiscuous process, by which a donor bacterium transfers a large portion of genetic material to a recipient cell. This mechanism of horizontal gene transfer plays an important role in bacterial evolution and in the ability of bacteria to acquire resistance to antimicrobial drugs and disinfectants. Bacterial conjugation is a complex and energy-consuming process, that is tightly regulated and largely affected by various environmental signals sensed by the bacterial cell. Comprehensive knowledge about bacterial conjugation and the ways it is affected by environmental cues is required to better understand bacterial ecology and evolution and to find new effective ways to counteract the threating dissemination of antibiotic resistance genes between bacterial populations. Moreover, characterizing this process under stress or suboptimal growth conditions such as elevated temperatures, high salinity or in the outer space, may provide insights relevant to future habitat environmental conditions.},
}
@article {pmid36993299,
year = {2023},
author = {Quinones-Olvera, N and Owen, SV and McCully, LM and Marin, MG and Rand, EA and Fan, AC and Martins Dosumu, OJ and Paul, K and Sanchez Castaño, CE and Petherbridge, R and Paull, JS and Baym, M},
title = {Diverse and abundant phages exploit conjugative plasmids.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {36993299},
issn = {2692-8205},
support = {R35 GM133700/GM/NIGMS NIH HHS/United States ; T32 GM135014/GM/NIGMS NIH HHS/United States ; },
abstract = {Phages exert profound evolutionary pressure on bacteria by interacting with receptors on the cell surface to initiate infection. While the majority of phages use chromosomally-encoded cell surface structures as receptors, plasmid-dependent phages exploit plasmid-encoded conjugation proteins, making their host range dependent on horizontal transfer of the plasmid. Despite their unique biology and biotechnological significance, only a small number of plasmid-dependent phages have been characterized. Here we systematically search for new plasmid-dependent phages targeting IncP and IncF plasmids using a targeted discovery platform, and find that they are common and abundant in wastewater, and largely unexplored in terms of their genetic diversity. Plasmid-dependent phages are enriched in non-canonical types of phages, and all but one of the 64 phages we isolated were non-tailed, and members of the lipid-containing tectiviruses, ssDNA filamentous phages or ssRNA phages. We show that plasmid-dependent tectiviruses exhibit profound differences in their host range which is associated with variation in the phage holin protein. Despite their relatively high abundance in wastewater, plasmid-dependent tectiviruses are missed by metaviromic analyses, underscoring the continued importance of culture-based phage discovery. Finally, we identify a tailed phage dependent on the IncF plasmid, and find related structural genes in phages that use the orthogonal type 4 pilus as a receptor, highlighting the promiscuous use of these distinct contractile structures by multiple groups of phages. Taken together, these results indicate plasmid-dependent phages play an under-appreciated evolutionary role in constraining horizontal gene transfer via conjugative plasmids.},
}
@article {pmid36990411,
year = {2023},
author = {Sánchez-Arroyo, A and Plaza-Vinuesa, L and Rivas, BL and Mancheño, JM and Muñoz, R},
title = {The salicylate 1,2-dioxygenase from Pseudaminobacter salicylatoxidans DSM 6986[T] is a bifunctional enzyme that inactivates the mycotoxin ochratoxin A by a novel amidohydrolase activity.},
journal = {International journal of biological macromolecules},
volume = {237},
number = {},
pages = {124230},
doi = {10.1016/j.ijbiomac.2023.124230},
pmid = {36990411},
issn = {1879-0003},
mesh = {Phyllobacteriaceae ; Salicylates/chemistry ; Molecular Docking Simulation ; *Mycotoxins ; Phenylalanine ; *Dioxygenases/genetics ; },
abstract = {The salicylate 1,2-dioxygenase from the bacterium Pseudaminobacter salicylatoxidans DSM 6986[T] (PsSDO) is a versatile metalloenzyme that participates in the aerobic biodegradation of aromatic compounds, such as gentisates and salicylates. Surprisingly, and unrelated to this metabolic role, it has been reported that PsSDO may transform the mycotoxin ochratoxin A (OTA), a molecule that appears in numerous food products that results in serious biotechnological concern. In this work, we show that PsSDO, together with its dioxygenase activity, behaves as an amidohydrolase with a marked specificity for substrates containing a C-terminal phenylalanine residue, similar to OTA, although its presence is not an absolute requirement. This side chain would establish aromatic stacking interactions with the indole ring of Trp104. PsSDO hydrolysed the amide bond of OTA rendering the much less toxic ochratoxin α and L-β-phenylalanine. The binding mode of OTA and of a diverse set of synthetic carboxypeptidase substrates these substrates have been characterized by molecular docking simulations, which has permitted us to propose a catalytic mechanism of hydrolysis by PsSDO that, similarly to metallocarboxypeptidases, assumes a water-induced pathway following a general acid/base mechanism in which the side chain of Glu82 would provide the solvent nucleophilicity required for the enzymatic reaction. Since the PsSDO chromosomal region, absent in other Pseudaminobacter strains, contained a set of genes present in conjugative plasmids, it could have been acquired by horizontal gene transfer, probably from a Celeribacter strain.},
}
@article {pmid36989191,
year = {2023},
author = {Rathnapala, JMSN and Ragab, W and Kawato, S and Furukawa, M and Nozaki, R and Kondo, H and Hirono, I},
title = {Genomic characterization and identification of virulence-related genes in Vibrio nigripulchritudo isolated from white leg shrimp Penaeus vannamei.},
journal = {Journal of fish diseases},
volume = {46},
number = {7},
pages = {779-790},
doi = {10.1111/jfd.13786},
pmid = {36989191},
issn = {1365-2761},
support = {//Japan Science and Technology Agency/ ; //Japan Society for the Promotion of Science London/ ; },
mesh = {Phylogeny ; Virulence/genetics ; Genomics ; Vibrio ; *Penaeidae ; *Fish Diseases ; Animals ; },
abstract = {Vibrio nigripulchritudo causes vibriosis in penaeid shrimps. Here, we used Illumina and Nanopore sequencing technologies to sequence the genomes of three of its strains (TUMSAT-V. nig1, TUMSAT-V. nig2, and TUMSAT-V. nig3) to explore opportunities for disease management. Putative virulence factors and mobile genetic elements were detected while evaluating the phylogenetic relationship of each isolated strain. The genomes consisted of two circular chromosomes (I and II) plus one or two plasmids. The size of chromosome I ranged from 4.02 to 4.07 Mb with an average GC content of 46%, while the number of predicted CDSs ranged from 3563 to 3644. The size of chromosome II ranged from 2.16 to 2.18 Mb, with an average GC content of 45.5%, and the number of predicted CDSs ranged from 1970 to 1987. Numerous virulence genes were identified related to adherence, antiphagocytosis, chemotaxis, motility, iron uptake, quorum sensing, secretion systems, and toxins in all three genomes. Higher numbers of prophages and genomic islands found in TUMSAT-V. nig1 suggest that the strain has experienced numerous horizontal gene transfer events. The presence of antimicrobial resistance genes suggests that the strains have multidrug resistance. Comparative genomic analysis showed that all three strains belonged to the same clade.},
}
@article {pmid36989040,
year = {2023},
author = {Sanow, S and Kuang, W and Schaaf, G and Huesgen, P and Schurr, U and Roessner, U and Watt, M and Arsova, B},
title = {Molecular Mechanisms of Pseudomonas-Assisted Plant Nitrogen Uptake: Opportunities for Modern Agriculture.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {36},
number = {9},
pages = {536-548},
doi = {10.1094/MPMI-10-22-0223-CR},
pmid = {36989040},
issn = {0894-0282},
abstract = {Pseudomonas spp. make up 1.6% of the bacteria in the soil and are found throughout the world. More than 140 species of this genus have been identified, some beneficial to the plant. Several species in the family Pseudomonadaceae, including Azotobacter vinelandii AvOP, Pseudomonas stutzeri A1501, Pseudomonas stutzeri DSM4166, Pseudomonas szotifigens 6HT33bT, and Pseudomonas sp. strain K1 can fix nitrogen from the air. The genes required for these reactions are organized in a nitrogen fixation island, obtained via horizontal gene transfer from Klebsiella pneumoniae, Pseudomonas stutzeri, and Azotobacter vinelandii. Today, this island is conserved in Pseudomonas spp. from different geographical locations, which, in turn, have evolved to deal with different geo-climatic conditions. Here, we summarize the molecular mechanisms behind Pseudomonas-driven plant growth promotion, with particular focus on improving plant performance at limiting nitrogen (N) and improving plant N content. We describe Pseudomonas-plant interaction strategies in the soil, noting that the mechanisms of denitrification, ammonification, and secondary metabolite signaling are only marginally explored. Plant growth promotion is dependent on the abiotic conditions and differs at sufficient and deficient N. The molecular controls behind different plant responses are not fully elucidated. We suggest that superposition of transcriptome, proteome, and metabolome data and their integration with plant phenotype development through time will help fill these gaps. The aim of this review is to summarize the knowledge behind Pseudomonas-driven nitrogen fixation and to point to possible agricultural solutions. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.},
}
@article {pmid36988519,
year = {2023},
author = {Low, WW and Seddon, C and Beis, K and Frankel, G},
title = {The Interaction of the F-Like Plasmid-Encoded TraN Isoforms with Their Cognate Outer Membrane Receptors.},
journal = {Journal of bacteriology},
volume = {205},
number = {4},
pages = {e0006123},
pmid = {36988519},
issn = {1098-5530},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Escherichia coli/genetics/metabolism ; *F Factor ; Amino Acid Sequence ; Conjugation, Genetic ; Plasmids/genetics ; Membrane Proteins/metabolism ; Protein Isoforms/genetics ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Horizontal gene transfer via conjugation plays a major role in bacterial evolution. In F-like plasmids, efficient DNA transfer is mediated by close association between donor and recipient bacteria. This process, known as mating pair stabilization (MPS), is mediated by interactions between the plasmid-encoded outer membrane (OM) protein TraN in the donor and chromosomally-encoded OM proteins in the recipient. We have recently reported the existence of 7 TraN sequence types, which are grouped into 4 structural types, that we named TraNα, TraNβ, TraNγ, and TraNδ. Moreover, we have shown specific pairing between TraNα and OmpW, TraNβ and OmpK36 of Klebsiella pneumoniae, TraNγ and OmpA, and TraNδ and OmpF. In this study, we found that, although structurally similar, TraNα encoded by the Salmonella enterica pSLT plasmid (TraNα2) binds OmpW in both Escherichia coli and Citrobacter rodentium, while TraNα encoded by the R100-1 plasmid (TraNα1) only binds OmpW in E. coli. AlphaFold2 predictions suggested that this specificity is mediated by a single amino acid difference in loop 3 of OmpW, which we confirmed experimentally. Moreover, we show that single amino acids insertions into loop 3 of OmpK36 affect TraNβ-mediated conjugation efficiency of the K. pneumoniae resistance plasmid pKpQIL. Lastly, we report that TraNβ can also mediate MPS by binding OmpK35, making it the first TraN variant that can bind more than one OM protein in the recipient. Together, these data show that subtle sequence differences in the OM receptors can impact TraN-mediated conjugation efficiency. IMPORTANCE Conjugation plays a central role in the spread of antimicrobial resistance genes among bacterial pathogens. Efficient conjugation is mediated by formation of mating pairs via a pilus, followed by mating pair stabilization (MPS), mediated by tight interactions between the plasmid-encoded outer membrane protein (OMP) TraN in the donor (of which there are 7 sequence types grouped into the 4 structural isoforms α, β, γ, and δ), and an OMP receptor in the recipient (OmpW, OmpK36, OmpA, and OmpF, respectively). In this study, we found that subtle differences in OmpW and OmpK36 have significant consequences on conjugation efficiency and specificity, highlighting the existence of selective pressure affecting plasmid-host compatibility and the flow of horizontal gene transfer in bacteria.},
}
@article {pmid36985115,
year = {2023},
author = {Gummalla, VS and Zhang, Y and Liao, YT and Wu, VCH},
title = {The Role of Temperate Phages in Bacterial Pathogenicity.},
journal = {Microorganisms},
volume = {11},
number = {3},
pages = {},
pmid = {36985115},
issn = {2076-2607},
support = {2030-42000-0055-000-D//Agricultural Research Service/ ; },
abstract = {Bacteriophages are viruses that infect bacteria and archaea and are classified as virulent or temperate phages based on their life cycles. A temperate phage, also known as a lysogenic phage, integrates its genomes into host bacterial chromosomes as a prophage. Previous studies have indicated that temperate phages are beneficial to their susceptible bacterial hosts by introducing additional genes to bacterial chromosomes, creating a mutually beneficial relationship. This article reviewed three primary ways temperate phages contribute to the bacterial pathogenicity of foodborne pathogens, including phage-mediated virulence gene transfer, antibiotic resistance gene mobilization, and biofilm formation. This study provides insights into mechanisms of phage-bacterium interactions in the context of foodborne pathogens and provokes new considerations for further research to avoid the potential of phage-mediated harmful gene transfer in agricultural environments.},
}
@article {pmid36983453,
year = {2023},
author = {Urquhart, AS and Idnurm, A},
title = {A Polyphasic Approach including Whole Genome Sequencing Reveals Paecilomyces paravariotii sp. nov. as a Cryptic Sister Species to P. variotii.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {3},
pages = {},
pmid = {36983453},
issn = {2309-608X},
abstract = {Whole genome sequencing is rapidly increasing phylogenetic resolution across many groups of fungi. To improve sequencing coverage in the genus Paecilomyces (Eurotiales), we report nine new Paecilomyces genomes representing five different species. Phylogenetic comparison between these genomes and those reported previously showed that Paecilomyces paravariotii is a distinct species from its close relative P. variotii. The independence of P. paravariotii is supported by analysis of overall gene identify (via BLAST), differences in secondary metabolism and an inability to form ascomata when paired with a fertile P. variotii strain of opposite mating type. Furthermore, whole genome sequencing resolves the P. formosus clade into three separate species, one of which lacked a valid name that is now provided.},
}
@article {pmid36982992,
year = {2023},
author = {Liu, W and Huang, Y and Zhang, H and Liu, Z and Huan, Q and Xiao, X and Wang, Z},
title = {Factors and Mechanisms Influencing Conjugation In Vivo in the Gastrointestinal Tract Environment: A Review.},
journal = {International journal of molecular sciences},
volume = {24},
number = {6},
pages = {},
pmid = {36982992},
issn = {1422-0067},
support = {32273055//National Natural Science Foundation of China/ ; },
mesh = {Drug Resistance, Microbial ; *Intestines ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Plasmids/genetics ; Conjugation, Genetic ; },
abstract = {The emergence and spread of antibiotic resistance genes (ARGs) have imposed a serious threat on global public health. Horizontal gene transfer (HGT) via plasmids is mainly responsible for the spread of ARGs, and conjugation plays an important role in HGT. The conjugation process is very active in vivo and its effect on the spreading of ARGs may be underestimated. In this review, factors affecting conjugation in vivo, especially in the intestinal environment, are summarized. In addition, the potential mechanisms affecting conjugation in vivo are summarized from the perspectives of bacterial colonization and the conjugation process.},
}
@article {pmid36980919,
year = {2023},
author = {Weltzer, ML and Wall, D},
title = {Social Diversification Driven by Mobile Genetic Elements.},
journal = {Genes},
volume = {14},
number = {3},
pages = {},
pmid = {36980919},
issn = {2073-4425},
support = {R35 GM140886/GM/NIGMS NIH HHS/United States ; },
mesh = {*Bacteria/genetics ; *Myxococcales/genetics ; Biological Evolution ; Genome ; Interspersed Repetitive Sequences/genetics ; },
abstract = {Social diversification in microbes is an evolutionary process where lineages bifurcate into distinct populations that cooperate with themselves but not with other groups. In bacteria, this is frequently driven by horizontal transfer of mobile genetic elements (MGEs). Here, the resulting acquisition of new genes changes the recipient's social traits and consequently how they interact with kin. These changes include discriminating behaviors mediated by newly acquired effectors. Since the producing cell is protected by cognate immunity factors, these selfish elements benefit from selective discrimination against recent ancestors, thus facilitating their proliferation and benefiting the host. Whether social diversification benefits the population at large is less obvious. The widespread use of next-generation sequencing has recently provided new insights into population dynamics in natural habitats and the roles MGEs play. MGEs belong to accessory genomes, which often constitute the majority of the pangenome of a taxon, and contain most of the kin-discriminating loci that fuel rapid social diversification. We further discuss mechanisms of diversification and its consequences to populations and conclude with a case study involving myxobacteria.},
}
@article {pmid36975806,
year = {2023},
author = {Desingu, PA and Nagarajan, K and Sundaresan, NR},
title = {Unique Tandem Repeats in the Inverted Terminal Repeat Regions of Monkeypox Viruses.},
journal = {Microbiology spectrum},
volume = {11},
number = {2},
pages = {e0319922},
pmid = {36975806},
issn = {2165-0497},
abstract = {The genetic diversity, especially in noncoding regions between clade I, clade IIa, and clade IIb monkeypox viruses (MPXVs), is still not fully understood. Here, we report that unique 16-nucleotide-length tandem repeats in MPXVs viruses are located in the noncoding regions of inverted terminal repeats (ITR), and the copy number of this repeat is different among clade I, clade IIa, and clade IIb viruses. It is noteworthy that tandem repeats containing these specific sequences (AACTAACTTATGACTT) are only present in MPXVs and are not found in other poxviruses. Also, the tandem repeats containing these specific sequences (AACTAACTTATGACTT) do not correspond to the tandem repeats present in the human and rodent (mice and rat) genomes. On the other hand, some of the reported tandem repeats in the human and rodent (mice and rat) genomes are present in the clade IIb-B.1 lineage of MPXV. In addition, it is noteworthy that the genes flanking these tandem repeats are lost and gained compared between clade I, clade IIa, and clade IIb MPXV. IMPORTANCE The different groups of MPXVs contain unique tandem repeats with different copy numbers in the ITR regions, and these repeats may be likely to play a role in the genetic diversity of the virus. Clade IIb (B) MPXV contains 38 and 32 repeats similar to the Tandem repeats reported in the human and rodent genome, respectively. However, none of these 38 (human) and 32 (rodent) tandem repeats matched the tandem repeats (AACTAACTTATGACTT) found in the present study. Finally, when developing attenuated or modified MPXV vaccine strains, these repeats in noncoding genomic regions can be exploited to incorporate foreign proteins (adjuvants/other virus proteins/racking fluorescent proteins such as green fluorescent protein) to carry out studies such as vaccine production and virus pathogenesis.},
}
@article {pmid36964199,
year = {2023},
author = {Kavagutti, VS and Chiriac, MC and Ghai, R and Salcher, MM and Haber, M},
title = {Isolation of phages infecting the abundant freshwater Actinobacteriota order 'Ca. Nanopelagicales'.},
journal = {The ISME journal},
volume = {17},
number = {6},
pages = {943-946},
pmid = {36964199},
issn = {1751-7370},
mesh = {*Bacteriophages ; Bacteria/genetics ; Gene Transfer, Horizontal ; Metagenome ; Fresh Water/microbiology ; Genome, Viral ; Phylogeny ; },
abstract = {Low-GC Actinobacteriota of the order 'Ca. Nanopelagicales' (also known as acI or hgcI clade) are abundant in freshwaters around the globe. Extensive predation pressure by phages has been assumed to be the reason for their high levels of microdiversity. So far, however, only a few metagenome-assembled phages have been proposed to infect them and no phages have been isolated. Taking advantage of recent advances in the cultivation of 'Ca. Nanopelagicales' we isolated a novel species of its genus 'Ca. Planktophila'. Using this isolate as bait, we cultivated the first two phages infecting this abundant bacterial order. Both genomes contained a whiB-like transcription factor and a RNA polymerase sigma-70 factor, which might aid in manipulating their host's metabolism. Both phages encoded a glycosyltransferase and one an anti-restriction protein, potential means to evade degradation of their DNA by nucleases present in the host genome. The two phage genomes shared only 6% of their genome with their closest relatives, with whom they form a previously uncultured family of actinophages within the Caudoviricetes. Read recruitment analyses against globally distributed metagenomes revealed the endemic distribution of this group of phages infecting 'Ca. Nanopelagicales'. The recruitment pattern against metagenomes from the isolation site and the modular distribution of shared genes between the two phages indicate high levels of horizontal gene transfer, likely mirroring the microdiversity of their host in the evolutionary arms race between host and phage.},
}
@article {pmid36961781,
year = {2023},
author = {Belal, NA and Heath, LS},
title = {A complete theoretical framework for inferring horizontal gene transfers using partial order sets.},
journal = {PloS one},
volume = {18},
number = {3},
pages = {e0281824},
pmid = {36961781},
issn = {1932-6203},
mesh = {Phylogeny ; *Gene Transfer, Horizontal ; *Evolution, Molecular ; },
abstract = {We present a method for detecting horizontal gene transfer (HGT) using partial orders (posets). The method requires a poset for each species/gene pair, where we have a set of species S, and a set of genes G. Given the posets, the method constructs a phylogenetic tree that is compatible with the set of posets; this is done for each gene. Also, the set of posets can be derived from the tree. The trees constructed for each gene are then compared and tested for contradicting information, where a contradiction suggests HGT.},
}
@article {pmid36958858,
year = {2023},
author = {Bird, SM and Ford, S and Thompson, CMA and Little, R and Hall, JPJ and Jackson, RW and Malone, J and Harrison, E and Brockhurst, MA},
title = {Compensatory mutations reducing the fitness cost of plasmid carriage occur in plant rhizosphere communities.},
journal = {FEMS microbiology ecology},
volume = {99},
number = {4},
pages = {},
pmid = {36958858},
issn = {1574-6941},
support = {BB/R014884/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R014884/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R018154/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/J/000PR9797/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Rhizosphere ; Plasmids/genetics ; Mutation ; *Pseudomonas fluorescens/genetics ; },
abstract = {Plasmids drive bacterial evolutionary innovation by transferring ecologically important functions between lineages, but acquiring a plasmid often comes at a fitness cost to the host cell. Compensatory mutations, which ameliorate the cost of plasmid carriage, promote plasmid maintenance in simplified laboratory media across diverse plasmid-host associations. Whether such compensatory evolution can occur in more complex communities inhabiting natural environmental niches where evolutionary paths may be more constrained is, however, unclear. Here, we show a substantial fitness cost of carrying the large conjugative plasmid pQBR103 in Pseudomonas fluorescens SBW25 in the plant rhizosphere. This plasmid fitness cost could be ameliorated by compensatory mutations affecting the chromosomal global regulatory system gacA/gacS, which arose rapidly in plant rhizosphere communities and were exclusive to plasmid carriers. These findings expand our understanding of the importance of compensatory evolution in plasmid dynamics beyond simplified lab media. Compensatory mutations contribute to plasmid survival in bacterial populations living within complex microbial communities in their environmental niche.},
}
@article {pmid36958158,
year = {2023},
author = {Saha, S and Xiong, JQ and Patil, SM and Ha, GS and Hoh, JK and Park, HK and Chung, W and Chang, SW and Khan, MA and Park, HB and Jeon, BH},
title = {Dissemination of sulfonamide resistance genes in digester microbiome during anaerobic digestion of food waste leachate.},
journal = {Journal of hazardous materials},
volume = {452},
number = {},
pages = {131200},
doi = {10.1016/j.jhazmat.2023.131200},
pmid = {36958158},
issn = {1873-3336},
mesh = {Anaerobiosis ; Food ; *Refuse Disposal ; *Microbiota/genetics ; Sewage/microbiology ; Bacteria/metabolism ; Sulfanilamide ; Anti-Bacterial Agents/metabolism ; *Chloroflexi ; Firmicutes ; Methane/metabolism ; Bioreactors ; },
abstract = {The preeminence of sulfonamide drug resistance genes in food waste (FW) and the increased utilization of high-strength organic FW in anaerobic digestion (AD) to enhance methane production have raised severe public health concerns in wastewater treatment plants worldwide. In this regard, the dissemination patterns of different sulfonamide resistance genes (sul1 and sul2) and their impact on the digester core microbiota during AD of FW leachate (FWL) were evaluated. The presence of various sulfonamide antibiotics (SAs) in FWL digesters improved the final methane yield by 37 % during AD compared with FWL digesters without SAs. Microbial population shifts towards hydrolytic, acidogenic, and acetogenic bacteria in the phyla Actinobacteriota, Bacteroidota, Chloroflexi, Firmicutes, Proteobacteria, and Synergistota occurred due to SA induced substrate digestion and absorption through active transport; butanoate, propanoate, and pyruvate metabolism; glycolysis; gluconeogenesis; the citrate cycle; and pentose phosphate pathway. The initial dominance of Methanosaeta (89-96 %) declined to 47-53 % as AD progressed and shifted towards Methanosarcina (40 %) in digesters with the highest SA concentrations at the end of AD. Dissemination of sul1 depended on class 1 integron gene (intl1)-based horizontal gene transfer to pathogenic members of Chloroflexi, Firmicutes, and Patescibacteria, whereas sul2 was transmitted to Synergistota independent of intl1. Low susceptibility and ability to utilize SAs during methanogenesis shielded methanogenic archaea against selection pressure, thus preventing them from interacting with sul or intl1 genes, thereby minimizing the risk of antibiotic resistance development. The observed emergence of cationic antimicrobial peptide, vancomycin, and β-lactam resistance in the core microbiota during AD of FWL in the presence of SAs suggests that multidrug resistance caused by bacterial transformation could lead to an increase in the environmental resistome through wastewater sludge treatment.},
}
@article {pmid36951100,
year = {2023},
author = {Lin, H and Moody, ERR and Williams, TA and Moreau, JW},
title = {On the Origin and Evolution of Microbial Mercury Methylation.},
journal = {Genome biology and evolution},
volume = {15},
number = {4},
pages = {},
pmid = {36951100},
issn = {1759-6653},
mesh = {*Mercury ; *Methylmercury Compounds ; Methylation ; Phylogeny ; Bacteria/genetics ; Archaea/genetics ; },
abstract = {The origin of microbial mercury methylation has long been a mystery. Here, we employed genome-resolved phylogenetic analyses to decipher the evolution of the mercury-methylating gene, hgcAB, constrain the ancestral origin of the hgc operon, and explain the distribution of hgc in Bacteria and Archaea. We infer the extent to which vertical inheritance and horizontal gene transfer have influenced the evolution of mercury methylators and hypothesize that evolution of this trait bestowed the ability to produce an antimicrobial compound (MeHg+) on a potentially resource-limited early Earth. We speculate that, in response, the evolution of MeHg+-detoxifying alkylmercury lyase (encoded by merB) reduced a selective advantage for mercury methylators and resulted in widespread loss of hgc in Bacteria and Archaea.},
}
@article {pmid36950985,
year = {2023},
author = {Ding, D and Wang, B and Zhang, X and Zhang, J and Zhang, H and Liu, X and Gao, Z and Yu, Z},
title = {The spread of antibiotic resistance to humans and potential protection strategies.},
journal = {Ecotoxicology and environmental safety},
volume = {254},
number = {},
pages = {114734},
doi = {10.1016/j.ecoenv.2023.114734},
pmid = {36950985},
issn = {1090-2414},
mesh = {Animals ; Humans ; *Bacteria/genetics ; *Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; },
abstract = {Antibiotic resistance is currently one of the greatest threats to human health. Widespread use and residues of antibiotics in humans, animals, and the environment can exert selective pressure on antibiotic resistance bacteria (ARB) and antibiotic resistance gene (ARG), accelerating the flow of antibiotic resistance. As ARG spreads to the population, the burden of antibiotic resistance in humans increases, which may have potential health effects on people. Therefore, it is critical to mitigate the spread of antibiotic resistance to humans and reduce the load of antibiotic resistance in humans. This review briefly described the information of global antibiotic consumption information and national action plans (NAPs) to combat antibiotic resistance and provided a set of feasible control strategies for the transmission of ARB and ARG to humans in three areas including (a) Reducing the colonization capacity of exogenous ARB, (b) Enhancing human colonization resistance and mitigating the horizontal gene transfer (HGT) of ARG, (c) Reversing ARB antibiotic resistance. With the hope of achieving interdisciplinary one-health prevention and control of bacterial resistance.},
}
@article {pmid36949816,
year = {2023},
author = {Guzmán-Herrador, DL and Fernández-Gómez, A and Llosa, M},
title = {Recruitment of heterologous substrates by bacterial secretion systems for transkingdom translocation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1146000},
pmid = {36949816},
issn = {2235-2988},
mesh = {Humans ; *Bacterial Secretion Systems/genetics ; *Bacteria/metabolism ; Virulence ; Bacterial Proteins/genetics/metabolism ; Type IV Secretion Systems/metabolism ; },
abstract = {Bacterial secretion systems mediate the selective exchange of macromolecules between bacteria and their environment, playing a pivotal role in processes such as horizontal gene transfer or virulence. Among the different families of secretion systems, Type III, IV and VI (T3SS, T4SS and T6SS) share the ability to inject their substrates into human cells, opening up the possibility of using them as customized injectors. For this to happen, it is necessary to understand how substrates are recruited and to be able to engineer secretion signals, so that the transmembrane machineries can recognize and translocate the desired substrates in place of their own. Other factors, such as recruiting proteins, chaperones, and the degree of unfolding required to cross through the secretion channel, may also affect transport. Advances in the knowledge of the secretion mechanism have allowed heterologous substrate engineering to accomplish translocation by T3SS, and to a lesser extent, T4SS and T6SS into human cells. In the case of T4SS, transport of nucleoprotein complexes adds a bonus to its biotechnological potential. Here, we review the current knowledge on substrate recognition by these secretion systems, the many examples of heterologous substrate translocation by engineering of secretion signals, and the current and future biotechnological and biomedical applications derived from this approach.},
}
@article {pmid36949153,
year = {2023},
author = {Wang, Q and Wei, S and Silva, AF and Madsen, JS},
title = {Cooperative antibiotic resistance facilitates horizontal gene transfer.},
journal = {The ISME journal},
volume = {17},
number = {6},
pages = {846-854},
pmid = {36949153},
issn = {1751-7370},
support = {794315/MCCC_/Marie Curie/United Kingdom ; },
mesh = {*Gene Transfer, Horizontal/drug effects/genetics ; *Drug Resistance, Microbial/drug effects/genetics ; Plasmids/drug effects/genetics ; beta-Lactamases/genetics/metabolism ; Genotype ; Conjugation, Genetic ; Chromosomes, Bacterial/genetics ; beta-Lactams/pharmacology ; Anti-Bacterial Agents/pharmacology ; *Bacteria/cytology/drug effects/genetics ; },
abstract = {The rise of β-lactam resistance among pathogenic bacteria, due to the horizontal transfer of plasmid-encoded β-lactamases, is a current global health crisis. Importantly, β-lactam hydrolyzation by β-lactamases, not only protects the producing cells but also sensitive neighboring cells cooperatively. Yet, how such cooperative traits affect plasmid transmission and maintenance is currently poorly understood. Here we experimentally show that KPC-2 β-lactamase expression and extracellular activity were higher when encoded on plasmids compared with the chromosome, resulting in the elevated rescue of sensitive non-producers. This facilitated efficient plasmid transfer to the rescued non-producers and expanded the potential plasmid recipient pool and the probability of plasmid transfer to new genotypes. Social conversion of non-producers by conjugation was efficient yet not absolute. Non-cooperative plasmids, not encoding KPC-2, were moderately more competitive than cooperative plasmids when β-lactam antibiotics were absent. However, in the presence of a β-lactam antibiotic, strains with non-cooperative plasmids were efficiently outcompeted. Moreover, plasmid-free non-producers were more competitive than non-producers imposed with the metabolic burden of a plasmid. Our results suggest that cooperative antibiotic resistance especially promotes the fitness of replicons that transfer horizontally such as conjugative plasmids.},
}
@article {pmid36949027,
year = {2023},
author = {Tanaka, E and Wajima, T and Nakaminami, H and Uchiya, KI},
title = {Contribution of amino acid substitutions in ParE to quinolone resistance in Haemophilus haemolyticus revealed through a horizontal transfer assay using Haemophilus influenzae.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {78},
number = {5},
pages = {1225-1230},
doi = {10.1093/jac/dkad074},
pmid = {36949027},
issn = {1460-2091},
mesh = {Amino Acid Substitution ; Levofloxacin ; DNA Topoisomerase IV/genetics ; Anti-Bacterial Agents/pharmacology ; Haemophilus influenzae ; Microbial Sensitivity Tests ; Humans ; Drug Resistance, Bacterial/genetics ; Haemophilus ; Child ; DNA Gyrase/genetics ; Agar ; *Quinolones/pharmacology ; },
abstract = {BACKGROUND: In 2019, a high-level quinolone-resistant Haemophilus haemolyticus strain (levofloxacin MIC = 16 mg/L) was isolated from a paediatric patient. In this study, we aimed to determine whether the quinolone resistance of H. haemolyticus could be transferred to Haemophilus influenzae and to identify the mechanism underlying the high-level quinolone resistance of H. haemolyticus.<br><br>METHODS: A horizontal gene transfer assay to H. influenzae was performed using genomic DNA or PCR-amplified quinolone-targeting genes from the high-level quinolone-resistant H. haemolyticus 2019-19 strain. The amino acids responsible for conferring quinolone resistance were identified through site-directed mutagenesis.<br><br>RESULTS: By adding the genomic DNA of H. haemolyticus 2019-19, resistant colonies were obtained on agar plates containing quinolones. Notably, H. influenzae grown on levofloxacin agar showed the same level of resistance as H. haemolyticus. Sequencing analysis showed that gyrA, parC and parE of H. influenzae were replaced by those of H. haemolyticus, suggesting that horizontal transfer occurred between the two strains. When the quinolone-targeting gene fragments were added sequentially, the addition of parE, as well as gyrA and parC, contributed to high-level resistance. In particular, amino acid substitutions at both the 439th and 502nd residues of ParE were associated with high-level resistance.<br><br>CONCLUSIONS: These findings indicate that quinolone resistance can be transferred between species and that amino acid substitutions at the 439th and 502nd residues of ParE, in addition to amino acid substitutions in both GyrA and ParC, contribute to high-level quinolone resistance.},
}
@article {pmid36948313,
year = {2023},
author = {Fenibo, EO and Selvarajan, R and Abia, ALK and Matambo, T},
title = {Medium-chain alkane biodegradation and its link to some unifying attributes of alkB genes diversity.},
journal = {The Science of the total environment},
volume = {877},
number = {},
pages = {162951},
doi = {10.1016/j.scitotenv.2023.162951},
pmid = {36948313},
issn = {1879-1026},
mesh = {Animals ; Humans ; *Alkanes/metabolism ; Biodegradation, Environmental ; Ecosystem ; Hydrocarbons/metabolism ; Iron ; Phylogeny ; *Pseudomonas putida/metabolism ; Genes, Bacterial ; },
abstract = {Hydrocarbon footprints in the environment, via biosynthesis, natural seepage, anthropogenic activities and accidents, affect the ecosystem and induce a shift in the healthy biogeochemical equilibrium that drives needed ecological services. In addition, these imbalances cause human diseases and reduce animal and microorganism diversity. Microbial bioremediation, which capitalizes on functional genes, is a sustainable mitigation option for cleaning hydrocarbon-impacted environments. This review focuses on the bacterial alkB functional gene, which codes for a non-heme di‑iron monooxygenase (AlkB) with a di‑iron active site that catalyzes C8-C16 medium-chain alkane metabolism. These enzymes are ubiquitous and share common attributes such as being controlled by global transcriptional regulators, being a component of most super hydrocarbon degraders, and their distributions linked to horizontal gene transfer (HGT) events. The phylogenetic approach used in the HGT detection suggests that AlkB tree topology clusters bacteria functionally and that a preferential gradient dictates gene distribution. The alkB gene also acts as a biomarker for bioremediation, although it is found in pristine environments and absent in some hydrocarbon degraders. For instance, a quantitative molecular method has failed to link alkB copy number to contamination concentration levels. This limitation may be due to AlkB homologues, which have other functions besides n-alkane assimilation. Thus, this review, which focuses on Pseudomonas putida GPo1 alkB, shows that AlkB proteins are diverse but have some unifying trends around hydrocarbon-degrading bacteria; it is erroneous to rely on alkB detection alone as a monitoring parameter for hydrocarbon degradation, alkB gene distribution are preferentially distributed among bacteria, and the plausible explanation for AlkB affiliation to broad-spectrum metabolism of hydrocarbons in super-degraders hitherto reported. Overall, this review provides a broad perspective of the ecology of alkB-carrying bacteria and their directed biodegradation pathways.},
}
@article {pmid36946779,
year = {2023},
author = {Johnston, EL and Zavan, L and Bitto, NJ and Petrovski, S and Hill, AF and Kaparakis-Liaskos, M},
title = {Planktonic and Biofilm-Derived Pseudomonas aeruginosa Outer Membrane Vesicles Facilitate Horizontal Gene Transfer of Plasmid DNA.},
journal = {Microbiology spectrum},
volume = {11},
number = {2},
pages = {e0517922},
pmid = {36946779},
issn = {2165-0497},
abstract = {Outer membrane vesicles (OMVs) produced by Gram-negative bacteria package various cargo, including DNA that can be transferred to other bacteria or to host cells. OMV-associated DNA has been implicated in mediating horizontal gene transfer (HGT) between bacteria, which includes the dissemination of antibiotic resistance genes within and between bacterial species. Despite the known ability of OMVs to mediate HGT, the mechanisms of DNA packaging into OMVs remain poorly characterized, as does the effect of bacterial growth conditions on the DNA cargo composition of OMVs and their subsequent abilities to mediate HGT. In this study, we examined the DNA content of OMVs produced by the opportunistic pathogen Pseudomonas aeruginosa grown in either planktonic or biofilm conditions. Analysis of planktonic growth-derived OMVs revealed their ability to package and protect plasmid DNA from DNase degradation and to transfer plasmid-encoded antibiotic resistance genes to recipient, antibiotic-sensitive P. aeruginosa bacteria at a greater efficiency than transformation with plasmid alone. Comparisons of planktonic and biofilm-derived P. aeruginosa OMVs demonstrated that biofilm-derived OMVs were smaller but were associated with more plasmid DNA than planktonic-derived OMVs. Additionally, biofilm-derived P. aeruginosa OMVs were more efficient in the transformation of competent P. aeruginosa bacteria, compared to transformations with an equivalent number of planktonic-derived OMVs. The findings of this study highlight the importance of bacterial growth conditions for the packaging of DNA within P. aeruginosa OMVs and their ability to facilitate HGT, thus contributing to the spread of antibiotic resistance genes between P. aeruginosa bacteria. IMPORTANCE Bacterial membrane vesicles (BMVs) mediate interbacterial communication, and their ability to package DNA specifically contributes to biofilm formation, antibiotic resistance, and HGT between bacteria. However, the ability of P. aeruginosa OMVs to mediate HGT has not yet been demonstrated. Here, we reveal that P. aeruginosa planktonic and biofilm-derived OMVs can deliver plasmid-encoded antibiotic resistance to recipient P. aeruginosa. Additionally, we demonstrated that P. aeruginosa biofilm-derived OMVs were associated with more plasmid DNA compared to planktonic-derived OMVs and were more efficient in the transfer of plasmid DNA to recipient bacteria. Overall, this demonstrated the ability of P. aeruginosa OMVs to facilitate the dissemination of antibiotic resistance genes, thereby enabling the survival of susceptible bacteria during antibiotic treatment. Investigating the roles of biofilm-derived BMVs may contribute to furthering our understanding of the role of BMVs in HGT and the spread of antibiotic resistance in the environment.},
}
@article {pmid36945052,
year = {2023},
author = {Wang, Y and Zhang, Y and Hu, Y and Liu, L and Liu, SJ and Zhang, T},
title = {Genome-centric metagenomics reveals the host-driven dynamics and ecological role of CPR bacteria in an activated sludge system.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {56},
pmid = {36945052},
issn = {2049-2618},
mesh = {Humans ; *Sewage/microbiology ; *Bacteria/genetics/metabolism ; Metagenomics ; Metagenome/genetics ; Metabolic Networks and Pathways ; Phylogeny ; },
abstract = {BACKGROUND: Candidate phyla radiation (CPR) constitutes highly diverse bacteria with small cell sizes and are likely obligate intracellular symbionts. Given their distribution and complex associations with bacterial hosts, genetic and biological features of CPR bacteria in low-nutrient environments have received increasing attention. However, CPR bacteria in wastewater treatment systems remain poorly understood. We utilized genome-centric metagenomics to answer how CPR communities shift over 11 years and what kind of ecological roles they act in an activated sludge system.<br><br>RESULTS: We found that approximately 9% (135) of the 1,526 non-redundant bacterial and archaeal metagenome-assembled genomes were affiliated with CPR. CPR bacteria were consistently abundant with a relative abundance of up to 7.5% in the studied activated sludge system. The observed striking fluctuations in CPR community compositions and the limited metabolic and biosynthetic capabilities in CPR bacteria collectively revealed the nature that CPR dynamics may be directly determined by the available hosts. Similarity-based network analysis further confirmed the broad bacterial hosts of CPR lineages. The proteome contents of activated sludge-associated CPR had a higher similarity to those of environmental-associated CPR than to those of human-associated ones. Comparative genomic analysis observed significant enrichment of genes for oxygen stress resistance in activated sludge-associated CPR bacteria. Furthermore, genes for carbon cycling and horizontal gene transfer were extensively identified in activated sludge-associated CPR genomes.<br><br>CONCLUSIONS: These findings highlight the presence of specific host interactions among CPR lineages in activated sludge systems. Despite the lack of key metabolic pathways, these small, yet abundant bacteria may have significant involvements in biogeochemical cycling and bacterial evolution in activated sludge systems. Video Abstract.},
}
@article {pmid36944262,
year = {2023},
author = {Milner, DS and Galindo, LJ and Irwin, NAT and Richards, TA},
title = {Transporter Proteins as Ecological Assets and Features of Microbial Eukaryotic Pangenomes.},
journal = {Annual review of microbiology},
volume = {77},
number = {},
pages = {45-66},
doi = {10.1146/annurev-micro-032421-115538},
pmid = {36944262},
issn = {1545-3251},
mesh = {*Eukaryota/genetics ; *Eukaryotic Cells ; Membrane Transport Proteins ; Gene Duplication ; Phenotype ; },
abstract = {Here we review two connected themes in evolutionary microbiology: (a) the nature of gene repertoire variation within species groups (pangenomes) and (b) the concept of metabolite transporters as accessory proteins capable of providing niche-defining "bolt-on" phenotypes. We discuss the need for improved sampling and understanding of pangenome variation in eukaryotic microbes. We then review the factors that shape the repertoire of accessory genes within pangenomes. As part of this discussion, we outline how gene duplication is a key factor in both eukaryotic pangenome variation and transporter gene family evolution. We go on to outline how, through functional characterization of transporter-encoding genes, in combination with analyses of how transporter genes are gained and lost from accessory genomes, we can reveal much about the niche range, the ecology, and the evolution of virulence of microbes. We advocate for the coordinated systematic study of eukaryotic pangenomes through genome sequencing and the functional analysis of genes found within the accessory gene repertoire.},
}
@article {pmid36943061,
year = {2023},
author = {Nielsen, FD and Skov, MN and Sydenham, TV and Justesen, US},
title = {Development and Clinical Application of a Multilocus Sequence Typing Scheme for Bacteroides fragilis Based on Whole-Genome Sequencing Data.},
journal = {Microbiology spectrum},
volume = {11},
number = {2},
pages = {e0511122},
pmid = {36943061},
issn = {2165-0497},
abstract = {Bacteroides fragilis is among the most abundant and pathogenic bacterial species in the gut microbiota and is associated with diarrheal disease in children, inflammatory bowel disease, and the development of colorectal cancer. It is increasingly resistant to potent antimicrobial agents such as carbapenems and metronidazole, making it among the most resistant anaerobic bacteria. These factors combined call for increased monitoring of B. fragilis and its population structure on a worldwide scale. Here, we present a possible solution through the development of a multilocus sequence typing scheme (MLST). The scheme is based on seven core gene fragments: groL (hsp60), rpoB, recA, dnaJ, rprX, prfA, and fusA. These gene fragments possess high discriminatory power while retaining concordance with whole core genome-based phylogenetic analysis. The scheme proved capable of differentiating B. fragilis isolates at the strain level. It offers a standardized method for molecular typing and can be applied to isolates from various sampling backgrounds, such as patient isolates, environmental samples, and strains obtained from food and animal sources. In total, 567 B. fragilis genomes were sequence typed and their isolate data collected. The MLST scheme clearly divided the B. fragilis population into two divisions based on the presence of the cfiA and cepA resistance genes. However, no other specific subpopulations within the analyzed genomes were found to be associated with any specific diseases or geographical location. With this MLST scheme, we hope to provide a powerful tool for the study and monitoring of B. fragilis on an international scale. IMPORTANCE Here, we present the first MLST scheme for Bacteroides fragilis, one of the most abundant pathogenic bacteria in the human gut microbiota. The scheme enables standard classification and monitoring of B. fragilis on a worldwide scale and groups the majority of current isolate data in one place. A more unified approach to the collection and analysis of B. fragilis data could provide crucial insights into how the pathogen operates and develops as a species. Close monitoring of B. fragilis is especially relevant, as it is increasingly resistant to potent antimicrobial agents and engages in horizontal gene transfer with other bacteria. Hopefully, this approach will guide new discoveries into how B. fragilis evolves and interacts with its human host. Additionally, the scheme could potentially be applied to other species of the genus Bacteroides.},
}
@article {pmid36943058,
year = {2023},
author = {Rao, YZ and Li, YX and Li, ZW and Qu, YN and Qi, YL and Jiao, JY and Shu, WS and Hua, ZS and Li, WJ},
title = {Metagenomic Discovery of "Candidatus Parvarchaeales"-Related Lineages Sheds Light on Adaptation and Diversification from Neutral-Thermal to Acidic-Mesothermal Environments.},
journal = {mSystems},
volume = {8},
number = {2},
pages = {e0125222},
pmid = {36943058},
issn = {2379-5077},
mesh = {*Metagenome/genetics ; Phylogeny ; *Biological Evolution ; Adaptation, Physiological/genetics ; Archaea/genetics ; Acids/metabolism ; Amino Acids/genetics ; },
abstract = {"Candidatus Parvarchaeales" microbes, representing a DPANN archaeal group with limited metabolic potential and reliance on hosts for their growth, were initially found in acid mine drainage (AMD). Due to the lack of representatives, however, their ecological roles and adaptation to extreme habitats such as AMD as well as how they diverge across the lineage remain largely unexplored. By applying genome-resolved metagenomics, 28 Parvarchaeales-associated metagenome-assembled genomes (MAGs) representing two orders and five genera were recovered. Among them, we identified three new genera and proposed the names "Candidatus Jingweiarchaeum," "Candidatus Haiyanarchaeum," and "Candidatus Rehaiarchaeum," with the former two belonging to a new order, "Candidatus Jingweiarchaeales." Further analyses of the metabolic potentials revealed substantial niche differentiation between Jingweiarchaeales and Parvarchaeales. Jingweiarchaeales may rely on fermentation, salvage pathways, partial glycolysis, and the pentose phosphate pathway (PPP) for energy conservation reservation, while the metabolic potentials of Parvarchaeales might be more versatile. Comparative genomic analyses suggested that Jingweiarchaeales favor habitats with higher temperatures and that Parvarchaeales are better adapted to acidic environments. We further revealed that the thermal adaptation of these lineages, especially Haiyanarchaeum, might rely on genomic features such as the usage of specific amino acids, genome streamlining, and hyperthermophile featured genes such as rgy. Notably, the adaptation of Parvarchaeales to acidic environments was possibly driven by horizontal gene transfer (HGT). The reconstruction of ancestral states demonstrated that both may have originated from thermal and neutral environments and later spread to mesothermal and acidic environments. These evolutionary processes may also be accompanied by adaptation to oxygen-rich environments via HGT. IMPORTANCE "Candidatus Parvarchaeales" microbes may represent a lineage uniquely distributed in extreme environments such as AMD and hot springs. However, little is known about the strategies and processes of how they adapted to these extreme environments. By the discovery of potential new order-level lineages, "Ca. Jingweiarchaeales," and in-depth comparative genomic analysis, we unveiled the functional differentiation of these lineages. Furthermore, we show that the adaptation of these lineages to high-temperature and acidic environments was driven by different strategies, with the former relying more on genomic characteristics such as genome streamlining and amino acid compositions and the latter relying more on the acquisition of genes associated with acid tolerance. Finally, by the reconstruction of the ancestral states of the optimal growth temperature (OGT) and isoelectric point (pI), we showed the potential evolutionary process of Parvarchaeales-related lineages with regard to the shift from the high-temperature environment of their common ancestors to low-temperature (potentially acidic) environments.},
}
@article {pmid36941487,
year = {2023},
author = {Bhakta, S and Bhattacharya, A},
title = {In silico evolutionary and structural analysis of cAMP response proteins (CARPs) from Leishmania major.},
journal = {Archives of microbiology},
volume = {205},
number = {4},
pages = {125},
pmid = {36941487},
issn = {1432-072X},
support = {AU/REG/2019-20/12/008//Adamas University/ ; SRG/2020/000702//Science and Engineering Research Board/ ; },
mesh = {Animals ; *Leishmania major/genetics/metabolism ; Cyclic AMP/metabolism ; Phylogeny ; Signal Transduction/physiology ; *Carps ; },
abstract = {With unidentified chemical triggers and novel-effectors, cAMP signaling is broadly noncanonical in kinetoplastida parasites. Though novel protein kinase A regulatory subunits (PKAR) have been identified earlier, cAMP Response Proteins (CARPs) have been identified as a unique and definite cAMP effector of trypanosomatids. CARP1-CARP4 emerged as critical regulatory components of cAMP signaling pathway in Trypanosoma with evidences that CARP3 can directly interact with a flagellar adenylate cyclase (AC). CARP-mediated regulations, identified so far, reflects the mechanistic diversity of cAMP signaling. Albeit the function of the orthologous is not yet delineated, in kinetoplastids like Leishmania, presence of CARP1, 2 and 4 orthologues suggests existence of conserved effector mechanisms. Targeting CARP orthologues in Leishmania, a comprehensive evolutionary analysis of CARPs have been aimed in this study which revealed phylogenetic relationship, codon adaptation and structural heterogeneity among the orthologues, warranting functional analysis in future to explore their involvement in infectivity.},
}
@article {pmid36941328,
year = {2023},
author = {Zumkeller, S and Polsakiewicz, M and Knoop, V},
title = {Rickettsial DNA and a trans-splicing rRNA group I intron in the unorthodox mitogenome of the fern Haplopteris ensiformis.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {296},
pmid = {36941328},
issn = {2399-3642},
mesh = {Introns/genetics ; *Ferns/genetics ; *Genome, Mitochondrial ; Trans-Splicing ; Plants/genetics ; DNA, Mitochondrial/genetics ; },
abstract = {Plant mitochondrial genomes can be complex owing to highly recombinant structures, lack of gene syntenies, heavy RNA editing and invasion of chloroplast, nuclear or even foreign DNA by horizontal gene transfer (HGT). Leptosporangiate ferns remained the last major plant clade without an assembled mitogenome, likely owing to a demanding combination of the above. We here present both organelle genomes now for Haplopteris ensiformis. More than 1,400 events of C-to-U RNA editing and over 500 events of reverse U-to-C edits affect its organelle transcriptomes. The Haplopteris mtDNA is gene-rich, lacking only the ccm gene suite present in ancestral land plant mitogenomes, but is highly unorthodox, indicating extraordinary recombinogenic activity. Although eleven group II introns known in disrupted trans-splicing states in seed plants exist in conventional cis-arrangements, a particularly complex structure is found for the mitochondrial rrnL gene, which is split into two parts needing reassembly on RNA level by a trans-splicing group I intron. Aside from ca. 80 chloroplast DNA inserts that complicated the mitogenome assembly, the Haplopteris mtDNA features as an idiosyncrasy 30 variably degenerated protein coding regions from Rickettiales bacteria indicative of heavy bacterial HGT on top of tRNA genes of chlamydial origin.},
}
@article {pmid36940043,
year = {2023},
author = {Chaudhary, S and Kishen, S and Singh, M and Jassal, S and Pathania, R and Bisht, K and Sareen, D},
title = {Phylogeny-guided genome mining of roseocin family lantibiotics to generate improved variants of roseocin.},
journal = {AMB Express},
volume = {13},
number = {1},
pages = {34},
pmid = {36940043},
issn = {2191-0855},
support = {09/135(0773)/2017-EMR-I//Council for Scientific and Industrial Research, New Delhi/ ; CRG/2018/004218//DST-SERB/ ; },
abstract = {Roseocin, the two-peptide lantibiotic from Streptomyces roseosporus, carries extensive intramolecular (methyl)lanthionine bridging in the peptides and exhibits synergistic antibacterial activity against clinically relevant Gram-positive pathogens. Both peptides have a conserved leader but a diverse core region. The biosynthesis of roseocin involves post-translational modification of the two precursor peptides by a single promiscuous lanthipeptide synthetase, RosM, to install an indispensable disulfide bond in the Rosα core along with four and six thioether rings in Rosα and Rosβ cores, respectively. RosM homologs in the phylum actinobacteria were identified here to reveal twelve other members of the roseocin family which diverged into three types of biosynthetic gene clusters (BGCs). Further, the evolutionary rate among the BGC variants and analysis of variability within the core peptide versus leader peptide revealed a phylum-dependent lanthipeptide evolution. Analysis of horizontal gene transfer revealed its role in the generation of core peptide diversity. The naturally occurring diverse congeners of roseocin peptides identified from the mined novel BGCs were carefully aligned to identify the conserved sites and the substitutions in the core peptide region. These selected sites in the Rosα peptide were mutated for permitted substitutions, expressed heterologously in E. coli, and post-translationally modified by RosM in vivo. Despite a limited number of generated variants, two variants, RosαL8F and RosαL8W exhibited significantly improved inhibitory activity in a species-dependent manner compared to the wild-type roseocin. Our study proves that a natural repository of evolved variants of roseocin is present in nature and the key variations can be used to generate improved variants.},
}
@article {pmid36937147,
year = {2023},
author = {Cao, H and Liang, S and Zhang, C and Liu, B and Fei, Y},
title = {Molecular Profiling of a Multi-Strain Hypervirulent Klebsiella pneumoniae Infection Within a Single Patient.},
journal = {Infection and drug resistance},
volume = {16},
number = {},
pages = {1367-1380},
pmid = {36937147},
issn = {1178-6973},
abstract = {BACKGROUND: The rising prevalence of infections caused by carbapenem-resistant and hypervirulent Klebsiella pneumoniae (CR-hvKP) has outpaced our understanding of their evolutionary diversity. By straining the antimicrobial options and constant horizontal gene transfer of various pathogenic elements, CR-hvKP poses a global health threat.<br><br>METHODS: Six KP isolates (KP1~KP6) from urine, sputum and groin infection secretion of a single patient were characterized phenotypically and genotypically. The antimicrobial susceptibility, carbapenemase production, hypermucoviscosity, serum resistance, virulence factors, MLST and serotypes were profiled. Genomic variations were identified by whole-genome sequencing and the phylogenetic differentiation was analyzed by Enterobacterial repetitive intergenic consensus (ERIC)-PCR.<br><br>RESULTS: All KP strains were multi-drug resistant. Four of them (KP1, KP3, KP5 and KP6) belonged to ST11-K64, with high genetic closeness (relatedness coefficient above 0.96), sharing most resistance and virulence genes. Compared with KP1, the later isolates KP3, KP5 and KP6 acquired bla KPC-1 and lost bla SHV-182 genes. KP2 and KP4 had the same clonal origin of ST35-K16 (relatedness coefficient 0.98), containing almost identical genes for resistance and virulence. They were non-mucoid and carried bla NDM-5 gene.<br><br>CONCLUSION: A co-infection with two types of CR-hvKP affiliated with different clades within a single patient amplified the treatment difficulties. In addition to source control and epidemiological surveillance, investigation of the in-host interactions between CR-hvKP variants may provide valuable treatment solutions.},
}
@article {pmid36933870,
year = {2023},
author = {Yang, Q and Zhu, Y and Schwarz, S and Wang, L and Liu, W and Yang, W and Liu, S and Zhang, W},
title = {Integrative and conjugative elements in streptococci can act as vectors for plasmids and translocatable units integrated via IS1216E.},
journal = {International journal of antimicrobial agents},
volume = {61},
number = {5},
pages = {106793},
doi = {10.1016/j.ijantimicag.2023.106793},
pmid = {36933870},
issn = {1872-7913},
mesh = {*Conjugation, Genetic ; Plasmids/genetics ; *Streptococcus/genetics ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; },
abstract = {Mobile genetic elements (MGEs), such as integrative and conjugative elements (ICEs), plasmids and translocatable units (TUs), are important drivers for the spread of antibiotic resistance. Although ICEs have been reported to support the spread of plasmids among different bacteria, their role in mobilizing resistance plasmids and TUs has not yet been fully explored. In this study, a novel TU bearing optrA, a novel non-conjugative plasmid p5303-cfrD carrying cfr(D) and a new member of the ICESa2603 family, ICESg5301 were identified in streptococci. Polymerase chain reaction (PCR) assays revealed that three different types of cointegrates can be formed by IS1216E-mediated cointegration between the three different MGEs, including ICESg5301::p5303-cfrD::TU, ICESg5301::p5303-cfrD, and ICESg5301::TU. Conjugation assays showed that ICEs carrying p5303-cfrD and/or TU successfully transferred into recipient strains, thereby confirming that ICEs can serve as vectors for other non-conjugative MGEs, such as TUs and p5303-cfrD. As neither the TU nor plasmid p5303-cfrD can spread on their own between different bacteria, their integration into an ICE via IS1216E-mediated cointegrate formation not only increases the plasticity of ICEs, but also furthers the dissemination of plasmids and TUs carrying oxazolidinone resistance genes.},
}
@article {pmid36932546,
year = {2023},
author = {Weaver, BP and Haselwandter, CA and Boedicker, JQ},
title = {Stochastic effects in bacterial communication mediated by extracellular vesicles.},
journal = {Physical review. E},
volume = {107},
number = {2-1},
pages = {024409},
doi = {10.1103/PhysRevE.107.024409},
pmid = {36932546},
issn = {2470-0053},
mesh = {*Bacteria ; Quorum Sensing/physiology ; Communication ; *Extracellular Vesicles ; },
abstract = {Quorum sensing (QS) allows bacterial cells to sense changes in local cell density and, hence, to regulate multicellular processes, including biofilm formation, regulation of virulence, and horizontal gene transfer. While, traditionally, QS was thought to involve the exchange of extracellular signal molecules free in solution, recent experiments have shown that for some bacterial systems a substantial fraction of signal molecules are packaged and delivered in extracellular vesicles. How the packaging of signal molecules in extracellular vesicles influences the ability of cells to communicate and coordinate multicellular behaviors remains largely unknown. We present here a stochastic reaction-diffusion model of QS that accounts for the exchange of both freely diffusing and vesicle-associated signal molecules. We find that the delivery of signal molecules via extracellular vesicles amplifies local fluctuations in the signal concentration, which can strongly affect the dynamics and spatial range of bacterial communication. For systems with multiple bacterial colonies, extracellular vesicles provide an alternate pathway for signal transport between colonies, and may be crucial for long-distance signal exchange in environments with strong degradation of free signal molecules.},
}
@article {pmid36931217,
year = {2023},
author = {Zhao, Q and Hu, Z and Zhang, J and Wang, Y},
title = {Determination of the fate of antibiotic resistance genes and the response mechanism of plants during enhanced antibiotic degradation in a bioelectrochemical-constructed wetland system.},
journal = {Journal of hazardous materials},
volume = {451},
number = {},
pages = {131207},
doi = {10.1016/j.jhazmat.2023.131207},
pmid = {36931217},
issn = {1873-3336},
mesh = {*Anti-Bacterial Agents/pharmacology/analysis ; *Wastewater ; Waste Disposal, Fluid ; Wetlands ; Genes, Bacterial ; Chloramphenicol/analysis ; Drug Resistance, Microbial/genetics ; },
abstract = {Chloramphenicol (CAP) has a high concentration and detection frequency in aquatic environments due to its insufficient degradation in traditional biological wastewater treatment processes. In this study, bioelectrochemical assistant-constructed wetland systems (BES-CWs) were developed as advanced processes for efficient CAP removal, in which the degradation and transfer of CAP and the fate of antibiotic resistance genes (ARGs) were evaluated. The CAP removal efficiency could reach as high as 90.2%, while the removed CAP can be partially adsorbed and bioaccumulated in plants, significantly affecting plant growth. The vertical gene transfer and horizontal gene transfer increased the abundance of ARGs under high voltage and CAP concentrations. Microbial community analysis showed that CAP pressure and electrical stimulation selected the functional bacteria to increase CAP removal and antibiotic resistance. CAP degradation species carrying ARGs could increase their opposition to the biotoxicity of CAP and maintain system performance. In addition, ARGs are transferred into the plant and upward, which can potentially enter the food chain. This study provides an essential reference for enhancing antibiotic degradation and offers fundamental support for the underlying mechanism and ARG proliferation during antibiotic biodegradation.},
}
@article {pmid36931215,
year = {2023},
author = {Lin, D and Zhu, L and Yao, Y and Zhu, L and Wang, M},
title = {The ecological and molecular mechanism underlying effective reduction of antibiotic resistance genes pollution in soil by fermentation broth from fruit and vegetable waste.},
journal = {Journal of hazardous materials},
volume = {451},
number = {},
pages = {131201},
doi = {10.1016/j.jhazmat.2023.131201},
pmid = {36931215},
issn = {1873-3336},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Vegetables ; Soil ; Fermentation ; Fruit ; Genes, Bacterial ; Tetracycline/pharmacology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Soil Microbiology ; },
abstract = {The strategies to relieve antibiotic resistance genes (ARGs) pollution are urgently needed. Fermentation broth from fruit and vegetable waste (FFVW), an agricultural amendment, exhibits a remarkable capacity to reduce ARG pollution; however, the underlying mechanism of this effect remains unclear. We performed microcosm experiments to reappear the phenomenon of FFVW-driven reduction in ARGs. Moderate-level FFVW reduced gene resistance to sulfonamide (41.2 %), macrolide-lincosamide-streptogramin (MLS) (47.2 %), chloramphenicol (63.2 %), and tetracycline (61.4 %). Binning and network analyses revealed that Actinobacteria comprise the primary hosts of ARGs in arable soil, and FFVW substantially inhibited the growth and metabolic activity of these organisms. Moreover, tetracycline and MLS production was partially/completely inhibited by FFVW, further reducing the transfer frequency by 52.9-86.1 % and 46.6-66.6 % in the intragenic and intergenic mating systems, respectively. Furthermore, the expression of genes related to conjugation pairing and plasmid transfer was downregulated. Thus, FFVW effectively reduces ARG pollution by inhibiting Actinobacteria proliferation, thereby reducing selective pressure and restricting horizontal gene transfer. Our findings highlight the important underlying mechanisms of FFVW involved in ARG reduction, supporting its use in arable soil.},
}
@article {pmid36928121,
year = {2023},
author = {Gandini, CL and Garcia, LE and Abbona, CC and Ceriotti, LF and Kushnir, S and Geelen, D and Sanchez-Puerta, MV},
title = {Break-induced replication is the primary recombination pathway in plant somatic hybrid mitochondria: a model for mitochondrial horizontal gene transfer.},
journal = {Journal of experimental botany},
volume = {74},
number = {12},
pages = {3503-3517},
doi = {10.1093/jxb/erad104},
pmid = {36928121},
issn = {1460-2431},
mesh = {*Gene Transfer, Horizontal ; *Mitochondria/genetics ; Nicotiana/genetics ; DNA Repair ; Homologous Recombination ; },
abstract = {Somatic hybrids between distant species offer a remarkable model to study genomic recombination events after mitochondrial fusion. Recently, we described highly chimeric mitogenomes in two somatic hybrids between the Solanaceae Nicotiana tabacum and Hyoscyamus niger resulting from interparental homologous recombination. To better examine the recombination map in somatic hybrid mitochondria, we developed a more sensitive bioinformatic strategy to detect recombination activity based on high-throughput sequencing without assembling the hybrid mitogenome. We generated a new intergeneric somatic hybrid between N. tabacum and Physochlaina orientalis, and re-analyzed the somatic hybrids that we previously generated. We inferred 213 homologous recombination events across repeats of 2.1 kb on average. Most of them (~80%) were asymmetrical, consistent with the break-induced replication pathway. Only rare (2.74%) non-homologous events were detected. Interestingly, independent events frequently occurred in the same regions within and across somatic hybrids, suggesting the existence of recombination hotspots in plant mitogenomes. Break-induced replication is the main pathway of interparental recombination in somatic hybrid mitochondria. Findings of this study are relevant to mitogenome editing assays and to mechanistic aspects of DNA integration following mitochondrial DNA horizontal transfer events.},
}
@article {pmid36927397,
year = {2024},
author = {Teklemariam, AD and Al Hindi, R and Qadri, I and Alharbi, MG and Hashem, AM and Alrefaei, AA and Basamad, NA and Haque, S and Alamri, T and Harakeh, S},
title = {Phage cocktails - an emerging approach for the control of bacterial infection with major emphasis on foodborne pathogens.},
journal = {Biotechnology &amp; genetic engineering reviews},
volume = {40},
number = {1},
pages = {36-64},
doi = {10.1080/02648725.2023.2178870},
pmid = {36927397},
issn = {2046-5556},
mesh = {*Phage Therapy/methods ; *Bacteriophages ; Humans ; *Foodborne Diseases/therapy/microbiology/prevention &amp; control ; *Bacterial Infections/therapy ; Bacteria/virology ; },
abstract = {Phage therapy has recently attracted a great deal of attention to counteract the rapid emergence of antibiotic-resistant bacteria. In comparison to monophage therapy, phage cocktails are typically used to treat individual and/or multi-bacterial infections since the bacterial agents are unlikely to become resistant as a result of exposure to multiple phages simultaneously. The bacteriolytic effect of phage cocktails may produce efficient killing effect in comparison to individual phage. However, multiple use of phages (complex cocktails) may lead to undesirable side effects such as dysbiosis, horizontal gene transfer, phage resistance, cross resistance, and/or higher cost of production. Cocktail formulation, therefore, representa compromise between limiting the complexity of the cocktail and achieving substantial bacterial load reduction towards the targeted host organisms. Despite some constraints, the applications of monophage therapy have been well documented in the literature. However, phage cocktails-based approaches and their role for the control of pathogens have not been well investigated. In this review, we discuss the principle of phage cocktail formulations, their optimization strategies, major phage cocktail preparations, and their efficacy in inactivating various food borne bacterial pathogens.},
}
@article {pmid36927158,
year = {2023},
author = {Karnkowska, A and Yubuki, N and Maruyama, M and Yamaguchi, A and Kashiyama, Y and Suzaki, T and Keeling, PJ and Hampl, V and Leander, BS},
title = {Euglenozoan kleptoplasty illuminates the early evolution of photoendosymbiosis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {12},
pages = {e2220100120},
pmid = {36927158},
issn = {1091-6490},
mesh = {*Photosynthesis/genetics ; Plastids/genetics/metabolism ; Eukaryota/genetics ; *Chlorophyta/genetics/metabolism ; Transcriptome ; Phylogeny ; Symbiosis/genetics ; },
abstract = {Kleptoplasts (kP) are distinct among photosynthetic organelles in eukaryotes (i.e., plastids) because they are routinely sequestered from prey algal cells and function only temporarily in the new host cell. Therefore, the hosts of kleptoplasts benefit from photosynthesis without constitutive photoendosymbiosis. Here, we report that the euglenozoan Rapaza viridis has only kleptoplasts derived from a specific strain of green alga, Tetraselmis sp., but no canonical plastids like those found in its sister group, the Euglenophyceae. R. viridis showed a dynamic change in the accumulation of cytosolic polysaccharides in response to light-dark cycles, and [13]C isotopic labeling of ambient bicarbonate demonstrated that these polysaccharides originate in situ via photosynthesis; these data indicate that the kleptoplasts of R. viridis are functionally active. We also identified 276 sequences encoding putative plastid-targeting proteins and 35 sequences of presumed kleptoplast transporters in the transcriptome of R. viridis. These genes originated in a wide range of algae other than Tetraselmis sp., the source of the kleptoplasts, suggesting a long history of repeated horizontal gene transfer events from different algal prey cells. Many of the kleptoplast proteins, as well as the protein-targeting system, in R. viridis were shared with members of the Euglenophyceae, providing evidence that the early evolutionary stages in the green alga-derived secondary plastids of euglenophytes also involved kleptoplasty.},
}
@article {pmid36925471,
year = {2023},
author = {Cerbino, GN and Traglia, GM and Ayala Nuñez, T and Parmeciano Di Noto, G and Ramírez, MS and Centrón, D and Iriarte, A and Quiroga, C},
title = {Comparative genome analysis of the genus Shewanella unravels the association of key genetic traits with known and potential pathogenic lineages.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1124225},
pmid = {36925471},
issn = {1664-302X},
abstract = {Shewanella spp. are Gram-negative rods widely disseminated in aquatic niches that can also be found in human-associated environments. In recent years, reports of infections caused by these bacteria have increased significantly. Mobilome and resistome analysis of a few species showed that they are versatile; however, comprehensive comparative studies in the genus are lacking. Here, we analyzed the genetic traits of 144 genomes from Shewanella spp. isolates focusing on the mobilome, resistome, and virulome to establish their evolutionary relationship and detect unique features based on their genome content and habitat. Shewanella spp. showed a great diversity of mobile genetic elements (MGEs), most of them associated with monophyletic lineages of clinical isolates. Furthermore, 79/144 genomes encoded at least one antimicrobial resistant gene with their highest occurrence in clinical-related lineages. CRISPR-Cas systems, which confer immunity against MGEs, were found in 41 genomes being I-E and I-F the more frequent ones. Virulome analysis showed that all Shewanella spp. encoded different virulence genes (motility, quorum sensing, biofilm, adherence, etc.) that may confer adaptive advantages for survival against hosts. Our data revealed that key accessory genes are frequently found in two major clinical-related groups, which encompass the opportunistic pathogens Shewanella algae and Shewanella xiamenensis together with several other species. This work highlights the evolutionary nature of Shewanella spp. genomes, capable of acquiring different key genetic traits that contribute to their adaptation to different niches and facilitate the emergence of more resistant and virulent isolates that impact directly on human and animal health.},
}
@article {pmid36922599,
year = {2023},
author = {Nyerges, A and Vinke, S and Flynn, R and Owen, SV and Rand, EA and Budnik, B and Keen, E and Narasimhan, K and Marchand, JA and Baas-Thomas, M and Liu, M and Chen, K and Chiappino-Pepe, A and Hu, F and Baym, M and Church, GM},
title = {A swapped genetic code prevents viral infections and gene transfer.},
journal = {Nature},
volume = {615},
number = {7953},
pages = {720-727},
pmid = {36922599},
issn = {1476-4687},
support = {R35 GM133700/GM/NIGMS NIH HHS/United States ; },
mesh = {*Amino Acids/genetics/metabolism ; Codon/genetics ; Ecosystem ; *Escherichia coli/genetics/virology ; *Genetic Code/genetics ; Leucine/genetics/metabolism ; *Protein Biosynthesis/genetics ; RNA, Transfer/genetics/metabolism ; Serine/genetics ; *Virus Diseases/genetics/prevention &amp; control ; *Host Microbial Interactions/genetics ; Organisms, Genetically Modified/genetics ; Genome, Bacterial/genetics ; *Gene Transfer, Horizontal/genetics ; Viral Proteins/genetics/metabolism ; },
abstract = {Engineering the genetic code of an organism has been proposed to provide a firewall from natural ecosystems by preventing viral infections and gene transfer[1-6]. However, numerous viruses and mobile genetic elements encode parts of the translational apparatus[7-9], potentially rendering a genetic-code-based firewall ineffective. Here we show that such mobile transfer RNAs (tRNAs) enable gene transfer and allow viral replication in Escherichia coli despite the genome-wide removal of 3 of the 64 codons and the previously essential cognate tRNA and release factor genes. We then establish a genetic firewall by discovering viral tRNAs that provide exceptionally efficient codon reassignment allowing us to develop cells bearing an amino acid-swapped genetic code that reassigns two of the six serine codons to leucine during translation. This amino acid-swapped genetic code renders cells resistant to viral infections by mistranslating viral proteomes and prevents the escape of synthetic genetic information by engineered reliance on serine codons to produce leucine-requiring proteins. As these cells may have a selective advantage over wild organisms due to virus resistance, we also repurpose a third codon to biocontain this virus-resistant host through dependence on an amino acid not found in nature[10]. Our results may provide the basis for a general strategy to make any organism safely resistant to all natural viruses and prevent genetic information flow into and out of genetically modified organisms.},
}
@article {pmid36915058,
year = {2023},
author = {Zumkeller, S and Knoop, V},
title = {Categorizing 161 plant (streptophyte) mitochondrial group II introns into 29 families of related paralogues finds only limited links between intron mobility and intron-borne maturases.},
journal = {BMC ecology and evolution},
volume = {23},
number = {1},
pages = {5},
pmid = {36915058},
issn = {2730-7182},
mesh = {Introns/genetics ; *Evolution, Molecular ; *Mitochondria/genetics ; Plants/genetics ; Cell Nucleus ; },
abstract = {Group II introns are common in the two endosymbiotic organelle genomes of the plant lineage. Chloroplasts harbor 22 positionally conserved group II introns whereas their occurrence in land plant (embryophyte) mitogenomes is highly variable and specific for the seven major clades: liverworts, mosses, hornworts, lycophytes, ferns, gymnosperms and flowering plants. Each plant group features "signature selections" of ca. 20-30 paralogues from a superset of altogether 105 group II introns meantime identified in embryophyte mtDNAs, suggesting massive intron gains and losses along the backbone of plant phylogeny. We report on systematically categorizing plant mitochondrial group II introns into "families", comprising evidently related paralogues at different insertion sites, which may even be more similar than their respective orthologues in phylogenetically distant taxa. Including streptophyte (charophyte) algae extends our sampling to 161 and we sort 104 streptophyte mitochondrial group II introns into 25 core families of related paralogues evidently arising from retrotransposition events. Adding to discoveries of only recently created intron paralogues, hypermobile introns and twintrons, our survey led to further discoveries including previously overlooked "fossil" introns in spacer regions or e.g., in the rps8 pseudogene of lycophytes. Initially excluding intron-borne maturase sequences for family categorization, we added an independent analysis of maturase phylogenies and find a surprising incongruence between intron mobility and the presence of intron-borne maturases. Intriguingly, however, we find that several examples of nuclear splicing factors meantime characterized simultaneously facilitate splicing of independent paralogues now placed into the same intron families. Altogether this suggests that plant group II intron mobility, in contrast to their bacterial counterparts, is not intimately linked to intron-encoded maturases.},
}
@article {pmid36914349,
year = {2023},
author = {Wang, D and Fletcher, GC and Gagic, D and On, SLW and Palmer, JS and Flint, SH},
title = {Comparative genome identification of accessory genes associated with strong biofilm formation in Vibrio parahaemolyticus.},
journal = {Food research international (Ottawa, Ont.)},
volume = {166},
number = {},
pages = {112605},
doi = {10.1016/j.foodres.2023.112605},
pmid = {36914349},
issn = {1873-7145},
mesh = {*Vibrio parahaemolyticus/genetics ; Biofilms ; Genomics ; Operon ; Cellulose ; },
abstract = {Vibrio parahaemolyticus biofilms on the seafood processing plant surfaces are a potential source of seafood contamination and subsequent food poisoning. Strains differ in their ability to form biofilm, but little is known about the genetic characteristics responsible for biofilm development. In this study, pangenome and comparative genome analysis of V. parahaemolyticus strains reveals genetic attributes and gene repertoire that contribute to robust biofilm formation. The study identified 136 accessory genes that were exclusively present in strong biofilm forming strains and these were functionally assigned to the Gene Ontology (GO) pathways of cellulose biosynthesis, rhamnose metabolic and catabolic processes, UDP-glucose processes and O antigen biosynthesis (p < 0.05). Strategies of CRISPR-Cas defence and MSHA pilus-led attachment were implicated via Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation. Higher levels of horizontal gene transfer (HGT) were inferred to confer more putatively novel properties on biofilm-forming V. parahaemolyticus. Furthermore, cellulose biosynthesis, a neglected potential virulence factor, was identified as being acquired from within the order Vibrionales. The cellulose synthase operons in V. parahaemolyticus were examined for their prevalence (22/138, 15.94 %) and were found to consist of the genes bcsG, bcsE, bcsQ, bcsA, bcsB, bcsZ, bcsC. This study provides insights into robust biofilm formation of V. parahaemolyticus at the genomic level and facilitates: identification of key attributes for robust biofilm formation, elucidation of biofilm formation mechanisms and development of potential targets for novel control strategies of persistent V. parahaemolyticus.},
}
@article {pmid36913905,
year = {2023},
author = {Despotovic, M and de Nies, L and Busi, SB and Wilmes, P},
title = {Reservoirs of antimicrobial resistance in the context of One Health.},
journal = {Current opinion in microbiology},
volume = {73},
number = {},
pages = {102291},
pmid = {36913905},
issn = {1879-0364},
mesh = {Animals ; Humans ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; *One Health ; Bacteria/genetics ; Genes, Bacterial ; },
abstract = {The emergence and spread of antimicrobial resistance (AMR) and resistant bacteria, are a global public health challenge. Through horizontal gene transfer, potential pathogens can acquire antimicrobial resistance genes (ARGs) that can subsequently be spread between human, animal, and environmental reservoirs. To understand the dissemination of ARGs and linked microbial taxa, it is necessary to map the resistome within different microbial reservoirs. By integrating knowledge on ARGs in the different reservoirs, the One Health approach is crucial to our understanding of the complex mechanisms and epidemiology of AMR. Here, we highlight the latest insights into the emergence and spread of AMR from the One Health perspective, providing a baseline of understanding for future scientific investigations into this constantly growing global health threat.},
}
@article {pmid36912846,
year = {2023},
author = {Qi, Q and Ghaly, TM and Penesyan, A and Rajabal, V and Stacey, JA and Tetu, SG and Gillings, MR},
title = {Uncovering Bacterial Hosts of Class 1 Integrons in an Urban Coastal Aquatic Environment with a Single-Cell Fusion-Polymerase Chain Reaction Technology.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {12},
pages = {4870-4879},
doi = {10.1021/acs.est.2c09739},
pmid = {36912846},
issn = {1520-5851},
mesh = {Humans ; *Integrons/genetics ; *Drug Resistance, Bacterial/genetics ; Cell Fusion ; Bacteria/genetics ; Polymerase Chain Reaction ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbor class 1 integrons. We developed a modified version of epicPCR (emulsion, paired isolation, and concatenation polymerase chain reaction (PCR)) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multigene loci of interest. We also identified the Rhizobacter genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts toward hotspots of class 1 integron-mediated dissemination of AMR.},
}
@article {pmid36912090,
year = {2023},
author = {Deng, L and Wang, C and Zhang, X and Yang, W and Tang, H and Chen, X and Du, S and Chen, X},
title = {Cell-to-cell natural transformation in Bacillus subtilis facilitates large scale of genomic exchanges and the transfer of long continuous DNA regions.},
journal = {Nucleic acids research},
volume = {51},
number = {8},
pages = {3820-3835},
pmid = {36912090},
issn = {1362-4962},
mesh = {*Bacillus subtilis/genetics ; DNA/genetics ; DNA, Bacterial/genetics ; Genome ; Genomics ; *Transformation, Bacterial ; },
abstract = {Natural transformation is one of the major mechanisms of horizontal gene transfer. Although it is usually studied using purified DNA in the laboratory, recent studies showed that many naturally competent bacteria acquired exogenous DNA from neighboring donor cells. Our previous work indicates that cell-to-cell natural transformation (CTCNT) using two different Bacillus subtilis strains is a highly efficient process; however, the mechanism is unclear. In this study, we further characterized CTCNT and mapped the transferred DNA in the recombinants using whole genome sequencing. We found that a recombinant strain generated by CTCNT received up to 66 transferred DNA segments; the average length of acquired continuous DNA stretches was approximately 27 kb with a maximum length of 347 kb. Moreover, up to 1.54 Mb genomic DNA (37% of the chromosome) was transferred from the donors into one recipient cell. These results suggest that B. subtilis CTCNT facilitates horizontal gene transfer by increasing the transfer of DNA segments and fostering the exchange of large continuous genomic regions. This indicates that the potency of bacterial natural transformation is underestimated using traditional approaches and reveals that DNA donor cells may play an important role in the transformation process in natural environments.},
}
@article {pmid36909625,
year = {2023},
author = {Verhoeve, VI and Lehman, SS and Driscoll, TP and Beckmann, JF and Gillespie, JJ},
title = {Metagenome diversity illuminates origins of pathogen effectors.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {36909625},
issn = {2692-8205},
support = {R21 AI126108/AI/NIAID NIH HHS/United States ; R21 AI146773/AI/NIAID NIH HHS/United States ; R21 AI156762/AI/NIAID NIH HHS/United States ; R21 AI166832/AI/NIAID NIH HHS/United States ; },
abstract = {Recent metagenome assembled genome (MAG) analyses have profoundly impacted Rickettsiology systematics. Discovery of basal lineages (Mitibacteraceae and Athabascaceae) with predicted extracellular lifestyles reveals an evolutionary timepoint for the transition to host dependency, which occurred independent of mitochondrial evolution. Notably, these basal rickettsiae carry the Rickettsiales vir homolog (rvh) type IV secretion system (T4SS) and purportedly use rvh to kill congener microbes rather than parasitize host cells as described for derived rickettsial pathogens. MAG analysis also substantially increased diversity for genus Rickettsia and delineated a basal lineage (Tisiphia) that stands to inform on the rise of human pathogens from protist and invertebrate endosymbionts. Herein, we probed Rickettsiales MAG and genomic diversity for the distribution of Rickettsia rvh effectors to ascertain their origins. A sparse distribution of most Rickettsia rvh effectors outside of Rickettsiaceae lineages indicates unique rvh evolution from basal extracellular species and other rickettsial families. Remarkably, nearly every effector was found in multiple divergent forms with variable architectures, illuminating profound roles for gene duplication and recombination in shaping effector repertoires in Rickettsia pathogens. Lateral gene transfer plays a prominent role shaping the rvh effector landscape, as evinced by the discover of many effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchange between Rickettsia and Legionella species. Our study exemplifies how MAGs can provide incredible insight on the origins of pathogen effectors and how their architectural modifications become tailored to eukaryotic host cell biology.},
}
@article {pmid36909515,
year = {2023},
author = {Boys, IN and Johnson, AG and Quinlan, M and Kranzusch, PJ and Elde, NC},
title = {Structural homology screens reveal poxvirus-encoded proteins impacting inflammasome-mediated defenses.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {36909515},
issn = {2692-8205},
support = {R01 CA260414/CA/NCI NIH HHS/United States ; R35 GM134936/GM/NIGMS NIH HHS/United States ; },
abstract = {Viruses acquire host genes via horizontal gene transfer and can express them to manipulate host biology during infections. Some viral and host homologs retain sequence identity, but evolutionary divergence can obscure host origins. We used structural modeling to compare vaccinia virus proteins with metazoan proteomes. We identified vaccinia A47L as a homolog of gasdermins, the executioners of pyroptosis. An X-ray crystal structure of A47 confirmed this homology and cell-based assays revealed that A47 inhibits pyroptosis. We also identified vaccinia C1L as the product of a cryptic gene fusion event coupling a Bcl-2 related fold with a pyrin domain. C1 associates with components of the inflammasome, a cytosolic innate immune sensor involved in pyroptosis, yet paradoxically enhances inflammasome activity, suggesting a benefit to poxvirus replication in some circumstances. Our findings demonstrate the potential of structural homology screens to reveal genes that viruses capture from hosts and repurpose to benefit viral fitness.},
}
@article {pmid36901726,
year = {2023},
author = {Sonnenberg, CB and Haugen, P},
title = {Bipartite Genomes in Enterobacterales: Independent Origins of Chromids, Elevated Openness and Donors of Horizontally Transferred Genes.},
journal = {International journal of molecular sciences},
volume = {24},
number = {5},
pages = {},
pmid = {36901726},
issn = {1422-0067},
mesh = {*Genome, Bacterial ; Plasmids ; Bacteria/genetics ; *Gammaproteobacteria ; Codon Usage ; Gene Transfer, Horizontal ; },
abstract = {Multipartite bacteria have one chromosome and one or more chromid. Chromids are believed to have properties that enhance genomic flexibility, making them a favored integration site for new genes. However, the mechanism by which chromosomes and chromids jointly contribute to this flexibility is not clear. To shed light on this, we analyzed the openness of chromosomes and chromids of the two bacteria, Vibrio and Pseudoalteromonas, both which belong to the Enterobacterales order of Gammaproteobacteria, and compared the genomic openness with that of monopartite genomes in the same order. We applied pangenome analysis, codon usage analysis and the HGTector software to detect horizontally transferred genes. Our findings suggest that the chromids of Vibrio and Pseudoalteromonas originated from two separate plasmid acquisition events. Bipartite genomes were found to be more open compared to monopartite. We found that the shell and cloud pangene categories drive the openness of bipartite genomes in Vibrio and Pseudoalteromonas. Based on this and our two recent studies, we propose a hypothesis that explains how chromids and the chromosome terminus region contribute to the genomic plasticity of bipartite genomes.},
}
@article {pmid36897935,
year = {2023},
author = {Carr, VR and Pissis, SP and Mullany, P and Shoaie, S and Gomez-Cabrero, D and Moyes, DL},
title = {Palidis: fast discovery of novel insertion sequences.},
journal = {Microbial genomics},
volume = {9},
number = {3},
pages = {},
pmid = {36897935},
issn = {2057-5858},
support = {BB/M009513/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S016899/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Humans ; *DNA Transposable Elements ; *Bacteria/genetics ; Computational Biology ; Genome, Microbial ; Metagenomics ; },
abstract = {The diversity of microbial insertion sequences, crucial mobile genetic elements in generating diversity in microbial genomes, needs to be better represented in current microbial databases. Identification of these sequences in microbiome communities presents some significant problems that have led to their underrepresentation. Here, we present a bioinformatics pipeline called Palidis that recognizes insertion sequences in metagenomic sequence data rapidly by identifying inverted terminal repeat regions from mixed microbial community genomes. Applying Palidis to 264 human metagenomes identifies 879 unique insertion sequences, with 519 being novel and not previously characterized. Querying this catalogue against a large database of isolate genomes reveals evidence of horizontal gene transfer events across bacterial classes. We will continue to apply this tool more widely, building the Insertion Sequence Catalogue, a valuable resource for researchers wishing to query their microbial genomes for insertion sequences.},
}
@article {pmid36897181,
year = {2023},
author = {Wackett, LP},
title = {Horizontal gene transfer (HGT) and microbial evolution: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology.},
journal = {Environmental microbiology},
volume = {25},
number = {3},
pages = {772-773},
doi = {10.1111/1462-2920.16053},
pmid = {36897181},
issn = {1462-2920},
mesh = {*Gene Transfer, Horizontal ; *Environmental Microbiology ; },
}
@article {pmid36896589,
year = {2023},
author = {Yu, R and Chen, X and Long, L and Jost, M and Zhao, R and Liu, L and Mower, JP and dePamphilis, CW and Wanke, S and Jiao, Y},
title = {De novo Assembly and Comparative Analyses of Mitochondrial Genomes in Piperales.},
journal = {Genome biology and evolution},
volume = {15},
number = {3},
pages = {},
pmid = {36896589},
issn = {1759-6653},
mesh = {*Genome, Mitochondrial ; Biological Evolution ; *Magnoliopsida/genetics ; Introns ; Gene Transfer, Horizontal ; Phylogeny ; },
abstract = {The mitochondrial genome of Liriodendron tulipifera exhibits many ancestral angiosperm features and a remarkably slow evolutionary rate, while mitochondrial genomes of other magnoliids remain yet to be characterized. We assembled nine new mitochondrial genomes, representing all genera of perianth-bearing Piperales, as well as for a member of the sister clade: three complete or nearly complete mitochondrial genomes from Aristolochiaceae and six additional draft assemblies including Thottea, Asaraceae, Lactoridaceae, and Hydnoraceae. For comparative purpose, a complete mitochondrial genome was assembled for Saururus, a member of the perianth-less Piperales. The average number of short repeats (50-99 bp) was much larger in genus Aristolochia than in other angiosperm mitochondrial genomes, and approximately 30% of repeats (<350 bp) were found to have the capacity to mediate recombination. We found mitochondrial genomes in perianth-bearing Piperales comprising conserved repertories of protein-coding genes and rRNAs but variable copy numbers of tRNA genes. We identified several shifts from cis- to trans-splicing of the Group II introns of nad1i728, cox2i373, and nad7i209. Two short regions of the cox1 and atp8 genes were likely derived from independent horizontal gene transfer events in perianth-bearing Piperales. We found biased enrichment of specific substitution types in different lineages of magnoliids and the Aristolochiaceae family showed the highest ratio of A:T > T:A substitutions of all other investigated angiosperm groups. Our study reports the first mitochondrial genomes for Piperales and uses this new information for a better understanding of the evolutionary patterns of magnoliids and angiosperms in general.},
}
@article {pmid36893903,
year = {2023},
author = {Khan, AA and Nema, V and Ashraf, MT},
title = {Host-microbiota interactions and oncogenesis: Crosstalk and its implications in etiology.},
journal = {Microbial pathogenesis},
volume = {178},
number = {},
pages = {106063},
doi = {10.1016/j.micpath.2023.106063},
pmid = {36893903},
issn = {1096-1208},
mesh = {Humans ; Carcinogenesis ; *Microbiota/genetics ; *Neoplasms ; Host Microbial Interactions ; },
abstract = {A number of articles have discussed the potential of microbiota in oncogenesis. Several of these have evaluated the modulation of microbiota and its influence on cancer development. Even in recent past, a plethora of studies have gathered in order to understand the difference in microbiota population among different cancer and normal individuals. Although in majority of studies, microbiota mediated oncogenesis has been primarily attributed to the inflammatory mechanisms, there are several other ways through which microbiota can influence oncogenesis. These relatively less discussed aspects including the hormonal modulation through estrobolome and endobolome, production of cyclomodulins, and lateral gene transfer need more attention of scientific community. We prepared this article to discuss the role of microbiota in oncogenesis in order to provide concise information on these relatively less discussed microbiota mediated oncogenesis mechanisms.},
}
@article {pmid36892288,
year = {2023},
author = {Große, C and Scherer, J and Schleuder, G and Nies, DH},
title = {Interplay between Two-Component Regulatory Systems Is Involved in Control of Cupriavidus metallidurans Metal Resistance Genes.},
journal = {Journal of bacteriology},
volume = {205},
number = {4},
pages = {e0034322},
pmid = {36892288},
issn = {1098-5530},
mesh = {*Bacterial Proteins/genetics/metabolism ; Metals/metabolism ; Zinc/metabolism ; *Cupriavidus/genetics/metabolism ; },
abstract = {Metal resistance of Cupriavidus metallidurans is based on determinants that were acquired in the past by horizontal gene transfer during evolution. Some of these determinants encode transmembrane metal efflux systems. Expression of most of the respective genes is controlled by two-component regulatory systems composed of a membrane-bound sensor/sensory histidine kinase (HK) and a cytoplasmic, DNA-binding response regulator (RR). Here, we investigated the interplay between the three closely related two-component regulatory systems CzcRS, CzcR2S2, and AgrRS. All three systems regulate the response regulator CzcR, while the RRs AgrR and CzcR2 were not involved in czc regulation. Target promoters were czcNp and czcPp for genes upstream and downstream of the central czc gene region. The two systems together repressed CzcRS-dependent upregulation of czcP-lacZ at low zinc concentrations in the presence of CzcS but activated this signal transmission at higher zinc concentrations. AgrRS and CzcR2S2 interacted to quench CzcRS-mediated expression of czcNp-lacZ and czcPp-lacZ. Together, cross talk between the three two-component regulatory systems enhanced the capabilities of the Czc systems by controlling expression of the additional genes czcN and czcP. IMPORTANCE Bacteria are able to acquire genes encoding resistance to metals and antibiotics by horizontal gene transfer. To bestow an evolutionary advantage on their host cell, new genes must be expressed, and their expression should be regulated so that resistance-mediating proteins are produced only when needed. Newly acquired regulators may interfere with those already present in a host cell. Such an event was studied here in the metal-resistant bacterium Cupriavidus metallidurans. The results demonstrate how regulation by the acquired genes interacts with the host's extant regulatory network. This leads to emergence of a new system level of complexity that optimizes the response of the cell to periplasmic signals.},
}
@article {pmid36892285,
year = {2023},
author = {Brown, PJB and Chang, JH and Fuqua, C},
title = {Agrobacterium tumefaciens: a Transformative Agent for Fundamental Insights into Host-Microbe Interactions, Genome Biology, Chemical Signaling, and Cell Biology.},
journal = {Journal of bacteriology},
volume = {205},
number = {4},
pages = {e0000523},
pmid = {36892285},
issn = {1098-5530},
support = {R01 GM120337/GM/NIGMS NIH HHS/United States ; },
mesh = {*Agrobacterium tumefaciens/genetics ; *Host Microbial Interactions ; Plant Tumors/microbiology ; Plant Diseases/microbiology ; Plants/microbiology ; Bacteria ; Biology ; },
abstract = {Agrobacterium tumefaciens incites the formation of readily visible macroscopic structures known as crown galls on plant tissues that it infects. Records from biologists as early as the 17th century noted these unusual plant growths and began examining the basis for their formation. These studies eventually led to isolation of the infectious agent, A. tumefaciens, and decades of study revealed the remarkable mechanisms by which A. tumefaciens causes crown gall through stable horizontal genetic transfer to plants. This fundamental discovery generated a barrage of applications in the genetic manipulation of plants that is still under way. As a consequence of the intense study of A. tumefaciens and its role in plant disease, this pathogen was developed as a model for the study of critical processes that are shared by many bacteria, including host perception during pathogenesis, DNA transfer and toxin secretion, bacterial cell-cell communication, plasmid biology, and more recently, asymmetric cell biology and composite genome coordination and evolution. As such, studies of A. tumefaciens have had an outsized impact on diverse areas within microbiology and plant biology that extend far beyond its remarkable agricultural applications. In this review, we attempt to highlight the colorful history of A. tumefaciens as a study system, as well as current areas that are actively demonstrating its value and utility as a model microorganism.},
}
@article {pmid36892101,
year = {2023},
author = {Sun, H and Li, H and Zhang, X and Liu, Y and Chen, H and Zheng, L and Zhai, Y and Zheng, H},
title = {The honeybee gut resistome and its role in antibiotic resistance dissemination.},
journal = {Integrative zoology},
volume = {18},
number = {6},
pages = {1014-1026},
doi = {10.1111/1749-4877.12714},
pmid = {36892101},
issn = {1749-4877},
support = {32000346//National Natural Science Foundation of China Projects/ ; 32170495//National Natural Science Foundation of China Projects/ ; },
mesh = {Animals ; Bees/genetics ; Drug Resistance, Microbial/genetics ; *Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome ; },
abstract = {There is now general concern about widespread antibiotic resistance, and growing evidence indicates that gut microbiota is critical in providing antibiotic resistance. Honeybee is an important pollinator; the incidence of antibiotic resistance genes in honeybee gut causes potential risks to not only its own health but also to public and animal health, for its potential disseminator role, thus receiving more attention from the public. Recent analysis results reveal that the gut of honeybee serves as a reservoir of antibiotic resistance genes, probably due to antibiotics application history in beekeeping and horizontal gene transfer from the highly polluted environment. These antibiotic resistance genes accumulate in the honeybee gut and could be transferred to the pathogen, even having the potential to spread during pollination, tending, social interactions, etc. Newly acquired resistance traits may cause fitness reduction in bacteria whereas facilitating adaptive evolution as well. This review outlines the current knowledge about the resistome in honeybee gut and emphasizes its role in antibiotic resistance dissemination.},
}
@article {pmid36889142,
year = {2023},
author = {Hussain, M and Etebari, K and Asgari, S},
title = {Analysing inhibition of dengue virus in Wolbachia-infected mosquito cells following the removal of Wolbachia.},
journal = {Virology},
volume = {581},
number = {},
pages = {48-55},
doi = {10.1016/j.virol.2023.02.017},
pmid = {36889142},
issn = {1096-0341},
mesh = {Animals ; *Dengue Virus/physiology ; *Wolbachia/physiology ; Virus Replication ; *RNA Viruses/genetics ; *Aedes ; *Dengue ; },
abstract = {Wolbachia pipientis is known to block replication of positive sense RNA viruses. Previously, we created an Aedes aegypti Aag2 cell line (Aag2.wAlbB) transinfected with the wAlbB strain of Wolbachia and a matching tetracycline-cured Aag2.tet cell line. While dengue virus (DENV) was blocked in Aag2.wAlbB cells, we found significant inhibition of DENV in Aag2.tet cells. RNA-Seq analysis of the cells confirmed removal of Wolbachia and lack of expression of Wolbachia genes that could have been due to lateral gene transfer in Aag2.tet cells. However, we noticed a substantial increase in the abundance of phasi charoen-like virus (PCLV) in Aag2.tet cells. When RNAi was used to reduce the PCLV levels, DENV replication was significantly increased. Further, we found significant changes in the expression of antiviral and proviral genes in Aag2.tet cells. Overall, the results reveal an antagonistic interaction between DENV and PCLV and how PCLV-induced changes could contribute to DENV inhibition.},
}
@article {pmid36889077,
year = {2023},
author = {Yang, X and Niu, Y and Yang, Y and Zhou, H and Li, J and Fu, X and Shen, Z and Wang, J and Qiu, Z},
title = {Pheromone effect of estradiol regulates the conjugative transfer of pCF10 carrying antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {451},
number = {},
pages = {131087},
doi = {10.1016/j.jhazmat.2023.131087},
pmid = {36889077},
issn = {1873-3336},
mesh = {*Anti-Bacterial Agents/metabolism ; *Pheromones/pharmacology/genetics/metabolism ; Estradiol/pharmacology/metabolism ; Plasmids/genetics ; Drug Resistance, Microbial/genetics ; Enterococcus faecalis/genetics/metabolism ; Gene Transfer, Horizontal ; },
abstract = {Horizontal gene transfer (HGT) mediated by conjugative plasmids greatly contributes to bacteria evolution and the transmission of antibiotic resistance genes (ARGs). In addition to the selective pressure imposed by extensive antibiotic use, environmental chemical pollutants facilitate the dissemination of antibiotic resistance, consequently posing a serious threat to the ecological environment. Presently, the majority of studies focus on the effects of environmental compounds on R plasmid-mediated conjugation transfer, and pheromone-inducible conjugation has largely been neglected. In this study, we explored the pheromone effect and potential molecular mechanisms of estradiol in promoting the conjugative transfer of pCF10 plasmid in Enterococcus faecalis. Environmentally relevant concentrations of estradiol significantly increased the conjugative transfer of pCF10 with a maximum frequency of 3.2 × 10[-2], up to 3.5-fold change compared to that of control. Exposure to estradiol induced the activation of pheromone signaling cascade by increasing the expression of ccfA. Furthermore, estradiol might directly bind to the pheromone receptor PrgZ and promote pCF10 induction and finally enhance the conjugative transfer of pCF10. These findings cast valuable insights on the roles of estradiol and its homolog in increasing antibiotic resistance and the potential ecological risk.},
}
@article {pmid36881118,
year = {2023},
author = {Veremeichik, GN and Bulgakov, DV and Solomatina, TO and Makhazen, DS},
title = {In the interkingdom horizontal gene transfer, the small rolA gene is a big mystery.},
journal = {Applied microbiology and biotechnology},
volume = {107},
number = {7-8},
pages = {2097-2109},
pmid = {36881118},
issn = {1432-0614},
support = {23-24-00215//Russian Science Foundation/ ; },
mesh = {Plants, Genetically Modified ; *Gene Transfer, Horizontal ; DNA ; Genetic Engineering ; Oncogenes ; *Rhizobium/genetics ; },
abstract = {The biological function of the agrobacterial oncogene rolA is very poorly understood compared to other components of the mechanism of horizontal gene transfer during agrobacterial colonization of plants. Research groups around the world have worked on this problem, and available information is reviewed in this review, but other rol oncogenes have been studied much more thoroughly. Having one unexplored element makes it impossible to form a complete picture. However, the limited data suggest that the rolA oncogene and its regulatory apparatus have great potential in plant biotechnology and genetic engineering. Here, we collect and discuss available experimental data about the function and structure of rolA. There is still no clear understanding of the mechanism of RolA and its structure and localization. We believe this is because of the nucleotide structure of a frameshift in the most well-studied rolA gene of the agropine type pRi. In fact, interest in the genes of agrobacteria as natural tools for the phenotypic or biochemical engineering of plants increased. We believe that a detailed understanding of the molecular mechanisms will be forthcoming. KEY POINTS: • Among pRi T-DNA oncogenes, rolA is the least understood in spite of many studies. • Frameshift may be the reason for the failure to elucidate the role of agropine rolA. • Understanding of rolA is promising for the phenotypic and biochemical engineering of plants.},
}
@article {pmid36880348,
year = {2023},
author = {Tholl, D and Rebholz, Z and Morozov, AV and O'Maille, PE},
title = {Terpene synthases and pathways in animals: enzymology and structural evolution in the biosynthesis of volatile infochemicals.},
journal = {Natural product reports},
volume = {40},
number = {4},
pages = {766-793},
doi = {10.1039/d2np00076h},
pmid = {36880348},
issn = {1460-4752},
mesh = {Animals ; Phylogeny ; *Alkyl and Aryl Transferases/genetics ; Terpenes/metabolism ; Pheromones ; Mammals ; },
abstract = {Covering: up to the beginning of 2023Many animals release volatile or semi-volatile terpenes as semiochemicals in intra- and inter-specific interactions. Terpenes are important constituents of pheromones and serve as chemical defenses to ward off predators. Despite the occurrence of terpene specialized metabolites from soft corals to mammals, the biosynthetic origin of these compounds has largely remained obscure. An increasing number of animal genome and transcriptome resources is facilitating the identification of enzymes and pathways that allow animals to produce terpenes independent of their food sources or microbial endosymbionts. Substantial evidence has emerged for the presence of terpene biosynthetic pathways such as in the formation of the iridoid sex pheromone nepetalactone in aphids. In addition, terpene synthase (TPS) enzymes have been discovered that are evolutionary unrelated to canonical plant and microbial TPSs and instead resemble precursor enzymes called isoprenyl diphosphate synthases (IDSs) in central terpene metabolism. Structural modifications of substrate binding motifs in canonical IDS proteins presumably facilitated the transition to TPS function at an early state in insect evolution. Other arthropods such as mites appear to have adopted their TPS genes from microbial sources via horizontal gene transfer. A similar scenario likely occurred in soft corals, where TPS families with closer resemblance to microbial TPSs have been discovered recently. Together, these findings will spur the identification of similar or still unknown enzymes in terpene biosynthesis in other lineages of animals. They will also help develop biotechnological applications for animal derived terpenes of pharmaceutical value or advance sustainable agricultural practices in pest management.},
}
@article {pmid36878032,
year = {2023},
author = {Yu, X and Zhou, ZC and Shuai, XY and Lin, ZJ and Liu, Z and Zhou, JY and Lin, YH and Zeng, GS and Ge, ZY and Chen, H},
title = {Microplastics exacerbate co-occurrence and horizontal transfer of antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {451},
number = {},
pages = {131130},
doi = {10.1016/j.jhazmat.2023.131130},
pmid = {36878032},
issn = {1873-3336},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Microplastics/toxicity ; *Genes, Bacterial ; Plastics/analysis ; Anti-Bacterial Agents/toxicity ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; },
abstract = {Microplastic pollution is a rising environmental issue worldwide. Microplastics can provide a niche for the microbiome, especially for antibiotic-resistant bacteria, which could increase the transmission of antibiotic resistance genes (ARGs). However, the interactions between microplastics and ARGs are still indistinct in environmental settings. Microplastics were found to be significantly correlated with ARGs (p < 0.001), based on the analysis of samples taken from a chicken farm and its surrounding farmlands. Analysis of chicken feces revealed the highest abundance of microplastics (14.9 items/g) and ARGs (6.24 ×10[8] copies/g), suggesting that chicken farms could be the hotspot for the co-spread of microplastics and ARGs. Conjugative transfer experiments were performed to investigate the effects of microplastic exposure for different concentrations and sizes on the horizontal gene transfer (HGT) of ARGs between bacteria. Results showed that the microplastics significantly enhanced the bacterial conjugative transfer frequency by 1.4-1.7 folds indicating that microplastics could aggravate ARG dissemination in the environment. Potential mechanisms related to the up-regulation of rpoS, ompA, ompC, ompF, trbBp, traF, trfAp, traJ, and down-regulation of korA, korB, and trbA were induced by microplastics. These findings highlighted the co-occurrence of microplastics and ARGs in the agricultural environment and the exacerbation of ARGs' prevalence via rising the HGT derived from microplastics.},
}
@article {pmid36874978,
year = {2023},
author = {Fuchsman, CA and Garcia Prieto, D and Hays, MD and Cram, JA},
title = {Associations between picocyanobacterial ecotypes and cyanophage host genes across ocean basins and depth.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e14924},
pmid = {36874978},
issn = {2167-8359},
mesh = {*Ecotype ; Phylogeny ; *Genes, Viral ; Genome, Viral ; Cycadopsida ; },
abstract = {BACKGROUND: Cyanophages, viruses that infect cyanobacteria, are globally abundant in the ocean's euphotic zone and are a potentially important cause of mortality for marine picocyanobacteria. Viral host genes are thought to increase viral fitness by either increasing numbers of genes for synthesizing nucleotides for virus replication, or by mitigating direct stresses imposed by the environment. The encoding of host genes in viral genomes through horizontal gene transfer is a form of evolution that links viruses, hosts, and the environment. We previously examined depth profiles of the proportion of cyanophage containing various host genes in the Eastern Tropical North Pacific Oxygen Deficient Zone (ODZ) and at the subtropical North Atlantic (BATS). However, cyanophage host genes have not been previously examined in environmental depth profiles across the oceans.<br><br>METHODOLOGY: We examined geographical and depth distributions of picocyanobacterial ecotypes, cyanophage, and their viral-host genes across ocean basins including the North Atlantic, Mediterranean Sea, North Pacific, South Pacific, and Eastern Tropical North and South Pacific ODZs using phylogenetic metagenomic read placement. We determined the proportion of myo and podo-cyanophage containing a range of host genes by comparing to cyanophage single copy core gene terminase (terL). With this large dataset (22 stations), network analysis identified statistical links between 12 of the 14 cyanophage host genes examined here with their picocyanobacteria host ecotypes.<br><br>RESULTS: Picyanobacterial ecotypes, and the composition and proportion of cyanophage host genes, shifted dramatically and predictably with depth. For most of the cyanophage host genes examined here, we found that the composition of host ecotypes predicted the proportion of viral host genes harbored by the cyanophage community. Terminase is too conserved to illuminate the myo-cyanophage community structure. Cyanophage cobS was present in almost all myo-cyanophage and did not vary in proportion with depth. We used the composition of cobS phylotypes to track changes in myo-cyanophage composition.<br><br>CONCLUSIONS: Picocyanobacteria ecotypes shift with changes in light, temperature, and oxygen and many common cyanophage host genes shift concomitantly. However, cyanophage phosphate transporter gene pstS appeared to instead vary with ocean basin and was most abundant in low phosphate regions. Abundances of cyanophage host genes related to nutrient acquisition may diverge from host ecotype constraints as the same host can live in varying nutrient concentrations. Myo-cyanophage community in the anoxic ODZ had reduced diversity. By comparison to the oxic ocean, we can see which cyanophage host genes are especially abundant (nirA, nirC, and purS) or not abundant (myo psbA) in ODZs, highlighting both the stability of conditions in the ODZ and the importance of nitrite as an N source to ODZ endemic LLV Prochlorococcus.},
}
@article {pmid36871940,
year = {2023},
author = {Yan, K and Wei, M and Li, F and Wu, C and Yi, S and Tian, J and Liu, Y and Lu, H},
title = {Diffusion and enrichment of high-risk antibiotic resistance genes (ARGs) via the transmission chain (mulberry leave, guts and feces of silkworm, and soil) in an ecological restoration area of manganese mining, China: Role of heavy metals.},
journal = {Environmental research},
volume = {225},
number = {},
pages = {115616},
doi = {10.1016/j.envres.2023.115616},
pmid = {36871940},
issn = {1096-0953},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Bombyx/genetics ; Manganese ; Genes, Bacterial ; *Morus/genetics ; Soil ; Escherichia coli ; Drug Resistance, Microbial/genetics ; *Metals, Heavy/toxicity ; Feces ; Mining ; },
abstract = {This study investigated the diffusion and enrichment of antibiotic resistance genes (ARGs) and pathogens via the transmission chain (mulberry leaves - silkworm guts - silkworm feces - soil) near a manganese mine restoration area (RA) and control area (CA, away from RA). Horizontal gene transfer (HGT) of ARGs was testified by an IncP a-type broad host range plasmid RP4 harboring ARGs (tetA) and conjugative genes (e.g., korB, trbA, and trbB) as an indicator. Compared to leaves, the abundances of ARGs and pathogens in feces after silkworms ingested leaves from RA increased by 10.8% and 52.3%, respectively, whereas their abundance in feces from CA dropped by 17.1% and 97.7%, respectively. The predominant ARG types in feces involved the resistances to β-lactam, quinolone, multidrug, peptide, and rifamycin. Therein, several high-risk ARGs (e.g., qnrB, oqxA, and rpoB) carried by pathogens were more enriched in feces. However, HGT mediated by plasmid RP4 in this transmission chain was not a main factor to promote the enrichment of ARGs due to the harsh survival environment of silkworm guts for the plasmid RP4 host E. coli. Notably, Zn, Mn, and As in feces and guts promoted the enrichment of qnrB and oqxA. Worriedly, the abundance of qnrB and oqxA in soil increased by over 4-fold after feces from RA were added into soil for 30 days regardless of feces with or without E. coli RP4. Overall, ARGs and pathogens could diffuse and enrich in environment via the sericulture transmission chain developed at RA, especially some high-risk ARGs carried by pathogens. Thus, greater attentions should be paid to dispel such high-risk ARGs to support benign development of sericulture industry in the safe utilization of some RAs.},
}
@article {pmid36871872,
year = {2023},
author = {Henoun Loukili, N and Loquet, A and Perrin, A and Gaillot, O and Bruandet, A and Sendid, B and Zahar, JR and Nseir, S},
title = {Time to intestinal clearance of carbapenemase-producing Enterobacterales in hospital patients: a longitudinal retrospective observational cohort study.},
journal = {The Journal of hospital infection},
volume = {135},
number = {},
pages = {4-10},
doi = {10.1016/j.jhin.2023.01.022},
pmid = {36871872},
issn = {1532-2939},
mesh = {Humans ; Female ; Retrospective Studies ; *Escherichia coli ; beta-Lactamases/genetics ; Bacterial Proteins/genetics ; Hospitals ; *Enterobacteriaceae Infections/epidemiology/drug therapy ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {BACKGROUND: Intestinal clearance of carbapenemase-producing Enterobacterales (CPE-IC) is a cornerstone to discontinue isolation precautions for CPE patients in hospitals. This study aimed to evaluate the time to spontaneous CPE-IC and identify its potential associated risk factors.<br><br>METHODS: This retrospective cohort study was carried out between January 2018 and September 2020 on all patients in a 3200-bed teaching referral hospital with confirmed CPE intestinal carriage. CPE-IC was defined as at least three consecutive CPE-negative rectal swab cultures without a subsequent positive result. A survival analysis was performed to determine the median time to CPE-IC. A multivariate Cox model was implemented to explore the factors associated with CPE-IC.<br><br>RESULTS: A total of 110 patients were positives for CPE, of whom 27 (24.5%) achieved CPE-IC. Median time to CPE-IC was 698 days. Univariate analysis showed that female sex (P=0.046), multiple CPE-species in index cultures (P=0.005), Escherichia coli or Klebsiella spp. (P=0.001 and P=0.028, respectively) were significantly associated with the time to CPE-IC. Multivariate analysis highlighted that identification of E. coli carbapenemase-producing or CPEs harbouring ESBL genes in index culture extended the median time to CPE-IC, respectively (adjusted hazard ratio (aHR)&#xa0;= 0.13 (95% confidence interval: 0.04-0.45]; P=0.001 and aHR&#xa0;= 0.34 (95% confidence interval: 0.12-0.90); P=0.031).<br><br>CONCLUSION: Intestinal decolonization of CPE can take several months to years to occur. Carbapenemase-producing E.&#xa0;coli are likely to play a key role in delaying intestinal decolonization, probably through horizontal gene transfer between species. Therefore, discontinuation of isolation precautions in CPE-patients should be considered with caution.},
}
@article {pmid36867924,
year = {2023},
author = {Mirtaleb, MS and Falak, R and Heshmatnia, J and Bakhshandeh, B and Taheri, RA and Soleimanjahi, H and Zolfaghari Emameh, R},
title = {An insight overview on COVID-19 mRNA vaccines: Advantageous, pharmacology, mechanism of action, and prospective considerations.},
journal = {International immunopharmacology},
volume = {117},
number = {},
pages = {109934},
pmid = {36867924},
issn = {1878-1705},
mesh = {Humans ; COVID-19 Vaccines ; *COVID-19/prevention &amp; control ; Pandemics/prevention &amp; control ; Prospective Studies ; SARS-CoV-2 ; RNA, Messenger ; mRNA Vaccines ; *Viral Vaccines ; },
abstract = {The worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has urged scientists to present some novel vaccine platforms during this pandemic to provide a rather prolonged immunity against this respiratory viral infection. In spite of many campaigns formed against the administration of mRNA-based vaccines, those platforms were the most novel types, which helped us meet the global demand by developing protection against COVID-19 and reducing the development of severe forms of this respiratory viral infection. Some societies are worry about the COVID-19 mRNA vaccine administration and the potential risk of genetic integration of inoculated mRNA into the human genome. Although the efficacy and long-term safety of mRNA vaccines have not yet been fully clarified, obviously their application has switched the mortality and morbidity of the COVID-19 pandemic. This study describes the structural features and technologies used in producing of COVID-19 mRNA-based vaccines as the most influential factor in controlling this pandemic and a successful pattern for planning to produce other kind of genetic vaccines against infections or cancers.},
}
@article {pmid36864029,
year = {2023},
author = {Lee, K and Raguideau, S and Sirén, K and Asnicar, F and Cumbo, F and Hildebrand, F and Segata, N and Cha, CJ and Quince, C},
title = {Population-level impacts of antibiotic usage on the human gut microbiome.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {1191},
pmid = {36864029},
issn = {2041-1723},
support = {BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Microbiota ; Metagenome/genetics ; Genome, Human ; },
abstract = {The widespread usage of antimicrobials has driven the evolution of resistance in pathogenic microbes, both increased prevalence of antimicrobial resistance genes (ARGs) and their spread across species by horizontal gene transfer (HGT). However, the impact on the wider community of commensal microbes associated with the human body, the microbiome, is less well understood. Small-scale studies have determined the transient impacts of antibiotic consumption but we conduct an extensive survey of ARGs in 8972 metagenomes to determine the population-level impacts. Focusing on 3096 gut microbiomes from healthy individuals not taking antibiotics we demonstrate highly significant correlations between both the total ARG abundance and diversity and per capita antibiotic usage rates across ten countries spanning three continents. Samples from China were notable outliers. We use a collection of 154,723 human-associated metagenome assembled genomes (MAGs) to link these ARGs to taxa and detect HGT. This reveals that the correlations in ARG abundance are driven by multi-species mobile ARGs shared between pathogens and commensals, within a highly connected central component of the network of MAGs and ARGs. We also observe that individual human gut ARG profiles cluster into two types or resistotypes. The less frequent resistotype has higher overall ARG abundance, is associated with certain classes of resistance, and is linked to species-specific genes in the Proteobacteria on the periphery of the ARG network.},
}
@article {pmid36863279,
year = {2023},
author = {Zhang, H and Song, J and Zheng, Z and Li, T and Shi, N and Han, Y and Zhang, L and Yu, Y and Fang, H},
title = {Fungicide exposure accelerated horizontal transfer of antibiotic resistance genes via plasmid-mediated conjugation.},
journal = {Water research},
volume = {233},
number = {},
pages = {119789},
doi = {10.1016/j.watres.2023.119789},
pmid = {36863279},
issn = {1879-2448},
mesh = {*Anti-Bacterial Agents/pharmacology ; Escherichia coli/genetics ; *Fungicides, Industrial ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Plasmids/genetics ; Gene Transfer, Horizontal ; },
abstract = {Co-pollution of soil with pesticide residues and antibiotic resistance genes (ARGs) is increasing due to the substantial usage of pesticides and organic fertilizers in greenhouse-based agricultural production. Non-antibiotic stresses, including those from agricultural fungicides, are potential co-selectors for the horizontal transfer of ARGs, but the underlying mechanism remains unclear. Intragenus and intergenus conjugative transfer systems of the antibiotic resistant plasmid RP4 were established to examine conjugative transfer frequency under stress from four widely used fungicides: triadimefon, chlorothalonil, azoxystrobin, and carbendazim. The mechanisms were elucidated at the cellular and molecular levels using transmission electron microscopy, flow cytometry, RT-qPCR, and RNA-seq techniques. The conjugative transfer frequency of plasmid RP4 between Escherichia coli strains increased with the rising exposure concentrations of chlorothalonil, azoxystrobin, and carbendazim, but was suppressed between E. coli and Pseudomonas putida by a high fungicide concentration (10 µg/mL). Triadimefon did not significantly affect conjugative transfer frequency. Exploration of the underlying mechanisms revealed that: (i) chlorothalonil exposure mainly promoted generation of intracellular reactive oxygen species, stimulated the SOS response, and increased cell membrane permeability, while (ii) azoxystrobin and carbendazim primarily enhanced expression of conjugation-related genes on the plasmid. These findings reveal the fungicide-triggered mechanisms associated with plasmid conjugation and highlight the potential role of non-bactericidal pesticides on the dissemination of ARGs.},
}
@article {pmid36863168,
year = {2023},
author = {Horne, T and Orr, VT and Hall, JP},
title = {How do interactions between mobile genetic elements affect horizontal gene transfer?.},
journal = {Current opinion in microbiology},
volume = {73},
number = {},
pages = {102282},
doi = {10.1016/j.mib.2023.102282},
pmid = {36863168},
issn = {1879-0364},
mesh = {*Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Bacteria/genetics ; Biological Evolution ; *Microbiota ; },
abstract = {Horizontal gene transfer is central to bacterial adaptation and is facilitated by mobile genetic elements (MGEs). Increasingly, MGEs are being studied as agents with their own interests and adaptations, and the interactions MGEs have with one another are recognised as having a powerful effect on the flow of traits between microbes. Collaborations and conflicts between MGEs are nuanced and can both promote and inhibit the acquisition of new genetic material, shaping the maintenance of newly acquired genes and the dissemination of important adaptive traits through microbiomes. We review recent studies that shed light on this dynamic and oftentimes interlaced interplay, highlighting the importance of genome defence systems in mediating MGE-MGE conflicts, and outlining the consequences for evolutionary change, that resonate from the molecular to microbiome and ecosystem levels.},
}
@article {pmid36863149,
year = {2023},
author = {Zhang, Y and Xiang, Y and Xu, R and Huang, J and Deng, J and Zhang, X and Wu, Z and Huang, Z and Yang, Z and Xu, J and Xiong, W and Li, H},
title = {Magnetic biochar promotes the risk of mobile genetic elements propagation in sludge anaerobic digestion.},
journal = {Journal of environmental management},
volume = {335},
number = {},
pages = {117492},
doi = {10.1016/j.jenvman.2023.117492},
pmid = {36863149},
issn = {1095-8630},
mesh = {*Sewage ; *Genes, Bacterial ; Anaerobiosis ; Anti-Bacterial Agents/pharmacology ; Interspersed Repetitive Sequences ; Magnetic Phenomena ; Manure/microbiology ; },
abstract = {Mobile genetic elements (MGEs) mediated horizontal gene transfer is the primary reason for the propagation of antibiotic resistance genes in environment. The behavior of MGEs under magnetic biochar pressure in sludge anaerobic digestion (AD) is still unknown. This study evaluated the effects of different dosage magnetic biochar on the MGEs in AD reactors. The results showed that the biogas yield was highest (106.68 ± 1.16 mL g[-1] VSadded) with adding optimal dosage of magnetic biochar (25 mg g[-1] TSadded), due to it increased the microorganism's abundance involved in hydrolysis and methanogenesis. While, the total absolute abundance of MGEs in the reactors with magnetic biochar addition increased by 11.58%-77.37% compared with the blank reactor. When the dosage of magnetic biochar was 12.5 mg g[-1] TSadded, the relative abundance of most MGEs was the highest. The enrichment effect on ISCR1 was the most significant, and the enrichment rate reached 158.90-214.16%. Only the intI1 abundance was reduced and the removal rates yield 14.38-40.00%, which was inversely proportional to the dosage of magnetic biochar. Co-occurrence network explored that Proteobacteria (35.64%), Firmicutes (19.80%) and Actinobacteriota (15.84%) were the main potential host of MGEs. Magnetic biochar changed MGEs abundance by affecting the potential MGEs-host community structure and abundance. Redundancy analysis and variation partitioning analysis showed that the combined effect of polysaccharides, protein and sCOD exhibited the greatest contribution (accounted for 34.08%) on MGEs variation. These findings demonstrated that magnetic biochar increases the risk of MGEs proliferation in AD system.},
}
@article {pmid36858028,
year = {2023},
author = {Martins, SJ and Pasche, J and Silva, HAO and Selten, G and Savastano, N and Abreu, LM and Bais, HP and Garrett, KA and Kraisitudomsook, N and Pieterse, CMJ and Cernava, T},
title = {The Use of Synthetic Microbial Communities to Improve Plant Health.},
journal = {Phytopathology},
volume = {113},
number = {8},
pages = {1369-1379},
doi = {10.1094/PHYTO-01-23-0016-IA},
pmid = {36858028},
issn = {0031-949X},
abstract = {Despite the numerous benefits plants receive from probiotics, maintaining consistent results across applications is still a challenge. Cultivation-independent methods associated with reduced sequencing costs have considerably improved the overall understanding of microbial ecology in the plant environment. As a result, now, it is possible to engineer a consortium of microbes aiming for improved plant health. Such synthetic microbial communities (SynComs) contain carefully chosen microbial species to produce the desired microbiome function. Microbial biofilm formation, production of secondary metabolites, and ability to induce plant resistance are some of the microbial traits to consider when designing SynComs. Plant-associated microbial communities are not assembled randomly. Ecological theories suggest that these communities have a defined phylogenetic organization structured by general community assembly rules. Using machine learning, we can study these rules and target microbial functions that generate desired plant phenotypes. Well-structured assemblages are more likely to lead to a stable SynCom that thrives under environmental stressors as compared with the classical selection of single microbial activities or taxonomy. However, ensuring microbial colonization and long-term plant phenotype stability is still one of the challenges to overcome with SynComs, as the synthetic community may change over time with microbial horizontal gene transfer and retained mutations. Here, we explored the advances made in SynCom research regarding plant health, focusing on bacteria, as they are the most dominant microbial form compared with other members of the microbiome and the most commonly found in SynCom studies.},
}
@article {pmid36853054,
year = {2023},
author = {Du, Y and Zou, J and Yin, Z and Chen, T},
title = {Pan-Chromosome and Comparative Analysis of Agrobacterium fabrum Reveal Important Traits Concerning the Genetic Diversity, Evolutionary Dynamics, and Niche Adaptation of the Species.},
journal = {Microbiology spectrum},
volume = {11},
number = {2},
pages = {e0292422},
pmid = {36853054},
issn = {2165-0497},
abstract = {Agrobacterium fabrum has been critical for the development of plant genetic engineering and agricultural biotechnology due to its ability to transform eukaryotic cells. However, the gene composition, evolutionary dynamics, and niche adaptation of this species is still unknown. Therefore, we established a comparative genomic analysis based on a pan-chromosome data set to evaluate the genetic diversity of A. fabrum. Here, 25 A. fabrum genomes were selected for analysis by core genome phylogeny combined with the average nucleotide identity (ANI), amino acid identity (AAI), and in silico DNA-DNA hybridization (DDH) values. An open pan-genome of A. fabrum exhibits genetic diversity with variable accessorial genes as evidenced by a consensus pan-genome of 12 representative genomes. The genomic plasticity of A. fabrum is apparent in its putative sequences for mobile genetic elements (MGEs), limited horizontal gene transfer barriers, and potentially horizontally transferred genes. The evolutionary constraints and functional enrichment in the pan-chromosome were measured by the Clusters of Orthologous Groups (COG) categories using eggNOG-mapper software, and the nonsynonymous/synonymous rate ratio (dN/dS) was determined using HYPHY software. Comparative analysis revealed significant differences in the functional enrichment and the degree of purifying selection between the core genome and non-core genome. We demonstrate that the core gene families undergo stronger purifying selection but have a significant bias to contain one or more positively selected sites. Furthermore, although they shared similar genetic diversity, we observed significant differences between chromosome 1 (Chr I) and the chromid in their functional features and evolutionary constraints. We demonstrate that putative genetic elements responsible for plant infection, ecological adaptation, and speciation represent the core genome, highlighting their importance in the adaptation of A. fabrum to plant-related niches. Our pan-chromosome analysis of A. fabrum provides comprehensive insights into the genetic properties, evolutionary patterns, and niche adaptation of the species. IMPORTANCE Agrobacterium spp. live in diverse plant-associated niches such as soil, the rhizosphere, and vegetation, which are challenged by multiple stressors such as diverse energy sources, plant defenses, and microbial competition. They have evolved the ability to utilize diverse resources, escape plant defenses, and defeat competitors. However, the underlying genetic diversity and evolutionary dynamics of Agrobacterium spp. remain unexplored. We examined the phylogeny and pan-genome of A. fabrum to define intraspecies evolutionary relationships. Our results indicate an open pan-genome and numerous MGEs and horizontally transferred genes among A. fabrum genomes, reflecting the flexibility of the chromosomes and the potential for genetic exchange. Furthermore, we observed significant differences in the functional features and evolutionary constraints between the core and accessory genomes and between Chr I and the chromid, respectively.},
}
@article {pmid36851563,
year = {2023},
author = {Elois, MA and Silva, RD and Pilati, GVT and Rodríguez-Lázaro, D and Fongaro, G},
title = {Bacteriophages as Biotechnological Tools.},
journal = {Viruses},
volume = {15},
number = {2},
pages = {},
pmid = {36851563},
issn = {1999-4915},
mesh = {*Bacteriophages/genetics ; Prophages ; Lysogeny ; Biofilms ; Biotechnology ; },
abstract = {Bacteriophages are ubiquitous organisms that can be specific to one or multiple strains of hosts, in addition to being the most abundant entities on the planet. It is estimated that they exceed ten times the total number of bacteria. They are classified as temperate, which means that phages can integrate their genome into the host genome, originating a prophage that replicates with the host cell and may confer immunity against infection by the same type of phage; and lytics, those with greater biotechnological interest and are viruses that lyse the host cell at the end of its reproductive cycle. When lysogenic, they are capable of disseminating bacterial antibiotic resistance genes through horizontal gene transfer. When professionally lytic-that is, obligately lytic and not recently descended from a temperate ancestor-they become allies in bacterial control in ecological imbalance scenarios; these viruses have a biofilm-reducing capacity. Phage therapy has also been advocated by the scientific community, given the uniqueness of issues related to the control of microorganisms and biofilm production when compared to other commonly used techniques. The advantages of using bacteriophages appear as a viable and promising alternative. This review will provide updates on the landscape of phage applications for the biocontrol of pathogens in industrial settings and healthcare.},
}
@article {pmid36847532,
year = {2023},
author = {Cooke, MB and Herman, C},
title = {Conjugation's Toolkit: the Roles of Nonstructural Proteins in Bacterial Sex.},
journal = {Journal of bacteriology},
volume = {205},
number = {3},
pages = {e0043822},
pmid = {36847532},
issn = {1098-5530},
support = {DP1 AI152073/AI/NIAID NIH HHS/United States ; },
mesh = {Plasmids ; *Type IV Secretion Systems/genetics ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Bacterial conjugation, a form of horizontal gene transfer, relies on a type 4 secretion system (T4SS) and a set of nonstructural genes that are closely linked. These nonstructural genes aid in the mobile lifestyle of conjugative elements but are not part of the T4SS apparatus for conjugative transfer, such as the membrane pore and relaxosome, or the plasmid maintenance and replication machineries. While these nonstructural genes are not essential for conjugation, they assist in core conjugative functions and mitigate the cellular burden on the host. This review compiles and categorizes known functions of nonstructural genes by the stage of conjugation they modulate: dormancy, transfer, and new host establishment. Themes include establishing a commensalistic relationship with the host, manipulating the host for efficient T4SS assembly and function and assisting in conjugative evasion of recipient cell immune functions. These genes, taken in a broad ecological context, play important roles in ensuring proper propagation of the conjugation system in a natural environment.},
}
@article {pmid36844929,
year = {2023},
author = {Nielsen, FD and Møller-Jensen, J and Jørgensen, MG},
title = {Adding context to the pneumococcal core genes using bioinformatic analysis of the intergenic pangenome of Streptococcus pneumoniae.},
journal = {Frontiers in bioinformatics},
volume = {3},
number = {},
pages = {1074212},
pmid = {36844929},
issn = {2673-7647},
abstract = {Introduction: Whole genome sequencing offers great opportunities for linking genotypes to phenotypes aiding in our understanding of human disease and bacterial pathogenicity. However, these analyses often overlook non-coding intergenic regions (IGRs). By disregarding the IGRs, crucial information is lost, as genes have little biological function without expression. Methods/Results: In this study, we present the first complete pangenome of the important human pathogen Streptococcus pneumoniae (pneumococcus), spanning both the genes and IGRs. We show that the pneumococcus species retains a small core genome of IGRs that are present across all isolates. Gene expression is highly dependent on these core IGRs, and often several copies of these core IGRs are found across each genome. Core genes and core IGRs show a clear linkage as 81% of core genes are associated with core IGRs. Additionally, we identify a single IGR within the core genome that is always occupied by one of two highly distinct sequences, scattered across the phylogenetic tree. Discussion: Their distribution indicates that this IGR is transferred between isolates through horizontal regulatory transfer independent of the flanking genes and that each type likely serves different regulatory roles depending on their genetic context.},
}
@article {pmid36841913,
year = {2023},
author = {Stockdale, SR and Shkoporov, AN and Khokhlova, EV and Daly, KM and McDonnell, SA and O' Regan, O and Nolan, JA and Sutton, TDS and Clooney, AG and Ryan, FJ and Sheehan, D and Lavelle, A and Draper, LA and Shanahan, F and Ross, RP and Hill, C},
title = {Interpersonal variability of the human gut virome confounds disease signal detection in IBD.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {221},
pmid = {36841913},
issn = {2399-3642},
support = {SFI/12/RC/2273//Science Foundation Ireland (SFI)/ ; 101001684//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; SFI/14/SP APC/B3032//Science Foundation Ireland (SFI)/ ; 220646/Z/20/Z//Wellcome Trust (Wellcome)/ ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Virome/genetics ; *Gastrointestinal Microbiome/genetics ; *Viruses/genetics ; *Colitis, Ulcerative/genetics/microbiology ; *Inflammatory Bowel Diseases/genetics ; },
abstract = {Viruses are increasingly recognised as important components of the human microbiome, fulfilling numerous ecological roles including bacterial predation, immune stimulation, genetic diversification, horizontal gene transfer, microbial interactions, and augmentation of metabolic functions. However, our current view of the human gut virome is tainted by previous sequencing requirements that necessitated the amplification of starting nucleic acids. In this study, we performed an original longitudinal analysis of 40 healthy control, 19 Crohn's disease, and 20 ulcerative colitis viromes over three time points without an amplification bias, which revealed and highlighted the interpersonal individuality of the human gut virome. In contrast to a 16 S rRNA gene analysis of matched samples, we show that α- and β-diversity metrics of unamplified viromes are not as efficient at discerning controls from patients with inflammatory bowel disease. Additionally, we explored the intrinsic properties of unamplified gut viromes and show there is considerable interpersonal variability in viral taxa, infrequent longitudinal persistence of intrapersonal viruses, and vast fluctuations in the abundance of temporal viruses. Together, these properties of unamplified faecal viromes confound the ability to discern disease associations but significantly advance toward an unbiased and accurate representation of the human gut virome.},
}
@article {pmid36840598,
year = {2023},
author = {Densi, A and Iyer, RS and Bhat, PJ},
title = {Synonymous and Nonsynonymous Substitutions in Dictyostelium discoideum Ammonium Transporter amtA Are Necessary for Functional Complementation in Saccharomyces cerevisiae.},
journal = {Microbiology spectrum},
volume = {11},
number = {2},
pages = {e0384722},
pmid = {36840598},
issn = {2165-0497},
abstract = {Ammonium transporters are present in all three domains of life. They have undergone extensive horizontal gene transfer (HGT), gene duplication, and functional diversification and therefore offer an excellent paradigm to study protein evolution. We attempted to complement a mep1Δmep2Δmep3Δ strain of Saccharomyces cerevisiae (triple-deletion strain), which otherwise cannot grow on ammonium as a sole nitrogen source at concentrations of <3 mM, with amtA of Dictyostelium discoideum, an orthologue of S. cerevisiae MEP2. We observed that amtA did not complement the triple-deletion strain of S. cerevisiae for growth on low-ammonium medium. We isolated two mutant derivatives of amtA (amtA M1 and amtA M2) from a PCR-generated mutant plasmid library that complemented the triple-deletion strain of S. cerevisiae. amtA M1 bears three nonsynonymous and two synonymous substitutions, which are necessary for its functionality. amtA M2 bears two nonsynonymous substitutions and one synonymous substitution, all of which are necessary for functionality. Interestingly, AmtA M1 transports ammonium but does not confer methylamine toxicity, while AmtA M2 transports ammonium and confers methylamine toxicity, demonstrating functional diversification. Preliminary biochemical analyses indicated that the mutants differ in their conformations as well as their mechanisms of ammonium transport. These intriguing results clearly point out that protein evolution cannot be fathomed by studying nonsynonymous and synonymous substitutions in isolation. The above-described observations have significant implications for various facets of biological processes and are discussed in detail. IMPORTANCE Functional diversification following gene duplication is one of the major driving forces of protein evolution. While the role of nonsynonymous substitutions in the functional diversification of proteins is well recognized, knowledge of the role of synonymous substitutions in protein evolution is in its infancy. Using functional complementation, we isolated two functional alleles of the D. discoideum ammonium transporter gene (amtA), which otherwise does not function in S. cerevisiae as an ammonium transporters. One of them is an ammonium transporter, while the other is an ammonium transporter that also confers methylammonium (ammonium analogue) toxicity, suggesting functional diversification. Surprisingly, both alleles require a combination of synonymous and nonsynonymous substitutions for their functionality. These results bring out a hitherto-unknown pathway of protein evolution and pave the way for not only understanding protein evolution but also interpreting single nucleotide polymorphisms (SNPs).},
}
@article {pmid36840559,
year = {2023},
author = {Winter, M and Harms, K and Johnsen, P and Vos, M},
title = {Collection of Annotated Acinetobacter Genome Sequences.},
journal = {Microbiology resource announcements},
volume = {12},
number = {3},
pages = {e0109422},
pmid = {36840559},
issn = {2576-098X},
support = {NE/T008083/1//UKRI | Natural Environment Research Council (NERC)/ ; NE/S007504/1//UKRI | Natural Environment Research Council (NERC)/ ; },
abstract = {The genus Acinetobacter contains environmental species as well as opportunistic pathogens of humans. Several species are competent for natural transformation, an important mechanism of horizontal gene transfer. Here, we present the genome sequences of 19 Acinetobacter strains used in past and upcoming studies of natural transformation.},
}
@article {pmid36838481,
year = {2023},
author = {Tsilipounidaki, K and Florou, Z and Skoulakis, A and Fthenakis, GC and Miriagou, V and Petinaki, E},
title = {Diversity of Bacterial Clones and Plasmids of NDM-1 Producing Escherichia coli Clinical Isolates in Central Greece.},
journal = {Microorganisms},
volume = {11},
number = {2},
pages = {},
pmid = {36838481},
issn = {2076-2607},
abstract = {The objective of the present study was to genetically characterize ten NDM-1 producing Escherichia coli isolates, recovered from patients in a hospital in Central Greece during the period 2017 to 2021.The isolates were studied by whole genome sequencing to obtain multi-locus sequencing typing (MLST), identification of blaNDM1-environment, resistome and plasmid content. MLST analysis showed the presence of eight sequence types: ST46* (two isolates), ST46, ST744, ST998, ST410, ST224, ST4380, ST683 and ST12 (one isolate each). Apart of the presence of blaNDM-1, the isolates carried a combination of various to β-lactams encoding resistance genes: blaTEM-1B, blaCTX-15, blaOXA-1, blaVIM-1, blaSHV-5, blaOXA-16, blaOXA-10 and blaVEB-1. Additionally, plurality of resistance genes to aminoglycosides, macrolides, rifamycin, phenicols, sulfonamides and tetracycline was detected. The presence of multiple replicons was observed, with predominance of IncFII and IncFIB. Analysis of blaNDM-1 genetic environment of the isolates showed that seven had 100% identity with the pS-3002cz plasmid (Accession Number KJ 958927), two with the pB-3002cz plasmid (Accession Number KJ958926) and one with the pEc19397-131 plasmid (Accession Number MG878866). Τhis latter plasmid was derived by the fusion of two, previously identified, plasmids, pAMPD2 and pLK75 (Accession Numbers CP078058 and KJ440076, respectively). The diversity of clones and plasmids of NDM-1 producing E. coli isolated from patients in Greece indicates a continuous horizontal gene transfer.},
}
@article {pmid36838414,
year = {2023},
author = {Zayed, AR and Bitar, DM and Steinert, M and Lück, C and Spröer, C and Brettar, I and Höfle, MG and Bunk, B},
title = {Comparative Genomics of Legionella pneumophila Isolates from the West Bank and Germany Support Molecular Epidemiology of Legionnaires' Disease.},
journal = {Microorganisms},
volume = {11},
number = {2},
pages = {},
pmid = {36838414},
issn = {2076-2607},
support = {HO-930/5-1/2//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Legionella pneumophila is an environmental bacterium and clinical pathogen that causes many life-threating outbreaks of an atypical pneumonia called Legionnaires' disease (LD). Studies of this pathogen have focused mainly on Europe and the United States. A shortage in L. pneumophila data is clearly observed for developing countries. To reduce this knowledge gap, L. pneumophila isolates were studied in two widely different geographical areas, i.e., the West Bank and Germany. For this study, we sequenced and compared the whole genome of 38 clinical and environmental isolates of L. pneumophila covering different MLVA-8(12) genotypes in the two areas. Sequencing was conducted using the Illumina HiSeq 2500 platform. In addition, two isolates (A194 and H3) were sequenced using a Pacific Biosciences (PacBio) RSII platform to generate complete reference genomes from each of the geographical areas. Genome sequences from 55 L. pneumophila strains, including 17 reference strains, were aligned with the genome sequence of the closest strain (L. pneumophila strain Alcoy). A whole genome phylogeny based on single nucleotide polymorphisms (SNPs) was created using the ParSNP software v 1.0. The reference genomes obtained for isolates A194 and H3 consisted of circular chromosomes of 3,467,904 bp and 3,691,263 bp, respectively. An average of 36,418 SNPs (min. 8569, max. 70,708 SNPs) against our reference strain L. pneumophila str. Alcoy, and 2367 core-genes were identified among the fifty-five strains. An analysis of the genomic population structure by SNP comparison divided the fifty-five L. pneumophila strains into six branches. Individual isolates in sub-lineages in these branches differed by less than 120 SNPs if they had the same MLVA genotype and were isolated from the same location. A bioinformatics analysis identified the genomic islands (GIs) for horizontal gene transfer and mobile genetic elements, demonstrating that L. pneumophila showed high genome plasticity. Four L. pneumophila isolates (H3, A29, A129 and L10-091) contained well-defined plasmids. On average, only about half of the plasmid genes could be matched to proteins in databases. In silico phage findings suggested that 43 strains contained at least one phage. However, none of them were found to be complete. BLASTp analysis of proteins from the type IV secretion Dot/Icm system showed those proteins highly conserved, with less than 25% structural differences in the new L. pneumophila isolates. Overall, we demonstrated that whole genome sequencing provides a molecular surveillance tool for L. pneumophila at the highest conceivable discriminatory level, i.e., two to eight SNPs were observed for isolates from the same location but several years apart.},
}
@article {pmid36838403,
year = {2023},
author = {Hirose, J},
title = {Diversity and Evolution of Integrative and Conjugative Elements Involved in Bacterial Aromatic Compound Degradation and Their Utility in Environmental Remediation.},
journal = {Microorganisms},
volume = {11},
number = {2},
pages = {},
pmid = {36838403},
issn = {2076-2607},
abstract = {Integrative and conjugative elements (ICEs) are mobile DNA molecules that can be transferred through excision, conjugation, and integration into chromosomes. They contribute to the horizontal transfer of genomic islands across bacterial species. ICEs carrying genes encoding aromatic compound degradation pathways are of interest because of their contribution to environmental remediation. Recent advances in DNA sequencing technology have increased the number of newly discovered ICEs in bacterial genomes and have enabled comparative analysis of their evolution. The two different families of ICEs carry various aromatic compound degradation pathway genes. ICEclc and its related ICEs contain a number of members with diverse catabolic capabilities. In addition, the Tn4371 family, which includes ICEs that carry the chlorinated biphenyl catabolic pathway, has been identified. It is apparent that they underwent evolution through the acquisition, deletion, or exchange of modules to adapt to an environmental niche. ICEs have the property of both stability and mobility in the chromosome. Perspectives on the use of ICEs in environmental remediation are also discussed.},
}
@article {pmid36838273,
year = {2023},
author = {Werner, KA and Feyen, L and Hübner, T and Brüggemann, N and Prost, K and Grohmann, E},
title = {Fate of Horizontal-Gene-Transfer Markers and Beta-Lactamase Genes during Thermophilic Composting of Human Excreta.},
journal = {Microorganisms},
volume = {11},
number = {2},
pages = {},
pmid = {36838273},
issn = {2076-2607},
support = {01DG18005//Federal Ministry of Education and Research/ ; 01DG17010//Federal Ministry of Education and Research/ ; 57354010//German Academic Exchange Service/ ; },
abstract = {Thermophilic composting is a suitable treatment for the recycling of organic wastes for agriculture. However, using human excreta as feedstock for composting raises concerns about antibiotic resistances. We analyzed samples from the start and end of a thermophilic composting trial of human excreta, together with green cuttings and straw, with and without biochar. Beta-lactamase genes blaCTX-M, blaIMP, and blaTEM conferring resistance to broad-spectrum beta-lactam antibiotics, as well as horizontal gene transfer marker genes, intI1 and korB, were quantified using qPCR. We found low concentrations of the beta-lactamase genes in all samples, with non-significant mean decreases in blaCTX-M and blaTEM copy numbers and a mean increase in blaIMP copy numbers. The decrease in both intI1 and korB genes from start to end of composting indicated that thermophilic composting can decrease the horizontal spread of resistance genes. Thus, thermophilic composting can be a suitable treatment for the recycling of human excreta.},
}
@article {pmid36835573,
year = {2023},
author = {Ngcobo, PE and Nkosi, BVZ and Chen, W and Nelson, DR and Syed, K},
title = {Evolution of Cytochrome P450 Enzymes and Their Redox Partners in Archaea.},
journal = {International journal of molecular sciences},
volume = {24},
number = {4},
pages = {},
pmid = {36835573},
issn = {1422-0067},
support = {C686//Universit of Zululand/ ; MND200527525406//National Research Foundation (NRF), South Africa/ ; },
mesh = {Humans ; *Ferredoxins/metabolism ; *Archaea/metabolism ; Phylogeny ; Oxidation-Reduction ; Cytochrome P-450 Enzyme System/metabolism ; Bacteria/metabolism ; },
abstract = {Cytochrome P450 monooxygenases (CYPs/P450s) and their redox partners, ferredoxins, are ubiquitous in organisms. P450s have been studied in biology for over six decades owing to their distinct catalytic activities, including their role in drug metabolism. Ferredoxins are ancient proteins involved in oxidation-reduction reactions, such as transferring electrons to P450s. The evolution and diversification of P450s in various organisms have received little attention and no information is available for archaea. This study is aimed at addressing this research gap. Genome-wide analysis revealed 1204 P450s belonging to 34 P450 families and 112 P450 subfamilies, where some families and subfamilies are expanded in archaea. We also identified 353 ferredoxins belonging to the four types 2Fe-2S, 3Fe-4S, 7Fe-4S and 2[4Fe-4S] in 40 archaeal species. We found that bacteria and archaea shared the CYP109, CYP147 and CYP197 families, as well as several ferredoxin subtypes, and that these genes are co-present on archaeal plasmids and chromosomes, implying the plasmid-mediated lateral transfer of these genes from bacteria to archaea. The absence of ferredoxins and ferredoxin reductases in the P450 operons suggests that the lateral transfer of these genes is independent. We present different scenarios for the evolution and diversification of P450s and ferredoxins in archaea. Based on the phylogenetic analysis and high affinity to diverged P450s, we propose that archaeal P450s could have diverged from CYP109, CYP147 and CYP197. Based on this study's results, we propose that all archaeal P450s are bacterial in origin and that the original archaea had no P450s.},
}
@article {pmid36833369,
year = {2023},
author = {Wittich, RM and Haïdour, A and Aguilar-Romero, I and de la Torre-Zúñiga, J and van Dillewijn, P},
title = {Biodegradation of Microtoxic Phenylpropanoids (Phenylpropanoic Acid and Ibuprofen) by Bacteria and the Relevance for Their Removal from Wastewater Treatment Plants.},
journal = {Genes},
volume = {14},
number = {2},
pages = {},
pmid = {36833369},
issn = {2073-4425},
mesh = {*Ibuprofen/chemistry/metabolism ; Anti-Inflammatory Agents, Non-Steroidal ; Bacteria/metabolism ; Biodegradation, Environmental ; *Water Purification ; },
abstract = {The NSAID ibuprofen (2-(4-isobutylphenyl)propanoic acid) and the structurally related 3-phenylpropanoic acid (3PPA), are widely used pharmaceutical and personal care products (PPCPs) which enter municipal waste streams but whose relatively low rates of elimination by wastewater treatment plants (WWTPs) are leading to the contamination of aquatic resources. Here, we report the isolation of three bacterial strains from a municipal WWTP, which as a consortium are capable of mineralizing ibuprofen. These were identified as the Pseudomonas citronellolis species, termed RW422, RW423 and RW424, in which the first two of these isolates were shown to contain the catabolic ipf operon responsible for the first steps of ibuprofen mineralization. These ipf genes which are associated with plasmids could, experimentally, only be transferred between other Sphingomonadaceae species, such as from the ibuprofen degrading Sphingopyxis granuli RW412 to the dioxins degrading Rhizorhabdus wittichii RW1, generating RW421, whilst a transfer from the P. citronellolis isolates to R. wittichii RW1 was not observed. RW412 and its derivative, RW421, as well as the two-species consortium RW422/RW424, can also mineralize 3PPA. We show that IpfF can convert 3PPA to 3PPA-CoA; however, the growth of RW412 with 3PPA produces a major intermediate that was identified by NMR to be cinnamic acid. This and the identification of other minor products from 3PPA allows us to propose the major pathway used by RW412 to mineralize 3PPA. Altogether, the findings in this study highlight the importance of ipf genes, horizontal gene transfer, and alternative catabolic pathways in the bacterial populations of WWTPs to eliminate ibuprofen and 3PPA.},
}
@article {pmid36833214,
year = {2023},
author = {Gosselin, SP and Arsenault, DR and Jennings, CA and Gogarten, JP},
title = {The Evolutionary History of a DNA Methylase Reveals Frequent Horizontal Transfer and Within-Gene Recombination.},
journal = {Genes},
volume = {14},
number = {2},
pages = {},
pmid = {36833214},
issn = {2073-4425},
mesh = {*Evolution, Molecular ; *Inteins/genetics ; Gene Transfer, Horizontal ; Endonucleases/genetics ; DNA ; },
abstract = {Inteins, often referred to as protein introns, are highly mobile genetic elements that invade conserved genes throughout the tree of life. Inteins have been found to invade a wide variety of key genes within actinophages. While in the process of conducting a survey of these inteins in actinophages, we discovered that one protein family of methylases contained a putative intein, and two other unique insertion elements. These methylases are known to occur commonly in phages as orphan methylases (possibly as a form of resistance to restriction-modification systems). We found that the methylase family is not conserved within phage clusters and has a disparate distribution across divergent phage groups. We determined that two of the three insertion elements have a patchy distribution within the methylase protein family. Additionally, we found that the third insertion element is likely a second homing endonuclease, and that all three elements (the intein, the homing endonuclease, and what we refer to as the ShiLan domain) have different insertion sites that are conserved in the methylase gene family. Furthermore, we find strong evidence that both the intein and ShiLan domain are partaking in long-distance horizontal gene transfer events between divergent methylases in disparate phage hosts within the already dispersed methylase distribution. The reticulate evolutionary history of methylases and their insertion elements reveals high rates of gene transfer and within-gene recombination in actinophages.},
}
@article {pmid36833201,
year = {2023},
author = {Liu, S and Jiao, J and Tian, CF},
title = {Adaptive Evolution of Rhizobial Symbiosis beyond Horizontal Gene Transfer: From Genome Innovation to Regulation Reconstruction.},
journal = {Genes},
volume = {14},
number = {2},
pages = {},
pmid = {36833201},
issn = {2073-4425},
mesh = {*Rhizobium/genetics ; Symbiosis/genetics ; Gene Transfer, Horizontal ; Ecosystem ; Nitrogen Fixation/genetics ; *Fabaceae/microbiology ; },
abstract = {There are ubiquitous variations in symbiotic performance of different rhizobial strains associated with the same legume host in agricultural practices. This is due to polymorphisms of symbiosis genes and/or largely unexplored variations in integration efficiency of symbiotic function. Here, we reviewed cumulative evidence on integration mechanisms of symbiosis genes. Experimental evolution, in concert with reverse genetic studies based on pangenomics, suggests that gain of the same circuit of key symbiosis genes through horizontal gene transfer is necessary but sometimes insufficient for bacteria to establish an effective symbiosis with legumes. An intact genomic background of the recipient may not support the proper expression or functioning of newly acquired key symbiosis genes. Further adaptive evolution, through genome innovation and reconstruction of regulation networks, may confer the recipient of nascent nodulation and nitrogen fixation ability. Other accessory genes, either co-transferred with key symbiosis genes or stochastically transferred, may provide the recipient with additional adaptability in ever-fluctuating host and soil niches. Successful integrations of these accessory genes with the rewired core network, regarding both symbiotic and edaphic fitness, can optimize symbiotic efficiency in various natural and agricultural ecosystems. This progress also sheds light on the development of elite rhizobial inoculants using synthetic biology procedures.},
}
@article {pmid36830600,
year = {2023},
author = {Zhao, B and van Bodegom, PM and Trimbos, KB},
title = {Antibiotic Resistance Genes in Interconnected Surface Waters as Affected by Agricultural Activities.},
journal = {Biomolecules},
volume = {13},
number = {2},
pages = {},
pmid = {36830600},
issn = {2218-273X},
support = {201808310084//China Scholarship Council/ ; },
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Drug Resistance, Microbial ; Sulfonamides/pharmacology ; },
abstract = {Pastures have become one of the most important sources of antibiotic resistance genes (ARGs) pollution, bringing risks to human health through the environment and the food that is grown there. Another significant source of food production is greenhouse horticulture, which is typically located near pastures. Through waterways, pasture-originated ARGs may transfer to the food in greenhouses. However, how these pasture-originated ARGs spread to nearby waterways and greenhouses has been much less investigated, while this may pose risks to humans through agricultural products. We analyzed 29 ARGs related to the most used antibiotics in livestock in the Netherlands at 16 locations in an agricultural area, representing pastures, greenhouses and lakes. We found that ARGs were prevalent in all surface waters surrounding pastures and greenhouses and showed a similar composition, with sulfonamide ARGs being dominant. This indicates that both pastures and greenhouses cause antibiotic resistance pressures on neighboring waters. However, lower pressures were found in relatively larger and isolated lakes, suggesting that a larger water body or a non-agricultural green buffer zone could help reducing ARG impacts from agricultural areas. We also observed a positive relationship between the concentrations of the class 1 integron (intl1 gene)-used as a proxy for horizontal gene transfer-and ARG concentration and composition. This supports that horizontal gene transfer might play a role in dispersing ARGs through landscapes. In contrast, none of the measured four abiotic factors (phosphate, nitrate, pH and dissolved oxygen) showed any impact on ARG concentrations. ARGs from different classes co-occurred, suggesting simultaneous use of different antibiotics. Our findings help to understand the spatial patterns of ARGs, specifically the impacts of ARGs from pastures and greenhouses on each other and on nearby waterways. In this way, this study guides management aiming at reducing ARGs' risk to human health from agricultural products.},
}
@article {pmid36830312,
year = {2023},
author = {Bunduruș, IA and Balta, I and Ștef, L and Ahmadi, M and Peț, I and McCleery, D and Corcionivoschi, N},
title = {Overview of Virulence and Antibiotic Resistance in Campylobacter spp. Livestock Isolates.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {2},
pages = {},
pmid = {36830312},
issn = {2079-6382},
abstract = {Campylobacter remains the most prevalent foodborne pathogen bacterium responsible for causing gastroenteritis worldwide. Specifically, this pathogen colonises a ubiquitous range of environments, from poultry, companion pets and livestock animals to humans. The bacterium is uniquely adaptable to various niches, leading to complicated gastroenteritis and, in some cases, difficult to treat due to elevated resistance to certain antibiotics. This increased resistance is currently detected via genomic, clinical or epidemiological studies, with the results highlighting worrying multi-drug resistant (MDR) profiles in many food and clinical isolates. The Campylobacter genome encodes a rich inventory of virulence factors offering the bacterium the ability to influence host immune defences, survive antimicrobials, form biofilms and ultimately boost its infection-inducing potential. The virulence traits responsible for inducing clinical signs are not sufficiently defined because several populations have ample virulence genes with physiological functions that reflect their pathogenicity differences as well as a complement of antimicrobial resistance (AMR) systems. Therefore, exhaustive knowledge of the virulence factors associated with Campylobacter is crucial for collecting molecular insights into the infectivity processes, which could pave the way for new therapeutical targets to combat and control the infection and mitigate the spread of MDR bacteria. This review provides an overview of the spread and prevalence of genetic determinants associated with virulence and antibiotic resistance from studies performed on livestock animals. In addition, we have investigated the relevant coincidental associations between the prevalence of the genes responsible for pathogenic virulence, horizontal gene transfer (HGT) and transmissibility of highly pathogenic Campylobacter strains.},
}
@article {pmid36830244,
year = {2023},
author = {Shi, H and Hu, X and Li, W and Zhang, J and Hu, B and Lou, L},
title = {Soil Component: A Potential Factor Affecting the Occurrence and Spread of Antibiotic Resistance Genes.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {2},
pages = {},
pmid = {36830244},
issn = {2079-6382},
support = {2020YFC1806903//National Key Research and Development Program of China/ ; 41877463//National Natural Science Foundation of China/ ; 22193061//National Natural Science Foundation of China/ ; },
abstract = {In recent years, antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in soil have become research hotspots in the fields of public health and environmental ecosystems, but the effects of soil types and soil components on the occurrence and spread of ARGs still lack systematic sorting and in-depth research. Firstly, investigational information about ARB and ARGs contamination of soil was described. Then, existing laboratory studies about the influence of the soil component on ARGs were summarized in the following aspects: the influence of soil types on the occurrence of ARGs during natural or human activities and the control of exogenously added soil components on ARGs from the macro perspectives, the effects of soil components on the HGT of ARGs in a pure bacterial system from the micro perspectives. Following that, the similarities in pathways by which soil components affect HGT were identified, and the potential mechanisms were discussed from the perspectives of intracellular responses, plasmid activity, quorum sensing, etc. In the future, related research on multi-component systems, multi-omics methods, and microbial communities should be carried out in order to further our understanding of the occurrence and spread of ARGs in soil.},
}
@article {pmid36830238,
year = {2023},
author = {Michaelis, C and Grohmann, E},
title = {Horizontal Gene Transfer of Antibiotic Resistance Genes in Biofilms.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {2},
pages = {},
pmid = {36830238},
issn = {2079-6382},
abstract = {Most bacteria attach to biotic or abiotic surfaces and are embedded in a complex matrix which is known as biofilm. Biofilm formation is especially worrisome in clinical settings as it hinders the treatment of infections with antibiotics due to the facilitated acquisition of antibiotic resistance genes (ARGs). Environmental settings are now considered as pivotal for driving biofilm formation, biofilm-mediated antibiotic resistance development and dissemination. Several studies have demonstrated that environmental biofilms can be hotspots for the dissemination of ARGs. These genes can be encoded on mobile genetic elements (MGEs) such as conjugative and mobilizable plasmids or integrative and conjugative elements (ICEs). ARGs can be rapidly transferred through horizontal gene transfer (HGT) which has been shown to occur more frequently in biofilms than in planktonic cultures. Biofilm models are promising tools to mimic natural biofilms to study the dissemination of ARGs via HGT. This review summarizes the state-of-the-art of biofilm studies and the techniques that visualize the three main HGT mechanisms in biofilms: transformation, transduction, and conjugation.},
}
@article {pmid36830192,
year = {2023},
author = {Sánchez-Osuna, M and Barbé, J and Erill, I},
title = {Systematic In Silico Assessment of Antimicrobial Resistance Dissemination across the Global Plasmidome.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {2},
pages = {},
pmid = {36830192},
issn = {2079-6382},
abstract = {The emergence of pathogenic strains resistant to multiple antimicrobials is a pressing problem in modern healthcare. Antimicrobial resistance is mediated primarily by dissemination of resistance determinants via horizontal gene transfer. The dissemination of some resistance genes has been well documented, but few studies have analyzed the patterns underpinning the dissemination of antimicrobial resistance genes. Analyzing the %GC content of plasmid-borne antimicrobial resistance genes relative to their host genome %GC content provides a means to efficiently detect and quantify dissemination of antimicrobial resistance genes. In this work we automate %GC content analysis to perform a comprehensive analysis of known antimicrobial resistance genes in publicly available plasmid sequences. We find that the degree to which antimicrobial resistance genes are disseminated depends primarily on the resistance mechanism. Our analysis identifies conjugative plasmids as primary dissemination vectors and indicates that most broadly disseminated genes have spread from single genomic backgrounds. We show that resistance dissemination profiles vary greatly among antimicrobials, oftentimes reflecting stewardship measures. Our findings establish %GC content analysis as a powerful, intuitive and scalable method to monitor the dissemination of resistance determinants using publicly available sequence data.},
}
@article {pmid36829548,
year = {2023},
author = {Tang, J and Yao, D and Zhou, H and Wang, M and Daroch, M},
title = {Distinct Molecular Patterns of Two-Component Signal Transduction Systems in Thermophilic Cyanobacteria as Revealed by Genomic Identification.},
journal = {Biology},
volume = {12},
number = {2},
pages = {},
pmid = {36829548},
issn = {2079-7737},
support = {31970092//National Natural Science Foundation of China/ ; 32071480//National Natural Science Foundation of China/ ; 3221101094//National Natural Science Foundation of China/ ; GXWD20201231165807007-20200806170221001//Shenzhen Fundamental Research Program/ ; },
abstract = {Two-component systems (TCSs) play crucial roles in sensing and responding to environmental signals, facilitating the acclimation of cyanobacteria to hostile niches. To date, there is limited information on the TCSs of thermophilic cyanobacteria. Here, genome-based approaches were used to gain insights into the structure and architecture of the TCS in 17 well-described thermophilic cyanobacteria, namely strains from the genus Leptodesmis, Leptolyngbya, Leptothermofonsia, Thermoleptolyngbya, Thermostichus, and Thermosynechococcus. The results revealed a fascinating complexity and diversity of the TCSs. A distinct composition of TCS genes existed among these thermophilic cyanobacteria. A majority of TCS genes were classified as orphan, followed by the paired and complex cluster. A high proportion of histidine kinases (HKs) were predicted to be cytosolic subcellular localizations. Further analyses suggested diversified domain architectures of HK and response regulators (RRs), putatively in association with various functions. Comparative and evolutionary genomic analyses indicated that the horizontal gene transfer, as well as duplications events, might be involved in the evolutionary history of TCS genes in Thermostichus and Thermosynechococcus strains. A comparative analysis between thermophilic and mesophilic cyanobacteria indicated that one HK cluster and one RR cluster were uniquely shared by all the thermophilic cyanobacteria studied, while two HK clusters and one RR cluster were common to all the filamentous thermophilic cyanobacteria. These results suggested that these thermophile-unique clusters may be related to thermal characters and morphology. Collectively, this study shed light on the TCSs of thermophilic cyanobacteria, which may confer the necessary regulatory flexibility; these findings highlight that the genomes of thermophilic cyanobacteria have a broad potential for acclimations to environmental fluctuations.},
}
@article {pmid36827095,
year = {2023},
author = {Pardo-De la Hoz, CJ and Magain, N and Piatkowski, B and Cornet, L and Dal Forno, M and Carbone, I and Miadlikowska, J and Lutzoni, F},
title = {Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria.},
journal = {Systematic biology},
volume = {72},
number = {3},
pages = {694-712},
doi = {10.1093/sysbio/syad008},
pmid = {36827095},
issn = {1076-836X},
support = {1929994//National Science Foundation/ ; },
mesh = {Phylogeny ; *Genome ; Biological Evolution ; Prokaryotic Cells ; *Cyanobacteria/genetics ; },
abstract = {Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies. [Anomaly zone; bacteria; horizontal gene transfer; incomplete lineage sorting; Nostocales; phylogenomic conflict; rapid radiation; Rhizonema.].},
}
@article {pmid36824529,
year = {2022},
author = {Shippy, TD and Miller, S and Tamayo, B and Hosmani, PS and Flores-Gonzalez, M and Mueller, LA and Hunter, WB and Brown, SJ and D'Elia, T and Saha, S},
title = {Manual curation and phylogenetic analysis of chitinase family genes in the Asian citrus psyllid, Diaphorina citri.},
journal = {GigaByte (Hong Kong, China)},
volume = {2022},
number = {},
pages = {gigabyte46},
pmid = {36824529},
issn = {2709-4715},
support = {P20 GM103418/GM/NIGMS NIH HHS/United States ; },
abstract = {Chitinases are enzymes that digest the polysaccharide polymer chitin. During insect development, breakdown of chitin is an essential step in molting of the exoskeleton. Knockdown of chitinases required for molting is lethal to insects, making chitinase genes an interesting target for RNAi-based pest control methods. The Asian citrus psyllid, Diaphorina citri, carries the bacterium causing Huanglongbing, or citrus greening disease, a devastating citrus disease. We identified and annotated 12 chitinase family genes from D. citri as part of a community effort to create high-quality gene models to aid the design of interdictory molecules for pest control. We categorized the D. citri chitinases according to an established classification scheme and re-evaluated the classification of chitinases in other hemipterans. In addition to chitinases from known groups, we identified a novel class of chitinases present in D. citri and several related hemipterans that appears to be the result of horizontal gene transfer.},
}
@article {pmid36823453,
year = {2023},
author = {Webb, EA and Held, NA and Zhao, Y and Graham, ED and Conover, AE and Semones, J and Lee, MD and Feng, Y and Fu, FX and Saito, MA and Hutchins, DA},
title = {Importance of mobile genetic element immunity in numerically abundant Trichodesmium clades.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {15},
pmid = {36823453},
issn = {2730-6151},
support = {1657757//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1851222//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1851222//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1850719//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1850719//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1850719//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 2125191//NSF | Directorate for Biological Sciences (BIO)/ ; },
abstract = {The colony-forming cyanobacteria Trichodesmium spp. are considered one of the most important nitrogen-fixing genera in the warm, low nutrient ocean. Despite this central biogeochemical role, many questions about their evolution, physiology, and trophic interactions remain unanswered. To address these questions, we describe Trichodesmium pangenomic potential via significantly improved genomic assemblies from two isolates and 15 new >50% complete Trichodesmium metagenome-assembled genomes from hand-picked, Trichodesmium colonies spanning the Atlantic Ocean. Phylogenomics identified ~four N2 fixing clades of Trichodesmium across the transect, with T. thiebautii dominating the colony-specific reads. Pangenomic analyses showed that all T. thiebautii MAGs are enriched in COG defense mechanisms and encode a vertically inherited Type III-B Clustered Regularly Interspaced Short Palindromic Repeats and associated protein-based immunity system (CRISPR-Cas). Surprisingly, this CRISPR-Cas system was absent in all T. erythraeum genomes, vertically inherited by T. thiebautii, and correlated with increased signatures of horizontal gene transfer. Additionally, the system was expressed in metaproteomic and transcriptomic datasets and CRISPR spacer sequences with 100% identical hits to field-assembled, putative phage genome fragments were identified. While the currently CO2-limited T. erythraeum is expected to be a 'winner' of anthropogenic climate change, their genomic dearth of known phage resistance mechanisms, compared to T. thiebautii, could put this outcome in question. Thus, the clear demarcation of T. thiebautii maintaining CRISPR-Cas systems, while T. erythraeum does not, identifies Trichodesmium as an ecologically important CRISPR-Cas model system, and highlights the need for more research on phage-Trichodesmium interactions.},
}
@article {pmid36823299,
year = {2023},
author = {Baek, MG and Kim, KW and Yi, H},
title = {Subspecies-level genome comparison of Lactobacillus delbrueckii.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {3171},
pmid = {36823299},
issn = {2045-2322},
mesh = {*Lactobacillus delbrueckii/classification/genetics ; *Genome, Bacterial ; Gene Transfer, Horizontal ; Biological Evolution ; },
abstract = {Lactobacillus delbrueckii comprises six subspecies, L. delbrueckii subsp. bulgaricus, L. delbrueckii subsp. lactis, L. delbrueckii subsp. jakobsenii, L. delbrueckii subsp. delbrueckii, L. delbrueckii subsp. sunkii, and L. delbrueckii subsp. indicus. We investigated the evolution of the six subspecies of L. delbrueckii using comparative genomics. While the defining feature of the species was the gene number increment driven by mobile elements and gene fragmentation, the repertoire of subspecies-specific gene gains and losses differed among the six subspecies. The horizontal gene transfer analyses indicated that frequent gene transfers between different subspecies had occurred when the six subspecies first diverged from the common ancestor, but recent gene exchange was confined to a subspecies implying independent evolution of the six subspecies. The subspecies bulgaricus is a homogeneous group that diverged from the other subspecies a long time ago and underwent convergent evolution. The subspecies lactis, jakobsenii, delbrueckii, and sunkii were more closely related to each other than to other subspecies. The four subspecies commonly show increasing genetic variability with increasing genome size. However, the four subspecies were distinguished by specific gene contents. The subspecies indicus forms a branch distant from the other subspecies and shows an independent evolutionary trend. These results could explain the differences in the habitat and nutritional requirements of the subspecies of L. delbrueckii.},
}
@article {pmid36822312,
year = {2023},
author = {Sun, L and Tang, D and Tai, X and Wang, J and Long, M and Xian, T and Jia, H and Wu, R and Ma, Y and Jiang, Y},
title = {Effect of composted pig manure, biochar, and their combination on antibiotic resistome dissipation in swine wastewater-treated soil.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {323},
number = {},
pages = {121323},
doi = {10.1016/j.envpol.2023.121323},
pmid = {36822312},
issn = {1873-6424},
mesh = {*Composting ; *Manure ; *Drug Resistance, Bacterial ; Brassica/microbiology ; Interspersed Repetitive Sequences ; Soil Microbiology ; *Agriculture/methods ; *Swine ; Animals ; Soil/chemistry ; },
abstract = {The prevalence of antibiotic resistance genes (ARGs), owing to irrigation using untreated swine wastewater, in vegetable-cultivated soils around swine farms poses severe threats to human health. Furthermore, at the field scale, the remediation of such soils is still challenging. Therefore, here, we performed field-scale experiments involving the cultivation of Brassica pekinensis in a swine wastewater-treated soil amended with composted pig manure, biochar, or their combination. Specifically, the ARG and mobile genetic element (MGE) profiles of bulk soil (BS), rhizosphere soil (RS), and root endophyte (RE) samples were examined using high-throughput quantitative polymerase chain reaction. In total, 117 ARGs and 22 MGEs were detected. Moreover, we observed that soil amendment using composted pig manure, biochar, or their combination decreased the absolute abundance of ARGs in BS and RE after 90 days of treatment. However, the decrease in the abundance of ARGs in RS was not significant. We also observed that the manure and biochar co-application showed a minimal synergistic effect. To clarify this observation, we performed network and Spearman correlation analyses and used structure equation models to explore the correlations among ARGs, MGEs, bacterial composition, and soil properties. The results revealed that the soil amendments reduced the abundances of MGEs and potential ARG-carrying bacteria. Additionally, weakened horizontal gene transfer was responsible for the dissipation of ARGs. Thus, our results indicate that composted manure application, with or without biochar, is a useful strategy for soil nutrient supplementation and alleviating farmland ARG pollution, providing a justification for using an alternative to the common agricultural practice of treating the soil using only untreated swine wastewater. Additionally, our results are important in the context of soil health for sustainable agriculture.},
}
@article {pmid36821031,
year = {2023},
author = {Milligan, EG and Calarco, J and Davis, BC and Keenum, IM and Liguori, K and Pruden, A and Harwood, VJ},
title = {A Systematic Review of Culture-Based Methods for Monitoring Antibiotic-Resistant Acinetobacter, Aeromonas, and Pseudomonas as Environmentally Relevant Pathogens in Wastewater and Surface Water.},
journal = {Current environmental health reports},
volume = {10},
number = {2},
pages = {154-171},
pmid = {36821031},
issn = {2196-5412},
mesh = {Humans ; *Wastewater ; Genes, Bacterial ; *Aeromonas/genetics ; Pseudomonas/genetics ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents/pharmacology ; },
abstract = {PURPOSE OF REVIEW: Mounting evidence indicates that habitats such as wastewater and environmental waters are pathways for the spread of antibiotic-resistant bacteria (ARB) and mobile antibiotic resistance genes (ARGs). We identified antibiotic-resistant members of the genera Acinetobacter, Aeromonas, and Pseudomonas as key opportunistic pathogens that grow or persist in built (e.g., wastewater) or natural aquatic environments. Effective methods for monitoring these ARB in the environment are needed to understand their influence on dissemination of ARB and ARGs, but standard methods have not been developed. This systematic review considers peer-reviewed papers where the ARB above were cultured from wastewater or surface water, focusing on the accuracy of current methodologies.<br><br>RECENT FINDINGS: Recent studies suggest that many clinically important ARGs were originally acquired from environmental microorganisms. Acinetobacter, Aeromonas, and Pseudomonas species are of interest because their ability to persist and grow in the environment provides opportunities to engage in horizontal gene transfer with other environmental bacteria. Pathogenic strains of these organisms resistant to multiple, clinically relevant drug classes have been identified as an urgent threat. However, culture methods for these bacteria were generally developed for clinical samples and are not well-vetted for environmental samples. The search criteria yielded 60 peer-reviewed articles over the past 20&#xa0;years, which reported a wide variety of methods for isolation, confirmation, and antibiotic resistance assays. Based on a systematic comparison of the reported methods, we suggest a path forward for standardizing methodologies for monitoring antibiotic resistant strains of these bacteria in water environments.},
}
@article {pmid36818863,
year = {2023},
author = {Matveeva, T and Аndronov, E and Chen, K},
title = {Editorial: Rhizobiaceae mediated HGT: Facts, mechanisms, and evolutionary consequences.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1149426},
doi = {10.3389/fpls.2023.1149426},
pmid = {36818863},
issn = {1664-462X},
}
@article {pmid36813198,
year = {2023},
author = {Huang, Q and Liu, Z and Guo, Y and Li, B and Yang, Z and Liu, X and Ni, J and Li, X and Zhang, X and Zhou, N and Yin, H and Jiang, C and Hao, L},
title = {Coal-source acid mine drainage reduced the soil multidrug-dominated antibiotic resistome but increased the heavy metal(loid) resistome and energy production-related metabolism.},
journal = {The Science of the total environment},
volume = {873},
number = {},
pages = {162330},
doi = {10.1016/j.scitotenv.2023.162330},
pmid = {36813198},
issn = {1879-1026},
mesh = {*Soil ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; *Metals, Heavy ; Coal ; },
abstract = {A recent global scale study found that mining-impacted environments have multi-antibiotic resistance gene (ARG)-dominated resistomes with an abundance similar to urban sewage but much higher than freshwater sediment. These findings raised concern that mining may increase the risk of ARG environmental proliferation. The current study assessed how typical multimetal(loid)-enriched coal-source acid mine drainage (AMD) contamination affects soil resistomes by comparing with background soils unaffected by AMD. Both contaminated and background soils have multidrug-dominated antibiotic resistomes attributed to the acidic environment. AMD-contaminated soils had a lower relative abundance of ARGs (47.45 ± 23.34 ×/Gb) than background soils (85.47 ± 19.71 ×/Gb) but held high-level heavy metal(loid) resistance genes (MRGs, 133.29 ± 29.36 ×/Gb) and transposase- and insertion sequence-dominated mobile genetic elements (MGEs, 188.51 ± 21.81 ×/Gb), which was 56.26 % and 412.12 % higher than background soils, respectively. Procrustes analysis showed that the microbial community and MGEs exerted more influence on driving heavy metal(loid) resistome variation than antibiotic resistome. The microbial community increased energy production-related metabolism to fulfill the increasing energy needs required by acid and heavy metal(loid) resistance. Horizontal gene transfer (HGT) events primarily exchanged energy- and information-related genes to adapt to the harsh AMD environment. These findings provide new insight into the risk of ARG proliferation in mining environments.},
}
@article {pmid36809063,
year = {2023},
author = {Li, Y and Li, D and Liang, Y and Cui, J and He, K and He, D and Liu, J and Hu, G and Yuan, L},
title = {Characterization of a Tigecycline-Resistant and blaCTX-M-Bearing Klebsiella pneumoniae Strain from a Peacock in a Chinese Zoo.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {3},
pages = {e0176422},
pmid = {36809063},
issn = {1098-5336},
mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; beta-Lactamases/genetics ; Colistin ; Drug Resistance, Multiple, Bacterial/genetics ; *Klebsiella Infections/veterinary/microbiology ; *Klebsiella pneumoniae/drug effects/genetics ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Plasmids/genetics ; Tigecycline/pharmacology ; Animals ; Birds/microbiology ; },
abstract = {In Chinese zoos, there are usually specially designed bird parks, similar to petting zoos, that allow children and adults to interact with diverse birds. However, such behaviors present a risk for the transmission of zoonotic pathogens. Recently, we isolated eight strains of Klebsiella pneumoniae and identified two blaCTX-M-positive strains from 110 birds, including parrots, peacocks, and ostriches, using anal or nasal swabs in a bird park of a zoo in China. There, K. pneumoniae LYS105A was obtained from a diseased peacock with chronic respiratory diseases by a nasal swab, which harbored the blaCTX-M-3 gene and exhibited resistance to amoxicillin, cefotaxime, gentamicin, oxytetracycline, doxycycline, tigecycline, florfenicol, and enrofloxacin. According to an analysis by whole-genome sequencing, K. pneumoniae LYS105A belongs to serotype ST859 (sequence type 859)-K19 (capsular serotype 19) and contains two plasmids, of which pLYS105A-2 can be transferred by electrotransformation and harbors numerous resistance genes such as blaCTX-M-3, aac(6')-Ib-cr5, and qnrB91. The above-mentioned genes are located in a novel mobile composite transposon, Tn7131, which makes horizontal transfer more flexible. Although no known genes were identified in the chromosome, a significant increase in SoxS upregulated the expression levels of phoPQ, acrEF-tolC, and oqxAB, which contributed to strain LYS105A acquiring resistance to tigecycline (MIC = 4 mg/L) and intermediate resistance to colistin (MIC = 2 mg/L). Altogether, our findings show that bird parks in zoos may act as important vehicles for the spread of multidrug-resistant bacteria from birds to humans and vice versa. IMPORTANCE A multidrug-resistant ST859-K19 K. pneumoniae strain, LYS105A, was obtained from a diseased peacock in a Chinese zoo. In addition, multiple resistance genes such as blaCTX-M-3, aac(6')-Ib-cr5, and qnrB91 were located in a novel composite transposon, Tn7131, of a mobile plasmid, implying that most of the resistance genes in strain LYS105A can be moved easily via horizontal gene transfer. Meanwhile, an increase in SoxS can further positively regulate the expression of phoPQ, acrEF-tolC, and oqxAB, which is the key factor for strain LYS105A to develop resistance to tigecycline and colistin. Taken together, these findings enrich our understanding of the horizontal cross-species spread of drug resistance genes, which will help us curb the development of bacterial resistance.},
}
@article {pmid36808308,
year = {2023},
author = {Zhu, Y and Wang, T and Zhu, W and Wei, Q},
title = {Influence of class 2 integron integrase concentration on gene cassette insertion and excision in vivo.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {54},
number = {2},
pages = {645-653},
pmid = {36808308},
issn = {1678-4405},
support = {EP-C-15-001/EPA/EPA/United States ; },
mesh = {*Integrons/genetics ; *Integrases/genetics/metabolism ; Mutagenesis, Insertional ; Promoter Regions, Genetic ; Plasmids/genetics ; },
abstract = {Integron can capture and express antimicrobial resistance gene cassettes and plays important roles in horizontal gene transfer. The establishment of a complete in vitro reaction system will help to reveal integron integrase mediated site-specific recombination process and regulation mechanism. As an enzymatic reaction, the concentration of integrase is assumed to have a great influence on the reaction rate. To determine the influence of different concentrations of integrase on the reaction rate and to find the best range of enzyme concentration were essential to optimizing the in vitro reaction system. In this study, plasmids with gradient transcription levels of class 2 integron integrase gene intI2 under different promoters were constructed. Among plasmids pI2W16, pINTI2N, pI2W, and pI2NW, intI2 transcription levels ranged from about 0.61-fold to 49.65-fold of that in pINTI2N. And the frequencies of gene cassette sat2 integration and excision catalyzed by IntI2 were positively correlated with the transcription levels of intI2 within this range. Western blotting results indicated high expression of IntI2 partly existed in the form of an inclusion body. When compared with Pc of class 1 integron, the spacer sequence of PintI2 can increase the strength of PcW but decrease the strength of PcS. In conclusion, the frequencies of gene cassette integration and excision were positively correlated with the concentration of IntI2. intI2 driving by PcW with PintI2 spacer sequence can obtain the optimum IntI2 concentration required to achieve the maximum recombination efficiency in vivo in this study.},
}
@article {pmid36805559,
year = {2023},
author = {Huang, Y and Sheth, RU and Zhao, S and Cohen, LA and Dabaghi, K and Moody, T and Sun, Y and Ricaurte, D and Richardson, M and Velez-Cortes, F and Blazejewski, T and Kaufman, A and Ronda, C and Wang, HH},
title = {High-throughput microbial culturomics using automation and machine learning.},
journal = {Nature biotechnology},
volume = {41},
number = {10},
pages = {1424-1433},
pmid = {36805559},
issn = {1546-1696},
support = {R01 AI132403/AI/NIAID NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; R21 AI146817/AI/NIAID NIH HHS/United States ; T32 GM007367/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Genomics/methods ; *Microbiota/genetics ; Bacteria ; Automation ; Machine Learning ; },
abstract = {Pure bacterial cultures remain essential for detailed experimental and mechanistic studies in microbiome research, and traditional methods to isolate individual bacteria from complex microbial ecosystems are labor-intensive, difficult-to-scale and lack phenotype-genotype integration. Here we describe an open-source high-throughput robotic strain isolation platform for the rapid generation of isolates on demand. We develop a machine learning approach that leverages colony morphology and genomic data to maximize the diversity of microbes isolated and enable targeted picking of specific genera. Application of this platform on fecal samples from 20 humans yields personalized gut microbiome biobanks totaling 26,997 isolates that represented >80% of all abundant taxa. Spatial analysis on >100,000 visually captured colonies reveals cogrowth patterns between Ruminococcaceae, Bacteroidaceae, Coriobacteriaceae and Bifidobacteriaceae families that suggest important microbial interactions. Comparative analysis of 1,197 high-quality genomes from these biobanks shows interesting intra- and interpersonal strain evolution, selection and horizontal gene transfer. This culturomics framework should empower new research efforts to systematize the collection and quantitative analysis of imaging-based phenotypes with high-resolution genomics data for many emerging microbiome studies.},
}
@article {pmid36805463,
year = {2023},
author = {Engin, AB and Engin, ED and Engin, A},
title = {Effects of co-selection of antibiotic-resistance and metal-resistance genes on antibiotic-resistance potency of environmental bacteria and related ecological risk factors.},
journal = {Environmental toxicology and pharmacology},
volume = {98},
number = {},
pages = {104081},
doi = {10.1016/j.etap.2023.104081},
pmid = {36805463},
issn = {1872-7077},
mesh = {*Genes, Bacterial ; Bacteria ; Drug Resistance, Microbial/genetics ; *Metals, Heavy ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The inadequate elimination of micropollutants in wastewater treatment plants (WWTP), cause to increase in the incidence of antibiotic resistant bacterial strains. Growth of microbial pathogens in WWTP is one of the serious public health problems. The widespread and simultaneous emergence of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in the environment with heavy metals create persistent and selective pressure for co-selection of both genes on environmental microorganisms. Co-localization of ARGs and HMRGs on the same horizontal mobile genetic elements (MGEs) allows the spreading of numerous antibiotic-resistant strains of bacteria in aquatic and terrestrial environment. The biofilm formation and colonization potential of environmental bacteria leads to the co-selection of multi-antibiotic resistance and multi-metal tolerance. Horizontal gene transfer (HGT), co-localization of both ARGs and HMRGs on the same MGEs, and the shared resistomes are important bacteria-associated ecological risks factors, which reduce the effectiveness of antibiotics against bacterial infections.},
}
@article {pmid36805209,
year = {2023},
author = {Rius, M and Rest, JS and Filloramo, GV and Novák Vanclová, AMG and Archibald, JM and Collier, JL},
title = {Horizontal Gene Transfer and Fusion Spread Carotenogenesis Among Diverse Heterotrophic Protists.},
journal = {Genome biology and evolution},
volume = {15},
number = {3},
pages = {},
pmid = {36805209},
issn = {1759-6653},
mesh = {*Carotenoids ; beta Carotene/genetics ; Gene Transfer, Horizontal ; *Stramenopiles ; Bacteria/genetics ; },
abstract = {Thraustochytrids (phylum: Labyrinthulomycota) are nonphotosynthetic marine protists. Some thraustochytrids have crtIBY, a trifunctional fusion gene encoding a protein capable of β-carotene biosynthesis from geranylgeranyl pyrophosphate. Here we show that crtIBY is essential in, and encodes the sole pathway for, carotenoid biosynthesis in the thraustochytrid Aurantiochytrium limacinum ATCC MYA-1381. We explore the evolutionary origins of CrtIBY and discover that the closest related protein domains are present in a small but diverse group of other heterotrophic protists, including the apusomonad Thecamonas trahens and the dinoflagellates Oxyrrhis marina and Noctiluca scintillans. Each organism within this cluster also contains one or more β-carotene 15-15' oxygenase genes (blh and rpe65), suggesting that the acquisition of β-carotene biosynthesis genes may have been related to the production of retinal. Our findings support a novel origin of eukaryotic (apo)carotenoid biosynthesis by horizontal gene transfer from Actinobacteria, Bacteroidetes, and/or Archaea. This reveals a remarkable case of parallel evolution of eukaryotic (apo)carotenogenesis in divergent protistan lineages by repeated gene transfers.},
}
@article {pmid36798152,
year = {2023},
author = {Kosmopoulos, JC and Campbell, DE and Whitaker, RJ and Wilbanks, EG},
title = {Horizontal gene transfer and CRISPR targeting drive phage-bacterial host interactions and coevolution in pink berry marine microbial aggregates.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.02.06.527410},
pmid = {36798152},
issn = {2692-8205},
abstract = {UNLABELLED: Bacteriophages (phages), viruses that infect bacteria, are the most abundant components of microbial communities and play roles in community dynamics and host evolution. The study of phage-host interactions, however, is made difficult by a paucity of model systems from natural environments and known and cultivable phage-host pairs. Here, we investigate phage-host interactions in the "pink berry" consortia, naturally-occurring, low-diversity, macroscopic aggregates of bacteria found in the Sippewissett Salt Marsh (Falmouth, MA, USA). We leverage metagenomic sequence data and a comparative genomics approach to identify eight compete phage genomes, infer their bacterial hosts from host-encoded clustered regularly interspaced short palindromic repeats (CRISPR), and observe the potential evolutionary consequences of these interactions. Seven of the eight phages identified infect the known pink berry symbionts Desulfofustis sp. PB-SRB1, Thiohalocapsa sp. PB-PSB1, and Rhodobacteraceae sp. A2, and belong to entirely novel viral taxa, except for one genome which represents the second member of the Knuthellervirus genus. We further observed increased nucleotide variation over a region of a conserved phage capsid gene that is commonly targeted by host CRISPR systems, suggesting that CRISPRs may drive phage evolution in pink berries. Finally, we identified a predicted phage lysin gene that was horizontally transferred to its bacterial host, potentially via a transposon intermediary, emphasizing the role of phages in bacterial evolution in pink berries. Taken together, our results demonstrate that pink berry consortia contain diverse and variable phages, and provide evidence for phage-host co-evolution via multiple mechanisms in a natural microbial system.<br><br>IMPORTANCE: Phages (viruses that infect bacteria) are important components of all microbial systems, where they drive the turnover of organic matter by lysing host cells, facilitate horizontal gene transfer (HGT), and co-evolve with their bacterial hosts. Bacteria resist phage infection, which is often costly or lethal, through a diversity of mechanisms. One of these mechanisms are CRISPR systems, which encode arrays of phage-derived sequences from past infections to block subsequent infection with related phages. Here, we investigate bacteria and phage populations from a simple marine microbial community known as "pink berries" found in salt marshes of Falmouth, Massachusetts, as a model of phage-host co-evolution. We identify eight novel phages, and characterize a case of putative CRISPR-driven phage evolution and an instance of HGT between phage and host, together suggesting that phages have large evolutionary impacts in a naturally-occuring microbial community.},
}
@article {pmid36795748,
year = {2023},
author = {Johnston, CHG and Hope, R and Soulet, AL and Dewailly, M and De Lemos, D and Polard, P},
title = {The RecA-directed recombination pathway of natural transformation initiates at chromosomal replication forks in the pneumococcus.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {8},
pages = {e2213867120},
pmid = {36795748},
issn = {1091-6490},
mesh = {*Streptococcus pneumoniae/genetics/metabolism ; *Rec A Recombinases/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Chromosomes/metabolism ; DNA/metabolism ; DNA, Single-Stranded/genetics/metabolism ; },
abstract = {Homologous recombination (HR) is a crucial mechanism of DNA strand exchange that promotes genetic repair and diversity in all kingdoms of life. Bacterial HR is driven by the universal recombinase RecA, assisted in the early steps by dedicated mediators that promote its polymerization on single-stranded DNA (ssDNA). In bacteria, natural transformation is a prominent HR-driven mechanism of horizontal gene transfer specifically dependent on the conserved DprA recombination mediator. Transformation involves internalization of exogenous DNA as ssDNA, followed by its integration into the chromosome by RecA-directed HR. How DprA-mediated RecA filamentation on transforming ssDNA is spatiotemporally coordinated with other cellular processes remains unknown. Here, we tracked the localization of fluorescent fusions to DprA and RecA in Streptococcus pneumoniae and revealed that both accumulate in an interdependent manner with internalized ssDNA at replication forks. In addition, dynamic RecA filaments were observed emanating from replication forks, even with heterologous transforming DNA, which probably represent chromosomal homology search. In conclusion, this unveiled interaction between HR transformation and replication machineries highlights an unprecedented role for replisomes as landing pads for chromosomal access of tDNA, which would define a pivotal early HR step for its chromosomal integration.},
}
@article {pmid36792883,
year = {2023},
author = {Lau, DYL and Aguirre Sánchez, JR and Baker-Austin, C and Martinez-Urtaza, J},
title = {What Whole Genome Sequencing Has Told Us About Pathogenic Vibrios.},
journal = {Advances in experimental medicine and biology},
volume = {1404},
number = {},
pages = {337-352},
pmid = {36792883},
issn = {0065-2598},
mesh = {Humans ; Phylogeny ; *Vibrio cholerae/genetics ; *Vibrio parahaemolyticus/genetics ; *Vibrio vulnificus/genetics ; Whole Genome Sequencing ; },
abstract = {When the first microbial genome sequences were published just 20 years ago, our understanding regarding the microbial world changed dramatically. The genomes of the first pathogenic vibrios sequenced, including Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus revealed a functional and phylogenetic diversity previously unimagined as well as a genome structure indelibly shaped by horizontal gene transfer. The initial glimpses into these organisms also revealed a genomic plasticity that allowed these bacteria to thrive in challenging and varied aquatic and marine environments, but critically also a suite of pathogenicity attributes. In this review we outline how our understanding of vibrios has changed over the last two decades with the advent of genomics and advances in bioinformatic and data analysis techniques, it has become possible to provide a more cohesive understanding regarding these bacteria: how these pathogens have evolved and emerged from environmental sources, their evolutionary routes through time and space, how they interact with other bacteria and the human host, as well as initiate disease. We outline novel approaches to the use of whole genome sequencing for this important group of bacteria and how new sequencing technologies may be applied to study these organisms in future studies.},
}
@article {pmid36792876,
year = {2023},
author = {Amaro, C and Carmona-Salido, H},
title = {Vibrio vulnificus, an Underestimated Zoonotic Pathogen.},
journal = {Advances in experimental medicine and biology},
volume = {1404},
number = {},
pages = {175-194},
pmid = {36792876},
issn = {0065-2598},
mesh = {Humans ; Animals ; *Vibrio vulnificus/genetics ; *Vibrio Infections/veterinary/epidemiology ; Aquaculture ; Gene Transfer, Horizontal ; Virulence/genetics ; },
abstract = {V. vulnificus, continues being an underestimated yet lethal zoonotic pathogen. In this chapter, we provide a comprehensive review of numerous aspects of the biology, epidemiology, and virulence mechanisms of this poorly understood pathogen. We will emphasize the widespread role of horizontal gene transfer in V. vulnificus specifically virulence plasmids and draw parallels from aquaculture farms to human health. By placing current findings in the context of climate change, we will also contend that fish farms act as evolutionary drivers that accelerate species evolution and the emergence of new virulent groups. Overall, we suggest that on-farm control measures should be adopted both to protect animals from Vibriosis, and also as a public health measure to prevent the emergence of new zoonotic groups.},
}
@article {pmid36792581,
year = {2023},
author = {Filée, J and Becker, HF and Mellottee, L and Eddine, RZ and Li, Z and Yin, W and Lambry, JC and Liebl, U and Myllykallio, H},
title = {Bacterial origins of thymidylate metabolism in Asgard archaea and Eukarya.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {838},
pmid = {36792581},
issn = {2041-1723},
mesh = {*Archaea/metabolism ; *Eukaryota/genetics/metabolism ; Phylogeny ; Thymidylate Synthase/genetics/metabolism ; Bacteria/genetics/metabolism ; Amino Acids/metabolism ; Folic Acid/metabolism ; DNA/metabolism ; },
abstract = {Asgard archaea include the closest known archaeal relatives of eukaryotes. Here, we investigate the evolution and function of Asgard thymidylate synthases and other folate-dependent enzymes required for the biosynthesis of DNA, RNA, amino acids and vitamins, as well as syntrophic amino acid utilization. Phylogenies of Asgard folate-dependent enzymes are consistent with their horizontal transmission from various bacterial groups. We experimentally validate the functionality of thymidylate synthase ThyX of the cultured 'Candidatus Prometheoarchaeum syntrophicum'. The enzyme efficiently uses bacterial-like folates and is inhibited by mycobacterial ThyX inhibitors, even though the majority of experimentally tested archaea are known to use carbon carriers distinct from bacterial folates. Our phylogenetic analyses suggest that the eukaryotic thymidylate synthase, required for de novo DNA synthesis, is not closely related to archaeal enzymes and might have been transferred from bacteria to protoeukaryotes during eukaryogenesis. Altogether, our study suggests that the capacity of eukaryotic cells to duplicate their genetic material is a sum of archaeal (replisome) and bacterial (thymidylate synthase) characteristics. We also propose that recent prevalent lateral gene transfer from bacteria has markedly shaped the metabolism of Asgard archaea.},
}
@article {pmid36792019,
year = {2023},
author = {Lekired, A and Cherif-Silini, H and Silini, A and Ben Yahia, H and Ouzari, HI},
title = {Comparative genomics reveals the acquisition of mobile genetic elements by the plant growth-promoting Pantoea eucrina OB49 in polluted environments.},
journal = {Genomics},
volume = {115},
number = {2},
pages = {110579},
doi = {10.1016/j.ygeno.2023.110579},
pmid = {36792019},
issn = {1089-8646},
mesh = {*Metals, Heavy ; *Pantoea/genetics ; Biodegradation, Environmental ; Interspersed Repetitive Sequences ; Genomics ; },
abstract = {Heavy metal-tolerant plant growth-promoting bacteria (PGPB) have gained popularity in bioremediation in recent years. A genome-assisted study of a heavy metal-tolerant PGPB Pantoea eucrina OB49 isolated from the rhizosphere of wheat grown on a heavy metal-contaminated site is presented. Comparative pan-genome analysis indicated that OB49 acquired heavy metal resistance genes through horizontal gene transfer. On contigs S10 and S12, OB49 has two arsRBCH operons that give arsenic resistance. On the S12 contig, an arsRBCH operon was discovered in conjunction with the merRTPCADE operon, which provides mercury resistance. P. eucrina OB49 may be involved in an ecological alternative for heavy metal remediation and growth promotion of wheat grown in metal-polluted soils. Our results suggested the detection of mobile genetic elements that harbour the ars operon and the fluoride resistance genes adjacent to the mer operon.},
}
@article {pmid36791498,
year = {2023},
author = {Sharma, A and Gupta, S and Paul, K},
title = {Evolution of codon and amino acid usage in bacterial protein toxins.},
journal = {Biochemical and biophysical research communications},
volume = {651},
number = {},
pages = {47-55},
doi = {10.1016/j.bbrc.2023.02.001},
pmid = {36791498},
issn = {1090-2104},
mesh = {*Bacterial Proteins/genetics/metabolism ; Amino Acids/metabolism ; *Bacterial Toxins/chemistry ; Bacteria/genetics/metabolism ; Codon/genetics ; },
abstract = {Toxin proteins are secreted by most pathogens as an integral part of pathogenic mechanism(s). The toxins act by either damaging the host cell membrane (for example, pore-forming toxins and RTX toxins) or by modulation of important cellular pathways (for example, inhibition of protein translation by ribosome-inactivating proteins). The mechanism of action of these toxins provides the pathogen with strategies for adaptation in the unfavorable host environment. Though, secreted by different pathogenic species, the protein toxins seem to share common features that allow the protein to bind to specific molecules and enter the host cell. Earlier studies have suggested role of several events like horizontal gene transfer and insertion-deletion mutations in evolution of protein toxins. The present study involving 125 bacterial protein toxins secreted by 49 pathogenic bacteria focuses on the role and constraints of the bacterial genome on evolution of codon and amino acid usage in respective bacterial protein toxins. We compare the nucleotide composition, codon and dinucleotide usage trends between different classes of bacterial protein toxins and between individual toxins and the parent bacterial genome expressing the toxin(s).},
}
@article {pmid36790109,
year = {2023},
author = {van Rooijen, LE and Tromer, EC and van Hooff, JJE and Kops, GJPL and Snel, B},
title = {Increased Sampling and Intracomplex Homologies Favor Vertical Over Horizontal Inheritance of the Dam1 Complex.},
journal = {Genome biology and evolution},
volume = {15},
number = {3},
pages = {},
pmid = {36790109},
issn = {1759-6653},
mesh = {Humans ; *Kinetochores ; Microtubule-Associated Proteins/genetics ; Phylogeny ; Microtubules ; Cell Division ; Cell Cycle Proteins/genetics ; *Saccharomyces cerevisiae Proteins/genetics ; Chromosomal Proteins, Non-Histone/genetics ; },
abstract = {Kinetochores connect chromosomes to spindle microtubules to ensure their correct segregation during cell division. Kinetochores of human and yeasts are largely homologous, their ability to track depolymerizing microtubules, however, is carried out by the nonhomologous complexes Ska1-C and Dam1-C, respectively. We previously reported the unique anti-correlating phylogenetic profiles of Dam1-C and Ska-C found among a wide variety of eukaryotes. Based on these profiles and the limited presence of Dam1-C, we speculated that horizontal gene transfer could have played a role in the evolutionary history of Dam1-C. Here, we present an expanded analysis of Dam1-C evolution, using additional genome as well as transcriptome sequences and recently published 3D structures. This analysis revealed a wider and more complete presence of Dam1-C in Cryptista, Rhizaria, Ichthyosporea, CRuMs, and Colponemidia. The fungal Dam1-C cryo-EM structure supports earlier hypothesized intracomplex homologies, which enables the reconstruction of rooted and unrooted phylogenies. The rooted tree of concatenated Dam1-C subunits is statistically consistent with the species tree of eukaryotes, suggesting that Dam1-C is ancient, and that the present-day phylogenetic distribution is best explained by multiple, independent losses and no horizontal gene transfer was involved. Furthermore, we investigated the ancient origin of Dam1-C via profile-versus-profile searches. Homology among 8 out of the 10 Dam1-C subunits suggests that the complex largely evolved from a single multimerizing subunit that diversified into a hetero-octameric core via stepwise subunit duplication and subfunctionalization of the subunits before the origin of the last eukaryotic common ancestor.},
}
@article {pmid36788632,
year = {2023},
author = {Sezmis, AL and Woods, LC and Peleg, AY and McDonald, MJ},
title = {Horizontal Gene Transfer, Fitness Costs and Mobility Shape the Spread of Antibiotic Resistance Genes into Experimental Populations of Acinetobacter Baylyi.},
journal = {Molecular biology and evolution},
volume = {40},
number = {3},
pages = {},
pmid = {36788632},
issn = {1537-1719},
support = {FT170100441//Australia Research Council Future Fellowship/ ; APP1186140//National Health Medical Research Council/ ; },
mesh = {Acinetobacter ; Plasmids ; Gene Transfer, Horizontal ; Drug Resistance, Microbial ; *Anti-Bacterial Agents ; *Acinetobacter baumannii/genetics ; },
abstract = {Horizontal gene transfer (HGT) is important for microbial evolution, but how evolutionary forces shape the frequencies of horizontally transferred genetic variants in the absence of strong selection remains an open question. In this study, we evolve laboratory populations of Acinetobacter baylyi (ADP1) with HGT from two clinically relevant strains of multidrug-resistant Acinetobacter baumannii (AB5075 and A9844). We find that DNA can cross the species barrier, even without strong selection, and despite substantial DNA sequence divergence between the two species. Our results confirm previous findings that HGT can drive the spread of antibiotic resistance genes (ARGs) without selection for that antibiotic, but not for all of the resistance genes present in the donor genome. We quantify the costs and benefits of horizontally transferred variants and use whole population sequencing to track the spread of ARGs from HGT donors into antibiotic-sensitive recipients. We find that even though most ARGs are taken up by populations of A. baylyi, the long-term fate of an individual gene depends both on its fitness cost and on the type of genetic element that carries the gene. Interestingly, we also found that an integron, but not its host plasmid, is able to spread in A. baylyi populations despite its strong deleterious effect. Altogether, our results show how HGT provides an evolutionary advantage to evolving populations by facilitating the spread of non-selected genetic variation including costly ARGs.},
}
@article {pmid36787297,
year = {2023},
author = {Thompson, CMA and Hall, JPJ and Chandra, G and Martins, C and Saalbach, G and Panturat, S and Bird, SM and Ford, S and Little, RH and Piazza, A and Harrison, E and Jackson, RW and Brockhurst, MA and Malone, JG},
title = {Plasmids manipulate bacterial behaviour through translational regulatory crosstalk.},
journal = {PLoS biology},
volume = {21},
number = {2},
pages = {e3001988},
pmid = {36787297},
issn = {1545-7885},
support = {BB/R018154/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/J/000PR9797/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T004363/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R014884/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R014884/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T010568/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Proteomics ; Plasmids/genetics ; *Bacteria/genetics ; Conjugation, Genetic/genetics ; Gene Transfer, Horizontal ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Beyond their role in horizontal gene transfer, conjugative plasmids commonly encode homologues of bacterial regulators. Known plasmid regulator homologues have highly targeted effects upon the transcription of specific bacterial traits. Here, we characterise a plasmid translational regulator, RsmQ, capable of taking global regulatory control in Pseudomonas fluorescens and causing a behavioural switch from motile to sessile lifestyle. RsmQ acts as a global regulator, controlling the host proteome through direct interaction with host mRNAs and interference with the host's translational regulatory network. This mRNA interference leads to large-scale proteomic changes in metabolic genes, key regulators, and genes involved in chemotaxis, thus controlling bacterial metabolism and motility. Moreover, comparative analyses found RsmQ to be encoded on a large number of divergent plasmids isolated from multiple bacterial host taxa, suggesting the widespread importance of RsmQ for manipulating bacterial behaviour across clinical, environmental, and agricultural niches. RsmQ is a widespread plasmid global translational regulator primarily evolved for host chromosomal control to manipulate bacterial behaviour and lifestyle.},
}
@article {pmid36786613,
year = {2023},
author = {Yang, D and Yang, Y and Qiao, P and Jiang, F and Zhang, X and Zhao, Z and Cai, T and Li, G and Cai, W},
title = {Genomic Island-Encoded Histidine Kinase and Response Regulator Coordinate Mannose Utilization with Virulence in Enterohemorrhagic Escherichia coli.},
journal = {mBio},
volume = {14},
number = {2},
pages = {e0315222},
pmid = {36786613},
issn = {2150-7511},
mesh = {Animals ; Mice ; Humans ; *Enterohemorrhagic Escherichia coli/metabolism ; Virulence/genetics ; Histidine Kinase/genetics/metabolism ; Genomic Islands ; Mannose ; HeLa Cells ; *Escherichia coli Proteins/genetics/metabolism ; Type III Secretion Systems/metabolism ; *Escherichia coli Infections/microbiology ; Gene Expression Regulation, Bacterial ; },
abstract = {Enterohemorrhagic Escherichia coli (EHEC) is a highly adaptive pathogen and has acquired diverse genetic elements, such as genomic islands and prophages, via horizontal gene transfer to promote fitness in vivo. Two-component signaling systems (TCSs) allow bacteria to sense, respond to, and adapt to various environments. This study identified a putative two-component signaling system composed of the histidine kinase EDL5436 (renamed LmvK) and the response regulator EDL5428 (renamed LmvR) in EHEC. lmvK and lmvR along with EDL5429 to EDL5434 (EDL5429-5434) between them constitute the OI167 genomic island and are highly associated with the EHEC pathotype. EDL5429-5434 encode transporters and metabolic enzymes that contribute to growth on mannose and are directly upregulated by LmvK/LmvR in the presence of mannose, as revealed by quantitative PCR (qPCR) and DNase I footprint assays. Moreover, LmvR directly activates the expression of the type III secretion system in response to mannose and promotes the formation of attaching and effacing lesions on HeLa cells. Using human colonoid and mouse infection models, we show that lmvK and lmvR contributed greatly to adherence and microcolony (MC) formation ex vivo and colonization in vivo. Finally, RNA sequencing and chromatin immunoprecipitation coupled with sequencing analyses identified additional direct targets of LmvR, most of which are involved in metabolism. Given that mannose is a mucus-derived sugar that induces virulence and is preferentially used by EHEC during infection, our data revealed a previously unknown mechanism by which EHEC recognizes the host metabolic landscape and regulates virulence expression accordingly. Our findings provide insights into how pathogenic bacteria evolve by acquiring genetic elements horizontally to adapt to host environments. IMPORTANCE The gastrointestinal tract represents a complex and challenging environment for enterohemorrhagic Escherichia coli (EHEC). However, EHEC is a highly adaptable pathogen, requiring only 10 to 100 CFUs to cause infection. This ability was achieved partially by acquiring mobile genetic elements, such as genomic islands, that promote overall fitness. Mannose is an intestinal mucus-derived sugar that stimulates virulence and is preferentially used by EHEC during infection. Here, we characterize the OI167 genomic island of EHEC, which encodes a novel two-component signaling system (TCS) and transporters and metabolic enzymes (EDL5429-5434) involved in mannose utilization. The TCS directly upregulates EDL5429-5434 and genes encoding the type III secretion system in the presence of mannose. Moreover, the TCS contributes greatly to EHEC virulence ex vivo and in vivo. Our data demonstrate an elegant example in which EHEC strains evolve by acquiring genetic elements horizontally to recognize the host metabolic landscape and regulate virulence expression accordingly, leading to successful infections.},
}
@article {pmid36781732,
year = {2023},
author = {Suzuki, M and Hashimoto, Y and Hirabayashi, A and Yahara, K and Yoshida, M and Fukano, H and Hoshino, Y and Shibayama, K and Tomita, H},
title = {Genomic Epidemiological Analysis of Antimicrobial-Resistant Bacteria with Nanopore Sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2632},
number = {},
pages = {227-246},
pmid = {36781732},
issn = {1940-6029},
mesh = {*Nanopore Sequencing ; Bacteria/genetics ; Plasmids/genetics ; Genomics ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {Antimicrobial-resistant (AMR) bacterial infections caused by clinically important bacteria, including ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) and mycobacteria (Mycobacterium tuberculosis and nontuberculous mycobacteria), have become a global public health threat. Their epidemic and pandemic clones often accumulate useful accessory genes in their genomes, such as AMR genes (ARGs) and virulence factor genes (VFGs). This process is facilitated by horizontal gene transfer among microbial communities via mobile genetic elements (MGEs), such as plasmids and phages. Nanopore long-read sequencing allows easy and inexpensive analysis of complex bacterial genome structures, although some aspects of sequencing data calculation and genome analysis methods are not systematically understood. Here we describe the latest and most recommended experimental and bioinformatics methods available for the construction of complete bacterial genomes from nanopore sequencing data and the detection and classification of genotypes of bacterial chromosomes, ARGs, VFGs, plasmids, and other MGEs based on their genomic sequences for genomic epidemiological analysis of AMR bacteria.},
}
@article {pmid36780569,
year = {2023},
author = {McKeithen-Mead, SA and Grossman, AD},
title = {Timing of integration into the chromosome is critical for the fitness of an integrative and conjugative element and its bacterial host.},
journal = {PLoS genetics},
volume = {19},
number = {2},
pages = {e1010524},
pmid = {36780569},
issn = {1553-7404},
support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; R35 GM122538/GM/NIGMS NIH HHS/United States ; T32 GM007287/GM/NIGMS NIH HHS/United States ; },
mesh = {DNA, Bacterial/genetics ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; Chromosomes/metabolism ; Bacteria/genetics ; DNA Transposable Elements ; },
abstract = {Integrative and conjugative elements (ICEs) are major contributors to genome plasticity in bacteria. ICEs reside integrated in the chromosome of a host bacterium and are passively propagated during chromosome replication and cell division. When activated, ICEs excise from the chromosome and may be transferred through the ICE-encoded conjugation machinery into a recipient cell. Integration into the chromosome of the new host generates a stable transconjugant. Although integration into the chromosome of a new host is critical for the stable acquisition of ICEs, few studies have directly investigated the molecular events that occur in recipient cells during generation of a stable transconjugant. We found that integration of ICEBs1, an ICE of Bacillus subtilis, occurred several generations after initial transfer to a new host. Premature integration in new hosts led to cell death and hence decreased fitness of the ICE and transconjugants. Host lethality due to premature integration was caused by rolling circle replication that initiated in the integrated ICEBs1 and extended into the host chromosome, resulting in catastrophic genome instability. Our results demonstrate that the timing of integration of an ICE is linked to cessation of autonomous replication of the ICE, and that perturbing this linkage leads to a decrease in ICE and host fitness due to a loss of viability of transconjugants. Linking integration to cessation of autonomous replication appears to be a conserved regulatory scheme for mobile genetic elements that both replicate and integrate into the chromosome of their host.},
}
@article {pmid36779718,
year = {2023},
author = {Kuntová, L and Mašlaňová, I and Obořilová, R and Šimečková, H and Finstrlová, A and Bárdy, P and Šiborová, M and Troianovska, L and Botka, T and Gintar, P and Šedo, O and Farka, Z and Doškař, J and Pantůček, R},
title = {Staphylococcus aureus Prophage-Encoded Protein Causes Abortive Infection and Provides Population Immunity against Kayviruses.},
journal = {mBio},
volume = {14},
number = {2},
pages = {e0249022},
pmid = {36779718},
issn = {2150-7511},
support = {224067/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Prophages/genetics ; Staphylococcus aureus/genetics ; Lysogeny ; *Staphylococcal Infections/microbiology ; Staphylococcus ; Staphylococcus Phages/genetics ; Membrane Proteins/genetics ; },
abstract = {Both temperate and obligately lytic phages have crucial roles in the biology of staphylococci. While superinfection exclusion among closely related temperate phages is a well-characterized phenomenon, the interactions between temperate and lytic phages in staphylococci are not understood. Here, we present a resistance mechanism toward lytic phages of the genus Kayvirus, mediated by the membrane-anchored protein designated PdpSau encoded by Staphylococcus aureus prophages, mostly of the Sa2 integrase type. The prophage accessory gene pdpSau is strongly linked to the lytic genes for holin and ami2-type amidase and typically replaces genes for the toxin Panton-Valentine leukocidin (PVL). The predicted PdpSau protein structure shows the presence of a membrane-binding α-helix in its N-terminal part and a cytoplasmic positively charged C terminus. We demonstrated that the mechanism of action of PdpSau does not prevent the infecting kayvirus from adsorbing onto the host cell and delivering its genome into the cell, but phage DNA replication is halted. Changes in the cell membrane polarity and permeability were observed from 10 min after the infection, which led to prophage-activated cell death. Furthermore, we describe a mechanism of overcoming this resistance in a host-range Kayvirus mutant, which was selected on an S. aureus strain harboring prophage 53 encoding PdpSau, and in which a chimeric gene product emerged via adaptive laboratory evolution. This first case of staphylococcal interfamily phage-phage competition is analogous to some other abortive infection defense systems and to systems based on membrane-destructive proteins. IMPORTANCE Prophages play an important role in virulence, pathogenesis, and host preference, as well as in horizontal gene transfer in staphylococci. In contrast, broad-host-range lytic staphylococcal kayviruses lyse most S. aureus strains, and scientists worldwide have come to believe that the use of such phages will be successful for treating and preventing bacterial diseases. The effectiveness of phage therapy is complicated by bacterial resistance, whose mechanisms related to therapeutic staphylococcal phages are not understood in detail. In this work, we describe a resistance mechanism targeting kayviruses that is encoded by a prophage. We conclude that the defense mechanism belongs to a broader group of abortive infections, which is characterized by suicidal behavior of infected cells that are unable to produce phage progeny, thus ensuring the survival of the host population. Since the majority of staphylococcal strains are lysogenic, our findings are relevant for the advancement of phage therapy.},
}
@article {pmid36778249,
year = {2023},
author = {Zhou, W and Karan, KR and Gu, W and Klein, HU and Sturm, G and De Jager, PL and Bennett, DA and Hirano, M and Picard, M and Mills, RE},
title = {Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {36778249},
issn = {2692-8205},
support = {P30 AG072975/AG/NIA NIH HHS/United States ; U01 AG046152/AG/NIA NIH HHS/United States ; R01 AG066828/AG/NIA NIH HHS/United States ; U01 AG061356/AG/NIA NIH HHS/United States ; R01 AG017917/AG/NIA NIH HHS/United States ; P30 AG010161/AG/NIA NIH HHS/United States ; R21 HG011493/HG/NHGRI NIH HHS/United States ; P30 AG072931/AG/NIA NIH HHS/United States ; R01 AG015819/AG/NIA NIH HHS/United States ; },
abstract = {The transfer of mitochondrial DNA into the nuclear genomes of eukaryotes (Numts) has been linked to lifespan in non-human species [1-3] and recently demonstrated to occur in rare instances from one human generation to the next [4]. Here we investigated numtogenesis dynamics in humans in two ways. First, we quantified Numts in 1,187 post-mortem brain and blood samples from different individuals. Compared to circulating immune cells (n=389), post-mitotic brain tissue (n=798) contained more Numts, consistent with their potential somatic accumulation. Within brain samples we observed a 5.5-fold enrichment of somatic Numt insertions in the dorsolateral prefrontal cortex compared to cerebellum samples, suggesting that brain Numts arose spontaneously during development or across the lifespan. Moreover, more brain Numts was linked to earlier mortality. The brains of individuals with no cognitive impairment who died at younger ages carried approximately 2 more Numts per decade of life lost than those who lived longer. Second, we tested the dynamic transfer of Numts using a repeated-measures WGS design in a human fibroblast model that recapitulates several molecular hallmarks of aging [5]. These longitudinal experiments revealed a gradual accumulation of one Numt every ~13 days. Numtogenesis was independent of large-scale genomic instability and unlikely driven cell clonality. Targeted pharmacological perturbations including chronic glucocorticoid signaling or impairing mitochondrial oxidative phosphorylation (OxPhos) only modestly increased the rate of numtogenesis, whereas patient-derived SURF1-mutant cells exhibiting mtDNA instability accumulated Numts 4.7-fold faster than healthy donors. Combined, our data document spontaneous numtogenesis in human cells and demonstrate an association between brain cortical somatic Numts and human lifespan. These findings open the possibility that mito-nuclear horizontal gene transfer among human post-mitotic tissues produce functionally-relevant human Numts over timescales shorter than previously assumed.},
}
@article {pmid36778052,
year = {2022},
author = {Seshadri, R and Roux, S and Huber, KJ and Wu, D and Yu, S and Udwary, D and Call, L and Nayfach, S and Hahnke, RL and Pukall, R and White, JR and Varghese, NJ and Webb, C and Palaniappan, K and Reimer, LC and Sardà, J and Bertsch, J and Mukherjee, S and Reddy, TBK and Hajek, PP and Huntemann, M and Chen, IA and Spunde, A and Clum, A and Shapiro, N and Wu, ZY and Zhao, Z and Zhou, Y and Evtushenko, L and Thijs, S and Stevens, V and Eloe-Fadrosh, EA and Mouncey, NJ and Yoshikuni, Y and Whitman, WB and Klenk, HP and Woyke, T and Göker, M and Kyrpides, NC and Ivanova, NN},
title = {Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes.},
journal = {Cell genomics},
volume = {2},
number = {12},
pages = {100213},
pmid = {36778052},
issn = {2666-979X},
abstract = {The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%-50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences.},
}
@article {pmid36772873,
year = {2023},
author = {Molina-Santiago, C and Bernal, P},
title = {Nanotube-mediated plasmid transfer as a natural alternative for the improvement of industrially relevant bacteria.},
journal = {Microbial biotechnology},
volume = {16},
number = {4},
pages = {706-708},
pmid = {36772873},
issn = {1751-7915},
mesh = {Plasmids ; DNA, Bacterial ; *Bacteria/genetics ; *Gene Transfer, Horizontal ; Conjugation, Genetic ; },
}
@article {pmid36772829,
year = {2023},
author = {Shen, M and Goldlust, K and Daniel, S and Lesterlin, C and Yamaichi, Y},
title = {Recipient UvrD helicase is involved in single- to double-stranded DNA conversion during conjugative plasmid transfer.},
journal = {Nucleic acids research},
volume = {51},
number = {6},
pages = {2790-2799},
pmid = {36772829},
issn = {1362-4962},
mesh = {Conjugation, Genetic/genetics ; DNA ; *DNA Helicases/genetics/metabolism ; DNA, Bacterial/genetics/metabolism ; *DNA, Single-Stranded/genetics ; Escherichia coli/genetics/metabolism ; *Escherichia coli Proteins/genetics ; Gene Transfer, Horizontal/genetics ; Plasmids/genetics ; },
abstract = {Dissemination of antibiotic resistance, a current societal challenge, is often driven by horizontal gene transfer through bacterial conjugation. During conjugative plasmid transfer, single-stranded (ss) DNA is transferred from the donor to the recipient cell. Subsequently, a complete double-stranded (ds) plasmid molecule is generated and plasmid-encoded genes are expressed, allowing successful establishment of the transconjugant cell. Such dynamics of transmission can be modulated by host- or plasmid-encoded factors, either in the donor or in the recipient cell. We applied transposon insertion sequencing to identify host-encoded factors that affect conjugative transfer frequency in Escherichia coli. Disruption of the recipient uvrD gene decreased the acquisition frequency of conjugative plasmids belonging to different incompatibility groups. Results from various UvrD mutants suggested that dsDNA binding activity and interaction with RNA polymerase are dispensable, but ATPase activity is required for successful plasmid establishment of transconjugant cells. Live-cell microscopic imaging showed that the newly transferred ssDNA within a uvrD- recipient often failed to be converted to dsDNA. Our work suggested that in addition to its role in maintaining genome integrity, UvrD is also key for the establishment of horizontally acquired plasmid DNA that drives genome diversity and evolution.},
}
@article {pmid36768888,
year = {2023},
author = {Zhang, C and Jiao, C and Sun, X and Li, X},
title = {A MYB Transcription Factor Atlas Provides Insights into the Evolution of Environmental Adaptations in Plants.},
journal = {International journal of molecular sciences},
volume = {24},
number = {3},
pages = {},
pmid = {36768888},
issn = {1422-0067},
support = {32102318//National Natural Science Foundation of China/ ; 2022LFR048//Development Foundation of Zhejiang A &amp; F University/ ; },
mesh = {*Transcription Factors/genetics/metabolism ; Phylogeny ; DNA Copy Number Variations ; Plants/genetics/metabolism ; Genome, Plant ; *Magnoliopsida/genetics ; Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant ; Evolution, Molecular ; },
abstract = {The MYB transcription factor superfamily includes key regulators of plant development and responses to environmental changes. The diversity of lifestyles and morphological characteristics exhibited by plants are potentially associated with the genomic dynamics of the MYB superfamily. With the release of the plant genomes, a comprehensive phylogenomic analysis of the MYB superfamily across Viridiplantae is allowed. The present study performed phylogenetic, phylogenomic, syntenic, horizontal gene transfer, and neo/sub-functionalization analysis of the MYB superfamily to explore the evolutionary contributions of MYB members to species diversification, trait formation, and environmental adaptation in 437 different plant species. We identified major changes in copy number variation and genomic context within subclades across lineages. Multiple MYB subclades showed highly conserved copy number patterns and synteny across flowering plants, whereas others were more dynamic and showed lineage-specific patterns. As examples of lineage-specific morphological divergence, we hypothesize that the gain of a MYB orthogroup associated with flower development and environmental responses and an orthogroup associated with auxin and wax biosynthesis in angiosperms were correlated with the emergence of flowering plants, unbiased neo-/sub-functionalization of gene duplicates contributed to environmental adaptation, and species-specific neo-/sub-functionalization contributed to phenotype divergence between species. Transposable element insertion in promoter regions may have facilitated the sub-/neo-functionalization of MYB genes and likely played a tissue-specific role contributing to sub-/neo-functionalization in plant root tissues. This study provides new insights into the evolutionary divergence of the MYB superfamily across major flowering and non-flowering lineages and emphasizes the need for lineage-/tissue-specific characterization to further understand trait variability and environmental adaptation.},
}
@article {pmid36764681,
year = {2023},
author = {Van Etten, J and Benites, LF and Stephens, TG and Yoon, HS and Bhattacharya, D},
title = {Algae obscura: The potential of rare species as model systems.},
journal = {Journal of phycology},
volume = {59},
number = {2},
pages = {293-300},
doi = {10.1111/jpy.13321},
pmid = {36764681},
issn = {1529-8817},
mesh = {Phylogeny ; *Biological Evolution ; Plants ; Eukaryota/genetics ; *Rhodophyta/genetics ; Plastids/genetics ; Symbiosis/genetics ; },
abstract = {Model organism research has provided invaluable knowledge about foundational biological principles. However, most of these studies have focused on species that are in high abundance, easy to cultivate in the lab, and represent only a small fraction of extant biodiversity. Here, we present three examples of rare algae with unusual features that we refer to as "algae obscura." The Cyanidiophyceae (Rhodophyta), Glaucophyta, and Paulinella (rhizarian) lineages have all transitioned out of obscurity to become models for fundamental evolutionary research. Insights have been gained into the prevalence and importance of eukaryotic horizontal gene transfer, early Earth microbial community dynamics, primary plastid endosymbiosis, and the origin of Archaeplastida. By reviewing the research that has come from the exploration of these organisms, we demonstrate that underappreciated algae have the potential to help us formulate, refine, and substantiate core hypotheses and that such organisms should be considered when establishing future model systems.},
}
@article {pmid36764395,
year = {2023},
author = {Van Dijck, C and Laumen, JGE and de Block, T and Abdellati, S and De Baetselier, I and Tsoumanis, A and Malhotra-Kumar, S and Manoharan-Basil, SS and Kenyon, C and Xavier, BB},
title = {The oropharynx of men using HIV pre-exposure prophylaxis is enriched with antibiotic resistance genes: A cross-sectional observational metagenomic study.},
journal = {The Journal of infection},
volume = {86},
number = {4},
pages = {329-337},
doi = {10.1016/j.jinf.2023.02.006},
pmid = {36764395},
issn = {1532-2742},
mesh = {Male ; Humans ; Homosexuality, Male ; Sexual Behavior ; *Pre-Exposure Prophylaxis ; *HIV Infections/prevention &amp; control/epidemiology ; Anti-Bacterial Agents/pharmacology ; Cross-Sectional Studies ; *Sexual and Gender Minorities ; Oropharynx ; Drug Resistance, Microbial ; Fluoroquinolones ; Macrolides ; },
abstract = {BACKGROUND: Phenotypic studies have found high levels of antimicrobial resistance to cephalosporins, macrolides and fluoroquinolones in commensal Neisseria species in the oropharynx of men who have sex with men (MSM) using HIV pre-exposure prophylaxis (PrEP). These species include Neisseria subflava and Neisseria mucosa. This may represent a risk to pathogens like Neisseria gonorrhoeae which tend to take up antibiotic resistance genes (ARGs) from other bacteria. We aimed to explore to what extent the oropharyngeal resistome of MSM using PrEP differed from the general population.<br><br>METHODS: We collected oropharyngeal swabs from 32 individuals of the general population and from 64 MSM using PrEP. Thirty-two MSM had consumed antibiotics in the previous six months, whereas none of the other participants had. Samples underwent shotgun metagenomic sequencing. Sequencing reads were mapped against MEGARes 2.0 to estimate ARG abundance. ARG abundance was compared between groups by zero-inflated negative binomial regression.<br><br>FINDINGS: ARG abundance was significantly lower in the general population than in MSM (ratio 0.41, 95% CI 0.26-0.65). More specifically, this was the case for fluoroquinolones (0.33, 95% CI 0.15-0.69), macrolides (0.37, 95% CI 0.25-0.56), tetracyclines (0.41, 95% CI 0.25-0.69), and multidrug efflux pumps (0.11, 95% CI 0.03-0.33), but not for beta-lactams (1.38, 95% CI 0.73-2.61). There were no significant differences in ARG abundance between MSM who had used antibiotics and those that had not.<br><br>INTERPRETATION: The resistome of MSM using PrEP is enriched with ARGs, independent of recent antibiotic use. Stewardship campaigns should aim to reduce antibiotic consumption in populations at high risk for STIs.},
}
@article {pmid36762480,
year = {2023},
author = {Arbel-Goren, R and McKeithen-Mead, SA and Voglmaier, D and Afremov, I and Teza, G and Grossman, AD and Stavans, J},
title = {Target search by an imported conjugative DNA element for a unique integration site along a bacterial chromosome during horizontal gene transfer.},
journal = {Nucleic acids research},
volume = {51},
number = {7},
pages = {3116-3129},
pmid = {36762480},
issn = {1362-4962},
support = {R35 GM122538/GM/NIGMS NIH HHS/United States ; T32 GM007287/GM/NIGMS NIH HHS/United States ; R01 GM050895/GM/NIGMS NIH HHS/United States ; },
mesh = {*Gene Transfer, Horizontal ; *DNA ; DNA Replication ; Chromosomes, Bacterial/genetics ; Chemical Phenomena ; Conjugation, Genetic ; DNA, Bacterial/genetics ; },
abstract = {Integrative and conjugative elements (ICEs) are mobile genetic elements that can transfer by conjugation to recipient cells. Some ICEs integrate into a unique site in the genome of their hosts. We studied quantitatively the process by which an ICE searches for its unique integration site in the Bacillus subtilis chromosome. We followed the motion of both ICEBs1 and the chromosomal integration site in real time within individual cells. ICEBs1 exhibited a wide spectrum of dynamical behaviors, ranging from rapid sub-diffusive displacements crisscrossing the cell, to kinetically trapped states. The chromosomal integration site moved sub-diffusively and exhibited pronounced dynamical asymmetry between longitudinal and transversal motions, highlighting the role of chromosomal structure and the heterogeneity of the bacterial interior in the search. The successful search for and subsequent recombination into the integration site is a key step in the acquisition of integrating mobile genetic elements. Our findings provide new insights into intracellular transport processes involving large DNA molecules.},
}
@article {pmid36762093,
year = {2022},
author = {Li, Z and Shen, J and Wang, F and Wang, M and Shen, J and Li, Y and Zhu, Q and Wu, J},
title = {Impacts of organic materials amendment on the soil antibiotic resistome in subtropical paddy fields.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1075234},
pmid = {36762093},
issn = {1664-302X},
abstract = {The organic material amendment has been proven to change the soil antibiotic resistance genes (ARGs) profile, which may threaten human health through the food chain, but the effects and mechanisms of different organic materials on ARGs in paddy soils are less explored. In this study, a field experiment was set up with the treatments of conventional chemical fertilization (NPK) and common organic material amendment [rice straw (RS), swine manure (SM), and biochar (BC)] to explore the effects and mechanisms. In total, 84 unique ARGs were found across the soil samples with different organic material amendments, and they conferred resistance to the major antibiotic classes. Compared with NPK, SM significantly increased the detected number and relative abundance of ARGs. A higher detected number of ARGs than NPK was observed in BC, whereas BC had a lower relative abundance of ARGs than NPK. Compared with NPK, a detected number decrease was observed in RS, although abundance showed no significant differences. Compared with other treatments, a higher detected number and relative abundance of mobile genetic elements (MGEs) were observed in BC, indicating a higher potential for horizontal gene transfer. There were significantly positive relationships between the relative abundances of total ARGs and MGEs and the bacterial abundance. The network analysis suggested the important role of MGEs and bacterial communities in shaping the ARGs profile. Mantel test and redundancy analysis (RDA) suggested that soil carbon, nitrogen, and C/N were the major chemical drivers of the ARGs profile. The risk of ARGs spreading to the food chain should be considered when applying SM and biochar, which shifted the ARGs and MGEs profiles, respectively. Pre-treatment measures need to be studied to reduce the dissemination of ARGs in paddy fields.},
}
@article {pmid36758922,
year = {2023},
author = {Wang, M and Lian, Y and Wang, Y and Zhu, L},
title = {The role and mechanism of quorum sensing on environmental antimicrobial resistance.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {322},
number = {},
pages = {121238},
doi = {10.1016/j.envpol.2023.121238},
pmid = {36758922},
issn = {1873-6424},
mesh = {*Quorum Sensing ; *Anti-Bacterial Agents/toxicity ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; Genes, Bacterial ; },
abstract = {As more environmental contaminants emerging, antibiotics and antibiotic resistance genes (ARGs) have caused a substantial increase of antimicrobial resistance (AMR) in environment. Quorum sensing (QS) is a bacterial cell-to-cell communication process that regulates many traits and gene expression, including ARGs and the related genes that contribute to AMR development. Herein, we summarize the role, physiology, and genetic mechanisms of bacterial QS in AMR development in the environment. First, the effect of QS on AMR is introduced. Next, the role of QS in bacterial physiological behaviors that promote AMR development, including membrane permeability, tactic movement, biofilm formation, persister formation, and small colony variants (SCVs), is systematically analyzed. Furthermore, the regulation of QS on the expression of ARGs, generation of reactive oxygen species (ROS), which affects ARGs formation, and horizontal gene transfer (HGT), which accelerates the transmission of ARGs, are discussed to reveal the molecular mechanism for AMR development. This review provides a reference for a better understanding of AMR evolution and novel insights into AMR prevention.},
}
@article {pmid36758429,
year = {2023},
author = {Li, X and Lu, H and Yang, K and Zhu, L},
title = {Attenuation of tetracyclines and related resistance genes in soil when exposed to nanoscale zero-valent iron.},
journal = {Journal of hazardous materials},
volume = {448},
number = {},
pages = {130867},
doi = {10.1016/j.jhazmat.2023.130867},
pmid = {36758429},
issn = {1873-3336},
mesh = {Humans ; *Tetracyclines/pharmacology ; Soil ; Iron ; Anti-Bacterial Agents/pharmacology ; Biodegradation, Environmental ; *Environmental Restoration and Remediation ; },
abstract = {Antibiotics pollution in soil poses increasing threats to human health due to stimulated proliferation and transmission of antibiotic resistance genes (ARGs). Nanoscale zero-valent iron (NZVI) is a promising material for the remediation of antibiotics, but how NZVI affects the diversity, abundance, and horizontal gene transfer potentials of ARGs remains unclear. Herein, the biotic and abiotic effects of NZVI at different concentrations on tetracyclines (TCs) and the associated ARGs were investigated. Results showed NZVI could effectively accelerate the degradation of TCs, which increased from 51.38% (without NZVI) to 57.96%- 71.66% (1-10 g NZVI/kg) in 20 days. Biotic degradation contributed to 66.10%- 76.30% of the total TCs removal. NZVI induced TCs biodegradation was probably due to alleviated toxicity of TCs on cells and increased microbial biomass and enzyme activities. Additionally, TCs-related ARGs were attenuated with decreased horizontal gene transfer potentials of intI1 and ISCR1, but opposite effects were observed for non TC-related ARGs, especially during excess exposure to NZVI. This study illustrated the possibility of remediating of antibiotic contaminated soil by NZVI and meanwhile reducing the potential risks of ARGs.},
}
@article {pmid36756971,
year = {2024},
author = {Chen, Y and Jia, B and Li, JY and Li, D and He, W},
title = {Characteristics and driving factors of antibiotic resistance genes in aquaculture products from freshwater ponds in China Yangtze River Delta.},
journal = {Environmental technology},
volume = {45},
number = {12},
pages = {2459-2470},
doi = {10.1080/09593330.2023.2176261},
pmid = {36756971},
issn = {1479-487X},
mesh = {Humans ; *Ponds/analysis ; *Genes, Bacterial ; Anti-Bacterial Agents/analysis ; RNA, Ribosomal, 16S ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; China ; Aquaculture ; },
abstract = {Antibiotic resistance genes (ARGs) are widespread in aquaculture and pose a huge threat to aquaculture organisms and human health. In this study, occurrences and relative abundances of ARGs were analysed in the guts of products cultured in freshwater ponds in the Yangtze River Delta region in China. A total of 29 ARGs were found in the gut samples, with detection frequencies ranging from 4.8% to 81%, and the relative abundances (ARGs/16S rRNA) ranging from 10[-7] to 1. In addition, the human dietary intake of ARGs via aquaculture products was assessed, where the daily intake of most ARGs via aquaculture products was higher than those via PM2.5 and drinking water, but lower than that via vegetables. The relative abundances of MGE (IS613, Tp614, tnpA and int1) were significantly correlated with those of multiple ARGs, indicating the horizontal gene transfer (HGT) of ARGs among gut microorganisms. Proteobacteria, Firmicutes and Actinobacteria were the dominated microbial communities found in the guts of aquaculture products. In addition, significant correlations were found between Cyanobacteria and int1, between Nitrospira and tetE, and between sul2 and aadA2, indicating potential same hosts of these genes. In addition, results from co-correlation indicated both HGT (dominated by MGEs) of ARGs and the enrichment of ARGs in bacteria. MGEs, mostly int1, were more effective than bacteria in increasing the ARG abundance. This study could provide a better understanding of the transmission of ARGs in the aquaculture environment and improve the quality of aquaculture products and the ecology.},
}
@article {pmid36753420,
year = {2023},
author = {Beamud, B and García-González, N and Gómez-Ortega, M and González-Candelas, F and Domingo-Calap, P and Sanjuan, R},
title = {Genetic determinants of host tropism in Klebsiella phages.},
journal = {Cell reports},
volume = {42},
number = {2},
pages = {112048},
pmid = {36753420},
issn = {2211-1247},
mesh = {Humans ; *Klebsiella/genetics ; *Bacteriophages/genetics ; Viral Tropism ; Klebsiella pneumoniae/genetics ; Genome, Viral ; },
abstract = {Bacteriophages play key roles in bacterial ecology and evolution and are potential antimicrobials. However, the determinants of phage-host specificity remain elusive. Here, we isolate 46 phages to challenge 138 representative clinical isolates of Klebsiella pneumoniae, a widespread opportunistic pathogen. Spot tests show a narrow host range for most phages, with <2% of 6,319 phage-host combinations tested yielding detectable interactions. Bacterial capsule diversity is the main factor restricting phage host range. Consequently, phage-encoded depolymerases are key determinants of host tropism, and depolymerase sequence types are associated with the ability to infect specific capsular types across phage families. However, all phages with a broader host range found do not encode canonical depolymerases, suggesting alternative modes of entry. These findings expand our knowledge of the complex interactions between bacteria and their viruses and point out the feasibility of predicting the first steps of phage infection using bacterial and phage genome sequences.},
}
@article {pmid36752380,
year = {2023},
author = {Yuan, L and Lu, H and Li, F and Nielsen, J and Kerkhoven, EJ},
title = {HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer.},
journal = {Briefings in bioinformatics},
volume = {24},
number = {2},
pages = {},
pmid = {36752380},
issn = {1477-4054},
mesh = {Phylogeny ; *Gene Transfer, Horizontal ; *Genomics ; Genome ; Evolution, Molecular ; },
abstract = {BACKGROUND: Horizontal gene transfer (HGT) is an important driver in genome evolution, gain-of-function, and metabolic adaptation to environmental niches. Genome-wide identification of putative HGT events has become increasingly practical, given the rapid growth of genomic data. However, existing HGT analysis toolboxes are not widely used, limited by their inability to perform phylogenetic reconstruction to explore potential donors, and the detection of HGT from both evolutionarily distant and closely related species.<br><br>RESULTS: In this study, we have developed HGTphyloDetect, which is a versatile computational toolbox that combines high-throughput analysis with phylogenetic inference, to facilitate comprehensive investigation of HGT events. Two case studies with Saccharomyces cerevisiae and Candida versatilis demonstrate the ability of HGTphyloDetect to identify horizontally acquired genes with high accuracy. In addition, HGTphyloDetect enables phylogenetic analysis to illustrate a likely path of gene transmission among the evolutionarily distant or closely related species.<br><br>CONCLUSIONS: The HGTphyloDetect computational toolbox is designed for ease of use and can accurately find HGT events with a very low false discovery rate in a high-throughput manner. The HGTphyloDetect toolbox and its related user tutorial are freely available at https://github.com/SysBioChalmers/HGTphyloDetect.},
}
@article {pmid36750723,
year = {2023},
author = {Beltran, LC and Cvirkaite-Krupovic, V and Miller, J and Wang, F and Kreutzberger, MAB and Patkowski, JB and Costa, TRD and Schouten, S and Levental, I and Conticello, VP and Egelman, EH and Krupovic, M},
title = {Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {666},
pmid = {36750723},
issn = {2041-1723},
support = {/WT_/Wellcome Trust/United Kingdom ; K99 GM138756/GM/NIGMS NIH HHS/United States ; U24 GM116790/GM/NIGMS NIH HHS/United States ; R35 GM122510/GM/NIGMS NIH HHS/United States ; R00 GM138756/GM/NIGMS NIH HHS/United States ; S10 RR025067/RR/NCRR NIH HHS/United States ; P30 CA044579/CA/NCI NIH HHS/United States ; G20 RR031199/RR/NCRR NIH HHS/United States ; },
mesh = {*Agrobacterium tumefaciens/genetics ; Bacterial Proteins/genetics ; *Conjugation, Genetic ; Cryoelectron Microscopy ; *DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Plasmids ; *Aeropyrum/genetics ; *Pyrobaculum/genetics ; },
abstract = {Conjugation is a major mechanism of horizontal gene transfer promoting the spread of antibiotic resistance among human pathogens. It involves establishing a junction between a donor and a recipient cell via an extracellular appendage known as the mating pilus. In bacteria, the conjugation machinery is encoded by plasmids or transposons and typically mediates the transfer of cognate mobile genetic elements. Much less is known about conjugation in archaea. Here, we determine atomic structures by cryo-electron microscopy of three conjugative pili, two from hyperthermophilic archaea (Aeropyrum pernix and Pyrobaculum calidifontis) and one encoded by the Ti plasmid of the bacterium Agrobacterium tumefaciens, and show that the archaeal pili are homologous to bacterial mating pili. However, the archaeal conjugation machinery, known as Ced, has been 'domesticated', that is, the genes for the conjugation machinery are encoded on the chromosome rather than on mobile genetic elements, and mediates the transfer of cellular DNA.},
}
@article {pmid36748704,
year = {2023},
author = {Anbo, M and Jelsbak, L},
title = {A bittersweet fate: detection of serotype switching in Pseudomonas aeruginosa.},
journal = {Microbial genomics},
volume = {9},
number = {1},
pages = {},
pmid = {36748704},
issn = {2057-5858},
mesh = {Serogroup ; *Pseudomonas aeruginosa ; Drug Resistance, Microbial ; *Gene Transfer, Horizontal ; },
abstract = {High-risk clone types in Pseudomonas aeruginosa are problematic global multidrug-resistant clones. However, apart from their ability to resist antimicrobial treatment, not much is known about what sets these clones apart from the multitude of other clones. In high-risk clone ST111, it has previously been shown that replacement of the native serotype biosynthetic gene cluster (O4) by a different gene cluster (O12) by horizontal gene transfer and recombination may have contributed to the global success of this clone. However, the extent to which isolates undergo this type of serotype switching has not been adequately explored in P. aeruginosa. In the present study, a bioinformatics tool has been developed and utilized to provide a first estimate of serotype switching in groups of multidrug resistant (MDR) clinical isolates. The tool detects serotype switching by analysis of core-genome phylogeny and in silico serotype. Analysis of a national survey of MDR isolates found a prevalence of 3.9 % of serotype-switched isolates in high-risk clone types ST111, ST244 and ST253. A global survey of MDR isolates was additionally analysed, and it was found that 2.3 % of isolates had undergone a serotype switch. To further understand this process, we determined the exact boundaries of the horizontally transferred serotype O12 island. We found that the size of the serotype island correlates with the clone type of the receiving isolate and additionally we found intra-clone type variations in size and boundaries. This suggests multiple serotype switch events. Moreover, we found that the housekeeping gene gyrA is co-transferred with the O12 serotype island, which prompted us to analyse this allele for all serotype O12 isolates. We found that 95 % of ST111 O12 isolates had a resistant gyrA allele and 86 % of all O12 isolates had a resistant gyrA allele. The rates of resistant gyrA alleles in isolates with other prevalent serotypes are all lower. Together, these results show that the transfer and acquisition of serotype O12 in high-risk clone ST111 has happened multiple times and may be facilitated by multiple donors, which clearly suggests a strong selection pressure for this process. However, gyrA-mediated antibiotic resistance may not be the only evolutionary driver.},
}
@article {pmid36748580,
year = {2022},
author = {Wietz, M and López-Pérez, M and Sher, D and Biller, SJ and Rodriguez-Valera, F},
title = {Microbe Profile: Alteromonas macleodii - a widespread, fast-responding, 'interactive' marine bacterium.},
journal = {Microbiology (Reading, England)},
volume = {168},
number = {11},
pages = {},
doi = {10.1099/mic.0.001236},
pmid = {36748580},
issn = {1465-2080},
mesh = {*Genome, Bacterial/genetics ; *Alteromonas/genetics/metabolism ; Phenotype ; Adaptation, Physiological ; Phylogeny ; Seawater/microbiology ; },
abstract = {Alteromonas macleodii is a marine heterotrophic bacterium with widespread distribution - from temperate to tropical oceans, and from surface to deep waters. Strains of A. macleodii exhibit considerable genomic and metabolic variability, and can grow rapidly on diverse organic compounds. A. macleodii is a model organism for the study of population genomics, physiological adaptations and microbial interactions, with individual genomes encoding diverse phenotypic traits influenced by recombination and horizontal gene transfer.},
}
@article {pmid36748576,
year = {2022},
author = {Kupczok, A and Bailey, ZM and Refardt, D and Wendling, CC},
title = {Co-transfer of functionally interdependent genes contributes to genome mosaicism in lambdoid phages.},
journal = {Microbial genomics},
volume = {8},
number = {11},
pages = {},
pmid = {36748576},
issn = {2057-5858},
mesh = {*Bacteriophages/genetics ; Mosaicism ; Operon ; },
abstract = {Lambdoid (or Lambda-like) phages are a group of related temperate phages that can infect Escherichia coli and other gut bacteria. A key characteristic of these phages is their mosaic genome structure, which served as the basis for the 'modular genome hypothesis'. Accordingly, lambdoid phages evolve by transferring genomic regions, each of which constitutes a functional unit. Nevertheless, it is unknown which genes are preferentially transferred together and what drives such co-transfer events. Here we aim to characterize genome modularity by studying co-transfer of genes among 95 distantly related lambdoid (pro-)phages. Based on gene content, we observed that the genomes cluster into 12 groups, which are characterized by a highly similar gene content within the groups and highly divergent gene content across groups. Highly similar proteins can occur in genomes of different groups, indicating that they have been transferred. About 26 % of homologous protein clusters in the four known operons (i.e. the early left, early right, immunity and late operon) engage in gene transfer, which affects all operons to a similar extent. We identified pairs of genes that are frequently co-transferred and observed that these pairs tend to be near one another on the genome. We find that frequently co-transferred genes are involved in related functions and highlight interesting examples involving structural proteins, the cI repressor and Cro regulator, proteins interacting with DNA, and membrane-interacting proteins. We conclude that epistatic effects, where the functioning of one protein depends on the presence of another, play an important role in the evolution of the modular structure of these genomes.},
}
@article {pmid36748570,
year = {2023},
author = {Sengupta, S and Azad, RK},
title = {Leveraging comparative genomics to uncover alien genes in bacterial genomes.},
journal = {Microbial genomics},
volume = {9},
number = {1},
pages = {},
pmid = {36748570},
issn = {2057-5858},
mesh = {*Genome, Bacterial ; *Genomics/methods ; Algorithms ; Biological Evolution ; },
abstract = {A significant challenge in bacterial genomics is to catalogue genes acquired through the evolutionary process of horizontal gene transfer (HGT). Both comparative genomics and sequence composition-based methods have often been invoked to quantify horizontally acquired genes in bacterial genomes. Comparative genomics methods rely on completely sequenced genomes and therefore the confidence in their predictions increases as the databases become more enriched in completely sequenced genomes. Recent developments including in microbial genome sequencing call for reassessment of alien genes based on information-rich resources currently available. We revisited the comparative genomics approach and developed a new algorithm for alien gene detection. Our algorithm compared favourably with the existing comparative genomics-based methods and is capable of detecting both recent and ancient transfers. It can be used as a standalone tool or in concert with other complementary algorithms for comprehensively cataloguing alien genes in bacterial genomes.},
}
@article {pmid36748564,
year = {2023},
author = {Colombi, E and Hill, Y and Lines, R and Sullivan, JT and Kohlmeier, MG and Christophersen, CT and Ronson, CW and Terpolilli, JJ and Ramsay, JP},
title = {Population genomics of Australian indigenous Mesorhizobium reveals diverse nonsymbiotic genospecies capable of nitrogen-fixing symbioses following horizontal gene transfer.},
journal = {Microbial genomics},
volume = {9},
number = {1},
pages = {},
pmid = {36748564},
issn = {2057-5858},
mesh = {Gene Transfer, Horizontal ; *Mesorhizobium/genetics ; Symbiosis/genetics ; Metagenomics ; Nitrogen ; Australia ; *Lotus/microbiology ; Soil ; },
abstract = {Mesorhizobia are soil bacteria that establish nitrogen-fixing symbioses with various legumes. Novel symbiotic mesorhizobia frequently evolve following horizontal transfer of symbiosis-gene-carrying integrative and conjugative elements (ICESyms) to indigenous mesorhizobia in soils. Evolved symbionts exhibit a wide range in symbiotic effectiveness, with some fixing nitrogen poorly or not at all. Little is known about the genetic diversity and symbiotic potential of indigenous soil mesorhizobia prior to ICESym acquisition. Here we sequenced genomes of 144 Mesorhizobium spp. strains cultured directly from cultivated and uncultivated Australian soils. Of these, 126 lacked symbiosis genes. The only isolated symbiotic strains were either exotic strains used previously as legume inoculants, or indigenous mesorhizobia that had acquired exotic ICESyms. No native symbiotic strains were identified. Indigenous nonsymbiotic strains formed 22 genospecies with phylogenomic diversity overlapping the diversity of internationally isolated symbiotic Mesorhizobium spp. The genomes of indigenous mesorhizobia exhibited no evidence of prior involvement in nitrogen-fixing symbiosis, yet their core genomes were similar to symbiotic strains and they generally lacked genes for synthesis of biotin, nicotinate and thiamine. Genomes of nonsymbiotic mesorhizobia harboured similar mobile elements to those of symbiotic mesorhizobia, including ICESym-like elements carrying aforementioned vitamin-synthesis genes but lacking symbiosis genes. Diverse indigenous isolates receiving ICESyms through horizontal gene transfer formed effective symbioses with Lotus and Biserrula legumes, indicating most nonsymbiotic mesorhizobia have an innate capacity for nitrogen-fixing symbiosis following ICESym acquisition. Non-fixing ICESym-harbouring strains were isolated sporadically within species alongside effective symbionts, indicating chromosomal lineage does not predict symbiotic potential. Our observations suggest previously observed genomic diversity amongst symbiotic Mesorhizobium spp. represents a fraction of the extant diversity of nonsymbiotic strains. The overlapping phylogeny of symbiotic and nonsymbiotic clades suggests major clades of Mesorhizobium diverged prior to introduction of symbiosis genes and therefore chromosomal genes involved in symbiosis have evolved largely independent of nitrogen-fixing symbiosis.},
}
@article {pmid36748528,
year = {2022},
author = {Tamminga, SM and Völpel, SL and Schipper, K and Stehle, T and Pannekoek, Y and van Sorge, NM},
title = {Genetic diversity of Staphylococcus aureus wall teichoic acid glycosyltransferases affects immune recognition.},
journal = {Microbial genomics},
volume = {8},
number = {12},
pages = {},
pmid = {36748528},
issn = {2057-5858},
mesh = {Humans ; *Staphylococcus aureus/genetics/metabolism ; Glycosyltransferases/genetics/chemistry/metabolism ; Teichoic Acids/chemistry/metabolism ; Bacterial Proteins/metabolism ; *Staphylococcal Infections ; Codon, Nonsense/metabolism ; },
abstract = {Staphylococcus aureus is a leading cause of skin and soft tissue infections and systemic infections. Wall teichoic acids (WTAs) are cell wall-anchored glycopolymers that are important for S. aureus nasal colonization, phage-mediated horizontal gene transfer, and antibiotic resistance. WTAs consist of a polymerized ribitol phosphate (RboP) chain that can be glycosylated with N-acetylglucosamine (GlcNAc) by three glycosyltransferases: TarS, TarM, and TarP. TarS and TarP modify WTA with β-linked GlcNAc at the C-4 (β1,4-GlcNAc) and the C-3 position (β1,3-GlcNAc) of the RboP subunit, respectively, whereas TarM modifies WTA with α-linked GlcNAc at the C-4 position (α1,4-GlcNAc). Importantly, these WTA glycosylation patterns impact immune recognition and clearance of S. aureus. Previous studies suggest that tarS is near-universally present within the S. aureus population, whereas a smaller proportion co-contain either tarM or tarP. To gain more insight into the presence and genetic variation of tarS, tarM and tarP in the S. aureus population, we analysed a collection of 25 652 S. aureus genomes within the PubMLST database. Over 99 % of isolates contained tarS. Co-presence of tarS/tarM or tarS/tarP occurred in 37 and 7 % of isolates, respectively, and was associated with specific S. aureus clonal complexes. We also identified 26 isolates (0.1 %) that contained all three glycosyltransferase genes. At sequence level, we identified tar alleles with amino acid substitutions in critical enzymatic residues or with premature stop codons. Several tar variants were expressed in a S. aureus tar-negative strain. Analysis using specific monoclonal antibodies and human langerin showed that WTA glycosylation was severely attenuated or absent. Overall, our data provide a broad overview of the genetic diversity of the three WTA glycosyltransferases in the S. aureus population and the functional consequences for immune recognition.},
}
@article {pmid36748517,
year = {2022},
author = {Greig, DR and Bird, MT and Chattaway, MA and Langridge, GC and Waters, EV and Ribeca, P and Jenkins, C and Nair, S},
title = {Characterization of a P1-bacteriophage-like plasmid (phage-plasmid) harbouring bla CTX-M-15 in Salmonella enterica serovar Typhi.},
journal = {Microbial genomics},
volume = {8},
number = {12},
pages = {},
pmid = {36748517},
issn = {2057-5858},
support = {BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10348/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Salmonella typhi/genetics ; *Bacteriophages/genetics ; Bacteriophage P1/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Plasmids/genetics ; beta-Lactamases/genetics ; },
abstract = {Antimicrobial-resistance (AMR) genes can be transferred between microbial cells via horizontal gene transfer (HGT), which involves mobile and integrative elements such as plasmids, bacteriophages, transposons, integrons and pathogenicity islands. Bacteriophages are found in abundance in the microbial world, but their role in virulence and AMR has not fully been elucidated in the Enterobacterales. With short-read sequencing paving the way to systematic high-throughput AMR gene detection, long-read sequencing technologies now enable us to establish how such genes are structurally connected into meaningful genomic units, raising questions about how they might cooperate to achieve their biological function. Here, we describe a novel ~98 kbp circular P1-bacteriophage-like plasmid termed ph681355 isolated from a clinical Salmonella enterica serovar Typhi isolate. It carries bla CTX-M-15, an IncY plasmid replicon (repY gene) and the ISEcP1 mobile element and is, to our knowledge, the first reported P1-bacteriophage-like plasmid (phage-plasmid) in S. enterica Typhi. We compared ph681355 to two previously described phage-plasmids, pSJ46 from S. enterica serovar Indiana and pMCR-1-P3 from Escherichia coli, and found high nucleotide similarity across the backbone. However, we saw low ph681355 backbone similarity to plasmid p60006 associated with the extensively drug-resistant S. enterica Typhi outbreak isolate in Pakistan, providing evidence of an alternative route for bla CTX-M-15 transmission. Our discovery highlights the importance of utilizing long-read sequencing in interrogating bacterial genomic architecture to fully understand AMR mechanisms and their clinical relevance. It also raises questions regarding how widespread bacteriophage-mediated HGT might be, suggesting that the resulting genomic plasticity might be higher than previously thought.},
}
@article {pmid36744899,
year = {2023},
author = {Prasad, A and Ene, A and Jablonska, S and Du, J and Wolfe, AJ and Putonti, C},
title = {Comparative Genomic Study of Streptococcus anginosus Reveals Distinct Group of Urinary Strains.},
journal = {mSphere},
volume = {8},
number = {2},
pages = {e0068722},
pmid = {36744899},
issn = {2379-5042},
support = {R25 DK122954/DK/NIDDK NIH HHS/United States ; 5 R25 DK122954-04/NH/NIH HHS/United States ; },
mesh = {Female ; Humans ; *Streptococcus anginosus/genetics ; Streptococcus/genetics ; Genomics ; *Urinary Tract Infections ; Multilocus Sequence Typing ; },
abstract = {Streptococcus anginosus is a prevalent member of the human flora. While it has been found in the microbiota of "healthy" asymptomatic individuals, it has also been associated with genitourinary tract infections and bacteremia. Based upon multilocus sequence analysis, two subspecies and two genomosubspecies have been characterized for the species. We previously conducted whole-genome sequencing of 85 S. anginosus isolates from the urinary tract. Here, we present genomic analysis of this species, including isolates from the urinary tract as well as gut and fecal, vaginal, oral, respiratory, and blood and heart samples. Average nucleotide identity and core genome analysis revealed that these strains form two distinct groups. Group 1 is comprised of the S. anginosus type strain and other previously identified S. anginosus subspecies and genomosubspecies, including isolates from throughout the human body. In contrast, group 2 consists of predominantly urinary streptococci (n = 77; 85.6%). Both of these S. anginosus groups are distinct from other members of the Streptococcus anginosus group (SAG) species S. intermedius and S. constellatus. Genes conserved among all strains of one group but not in any strains in the other group were next identified. Group 1 strains included genes found in S. intermedius and S. constellatus, suggesting that they were lost within the ancestor of the group 2 strains. In contrast, genes unique to the group 2 strains were homologous to more distant streptococci, indicative of acquisition via horizontal gene transfer. These genes are ideal candidates for use as marker genes to distinguish between the two groups in the human microbiota. IMPORTANCE Whole-genome analysis of S. anginosus strains provides greater insight into the diversity of this species than from marker genes alone. Our investigation of 166 publicly available S. anginosus genomes via average nucleotide identity and core genome analysis revealed two phylogenomically distinct groups of this species, with one group almost exclusively consisting of isolates from the urinary tract. In contrast, only 8 urinary strains were identified within the other group, which contained the S. anginosus type strain, as well as all identified subspecies and genomosubspecies. While genomic analysis suggested that this urinary group of S. anginosus is genomically different from the previously characterized S. anginosus subspecies, phenotypic characterization is still needed. Given prior reports of the prevalence of S. anginosus in the urinary tract of both continent and incontinent females, future studies are needed to investigate if the symptom state of the urinary tract is associated with these two different groups.},
}
@article {pmid36744093,
year = {2023},
author = {Qi, Q and Rajabal, V and Ghaly, TM and Tetu, SG and Gillings, MR},
title = {Identification of integrons and gene cassette-associated recombination sites in bacteriophage genomes.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1091391},
pmid = {36744093},
issn = {1664-302X},
abstract = {Bacteriophages are versatile mobile genetic elements that play key roles in driving the evolution of their bacterial hosts through horizontal gene transfer. Phages co-evolve with their bacterial hosts and have plastic genomes with extensive mosaicism. In this study, we present bioinformatic and experimental evidence that temperate and virulent (lytic) phages carry integrons, including integron-integrase genes, attC/attI recombination sites and gene cassettes. Integrons are normally found in Bacteria, where they capture, express and re-arrange mobile gene cassettes via integron-integrase activity. We demonstrate experimentally that a panel of attC sites carried in virulent phage can be recognized by the bacterial class 1 integron-integrase (IntI1) and then integrated into the paradigmatic attI1 recombination site using an attC x attI recombination assay. With an increasing number of phage genomes projected to become available, more phage-associated integrons and their components will likely be identified in the future. The discovery of integron components in bacteriophages establishes a new route for lateral transfer of these elements and their cargo genes between bacterial host cells.},
}
@article {pmid36741554,
year = {2022},
author = {Lombard, L and van Doorn, R and Groenewald, JZ and Tessema, T and Kuramae, EE and Etolo, DW and Raaijmakers, JM and Crous, PW},
title = {Fusarium diversity associated with the Sorghum-Striga interaction in Ethiopia.},
journal = {Fungal systematics and evolution},
volume = {10},
number = {},
pages = {177-215},
pmid = {36741554},
issn = {2589-3831},
abstract = {Sorghum production is seriously threatened by the root parasitic weeds (RPWs) Striga hermonthica and Striga asiatica in sub-Saharan Africa. Research has shown that Striga control depends on eliminating its seed reserves in soil. Several species of the genus Fusarium (Nectriaceae, Hypocreales), which have been isolated from diseased Striga plants have proven to be highly pathogenic to all developmental stages of these RPWs. In the present study 439 isolates of Fusarium spp. were found associated with soils from Sorghum growing fields, Sorghum rhizosphere, or as endophytes with Sorghum roots and seeds, or as endophytes of Striga stems and seeds. Based on multi-locus phylogenies of combinations of CaM, tef1, rpb1 and rpb2 alignments, and morphological characteristics, 42 species were identified, including three species that are newly described, namely F. extenuatum and F. tangerinum from Sorghum soils, and F. pentaseptatum from seed of Striga hermonthica. Using a previously published AFLP-derived marker that is specific to detect isolates of F. oxysporum f.sp. strigae, an effective soil-borne biocontrol agent against Striga, we also detected the gene in several other Fusarium species. As these isolates were all associated with the Striga/Sorghum pathosystem, the possibility of horizontal gene transfer among these fusaria will be of interest to further investigate in future. Citation: Lombard L, van Doorn R, Groenewald JZ, Tessema T, Kuramae EE, Etolo DW, Raaijmakers JM, Crous PW (2022). Fusarium diversity associated with the Sorghum-Striga interaction in Ethiopia. Fungal Systematics and Evolution 10: 177-215. doi: 10.3114/fuse.2022.10.08.},
}
@article {pmid36740055,
year = {2023},
author = {Markowicz, A},
title = {The significance of metallic nanoparticles in the emerging, development and spread of antibiotic resistance.},
journal = {The Science of the total environment},
volume = {871},
number = {},
pages = {162029},
doi = {10.1016/j.scitotenv.2023.162029},
pmid = {36740055},
issn = {1879-1026},
mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; *Metal Nanoparticles/toxicity ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; },
abstract = {An ever-increasing number of newly synthesised nanoparticles have a constantly expanding range of applications. The large-scale implementation of nanoparticles will inevitably lead to intentional or accidental contamination of various environments. Since the major benefit of using several metallic nanoparticles is antimicrobial activity, these emerging contaminants may have a potentially hazardous impact on the development and spread of antibiotic resistance - a challenge that threats infection therapy worldwide. Few studies underline that metallic nanoparticles may affect the emergence and evolution of resistance via mutations and horizontal transfer between different bacterial species. Due to the complexity of factors and mechanisms involved in disseminating antibiotic resistance, it is crucial to investigate if metallic nanoparticles play a significant role in this process through co-selection ability and pressure exerted on bacteria. The aim of this review is to summarise the current research on mutations and three main horizontal gene transfer modes facilitated by nanoparticles. Here, the current results in the field are presented, major knowledge gaps and the necessity for more environmentally relevant studies are discussed.},
}
@article {pmid36739179,
year = {2023},
author = {Islam, T and Azad, RB and Kasfy, SH and Rahman, AA and Khan, TZ},
title = {Horizontal gene transfer from plant to whitefly.},
journal = {Trends in biotechnology},
volume = {41},
number = {7},
pages = {853-856},
doi = {10.1016/j.tibtech.2023.01.007},
pmid = {36739179},
issn = {1879-3096},
mesh = {Animals ; *Hemiptera/genetics ; Gene Transfer, Horizontal ; },
abstract = {The recent discovery of the horizontal transfer of a toxin-neutralizing gene from plant to whitefly (Bemisia tabaci), a polyphagous insect, sparked a new area of study. In this forum, we discuss some potential biotechnological applications of this newly discovered knowledge in the coevolutionary arms race between plants and whitefly.},
}
@article {pmid36738814,
year = {2023},
author = {Bhowmik, P and Bharatham, N and Murakami, S and Ramachandran, V and Datta, S},
title = {Identification of key amino acid residues in OqxB mediated efflux of fluoroquinolones using site-directed mutagenesis.},
journal = {Research in microbiology},
volume = {174},
number = {4},
pages = {104039},
doi = {10.1016/j.resmic.2023.104039},
pmid = {36738814},
issn = {1769-7123},
mesh = {*Fluoroquinolones/pharmacology ; *Amino Acids ; Anti-Bacterial Agents/pharmacology/metabolism ; Nitrofurantoin ; Escherichia coli/genetics/metabolism ; Mutagenesis, Site-Directed ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Bacterial Proteins/metabolism ; },
abstract = {OqxB belongs to the RND (Resistance-Nodulation-Division) efflux pump family, recognized widely as a major contributor towards enhancing antimicrobial resistance. It is known to be predominantly present in all Klebsiella spp. and is attributed for its role in increasing resistance against an array of antibiotics like nitrofurantoin, quinolones, β-lactams and colistin. However, the presence of oqxB encoding this efflux pump is not limited only to Klebsiella spp., but is also found to occur via horizontal gene transfer in other bacterial genera like Escherichia coli, Enterobacter cloacae and Salmonella spp. Recently, we reported the crystal structure of OqxB and its structure-function relationship required for the efflux of fluoroquinolones. Extending these findings further, we characterized the structural architecture of this efflux pump along with identifying some critical amino acids at the substrate binding domain of OqxB. Based on our in silico modelling studies, both hydrophobic residues (F180, L280, L621, F626) and polar residues (R48, E50, E184, R157, R774) were found to be located at this site. The present work reports the importance of these key amino acid residues and the crucial ion-pair interactions at the substrate-binding pocket, thereby establishing their role in OqxB mediated efflux and the resultant resistance development against fluoroquinolones.},
}
@article {pmid36738611,
year = {2023},
author = {Zhang, Y and Zhao, Z and Xu, H and Wang, L and Liu, R and Jia, X},
title = {Fate of antibiotic resistance genes and bacteria in a coupled water-processing system with wastewater treatment plants and constructed wetlands in coastal eco-industrial parks.},
journal = {Ecotoxicology and environmental safety},
volume = {252},
number = {},
pages = {114606},
doi = {10.1016/j.ecoenv.2023.114606},
pmid = {36738611},
issn = {1090-2414},
mesh = {*Anti-Bacterial Agents/pharmacology/analysis ; *Waste Disposal, Fluid ; Genes, Bacterial ; Wetlands ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Tetracycline/pharmacology ; Sulfanilamide ; Aminoglycosides/pharmacology ; },
abstract = {In coastal eco-industrial zones, wastewater treatment plants (WWTPs) and constructed wetlands (CWs) can alleviate the challenge of water shortage and the negative effect of sewage discharge, while the problems of antibiotic resistance genes (ARGs) have not attracted enough attention. In this research, the Wafergen SmartChip system was adopted to investigate the ARG profiles in a coupled system combined WWTPs and CWs in a coastal industrial park. Potential risks of antibiotic resistance in chemical industrial wastewater were confirmed due to the higher abundance of target ARGs (> 10[7] copies/mL). General decline with partial enrichment in absolute and relative abundance of ARGs from the WWTPs to CWs revealed the effective removal of ARGs in the coupled system, while the fate of different ARG types varied greatly. Aminoglycoside and sulfonamide ARGs were detected with higher abundance (up to 5.34 ×10[7] and 3.61 ×10[7] copies/mL), especially aac(6')-Ib and sul1. Denitrification, secondary sedimentation, and acid hydrolysis contributed to the removal of aminoglycoside, sulfonamide, β-lactamase, chloramphenicol, and multidrug ARGs. Catalytic ozonation contributed to the removal of tetracycline and MLSB ARGs. Subsurface CWs worked effectively for the removal of sulfonamide, tetracycline, and multidrug ARGs, especially tetX, cphA, tetG, and strB. Close correlations between ARGs and MGEs emphasized the vital roles of anthropogenic pollutants and horizontal gene transfer on the diffusion of ARGs. Actinobacteria, Bacteroidota, and Cyanobacteria were dominant in the CWs, while Proteobacteria, Firmicutes, and Planctomycetota were prevalent in the WWTPs. Redundancy analysis and variance partitioning analysis indicated that transposase and water quality posed greater influences on the distribution of ARGs. Co-occurrence network revealed that potential multiple antibiotic resistant pathogenic bacteria decreased in the CWs. The coupled system has a limited effect on the reduction of ARGs and potential ARG hosts, providing a comprehensive insight into the fate of ARGs in conventional water-processing systems.},
}
@article {pmid37938682,
year = {2022},
author = {Orevi, T and Sørensen, SJ and Kashtan, N},
title = {Droplet size and surface hydrophobicity enhance bacterial plasmid transfer rates in microscopic surface wetness.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {72},
pmid = {37938682},
issn = {2730-6151},
support = {#220020475//James S. McDonnell Foundation (McDonnell Foundation)/ ; #1396/19//Israel Science Foundation (ISF)/ ; NNF200C0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; },
abstract = {Conjugal plasmids constitute a major engine for horizontal gene transfer in bacteria, and are key drivers of the spread of antibiotic resistance, virulence, and metabolic functions. Bacteria in terrestrial habitats often inhabit surfaces that are not constantly water-saturated, where microscopic surface wetness (MSW), comprised of thin liquid films and microdroplets, permanently or intermittently occurs. How physical properties of microdroplets, and of the surfaces they reside on, affect plasmid transfer rates is not well understood. Here, building on microscopy-based microdroplet experiments, we examined the relation between droplet properties (size and spread) and plasmid transfer rates at single-cell and individual droplet resolution, using Pseudomonas putida as a model species. We show that transfer rates increase with droplet size, due to higher densities of cells on the surface in larger droplets, resulting from lower ratio between the area of the liquid-solid interface and droplet volumes. We further show that surface hydrophobicity promotes transfer rates via the same mechanism. Our results provide new insights into how physical properties of surfaces and MSW affect plasmid transfer rates, and more generally, microbial interactions mediated by cell-to-cell contact, with important implications for our understanding of the ecology and evolution of bacteria in unsaturated environments.},
}
@article {pmid37938745,
year = {2022},
author = {Kujawska, M and Raulo, A and Millar, M and Warren, F and Baltrūnaitė, L and Knowles, SCL and Hall, LJ},
title = {Bifidobacterium castoris strains isolated from wild mice show evidence of frequent host switching and diverse carbohydrate metabolism potential.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {20},
pmid = {37938745},
issn = {2730-6151},
support = {/WT_/Wellcome Trust/United Kingdom ; BBS/E/F/00044409/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {Members of the gut microbiota genus Bifidobacterium are widely distributed human and animal symbionts believed to exert beneficial effects on their hosts. However, in-depth genomic analyses of animal-associated species and strains are somewhat lacking, particularly in wild animal populations. Here, to examine patterns of host specificity and carbohydrate metabolism capacity, we sequenced whole genomes of Bifidobacterium isolated from wild-caught small mammals from two European countries (UK and Lithuania). Members of Bifidobacterium castoris, Bifidobacterium animalis and Bifodobacterium pseudolongum were detected in wild mice (Apodemus sylvaticus, Apodemus agrarius and Apodemus flavicollis), but not voles or shrews. B. castoris constituted the most commonly recovered Bifidobacterium (78% of all isolates), with the majority of strains only detected in a single population, although populations frequently harboured multiple co-circulating strains. Phylogenetic analysis revealed that the mouse-associated B. castoris clades were not specific to a particular location or host species, and their distribution across the host phylogeny was consistent with regular host shifts rather than host-microbe codiversification. Functional analysis, including in vitro growth assays, suggested that mouse-derived B. castoris strains encoded an extensive arsenal of carbohydrate-active enzymes, including putative novel glycosyl hydrolases such as chitosanases, along with genes encoding putative exopolysaccharides, some of which may have been acquired via horizontal gene transfer. Overall, these results provide a rare genome-level analysis of host specificity and genomic capacity among important gut symbionts of wild animals, and reveal that Bifidobacterium has a labile relationship with its host over evolutionary time scales.},
}
@article {pmid37334233,
year = {2021},
author = {Liguori, R and Rommel, SH and Bengtsson-Palme, J and Helmreich, B and Wurzbacher, C},
title = {Microbial retention and resistances in stormwater quality improvement devices treating road runoff.},
journal = {FEMS microbes},
volume = {2},
number = {},
pages = {xtab008},
pmid = {37334233},
issn = {2633-6685},
abstract = {Current knowledge about the microbial communities that occur in urban road runoff is scarce. Road runoff of trafficked roads can be heavily polluted and is treated by stormwater quality improvement devices (SQIDs). However, microbes may influence the treatment process of these devices or could lead to stress resistant opportunistic microbial strains. In this study, the microbial community in the influent, effluent and the filter materials used to remove dissolved heavy metals from two different SQIDs were analyzed to determine microbial load, retention, composition, and mobile resistance genes. Although the microbes were replaced by new taxa in the effluent, there was no major retention of microbial genera. Further, the bacterial abundance of the SQIDs effluent was relatively stable over time. The heavy metal content correlated with intl1 and with microbial genera. The filter media itself was enriched with Intl1 gene cassettes, carrying several heavy metal and multidrug resistance genes (e.g. czrA, czcA, silP, mexW and mexI), indicating that this is a hot spot for horizontal gene transfer. Overall, the results shed light on road runoff microbial communities, and pointed to distinct bacterial communities within the SQIDs, which subsequently influence the microbial community and the genes released with the treated water.},
}
@article {pmid37744100,
year = {2021},
author = {Stabel, M and Hagemeister, J and Heck, Z and Aliyu, H and Ochsenreither, K},
title = {Characterization and Phylogenetic Analysis of a Novel GH43 β-Xylosidase From Neocallimastix californiae.},
journal = {Frontiers in fungal biology},
volume = {2},
number = {},
pages = {692804},
pmid = {37744100},
issn = {2673-6128},
abstract = {Degradation of lignocellulosic materials to release fermentable mono- and disaccharides is a decisive step toward a sustainable bio-based economy, thereby increasing the demand of robust and highly active lignocellulolytic enzymes. Anaerobic fungi of the phylum Neocallimastigomycota are potent biomass degraders harboring a huge variety of such enzymes. Compared to cellulose, hemicellulose degradation has received much less attention; therefore, the focus of this study has been the enzymatic xylan degradation of anaerobic fungi as these organisms produce some of the most effective known hydrolytic enzymes. We report the heterologous expression of a GH43 xylosidase, Xyl43Nc, and a GH11 endoxylanase, X11Nc, from the anaerobic fungus Neocallimastix californiae in Escherichia coli. The enzymes were identified by screening of the putative proteome. Xyl43Nc was highly active against 4-Nitrophenol-xylopyranosides with a Km of 0.72 mM, a kcat of 29.28 s[-1], a temperature optimum of 32°C and a pH optimum of 6. When combined, Xyl43Nc and X11Nc released xylose from beechwood xylan and arabinoxylan from wheat. Phylogenetic analysis revealed that Xyl43Nc shares common ancestry with enzymes from Spirochaetes and groups separately from Ascomycete sequences in our phylogeny, highlighting the importance of horizontal gene transfer in the evolution of the anaerobic fungi.},
}
@article {pmid37223257,
year = {2021},
author = {Liu, J and Soler, N and Gorlas, A and Cvirkaite-Krupovic, V and Krupovic, M and Forterre, P},
title = {Extracellular membrane vesicles and nanotubes in Archaea.},
journal = {microLife},
volume = {2},
number = {},
pages = {uqab007},
pmid = {37223257},
issn = {2633-6693},
abstract = {Membrane-bound extracellular vesicles (EVs) are secreted by cells from all three domains of life and their implication in various biological processes is increasingly recognized. In this review, we summarize the current knowledge on archaeal EVs and nanotubes, and emphasize their biological significance. In archaea, the EVs and nanotubes have been largely studied in representative species from the phyla Crenarchaeota and Euryarchaeota. The archaeal EVs have been linked to several physiological processes such as detoxification, biomineralization and transport of biological molecules, including chromosomal, viral or plasmid DNA, thereby taking part in genome evolution and adaptation through horizontal gene transfer. The biological significance of archaeal nanotubes is yet to be demonstrated, although they could participate in EV biogenesis or exchange of cellular contents. We also discuss the biological mechanisms leading to EV/nanotube biogenesis in Archaea. It has been recently demonstrated that, similar to eukaryotes, EV budding in crenarchaea depends on the ESCRT machinery, whereas the mechanism of EV budding in euryarchaeal lineages, which lack the ESCRT-III homologues, remains unknown.},
}
@article {pmid37223255,
year = {2021},
author = {Afonina, I and Tien, B and Nair, Z and Matysik, A and Lam, LN and Veleba, M and Jie, AKJ and Rashid, R and Cazenave-Gassiot, A and Wenk, M and Wai, SN and Kline, KA},
title = {The composition and function of Enterococcus faecalis membrane vesicles.},
journal = {microLife},
volume = {2},
number = {},
pages = {uqab002},
pmid = {37223255},
issn = {2633-6693},
abstract = {Membrane vesicles (MVs) contribute to various biological processes in bacteria, including virulence factor delivery, antimicrobial resistance, host immune evasion and cross-species communication. MVs are frequently released from the surface of both Gram-negative and Gram-positive bacteria during growth. In some Gram-positive bacteria, genes affecting MV biogenesis have been identified, but the mechanism of MV formation is unknown. In Enterococcus faecalis, a causative agent of life-threatening bacteraemia and endocarditis, neither mechanisms of MV formation nor their role in virulence has been examined. Since MVs of many bacterial species are implicated in host-pathogen interactions, biofilm formation, horizontal gene transfer, and virulence factor secretion in other species, we sought to identify, describe and functionally characterize MVs from E. faecalis. Here, we show that E. faecalis releases MVs that possess unique lipid and protein profiles, distinct from the intact cell membrane and are enriched in lipoproteins. MVs of E. faecalis are specifically enriched in unsaturated lipids that might provide membrane flexibility to enable MV formation, providing the first insights into the mechanism of MV formation in this Gram-positive organism.},
}
@article {pmid36732595,
year = {2023},
author = {Bhattacharjee, AS and Schulz, F and Woyke, T and Orcutt, BN and Martínez Martínez, J},
title = {Genomics discovery of giant fungal viruses from subsurface oceanic crustal fluids.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {10},
pmid = {36732595},
issn = {2730-6151},
support = {GBMF5334//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; DE-AC02-05CH11231//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; DE-AC02-05CH11231//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; OCE-0939564//National Science Foundation (NSF)/ ; },
abstract = {The oceanic igneous crust is a vast reservoir for microbial life, dominated by diverse and active bacteria, archaea, and fungi. Archaeal and bacterial viruses were previously detected in oceanic crustal fluids at the Juan de Fuca Ridge (JdFR). Here we report the discovery of two eukaryotic Nucleocytoviricota genomes from the same crustal fluids by sorting and sequencing single virions. Both genomes have a tRNA[Tyr] gene with an intron (20 bps) at the canonical position between nucleotide 37 and 38, a common feature in eukaryotic and archaeal tRNA genes with short introns (<100 bps), and fungal genes acquired through horizontal gene transfer (HGT) events. The dominance of Ascomycota fungi as the main eukaryotes in crustal fluids and the evidence for HGT point to these fungi as the putative hosts, making these the first putative fungi-Nucleocytoviricota specific association. Our study suggests active host-viral dynamics for the only eukaryotic group found in the subsurface oceanic crust and raises important questions about the impact of viral infection on the productivity and biogeochemical cycling in this ecosystem.},
}
@article {pmid36727472,
year = {2023},
author = {Daveri, A and Benigno, V and van der Meer, JR},
title = {Characterization of an atypical but widespread type IV secretion system for transfer of the integrative and conjugative element (ICEclc) in Pseudomonas putida.},
journal = {Nucleic acids research},
volume = {51},
number = {5},
pages = {2345-2362},
pmid = {36727472},
issn = {1362-4962},
mesh = {*Pseudomonas putida/genetics ; Type IV Secretion Systems/genetics ; Bacterial Proteins/genetics ; Plasmids/genetics ; Conjugation, Genetic/genetics ; Gene Transfer, Horizontal ; },
abstract = {Conjugation of DNA relies on multicomponent protein complexes bridging two bacterial cytoplasmic compartments. Whereas plasmid conjugation systems have been well documented, those of integrative and conjugative elements (ICEs) have remained poorly studied. We characterize here the conjugation system of the ICEclc element in Pseudomonas putida UWC1 that is a model for a widely distributed family of ICEs. By in frame deletion and complementation, we show the importance on ICE transfer of 22 genes in a 20-kb conserved ICE region. Protein comparisons recognized seven homologs to plasmid type IV secretion system components, another six homologs to frequent accessory proteins, and the rest without detectable counterparts. Stationary phase imaging of P. putida ICEclc with in-frame fluorescent protein fusions to predicted type IV components showed transfer-competent cell subpopulations with multiple fluorescent foci, largely overlapping in dual-labeled subcomponents, which is suggestive for multiple conjugation complexes per cell. Cross-dependencies between subcomponents in ICE-type IV secretion system assembly were revealed by quantitative foci image analysis in a variety of ICEclc mutant backgrounds. In conclusion, the ICEclc family presents an evolutionary distinct type IV conjugative system with transfer competent cells specialized in efficient transfer.},
}
@article {pmid36726572,
year = {2022},
author = {Calero-Cáceres, W and Rodríguez, K and Medina, A and Medina, J and Ortuño-Gutiérrez, N and Sunyoto, T and Dias, CAG and Bastidas-Caldes, C and Ramírez, MS and Harries, AD},
title = {Genomic insights of mcr-1 harboring Escherichia coli by geographical region and a One-Health perspective.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1032753},
pmid = {36726572},
issn = {1664-302X},
abstract = {The importance of the One Health concept in attempting to deal with the increasing levels of multidrug-resistant bacteria in both human and animal health is a challenge for the scientific community, policymakers, and the industry. The discovery of the plasmid-borne mobile colistin resistance (mcr) in 2015 poses a significant threat because of the ability of these plasmids to move between different bacterial species through horizontal gene transfer. In light of these findings, the World Health Organization (WHO) recommends that countries implement surveillance strategies to detect the presence of plasmid-mediated colistin-resistant microorganisms and take suitable measures to control and prevent their dissemination. Seven years later, ten different variants of the mcr gene (mcr-1 to mcr-10) have been detected worldwide in bacteria isolated from humans, animals, foods, the environment, and farms. However, the possible transmission mechanisms of the mcr gene among isolates from different geographical origins and sources are largely unknown. This article presents an analysis of whole-genome sequences of Escherichia coli that harbor mcr-1 gene from different origins (human, animal, food, or environment) and geographical location, to identify specific patterns related to virulence genes, plasmid content and antibiotic resistance genes, as well as their phylogeny and their distribution with their origin. In general, E. coli isolates that harbor mcr-1 showed a wide plethora of ARGs. Regarding the plasmid content, the highest concentration of plasmids was found in animal samples. In turn, Asia was the continent that led with the largest diversity and occurrence of these plasmids. Finally, about virulence genes, terC, gad, and traT represent the most frequent virulence genes detected. These findings highlight the relevance of analyzing the environmental settings as an integrative part of the surveillance programs to understand the origins and dissemination of antimicrobial resistance.},
}
@article {pmid36726175,
year = {2023},
author = {Petersen, C and Sørensen, T and Nielsen, MR and Sondergaard, TE and Sørensen, JL and Fitzpatrick, DA and Frisvad, JC and Nielsen, KL},
title = {Comparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events.},
journal = {IMA fungus},
volume = {14},
number = {1},
pages = {3},
pmid = {36726175},
issn = {2210-6340},
support = {NNF18OC0034952//Novo Nordisk Fonden/ ; },
abstract = {The Penicillia are known to produce a wide range natural products-some with devastating outcome for the agricultural industry and others with unexploited potential in different applications. However, a large-scale overview of the biosynthetic potential of different species has been lacking. In this study, we sequenced 93 Penicillium isolates and, together with eleven published genomes that hold similar assembly characteristics, we established a species phylogeny as well as defining a Penicillium pangenome. A total of 5612 genes were shared between ≥ 98 isolates corresponding to approximately half of the average number of genes a Penicillium genome holds. We further identified 15 lateral gene transfer events that have occurred in this collection of Penicillium isolates, which might have played an important role, such as niche adaption, in the evolution of these fungi. The comprehensive characterization of the genomic diversity in the Penicillium genus supersedes single-reference genomes, which do not necessarily capture the entire genetic variation.},
}
@article {pmid36724669,
year = {2023},
author = {Adenaya, A and Berger, M and Brinkhoff, T and Ribas-Ribas, M and Wurl, O},
title = {Usage of antibiotics in aquaculture and the impact on coastal waters.},
journal = {Marine pollution bulletin},
volume = {188},
number = {},
pages = {114645},
doi = {10.1016/j.marpolbul.2023.114645},
pmid = {36724669},
issn = {1879-3363},
mesh = {Humans ; *Anti-Bacterial Agents/analysis ; Ecosystem ; Aquaculture ; *Environmental Pollutants ; Water ; },
abstract = {For decades, coastal marine ecosystems have been threatened by a wide range of anthropogenic pollutants. Recently, there has been increasing concern about the accumulation and impacts of antibiotic compounds on marine ecosystems. However, information regarding the accumulation of antibiotics and the impacts they may have on microbial communities in coastal water bodies and on human health is sparse in literature. Antibiotics from aquacultures are constantly discharged into marine environments via rivers. Large rivers transport tons of antibiotics every year into coastal waters, e.g., 12 tons of sulfonamide by the river Mekong. Here, we discuss a potential influence of such imported antibiotics on bacterial communities in coastal waters. Potential accumulation of antibiotics in the uppermost surface layer of aquatic ecosystems, the so-called sea surface microlayer (SML), is of interest. Because of the ability of the SML to accumulate anthropogenic pollutants, it may serve as a pool for antibiotics and correspondingly also for resistant organisms. Also, due to its biofilm-like structure, the SML could serve as a hotspot for horizontal gene transfer, speeding up the spread of antibiotic resistant strains to encompassing marine environments. The emergence of antibiotic resistant bacteria is a global threat and scientists projected that it could pave the way for the next pandemic that could ravage the world in the next decades. For this reason, it is time to focus research on understanding and minimizing the impact of antibiotics on the sustainability of coastal waters and on the health of humans who depend on coastal resources for food and recreational purposes. Also, knowledge about antibiotics in the SML is necessary to understand the effects they are likely to have on bacterial abundance, diversity, and metabolic activities in coastal water bodies.},
}
@article {pmid36724283,
year = {2023},
author = {Sarma, S and Bhattacharjee, A and Devi, MV and Panyang, PP and Singh, AK},
title = {Long-term adaptation of ParA, RelE/ParE partition system, replication protein and phage proteins encoding low-cost plasmids of Escherichia species isolated from diarrheic children of North East India.},
journal = {Journal of applied microbiology},
volume = {134},
number = {2},
pages = {},
doi = {10.1093/jambio/lxac065},
pmid = {36724283},
issn = {1365-2672},
support = {IF-170007//DST-INSPIRE/ ; OLP-2035//Council of Scientific and Industrial Research/ ; GPP-0329//Department of Science and Technology-SERB/ ; },
mesh = {Humans ; Child ; beta-Lactamases/genetics/metabolism ; Escherichia coli/genetics ; Klebsiella pneumoniae/genetics/metabolism ; Plasmids/genetics ; Klebsiella/metabolism ; India ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Bacterial Toxins ; *Escherichia coli Proteins/genetics ; },
abstract = {AIMS: The prevalent distribution of plasmid-mediated β-lactam resistance is the most pressing global problem in enteric diseases. The current work aims to characterize plasmid-carrying β-lactam resistant Enterobacteriaceae isolates from North East India for horizontal gene transfer (HGT) and plasmid adaptation study.<br><br>METHODS AND RESULTS: In vitro transconjugation and transformation showed overall high conjugation frequency (4.11&#xa0;&#xd7;&#xa0;10-1-9.2&#xa0;&#xd7;&#xa0;10-1) and moderate transformation efficiency/&#xb5;g DNA (1.02&#xa0;&#xd7;&#xa0;102 -1&#xa0;&#xd7;&#xa0;103), and the highest conjugation frequency (9.2&#xa0;&#xd7;&#xa0;10-1) and transformation efficiency (1&#xa0;&#xd7;&#xa0;103) for Escherichia species S-10. Intra/intergenus plasmid transformation efficiency was highest for the transformation of Klebsiella pneumoniae S-2 to Shigellaflexneri S-42 (1.3&#xa0;&#xd7;&#xa0;103) and lowest for Escherichia species S-10 to Escherichia fergusonii S-30 (2&#xa0;&#xd7;&#xa0;102). In the plasmid stability test, S-10 was detected with the highest plasmid carrying frequency (83.44%) and insignificant segregational loss rate (0.0004) until the 60th day with low plasmid cost on the host. The above findings were also validated by whole-plasmid sequencing of Escherichia species S-10. The genome was identified with two plasmids constituting multiple phage proteins, relaxosomal protein NikA, replication protein RepA, and the plasmid maintenance proteins (ParA, RelE/ParE), thus assisting stable plasmid maintenance.<br><br>CONCLUSIONS: The results thus indicate that the high conjugation ability and low plasmid fitness cost might lead to horizontal gene transfer of the plasmid to the environment due to their prolonged adaptation in nonselective conditions, intensifying the infection's severity.},
}
@article {pmid36722946,
year = {2023},
author = {Carrilero, L and Dunn, SJ and Moran, RA and McNally, A and Brockhurst, MA},
title = {Evolutionary Responses to Acquiring a Multidrug Resistance Plasmid Are Dominated by Metabolic Functions across Diverse Escherichia coli Lineages.},
journal = {mSystems},
volume = {8},
number = {1},
pages = {e0071322},
pmid = {36722946},
issn = {2379-5077},
support = {BB/R006253/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R006261/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /DH_/Department of Health/United Kingdom ; },
mesh = {*Escherichia coli/genetics ; Plasmids/genetics ; *Genome, Bacterial/genetics ; Drug Resistance, Multiple ; Genomics ; },
abstract = {Multidrug resistance (MDR) plasmids drive the spread of antibiotic resistance between bacterial lineages. The immediate impact of MDR plasmid acquisition on fitness and cellular processes varies among bacterial lineages, but how the evolutionary processes enabling the genomic integration of MDR plasmids vary is less well understood, particularly in clinical pathogens. Using diverse Escherichia coli lineages experimentally evolved for ~700 generations, we show that the evolutionary response to gaining the MDR plasmid pLL35 was dominated by chromosomal mutations affecting metabolic and regulatory functions, with both strain-specific and shared mutational targets. The expression of several of these functions, such as anaerobic metabolism, is known to be altered upon acquisition of pLL35. Interactions with resident mobile genetic elements, notably several IS-elements, potentiated parallel mutations, including insertions upstream of hns that were associated with its upregulation and the downregulation of the plasmid-encoded extended-spectrum beta-lactamase gene. Plasmid parallel mutations targeted conjugation-related genes, whose expression was also commonly downregulated in evolved clones. Beyond their role in horizontal gene transfer, plasmids can be an important selective force shaping the evolution of bacterial chromosomes and core cellular functions. IMPORTANCE Plasmids drive the spread of antimicrobial resistance genes between bacterial genomes. However, the evolutionary processes allowing plasmids to be assimilated by diverse bacterial genomes are poorly understood, especially in clinical pathogens. Using experimental evolution with diverse E. coli lineages and a clinical multidrug resistance plasmid, we show that although plasmids drove unique evolutionary paths per lineage, there was a surprising degree of convergence in the functions targeted by mutations across lineages, dominated by metabolic functions. Remarkably, these same metabolic functions show higher evolutionary rates in MDR-lineages in nature and in some cases, like anaerobic metabolism, their expression is directly manipulated by the plasmid. Interactions with other mobile elements resident in the genomes accelerated adaptation by disrupting genes and regulatory sequences that they inserted into. Beyond their role in horizontal gene transfer, plasmids are an important selective force driving the evolution of bacterial genomes and core cellular functions.},
}
@article {pmid36720410,
year = {2023},
author = {Zhao, H and Liu, X and Sun, Y and Liu, J and Waigi, MG},
title = {Effects and mechanisms of plant growth regulators on horizontal transfer of antibiotic resistance genes through plasmid-mediated conjugation.},
journal = {Chemosphere},
volume = {318},
number = {},
pages = {137997},
doi = {10.1016/j.chemosphere.2023.137997},
pmid = {36720410},
issn = {1879-1298},
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics ; Plant Growth Regulators/pharmacology ; Drug Resistance, Microbial/genetics ; Bacteria ; Genes, Bacterial ; Plasmids/genetics ; Gene Transfer, Horizontal ; },
abstract = {A vast number of bacteria occur in both soil and plants, with some of them harboring antibiotic resistance genes (ARGs). When bacteria congregate on the interface of soil particles or on plant root surfaces, these ARGs can be transferred between bacteria via conjugation, leading to the formation of antibiotic-resistant pathogens that threaten human health. Plant growth regulators (PGRs) are widely used in agricultural production, promoting plant growth and increasing crop yields. However, until now, little information has been known about the effects of PGRs on the horizontal gene transfer (HGT) of ARGs. In this study, with Escherichia coli DH5α (carrying RP4 plasmid with Tet[R], Amp[R], Kan[R]) as the donor and E. coli HB101 as the recipient, a series of diparental conjugation experiments were conducted to investigate the effects of indoleacetic acid (IAA), ethel (ETH) and gibberellin (GA3) on HGT of ARGs via plasmid-mediated conjugation. Furthermore, the mechanisms involved were also clarified. The results showed that all three PGRs affected the ARG transfer frequency by inducing the intracellular reactive oxygen species (ROS) formation, changing the cell membrane permeability, and regulating the gene transcription of traA, traL, trfAp, trbBp, kilA, and korA in plasmid RP4. In detail, 50-100 mg⋅L[-1] IAA, 20-50 mg⋅L[-1] ETH and 1500-2500 mg⋅L[-1] GA3 all significantly promoted the ARG conjugation. This study indicated that widespread use of PGRs in agricultural production could affect the HGT of ARGs via plasmid-mediated conjugation, and the application of reasonable concentrations of PGRs could reduce the ARG transmission in both soil environments and plants.},
}
@article {pmid36719227,
year = {2023},
author = {Cesa-Luna, C and Geudens, N and Girard, L and De Roo, V and Maklad, HR and Martins, JC and Höfte, M and De Mot, R},
title = {Charting the Lipopeptidome of Nonpathogenic Pseudomonas.},
journal = {mSystems},
volume = {8},
number = {1},
pages = {e0098822},
pmid = {36719227},
issn = {2379-5077},
mesh = {*Pseudomonas/genetics ; *Pseudomonas fluorescens/genetics ; Lipopeptides ; Phylogeny ; },
abstract = {A major source of pseudomonad-specialized metabolites is the nonribosomal peptide synthetases (NRPSs) assembling siderophores and lipopeptides. Cyclic lipopeptides (CLPs) of the Mycin and Peptin families are frequently associated with, but not restricted to, phytopathogenic species. We conducted an in silico analysis of the NRPSs encoded by lipopeptide biosynthetic gene clusters in nonpathogenic Pseudomonas genomes, covering 13 chemically diversified families. This global assessment of lipopeptide production capacity revealed it to be confined to the Pseudomonas fluorescens lineage, with most strains synthesizing a single type of CLP. Whereas certain lipopeptide families are specific for a taxonomic subgroup, others are found in distant groups. NRPS activation domain-guided peptide predictions enabled reliable family assignments, including identification of novel members. Focusing on the two most abundant lipopeptide families (Viscosin and Amphisin), a portion of their uncharted diversity was mapped, including characterization of two novel Amphisin family members (nepenthesin and oakridgin). Using NMR fingerprint matching, known Viscosin-family lipopeptides were identified in 15 (type) species spread across different taxonomic groups. A bifurcate genomic organization predominates among Viscosin-family producers and typifies Xantholysin-, Entolysin-, and Poaeamide-family producers but most families feature a single NRPS gene cluster embedded between cognate regulator and transporter genes. The strong correlation observed between NRPS system phylogeny and rpoD-based taxonomic affiliation indicates that much of the structural diversity is linked to speciation, providing few indications of horizontal gene transfer. The grouping of most NRPS systems in four superfamilies based on activation domain homology suggests extensive module dynamics driven by domain deletions, duplications, and exchanges. IMPORTANCE Pseudomonas species are prominent producers of lipopeptides that support proliferation in a multitude of environments and foster varied lifestyles. By genome mining of biosynthetic gene clusters (BGCs) with lipopeptide-specific organization, we mapped the global Pseudomonas lipopeptidome and linked its staggering diversity to taxonomy of the producers, belonging to different groups within the major Pseudomonas fluorescens lineage. Activation domain phylogeny of newly mined lipopeptide synthetases combined with previously characterized enzymes enabled assignment of predicted BGC products to specific lipopeptide families. In addition, novel peptide sequences were detected, showing the value of substrate specificity analysis for prioritization of BGCs for further characterization. NMR fingerprint matching proved an excellent tool to unequivocally identify multiple lipopeptides bioinformatically assigned to the Viscosin family, by far the most abundant one in Pseudomonas and with stereochemistry of all its current members elucidated. In-depth analysis of activation domains provided insight into mechanisms driving lipopeptide structural diversification.},
}
@article {pmid36717488,
year = {2023},
author = {Ishibashi, K and Tanaka, Y and Morishita, Y},
title = {Evolutionary Overview of Aquaporin Superfamily.},
journal = {Advances in experimental medicine and biology},
volume = {1398},
number = {},
pages = {81-98},
pmid = {36717488},
issn = {0065-2598},
mesh = {Phylogeny ; *Genome ; *Aquaporins/genetics/chemistry/metabolism ; },
abstract = {Aquaporins (AQPs) are present not only in three domains of life, bacteria, eukaryotes, and archaea, but also in viruses. With the accumulating arrays of AQP superfamily, the evolutional relationship has attracted much attention with multiple publications on "the genome-wide identification and phylogenetic analysis" of AQP superfamily. A pair of NPA boxes forming a pore is highly conserved throughout the evolution and renders key residues for the classification of AQP superfamily into four groups: AQP1-like, AQP3-like, AQP8-like, and AQP11-like. The complexity of AQP family has mostly been achieved in nematodes and subsequent evolution has been directed toward increasing the number of AQPs through whole-genome duplications (WGDs) to extend the tissue specific expression and regulation. The discovery of the intracellular AQP (iAQP: AQP8-like and AQP11-like) and substrate transports by the plasma membrane AQP (pAQP: AQP1-like and AQP3-like) have accelerated the AQP research much more toward the transport of substrates with complex profiles. This evolutionary overview based on a simple classification of AQPs into four subfamilies will provide putative structural, functional, and localization information and insights into the role of AQP as well as clues to understand the complex diversity of AQP superfamily.},
}
@article {pmid36715351,
year = {2023},
author = {Liu, H and Huang, W and Yu, Y and Chen, D},
title = {Lightning-Rod Effect on Nanowire Tips Reinforces Electroporation and Electrochemical Oxidation: An Efficient Strategy for Eliminating Intracellular Antibiotic Resistance Genes.},
journal = {ACS nano},
volume = {17},
number = {3},
pages = {3037-3046},
doi = {10.1021/acsnano.2c11811},
pmid = {36715351},
issn = {1936-086X},
mesh = {Angiotensin Receptor Antagonists/pharmacology ; Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Anti-Bacterial Agents/pharmacology ; Disinfection ; *Drinking Water ; Drug Resistance, Microbial/genetics ; Electroporation ; Genes, Bacterial ; *Lightning ; *Nanowires ; *Water Purification/methods ; Oxidation-Reduction ; Intracellular Space/metabolism ; },
abstract = {Conventional oxidative disinfection methods are usually inefficient to eliminate intracellular antibiotic resistance genes (i-ARGs) due to competitive oxidation of cellular components of antibiotic-resistant bacteria (ARB), resulting in the ubiquitous occurrence of ARGs in drinking water systems. Herein, we developed the strategy of coupling electroporation and electrochemical oxidation on a Co3O4-nanowires-modified electrode to destroy the multiresistant Escherichia coli cells and promote subsequent i-ARG (blaTEM-1 and aac(3)-II) degradation. The lightning-rod effect over nanowire tips can form finite regions with a locally enhanced electric field and highly concentrated charge density, in turn facilitating the electroporation for ARB cell damage and electrochemical reactivity for reactive chlorine/oxygen species generation. Characterization of the ARB membrane integrity and morphology revealed that electroporation-induced cell pores were further enlarged by the oxidation of reactive species, resulting in i-ARG removal at lower applied voltages and with 6-9 times lower energy consumption than the conventional electrochemical oxidation approach with a Co3O4-film-modified electrode. The satisfactory application and effective inhibition of horizontal gene transfer in tap water further demonstrated the great potential of our strategy in the control of the ARG dissemination risk in drinking water systems.},
}
@article {pmid36714980,
year = {2023},
author = {Cheng, YY and Zhou, Z and Papadopoulos, JM and Zuke, JD and Falbel, TG and Anantharaman, K and Burton, BM and Venturelli, OS},
title = {Efficient plasmid transfer via natural competence in a microbial co-culture.},
journal = {Molecular systems biology},
volume = {19},
number = {3},
pages = {e11406},
pmid = {36714980},
issn = {1744-4292},
support = {R35GM124774//HHS &#xa6; NIH &#xa6; National Institute of General Medical Sciences (NIGMS)/ ; T32 GM007215/GM/NIGMS NIH HHS/United States ; },
mesh = {Coculture Techniques ; Plasmids/genetics ; *DNA ; *Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; },
abstract = {The molecular and ecological factors shaping horizontal gene transfer (HGT) via natural transformation in microbial communities are largely unknown, which is critical for understanding the emergence of antibiotic-resistant pathogens. We investigate key factors shaping HGT in a microbial co-culture by quantifying extracellular DNA release, species growth, and HGT efficiency over time. In the co-culture, plasmid release and HGT efficiency are significantly enhanced than in the respective monocultures. The donor is a key determinant of HGT efficiency as plasmids induce the SOS response, enter a multimerized state, and are released in high concentrations, enabling efficient HGT. However, HGT is reduced in response to high donor lysis rates. HGT is independent of the donor viability state as both live and dead cells transfer the plasmid with high efficiency. In sum, plasmid HGT via natural transformation depends on the interplay of plasmid properties, donor stress responses and lysis rates, and interspecies interactions.},
}
@article {pmid36714722,
year = {2022},
author = {Zhu, X and Chen, WJ and Bhatt, K and Zhou, Z and Huang, Y and Zhang, LH and Chen, S and Wang, J},
title = {Innovative microbial disease biocontrol strategies mediated by quorum quenching and their multifaceted applications: A review.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {1063393},
pmid = {36714722},
issn = {1664-462X},
abstract = {With the increasing resistance exhibited by undesirable bacteria to traditional antibiotics, the need to discover alternative (or, at least, supplementary) treatments to combat chemically resistant bacteria is becoming urgent. Quorum sensing (QS) refers to a novel bacterial communication system for monitoring cell density and regulation of a network of gene expression that is mediated by a group of signaling molecules called autoinducers (AIs). QS-regulated multicellular behaviors include biofilm formation, horizontal gene transfer, and antibiotic synthesis, which are demonstrating increasing pathogenicity to plants and aquacultural animals as well as contamination of wastewater treatment devices. To inhibit QS-regulated microbial behaviors, the strategy of quorum quenching (QQ) has been developed. Different quorum quenchers interfere with QS through different mechanisms, such as competitively inhibiting AI perception (e.g., by QS inhibitors) and AI degradation (e.g., by QQ enzymes). In this review, we first introduce different signaling molecules, including diffusible signal factor (DSF) and acyl homoserine lactones (AHLs) for Gram-negative bacteria, AIPs for Gram-positive bacteria, and AI-2 for interspecies communication, thus demonstrating the mode of action of the QS system. We next exemplify the QQ mechanisms of various quorum quenchers, such as chemical QS inhibitors, and the physical/enzymatic degradation of QS signals. We devote special attention to AHL-degrading enzymes, which are categorized in detail according to their diverse catalytic mechanisms and enzymatic properties. In the final part, the applications and advantages of quorum quenchers (especially QQ enzymes and bacteria) are summarized in the context of agricultural/aquacultural pathogen biocontrol, membrane bioreactors for wastewater treatment, and the attenuation of human pathogenic bacteria. Taken together, we present the state-of-the-art in research considering QS and QQ, providing theoretical evidence and support for wider application of this promising environmentally friendly biocontrol strategy.},
}
@article {pmid36712336,
year = {2022},
author = {Kuroyanagi, T and Bulasag, AS and Fukushima, K and Ashida, A and Suzuki, T and Tanaka, A and Camagna, M and Sato, I and Chiba, S and Ojika, M and Takemoto, D},
title = {Botrytis cinerea identifies host plants via the recognition of antifungal capsidiol to induce expression of a specific detoxification gene.},
journal = {PNAS nexus},
volume = {1},
number = {5},
pages = {pgac274},
pmid = {36712336},
issn = {2752-6542},
abstract = {The gray mold pathogen Botrytis cinerea has a broad host range, causing disease in >400 plant species, but it is not known how this pathogen evolved this polyxenous nature. Botrytis cinerea can metabolize a wide range of phytoalexins, including the stilbenoid resveratrol in grape, and the sesquiterpenoids capsidiol in tobacco and rishitin in potato and tomato. In this study, we analyzed the metabolism of sesquiterpenoid phytoalexins by B. cinerea. Capsidiol was dehydrogenated to capsenone, which was then further oxidized, while rishitin was directly oxidized to epoxy- or hydroxyrishitins, indicating that B. cinerea has separate mechanisms to detoxify structurally similar sesquiterpenoid phytoalexins. RNA-seq analysis revealed that a distinct set of genes were induced in B. cinerea when treated with capsidiol or rishitin, suggesting that B. cinerea can distinguish structurally similar phytoalexins to activate appropriate detoxification mechanisms. The gene most highly upregulated by capsidiol treatment encoded a dehydrogenase, designated Bccpdh. Heterologous expression of Bccpdh in a capsidiol-sensitive plant symbiotic fungus, Epichloë festucae, resulted in an acquired tolerance of capsidiol and the ability to metabolize capsidiol to capsenone, while B. cinerea Δbccpdh mutants became relatively sensitive to capsidiol. The Δbccpdh mutant showed reduced virulence on the capsidiol producing Nicotiana and Capsicum species but remained fully pathogenic on potato and tomato. Homologs of Bccpdh are found in taxonomically distant Ascomycota fungi but not in related Leotiomycetes species, suggesting that B. cinerea acquired the ancestral Bccpdh by horizontal gene transfer, thereby extending the pathogenic host range of this polyxenous pathogen to capsidiol-producing plant species.},
}
@article {pmid36708845,
year = {2023},
author = {Xiao, R and Huang, D and Du, L and Song, B and Yin, L and Chen, Y and Gao, L and Li, R and Huang, H and Zeng, G},
title = {Antibiotic resistance in soil-plant systems: A review of the source, dissemination, influence factors, and potential exposure risks.},
journal = {The Science of the total environment},
volume = {869},
number = {},
pages = {161855},
doi = {10.1016/j.scitotenv.2023.161855},
pmid = {36708845},
issn = {1879-1026},
mesh = {Humans ; *Soil/chemistry ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Soil Microbiology ; },
abstract = {As an emerging environmental contaminant, the widespread of antibiotic resistance has caused a series of environmental issues and human health concerns. A load of antibiotic residues induced by agricultural practices have exerted selective pressure to bacterial communities in the soil-plant system, which facilitated the occurrence and dissemination of antibiotic resistance genes (ARGs) through horizontal gene transfer. As a result, the enrichment of ARGs within crops at harvest under the influence of food ingestion could lead to critical concerns of public health. In this review, the prevalence and dissemination of antibiotic resistance in the soil-plant system are highlighted. Moreover, different underlying mechanisms and detection methods for ARGs transfer between the soil environment and plant compartments are summarized and discussed. On the other hand, a wide range of influencing factors for the transfer and distribution of antibiotic resistance within the soil-plant system are also presented and discussed. In response to exposure of antibiotic residues and resistomes, corresponding hazard identification assessments have been summarized, which could provide beneficial guides of the toxicological tolerance for the general population. Finally, further research priorities for detection and management ARGs spread are also suggested.},
}
@article {pmid36706177,
year = {2023},
author = {Melamed, JR and Yerneni, SS and Arral, ML and LoPresti, ST and Chaudhary, N and Sehrawat, A and Muramatsu, H and Alameh, MG and Pardi, N and Weissman, D and Gittes, GK and Whitehead, KA},
title = {Ionizable lipid nanoparticles deliver mRNA to pancreatic β cells via macrophage-mediated gene transfer.},
journal = {Science advances},
volume = {9},
number = {4},
pages = {eade1444},
pmid = {36706177},
issn = {2375-2548},
support = {R01 AI153064/AI/NIAID NIH HHS/United States ; F32 EB029345/EB/NIBIB NIH HHS/United States ; DP2 HD098860/HD/NICHD NIH HHS/United States ; R01 AI124429/AI/NIAID NIH HHS/United States ; U19 AI142596/AI/NIAID NIH HHS/United States ; R01 AI146101/AI/NIAID NIH HHS/United States ; },
mesh = {RNA, Messenger/genetics ; *Insulin-Secreting Cells ; Lipids ; *Nanoparticles ; Macrophages ; },
abstract = {Systemic messenger RNA (mRNA) delivery to organs outside the liver, spleen, and lungs remains challenging. To overcome this issue, we hypothesized that altering nanoparticle chemistry and administration routes may enable mRNA-induced protein expression outside of the reticuloendothelial system. Here, we describe a strategy for delivering mRNA potently and specifically to the pancreas using lipid nanoparticles. Our results show that delivering lipid nanoparticles containing cationic helper lipids by intraperitoneal administration produces robust and specific protein expression in the pancreas. Most resultant protein expression occurred within insulin-producing β cells. Last, we found that pancreatic mRNA delivery was dependent on horizontal gene transfer by peritoneal macrophage exosome secretion, an underappreciated mechanism that influences the delivery of mRNA lipid nanoparticles. We anticipate that this strategy will enable gene therapies for intractable pancreatic diseases such as diabetes and cancer.},
}
@article {pmid36695602,
year = {2023},
author = {Anderson, REV and Chalmers, G and Murray, R and Mataseje, L and Pearl, DL and Mulvey, M and Topp, E and Boerlin, P},
title = {Characterization of Escherichia coli and Other Enterobacterales Resistant to Extended-Spectrum Cephalosporins Isolated from Dairy Manure in Ontario, Canada.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {2},
pages = {e0186922},
pmid = {36695602},
issn = {1098-5336},
mesh = {Animals ; Cattle ; Humans ; *Cephalosporins/pharmacology ; Escherichia coli/genetics ; Manure ; Anti-Bacterial Agents/pharmacology ; Ontario ; Multilocus Sequence Typing ; Phylogeny ; beta-Lactamases/genetics ; *Escherichia coli Infections/microbiology ; Plasmids/genetics ; },
abstract = {Extended-spectrum cephalosporins (ESCs) resistance genes, such as blaCTX-M, blaCMY, and blaSHV, have been found regularly in bacteria from livestock. However, information on their distribution in dairy cattle in Canada and on the associated genome sequences of ESC-resistant Enterobacterales is sparse. In this study, the diversity and distribution of ESC-resistant Escherichia coli throughout manure treatments in six farms in Southern Ontario were assessed over a one-year period, and their ESC-resistance plasmids were characterized. The manure samples were enriched using selective media. The resulting isolates were screened via polymerase chain reaction for blaCTX-M, blaCMY, and blaSHV. No E. coli carrying blaSHV were detected. Escherichia coli (n = 248) carrying blaCTX-M or blaCMY underwent whole-genome sequencing using an Illumina MiSeq/NextSeq. These isolates were typed using multilocus sequence typing (MLST) and their resistance gene profiles. A subset of E. coli (n = 28) were sequenced using Oxford Nanopore Technologies. Plasmids were assembled using Unicycler and characterized via the resistance genes pattern, replicon type, plasmid MLST, phylogenetic analysis, and Mauve alignments. The recovery of ESC-resistant Enterobacterales (18 species, 8 genera) was drastically reduced in manure outputs. However, multiple treatment stages were needed to attain a significant reduction. 62 sequence types were identified, with ST10, ST46, ST58, ST155, ST190, ST398, ST685, and ST8761 being detected throughout the treatment pipeline. These STs overlapped with those found on multiple farms. The ESC-resistance determinants included CTX-M-1, -14, -15, -17, -24, -32, -55, and CMY-2. The plasmids carrying blaCTX-M were more diverse than were the plasmids carrying blaCMY. Known "epidemic plasmids" were detected for both blaCTX-M and blaCMY. IMPORTANCE The increase in antimicrobial resistance is of concern for human and animal health, especially when resistance is conferred to extended-spectrum cephalosporins, which are used to treat serious infections in both human and veterinary medicine. Bacteria carrying extended-spectrum cephalosporin resistance genes, including blaCTX-M and blaCMY, are frequently found in dairy manure. Manure treatment influences the loads and diversity of bacteria, including those carrying antimicrobial resistance genes, such as Enterobacterales and Escherichia coli. Any bacteria that survive the treatment process are subsequently applied to the environment. Enterobacterales carrying blaCTX-M or blaCMY can contaminate soil and crops consumed by humans and animals, thereby increasing the potential for antimicrobial resistance genes to integrate into the human gut microflora through horizontal gene transfer. This furthers the dissemination of resistance. Therefore, it is imperative to understand the effects manure treatments have on ESC-resistance in environmentally applied manure.},
}
@article {pmid36692711,
year = {2023},
author = {Li, Y and Xiong, L and Yu, H and Xiang, Y and Wei, Y and Zhang, Q and Ji, X},
title = {Biogeochemical sulfur cycling of virus auxiliary metabolic genes involved in Napahai plateau wetland.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {15},
pages = {44430-44438},
pmid = {36692711},
issn = {1614-7499},
support = {32160294//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 31860147//Innovative Research Group Project of the National Natural Science Foundation of China/ ; },
mesh = {*Wetlands ; Phylogeny ; Oxidation-Reduction ; *Microbiota ; Sulfur/metabolism ; },
abstract = {Virus plays important roles in regulating microbial community structure, horizontal gene transfer, and promoting biological evolution, also augmenting host metabolism during infection via the expression of auxiliary metabolic genes (AMGs), and thus affect biogeochemical cycling in the oceans. As the "kidney of the earth," wetlands have rich biodiversity and abundant resources. Based on metagenomic data, 10 AMGs associated with sulfur cycling, i.e., tusA, moaD, dsrE, soxA, soxB, soxC, soxD, soxX, soxY, and soxZ, were analyzed in Napahai plateau wetland. The phylogenetic trees of AMGs involved in sulfur metabolism from different habitats and host origins were constructed. Combined with principal coordinate analysis, it revealed that most AMGs associated with sulfur metabolism clustered separately, indicating the abundance and uniqueness in this region. The sulfur metabolism pathways involved by AMGs were mainly SOX systems, among which sulfur oxidation was associated with moaD and dsrE genes, while sulfur transport was related to tusA genes. It provides an insight into the biogeochemical sulfur cycling in plateau wetlands and lays the foundation for further study on the co-evolution of virus and host.},
}
@article {pmid36692352,
year = {2023},
author = {Chen, M and Shao, Y and Luo, J and Yuan, L and Wang, M and Chen, M and Guo, Q},
title = {Penicillin and Cefotaxime Resistance of Quinolone-Resistant Neisseria meningitidis Clonal Complex 4821, Shanghai, China, 1965-2020.},
journal = {Emerging infectious diseases},
volume = {29},
number = {2},
pages = {341-350},
pmid = {36692352},
issn = {1080-6059},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Neisseria meningitidis/genetics ; Penicillins ; *Quinolones/pharmacology ; Cefotaxime/pharmacology ; China/epidemiology ; Neisseria/genetics ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Penicillin Resistance/genetics ; },
abstract = {Clonal complex 4821 (CC4821) Neisseria meningitidis, usually resistant to quinolones but susceptible to penicillin and third-generation cephalosporins, is increasing worldwide. To characterize the penicillin-nonsusceptible (Pen[NS]) meningococci, we analyzed 491 meningococci and 724 commensal Neisseria isolates in Shanghai, China, during 1965-2020. The Pen[NS] proportion increased from 0.3% in 1965-1985 to 7.0% in 2005-2014 and to 33.3% in 2015-2020. Of the 26 Pen[NS] meningococci, 11 (42.3%) belonged to the CC4821 cluster; all possessed mutations in penicillin-binding protein 2, mostly from commensal Neisseria. Genetic analyses and transformation identified potential donors of 6 penA alleles. Three Pen[NS] meningococci were resistant to cefotaxime, 2 within the CC4821 cluster. With 96% of the Pen[NS] meningococci beyond the coverage of scheduled vaccination and the cefotaxime-resistant isolates all from toddlers, quinolone-resistant CC4821 has acquired penicillin and cefotaxime resistance closely related to the internationally disseminated ceftriaxone-resistant gonococcal FC428 clone, posing a greater threat especially to young children.},
}
@article {pmid36690118,
year = {2023},
author = {Yue, Z and Zhang, J and Ding, C and Wang, Y and Zhou, Z and Yu, X and Zhang, T and Wang, X},
title = {Transfer and distribution of antibiotic resistance genes in the soil-peanut system receiving manure for years.},
journal = {The Science of the total environment},
volume = {869},
number = {},
pages = {161742},
doi = {10.1016/j.scitotenv.2023.161742},
pmid = {36690118},
issn = {1879-1026},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Soil ; Arachis ; Genes, Bacterial ; Manure/analysis ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Drug Resistance, Microbial/genetics ; },
abstract = {Antibiotic resistance gene (ARG)-contaminated food from manure application is gaining widespread interest, but little is known about the distribution and uptake of ARGs in peanuts that are subjected to manure routinely. In this study, the ARG profile and bacterial community in soil and peanut plants from a 7-year manure-fertilized field were investigated using high-throughput qPCR and 16S rRNA gene sequencing. Manure application increased the abundance of ARGs in soil and peanuts by 59-72 and 4-10 fold, respectively. The abundance of ARGs from high to low was as follows: manure, shell-sphere soil, rhizosphere soil, bulk soil, stems, shells, needles, kernels, and roots. Source-tracker analyses were used to investigate the potential source of ARGs in peanut kernels, which revealed that the ARGs in peanut kernels may be primarily absorbed by the roots from the soil. The horizontal gene transfer (HGT) of ARGs was the primary factor in the spread of ARGs, and Proteobacteria were the primary agents of HGT between different parts of peanut plants. Additionally, norank_Chloroplast from the phylum Cyanobacteria was the most important contributor to the abundance of ARGs in peanut kernels. Overall, our findings fill a gap in our understanding of the distribution patterns of ARGs in peanut plants and the migratory pathways of ARGs from soil to peanut kernels.},
}
@article {pmid36689882,
year = {2023},
author = {An, R and Qi, Y and Zhang, XX and Ma, L},
title = {Xenogenetic evolutionary of integrons promotes the environmental pollution of antibiotic resistance genes - Challenges, progress and prospects.},
journal = {Water research},
volume = {231},
number = {},
pages = {119629},
doi = {10.1016/j.watres.2023.119629},
pmid = {36689882},
issn = {1879-2448},
mesh = {Humans ; *Integrons/genetics ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Genes, Bacterial ; Environmental Pollution ; },
abstract = {Environmental pollution of antibiotic resistance genes (ARGs) has been a great public concern. Integrons, as mobile genetic elements, with versatile gene acquisition systems facilitate the horizontal gene transfer (HGT) and pollution disseminations of ARGs. However, little is understood about the characteristics of ARGs mediated by integrons, which hampers our monitoring and control of the mobile antimicrobial resistance risks. To address these issues, we reviewed 3,322 publications concerning detection methods and pipeline, ARG diversity and evolutionary progress, environmental and geographical distribution, bacterial hosts, gene cassettes arrangements, and based on which to identify ARGs with high risk levels mediated by integrons. Diverse ARGs of 516 subtypes attributed to 12 types were capable of being carried by integrons, with 62 core ARG subtypes prevalent in pollution source, natural and human-related environments. Hosts of ARG-carrying integrons reached 271 bacterial species, most frequently carried by opportunistic pathogens Escherichia coli, Pseudomonas aeruginosa and Klebsiella pneumoniae. Moreover, the observed emergence of ARGs together with their multiple arrangements indicated the accumulation of ARGs mediated by integrons, and thus pose increasing HGT risks under modern selective agents. With the concerns of public health, we urgently call for a better monitoring and control of these high-risk ARGs. Our identified Risk Rank I ARGs (aacA7, blaOXA10, catB3, catB8, dfrA5) with high mobility, reviewed key trends and noteworthy advancements, and proposed future directions could be reference and guidance for standard formulation.},
}
@article {pmid36688638,
year = {2023},
author = {Bhandari, M and Rathnayake, IU and Huygens, F and Jennison, AV},
title = {Clinical and Environmental Vibrio cholerae Non-O1, Non-O139 Strains from Australia Have Similar Virulence and Antimicrobial Resistance Gene Profiles.},
journal = {Microbiology spectrum},
volume = {11},
number = {1},
pages = {e0263122},
pmid = {36688638},
issn = {2165-0497},
mesh = {Humans ; *Cholera/epidemiology/microbiology ; *Vibrio cholerae non-O1/genetics ; Virulence/genetics ; Anti-Bacterial Agents/pharmacology ; Serogroup ; Phylogeny ; Travel ; Genetic Variation ; Drug Resistance, Bacterial/genetics ; },
abstract = {Cholera caused by pathogenic Vibrio cholerae is still considered one of the major health problems in developing countries including those in Asia and Africa. Australia is known to have unique V. cholerae strains in Queensland waterways, resulting in sporadic cholera-like disease being reported in Queensland each year. We conducted virulence and antimicrobial genetic characterization of O1 and non-O1, non-O139 V. cholerae (NOVC) strains (1983 to 2020) from Queensland with clinical significance and compared these to environmental strains that were collected as part of a V. cholerae monitoring project in 2012 of Queensland waterways. In this study, 87 V. cholerae strains were analyzed where O1 (n = 5) and NOVC (n = 54) strains from Queensland and international travel-associated NOVC (n = 2) (61 in total) strains were sequenced, characterized, and compared with seven previously sequenced O1 strains and 18 other publicly available NOVC strains from Australia and overseas to visualize the genetic context among them. Of the 61 strains, three clinical and environmental NOVC serogroup strains had cholera toxin-producing genes, namely, the CTX phage (identified in previous outbreaks) and the complete Vibrio pathogenicity island 1. Phylogenetic analysis based on core genome analysis showed more than 10 distinct clusters and interrelatedness between clinical and environmental V. cholerae strains from Australia. Moreover, 30 (55%) NOVC strains had the cholix toxin gene (chxA) while only 11 (20%) strains had the mshA gene. In addition, 18 (34%) NOVC strains from Australia had the type three secretion system and discrete expression of type six secretion system genes. Interestingly, four NOVC strains from Australia and one NOVC strain from Indonesia had intSXT, a mobile genetic element. Several strains were found to have beta-lactamase (blaCARB-9) and chloramphenicol acetyltransferase (catB9) genes. Our study suggests that Queensland waterways can harbor highly divergent V. cholerae strains and serve as a reservoir for various V. cholerae-associated virulence genes which could be shared among O1 and NOVC V. cholerae strains via mobile genetic elements or horizontal gene transfer. IMPORTANCE Australia has its own V. cholerae strains, both toxigenic and nontoxigenic, that are associated with cholera disease. This study aimed to characterize a collection of clinical and environmental NOVC strains from Australia to understand their virulence and antimicrobial resistance profile and to place strains from Australia in the genetic context of international strains. The findings from this study suggest the toxigenic V. cholerae strains in the Queensland River water system are of public health concern. Therefore, ongoing monitoring and genomic characterization of V. cholerae strains from the Queensland environment are important and would assist public health departments to track the source of cholera infection early and implement prevention strategies for future outbreaks. Understanding the genomics of V. cholerae could also inform the natural ecology and evolution of this bacterium in natural environments.},
}
@article {pmid36685277,
year = {2022},
author = {Gomis-Rüth, FX and Stöcker, W},
title = {Structural and evolutionary insights into astacin metallopeptidases.},
journal = {Frontiers in molecular biosciences},
volume = {9},
number = {},
pages = {1080836},
pmid = {36685277},
issn = {2296-889X},
abstract = {The astacins are a family of metallopeptidases (MPs) that has been extensively described from animals. They are multidomain extracellular proteins, which have a conserved core architecture encompassing a signal peptide for secretion, a prodomain or prosegment and a zinc-dependent catalytic domain (CD). This constellation is found in the archetypal name-giving digestive enzyme astacin from the European crayfish Astacus astacus. Astacin catalytic domains span ∼200 residues and consist of two subdomains that flank an extended active-site cleft. They share several structural elements including a long zinc-binding consensus sequence (HEXXHXXGXXH) immediately followed by an EXXRXDRD motif, which features a family-specific glutamate. In addition, a downstream SIMHY-motif encompasses a "Met-turn" methionine and a zinc-binding tyrosine. The overall architecture and some structural features of astacin catalytic domains match those of other more distantly related MPs, which together constitute the metzincin clan of metallopeptidases. We further analysed the structures of PRO-, MAM, TRAF, CUB and EGF-like domains, and described their essential molecular determinants. In addition, we investigated the distribution of astacins across kingdoms and their phylogenetic origin. Through extensive sequence searches we found astacin CDs in > 25,000 sequences down the tree of life from humans beyond Metazoa, including Choanoflagellata, Filasterea and Ichtyosporea. We also found < 400 sequences scattered across non-holozoan eukaryotes including some fungi and one virus, as well as in selected taxa of archaea and bacteria that are pathogens or colonizers of animal hosts, but not in plants. Overall, we propose that astacins originate in the root of Holozoa consistent with Darwinian descent and that the latter genes might be the result of horizontal gene transfer from holozoan donors.},
}
@article {pmid36684780,
year = {2022},
author = {Wang, Y and Shahid, MQ},
title = {Genome sequencing and resequencing identified three horizontal gene transfers and uncovered the genetic mechanism on the intraspecies adaptive evolution of Gastrodia elata Blume.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {1035157},
pmid = {36684780},
issn = {1664-462X},
abstract = {Horizontal gene transfer is a rare and useful genetic mechanism in higher plants. Gastrodia elata Blume (GE) (Orchidaceae), well known as traditional medicinal material in East Asia, adopts a heterotrophic lifestyle, thus being considered to be more prone to horizontal gene transfer (HGT). GE is a "polytypic species" that currently comprised of five recognized forms according to the plant morphology. G. elata Blume forma elata (GEE) and G. elata Bl.f.glauca (GEG) are two common forms that naturally grow in different habitats with difference in altitude and latitude. G. elata Bl.f.viridis (GEV) often occurs sporadically in cultivated populations of GEE and GEG. However, the genetic relationships and genetic mechanism underpinned the divergent ecological adaptations of GEE and GEG have not been revealed. Here, we assembled a chromosome-level draft genome of GEE with 1.04 Gb. Among predicted 17,895 protein coding genes, we identified three HGTs. Meanwhile, we resequenced 10 GEE accessions, nine GEG accessions, and 10 GEV accessions, and identified two independent genetic lineages: GEG_pedigree (GEG individuals and GEV individuals collected from GEG populations) and GEE_pedigree (GEE individuals and GEV individuals collected from GEE populations), which strongly support the taxonomic status of GEE and GEG as subspecies, not as different forms. In highly differentiated genomic regions of GEE_pedigree and GEG_pedigree, three chalcone synthase-encoding genes and one Phox/Bem1p (PB1) domain of encoding Auxin (AUX)/Indoleacetic acid (IAA) were identified in selection sweeping genome regions, which suggested that differentiation between GEE_pedigree and GEG_pedigree was promoted by the selection of genes related to photoresponse and growth and development. Overall, this new genome would be helpful for breeding and utilization of GE and the new findings would deepen the understanding about ecological adaptation and evolution of GE.},
}
@article {pmid36680934,
year = {2023},
author = {Tang, Y and Shi, Y and Jia, B and Zhang, Y and Wang, Q},
title = {Evolution and function analysis of glycerol kinase GlpK in Pseudomonasaeruginosa.},
journal = {Biochemical and biophysical research communications},
volume = {645},
number = {},
pages = {30-39},
doi = {10.1016/j.bbrc.2022.12.060},
pmid = {36680934},
issn = {1090-2104},
mesh = {Humans ; Glycerol/metabolism ; *Glycerol Kinase/genetics/metabolism ; Phosphorylation ; *Pseudomonas aeruginosa/enzymology/genetics ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Pseudomonas aeruginosa is a Gram-negative bacterium capable of widespread niches, which is also one of the main bacteria that cause patient infection. The metabolic diversity of Pseudomonas aeruginosa is an essential factor in adapting to a variety of environments. Based on the previous studies, adaptive genetic variation in the glycerol kinase GlpK, the glycerol 3-phosphotransferase, contributes to the fitness of bacteria in human bodies, such as Mycobacterium tuberculosis and Escherichia coli. Thus, this study aimed to explore the molecular evolution and function of glpK in P. aeruginosa. Using extensive population genomic data, we have identified the prevalence of two glpK copies in P. aeruginosa that clustered into distinct branches, which were later known as Clade 1 and 2. The evolution analysis revealed that glpK in Clade 1 derived from an ancestral P. aeruginosa species and the other from an ancient horizontal gene transfer event. In addition, we confirmed that the GlpK in Clade 2 still retained glycerol kinase activity but was much weaker than that of GlpK in Clade 1. We demonstrated the importance of the critical amino acid Q70 in GlpK glycerol kinase activity by point mutation. Furthermore, Co-expression network analysis implied that the two glpK copies of P. aeruginosa regulate separate networks and may be a strategy to improve fitness in P. aeruginosa.},
}
@article {pmid36680256,
year = {2023},
author = {Pchelin, IM and Tkachev, PV and Azarov, DV and Gorshkov, AN and Drachko, DO and Zlatogursky, VV and Dmitriev, AV and Goncharov, AE},
title = {A Genome of Temperate Enterococcus Bacteriophage Placed in a Space of Pooled Viral Dark Matter Sequences.},
journal = {Viruses},
volume = {15},
number = {1},
pages = {},
pmid = {36680256},
issn = {1999-4915},
mesh = {Humans ; *Bacteriophages ; Enterococcus/genetics ; Genome, Viral ; Sequence Analysis, DNA ; Phylogeny ; Myoviridae/genetics ; },
abstract = {In the human gut, temperate bacteriophages interact with bacteria through predation and horizontal gene transfer. Relying on taxonomic data, metagenomic studies have associated shifts in phage abundance with a number of human diseases. The temperate bacteriophage VEsP-1 with siphovirus morphology was isolated from a sample of river water using Enterococcus faecalis as a host. Starting from the whole genome sequence of VEsP-1, we retrieved related phage genomes in blastp searches of the tail protein and large terminase sequences, and blastn searches of the whole genome sequences, with matches compiled from several different databases, and visualized a part of viral dark matter sequence space. The genome network and phylogenomic analyses resulted in the proposal of a novel genus "Vespunovirus", consisting of temperate, mainly metagenomic phages infecting Enterococcus spp.},
}
@article {pmid36677319,
year = {2022},
author = {Shivaramu, S and Tomasch, J and Kopejtka, K and Nupur, and Saini, MK and Bokhari, SNH and Küpper, H and Koblížek, M},
title = {The Influence of Calcium on the Growth, Morphology and Gene Regulation in Gemmatimonas phototrophica.},
journal = {Microorganisms},
volume = {11},
number = {1},
pages = {},
pmid = {36677319},
issn = {2076-2607},
abstract = {The bacterium Gemmatimonas phototrophica AP64 isolated from a freshwater lake in the western Gobi Desert represents the first phototrophic member of the bacterial phylum Gemmatimonadota. This strain was originally cultured on agar plates because it did not grow in liquid medium. In contrast, the closely related species G. groenlandica TET16 grows both on solid and in liquid media. Here, we show that the growth of G. phototrophica in liquid medium can be induced by supplementing the medium with 20 mg CaCl2 L[-1]. When grown at a lower concentration of calcium (2 mg CaCl2 L[-1]) in the liquid medium, the growth was significantly delayed, cells were elongated and lacked flagella. The elevated requirement for calcium is relatively specific as it can be partially substituted by strontium, but not by magnesium. The transcriptome analysis documented that several groups of genes involved in flagella biosynthesis and transport of transition metals were co-activated after amendment of 20 mg CaCl2 L[-1] to the medium. The presented results document that G. phototrophica requires a higher concentration of calcium for its metabolism and growth compared to other Gemmatimonas species.},
}
@article {pmid36676100,
year = {2023},
author = {Lila, ASA and Rajab, AAH and Abdallah, MH and Rizvi, SMD and Moin, A and Khafagy, ES and Tabrez, S and Hegazy, WAH},
title = {Biofilm Lifestyle in Recurrent Urinary Tract Infections.},
journal = {Life (Basel, Switzerland)},
volume = {13},
number = {1},
pages = {},
pmid = {36676100},
issn = {2075-1729},
abstract = {Urinary tract infections (UTIs) represent one of the most common infections that are frequently encountered in health care facilities. One of the main mechanisms used by bacteria that allows them to survive hostile environments is biofilm formation. Biofilms are closed bacterial communities that offer protection and safe hiding, allowing bacteria to evade host defenses and hide from the reach of antibiotics. Inside biofilm communities, bacteria show an increased rate of horizontal gene transfer and exchange of resistance and virulence genes. Additionally, bacterial communication within the biofilm allows them to orchestrate the expression of virulence genes, which further cements the infestation and increases the invasiveness of the infection. These facts stress the necessity of continuously updating our information and understanding of the etiology, pathogenesis, and eradication methods of this growing public health concern. This review seeks to understand the role of biofilm formation in recurrent urinary tact infections by outlining the mechanisms underlying biofilm formation in different uropathogens, in addition to shedding light on some biofilm eradication strategies.},
}
@article {pmid36675876,
year = {2022},
author = {Li, Y and Qi, M and Zhang, Q and Xu, Z and Zhang, Y and Gao, Y and Qi, Y and Qiu, L and Wang, M},
title = {Phylogenesis of the Functional 1-Aminocyclopropane-1-Carboxylate Oxidase of Fungi and Plants.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {1},
pages = {},
pmid = {36675876},
issn = {2309-608X},
support = {202102110044//the Science and Technology Department of Henan Province/ ; 222102110302//the Science and Technology Department of Henan Province/ ; 32102455//the National Natural Science Foundation of China/ ; },
abstract = {The 1-aminocyclopropane-1-carboxylic acid (ACC) pathway that synthesizes ethylene is shared in seed plants, fungi and probably other organisms. However, the evolutionary relationship of the key enzyme ACC oxidase (ACO) in the pathway among organisms remains unknown. Herein, we cloned, expressed and characterized five ACOs from the straw mushroom (Volvariella volvacea) and the oyster mushroom (Pleurotus ostreatus): VvACO1-4 and PoACO. The five mushroom ACOs and the previously identified AbACO of the button mushroom contained all three conserved residues that bound to Fe(II) in plant ACOs. They also had variable residues that were conserved and bound to ascorbate and bicarbonate in plant ACOs and harbored only 1-2 of the five conserved ACO motifs in plant ACOs. Particularly, VvACO2 and AbACO had only one ACO motif 2. Additionally, VvACO4 shared 44.23% sequence identity with the cyanobacterium Hapalosiphon putative functional ACO. Phylogenetic analysis showed that the functional ACOs of monocotyledonous and dicotyledonous plants co-occurred in Type I, Type II and Type III, while putative functional gymnosperm ACOs also appeared in Type III. The putative functional bacterial ACO, functional fungi and slime mold ACOs were clustered in ancestral Type IV. These results indicate that ACO motif 2, ACC and Fe(II) are essential for ACO activity. The ACOs of the other organisms may come from the horizontal transfer of fungal ACOs, which were found ordinarily in basidiomycetes. It is mostly the first case for the horizontal gene transfers from fungi to seed plants. The horizontal transfer of ACOs from fungi to plants probably facilitates the fungal-plant symbioses, plant-land colonization and further evolution to form seeds.},
}
@article {pmid36671285,
year = {2023},
author = {Canellas, ALB and de Oliveira, BFR and Laport, MS},
title = {Hiding in Plain Sight: Characterization of Aeromonas Species Isolated from a Recreational Estuary Reveals the Carriage and Putative Dissemination of Resistance Genes.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {1},
pages = {},
pmid = {36671285},
issn = {2079-6382},
support = {306395/2020-7//National Council for Scientific and Technological Development/ ; E-26/200.948/2021//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; E-26/211.284/2021//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 88887.613830/2021-00//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; code 001//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; E26/211.554/2019//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; },
abstract = {Antimicrobial resistance (AMR) has become one of the greatest challenges worldwide, hampering the treatment of a plethora of infections. Indeed, the AMR crisis poses a threat to the achievement of the United Nations' Sustainable Development Goals and, due to its multisectoral character, a holistic approach is needed to tackle this issue. Thus, the investigation of environments beyond the clinic is of utmost importance. Here, we investigated thirteen strains of antimicrobial-resistant Aeromonas isolated from an urban estuary in Brazil. Most strains carried at least one antimicrobial resistance gene and 11 carried at least one heavy metal resistance gene. Noteworthy, four (30.7%) strains carried the blaKPC gene, coding for a carbapenemase. In particular, the whole-genome sequence of Aeromonas hydrophila strain 34SFC-3 was determined, revealing not only the presence of antimicrobial and heavy metal resistance genes but also a versatile virulome repertoire. Mobile genetic elements, including insertion sequences, transposons, integrative conjugative elements, and an IncQ1 plasmid were also detected. Considering the ubiquity of Aeromonas species, their genetic promiscuity, pathogenicity, and intrinsic features to endure environmental stress, our findings reinforce the concept that A. hydrophila truly is a "Jack of all trades'' that should not be overlooked under the One Health perspective.},
}
@article {pmid36671228,
year = {2022},
author = {Selvarajan, R and Obize, C and Sibanda, T and Abia, ALK and Long, H},
title = {Evolution and Emergence of Antibiotic Resistance in Given Ecosystems: Possible Strategies for Addressing the Challenge of Antibiotic Resistance.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {1},
pages = {},
pmid = {36671228},
issn = {2079-6382},
abstract = {Antibiotics were once considered the magic bullet for all human infections. However, their success was short-lived, and today, microorganisms have become resistant to almost all known antimicrobials. The most recent decade of the 20th and the beginning of the 21st century have witnessed the emergence and spread of antibiotic resistance (ABR) in different pathogenic microorganisms worldwide. Therefore, this narrative review examined the history of antibiotics and the ecological roles of antibiotics, and their resistance. The evolution of bacterial antibiotic resistance in different environments, including aquatic and terrestrial ecosystems, and modern tools used for the identification were addressed. Finally, the review addressed the ecotoxicological impact of antibiotic-resistant bacteria and public health concerns and concluded with possible strategies for addressing the ABR challenge. The information provided in this review will enhance our understanding of ABR and its implications for human, animal, and environmental health. Understanding the environmental dimension will also strengthen the need to prevent pollution as the factors influencing ABR in this setting are more than just antibiotics but involve others like heavy metals and biocides, usually not considered when studying ABR.},
}
@article {pmid36669850,
year = {2023},
author = {Tonkin-Hill, G and Gladstone, RA and Pöntinen, AK and Arredondo-Alonso, S and Bentley, SD and Corander, J},
title = {Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe.},
journal = {Genome research},
volume = {33},
number = {1},
pages = {129-140},
pmid = {36669850},
issn = {1549-5469},
support = {204016/Z/16/Z//Wellcome Trust/United Kingdom ; 206194//Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Phylogeny ; *Evolution, Molecular ; *Prokaryotic Cells ; Genome, Bacterial ; Gene Transfer, Horizontal ; },
abstract = {Horizontal gene transfer (HGT) plays a critical role in the evolution and diversification of many microbial species. The resulting dynamics of gene gain and loss can have important implications for the development of antibiotic resistance and the design of vaccine and drug interventions. Methods for the analysis of gene presence/absence patterns typically do not account for errors introduced in the automated annotation and clustering of gene sequences. In particular, methods adapted from ecological studies, including the pangenome gene accumulation curve, can be misleading as they may reflect the underlying diversity in the temporal sampling of genomes rather than a difference in the dynamics of HGT. Here, we introduce Panstripe, a method based on generalized linear regression that is robust to population structure, sampling bias, and errors in the predicted presence/absence of genes. We show using simulations that Panstripe can effectively identify differences in the rate and number of genes involved in HGT events, and illustrate its capability by analyzing several diverse bacterial genome data sets representing major human pathogens.},
}
@article {pmid36669792,
year = {2023},
author = {Breidenstein, A and Ter Beek, J and Berntsson, RP},
title = {Structural and functional characterization of TraI from pKM101 reveals basis for DNA processing.},
journal = {Life science alliance},
volume = {6},
number = {4},
pages = {},
pmid = {36669792},
issn = {2575-1077},
mesh = {*Escherichia coli Proteins/metabolism ; Type IV Secretion Systems ; Plasmids/genetics ; DNA ; Esterases/genetics ; },
abstract = {Type 4 secretion systems are large and versatile protein machineries that facilitate the spread of antibiotic resistance and other virulence factors via horizontal gene transfer. Conjugative type 4 secretion systems depend on relaxases to process the DNA in preparation for transport. TraI from the well-studied conjugative plasmid pKM101 is one such relaxase. Here, we report the crystal structure of the trans-esterase domain of TraI in complex with its substrate oriT DNA, highlighting the conserved DNA-binding mechanism of conjugative relaxases. In addition, we present an apo structure of the trans-esterase domain of TraI that includes most of the flexible thumb region. This allows us for the first time to visualize the large conformational change of the thumb subdomain upon DNA binding. We also characterize the DNA binding, nicking, and religation activity of the trans-esterase domain, helicase domain, and full-length TraI. Unlike previous indications in the literature, our results reveal that the TraI trans-esterase domain from pKM101 behaves in a conserved manner with its homologs from the R388 and F plasmids.},
}
@article {pmid36669117,
year = {2023},
author = {Ishikawa, M and Fujiwara, A and Kosetsu, K and Horiuchi, Y and Kamamoto, N and Umakawa, N and Tamada, Y and Zhang, L and Matsushita, K and Palfalvi, G and Nishiyama, T and Kitasaki, S and Masuda, Y and Shiroza, Y and Kitagawa, M and Nakamura, T and Cui, H and Hiwatashi, Y and Kabeya, Y and Shigenobu, S and Aoyama, T and Kato, K and Murata, T and Fujimoto, K and Benfey, PN and Hasebe, M and Kofuji, R},
title = {GRAS transcription factors regulate cell division planes in moss overriding the default rule.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {4},
pages = {e2210632120},
pmid = {36669117},
issn = {1091-6490},
support = {20H05891 21H02499 and 21K19250//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; No grant number//Howard Hughes Medical Institute (HHMI)/ ; MIRA 1R35GM131725//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35 GM131725/GM/NIGMS NIH HHS/United States ; 18H04846 20H04892 20H05430&#xa0;and 22H04738//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 20H05415//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 16H06378//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
mesh = {*Arabidopsis Proteins/metabolism ; *Arabidopsis/genetics ; Transcription Factors/genetics/metabolism ; Cell Division/genetics ; Plant Roots/metabolism ; Gene Expression Regulation, Plant ; },
abstract = {Plant cells are surrounded by a cell wall and do not migrate, which makes the regulation of cell division orientation crucial for development. Regulatory mechanisms controlling cell division orientation may have contributed to the evolution of body organization in land plants. The GRAS family of transcription factors was transferred horizontally from soil bacteria to an algal common ancestor of land plants. SHORTROOT (SHR) and SCARECROW (SCR) genes in this family regulate formative periclinal cell divisions in the roots of flowering plants, but their roles in nonflowering plants and their evolution have not been studied in relation to body organization. Here, we show that SHR cell autonomously inhibits formative periclinal cell divisions indispensable for leaf vein formation in the moss Physcomitrium patens, and SHR expression is positively and negatively regulated by SCR and the GRAS member LATERAL SUPPRESSOR, respectively. While precursor cells of a leaf vein lacking SHR usually follow the geometry rule of dividing along the division plane with the minimum surface area, SHR overrides this rule and forces cells to divide nonpericlinally. Together, these results imply that these bacterially derived GRAS transcription factors were involved in the establishment of the genetic regulatory networks modulating cell division orientation in the common ancestor of land plants and were later adapted to function in flowering plant and moss lineages for their specific body organizations.},
}
@article {pmid36668832,
year = {2022},
author = {Proctor, RH and Hao, G and Kim, HS and Whitaker, BK and Laraba, I and Vaughan, MM and McCormick, SP},
title = {A Novel Trichothecene Toxin Phenotype Associated with Horizontal Gene Transfer and a Change in Gene Function in Fusarium.},
journal = {Toxins},
volume = {15},
number = {1},
pages = {},
pmid = {36668832},
issn = {2072-6651},
mesh = {Phylogeny ; *Fusarium/metabolism ; Gene Transfer, Horizontal ; *Trichothecenes/metabolism ; *Mycotoxins/chemistry ; Phenotype ; },
abstract = {Fusarium trichothecenes are among the mycotoxins of most concern to food and feed safety. Production of these mycotoxins and presence of the trichothecene biosynthetic gene (TRI) cluster have been confirmed in only two multispecies lineages of Fusarium: the Fusarium incarnatum-equiseti (Incarnatum) and F. sambucinum (Sambucinum) species complexes. Here, we identified and characterized a TRI cluster in a species that has not been formally described and is represented by Fusarium sp. NRRL 66739. This fungus is reported to be a member of a third Fusarium lineage: the F. buharicum species complex. Cultures of NRRL 66739 accumulated only two trichothecenes, 7-hydroxyisotrichodermin and 7-hydroxyisotrichodermol. Although these are not novel trichothecenes, the production profile of NRRL 66739 is novel, because in previous reports 7-hydroxyisotrichodermin and 7-hydroxyisotrichodermol were components of mixtures of 6-8 trichothecenes produced by several Fusarium species in Sambucinum. Heterologous expression analysis indicated that the TRI13 gene in NRRL 66739 confers trichothecene 7-hydroxylation. This contrasts the trichothecene 4-hydroxylation function of TRI13 in other Fusarium species. Phylogenetic analyses suggest that NRRL 66739 acquired the TRI cluster via horizontal gene transfer from a close relative of Incarnatum and Sambucinum. These findings provide insights into evolutionary processes that have shaped the distribution of trichothecene production among Fusarium species and the structural diversity of the toxins.},
}
@article {pmid36655280,
year = {2023},
author = {Shin, H and Kim, Y and Han, S and Hur, HG},
title = {Resistome Study in Aquatic Environments.},
journal = {Journal of microbiology and biotechnology},
volume = {33},
number = {3},
pages = {277-287},
pmid = {36655280},
issn = {1738-8872},
mesh = {*Genes, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria/genetics ; },
abstract = {Since the first discovery of antibiotics, introduction of new antibiotics has been coupled with the occurrence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Rapid dissemination of ARB and ARGs in the aquatic environments has become a global concern. ARB and ARGs have been already disseminated in the aquatic environments via various routes. Main hosts of most of ARGs were found to belong to Gammaproteobacteria class, including clinically important potential pathogens. Transmission of ARGs also occurs by horizontal gene transfer (HGT) mechanisms between bacterial strains in the aquatic environments, resulting in ubiquity of ARGs. Thus, a few of ARGs and MGEs (e.g., strA, sul1, int1) have been suggested as indicators for global comparability of contamination level in the aquatic environments. With ARB and ARGs contamination, the occurrence of critical pathogens has been globally issued due to their widespread in the aquatic environments. Thus, active surveillance systems have been launched worldwide. In this review, we described advancement of methodologies for ARGs detection, and occurrence of ARB and ARGs and their dissemination in the aquatic environments. Even though numerous studies have been conducted for ARB and ARGs, there is still no clear strategy to tackle antibiotic resistance (AR) in the aquatic environments. At least, for consistent surveillance, a strict framework should be established for further research in the aquatic environments.},
}
@article {pmid36653393,
year = {2023},
author = {Couturier, A and Virolle, C and Goldlust, K and Berne-Dedieu, A and Reuter, A and Nolivos, S and Yamaichi, Y and Bigot, S and Lesterlin, C},
title = {Real-time visualisation of the intracellular dynamics of conjugative plasmid transfer.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {294},
pmid = {36653393},
issn = {2041-1723},
mesh = {DNA, Bacterial/genetics/metabolism ; *Escherichia coli/genetics/metabolism ; *Conjugation, Genetic ; Plasmids/genetics ; DNA ; DNA, Single-Stranded/genetics ; Gene Transfer, Horizontal ; },
abstract = {Conjugation is a contact-dependent mechanism for the transfer of plasmid DNA between bacterial cells, which contributes to the dissemination of antibiotic resistance. Here, we use live-cell microscopy to visualise the intracellular dynamics of conjugative transfer of F-plasmid in E. coli, in real time. We show that the transfer of plasmid in single-stranded form (ssDNA) and its subsequent conversion into double-stranded DNA (dsDNA) are fast and efficient processes that occur with specific timing and subcellular localisation. Notably, the ssDNA-to-dsDNA conversion determines the timing of plasmid-encoded protein production. The leading region that first enters the recipient cell carries single-stranded promoters that allow the early and transient synthesis of leading proteins immediately upon entry of the ssDNA plasmid. The subsequent conversion into dsDNA turns off leading gene expression, and activates the expression of other plasmid genes under the control of conventional double-stranded promoters. This molecular strategy allows for the timely production of factors sequentially involved in establishing, maintaining and disseminating the plasmid.},
}
@article {pmid36653270,
year = {2023},
author = {Murakami, H and Sano, K and Motomura, K and Kuroda, A and Hirota, R},
title = {Assessment of horizontal gene transfer-mediated destabilization of Synechococcus elongatus PCC 7942 biocontainment system.},
journal = {Journal of bioscience and bioengineering},
volume = {135},
number = {3},
pages = {190-195},
doi = {10.1016/j.jbiosc.2022.12.002},
pmid = {36653270},
issn = {1347-4421},
mesh = {*Gene Transfer, Horizontal ; Ecosystem ; *Synechococcus/metabolism ; Phosphates/metabolism ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Biological containment is a biosafety strategy that prevents the dispersal of genetically modified organisms in natural ecosystems. We previously established a biocontainment system that makes bacterial growth dependent on the availability of phosphite (Pt), an ecologically rare form of phosphorus (P), by introducing Pt metabolic pathway genes and disrupting endogenous phosphate and organic phosphate transporter genes. Although this system proved highly effective, horizontal gene transfer (HGT) mediated recovery of a P transporter gene is considered as a potential pathway to abolish the Pt-dependent growth, resulting in escape from the containment. Here, we assessed the risk of HGT driven escape using the Pt-dependent cyanobacterium Synechococcus elongatus PCC 7942. Transformation experiments revealed that the Pt-dependent strain could regain phosphate transporter genes from the S. elongatus PCC 7942 wild-type genome and from the genome of the closely related strain, S. elongatus UTEX 2973. Transformed S. elongatus PCC 7942 became viable in a phosphate-containing medium. Meanwhile, transformation of the Synechocystis sp. PCC 6803 genome or environmental DNA did not yield escape strains, suggesting that only genetic material derived from phylogenetically-close species confer high risk to generate escape. Eliminating a single gene necessary for natural competence from the Pt-dependent strain reduced the escape occurrence rate. These results demonstrate that natural competence could be a potential risk to destabilize Pt-dependence, and therefore inhibiting exogenous DNA uptake would be effective for enhancing the robustness of the gene disruption-dependent biocontainment.},
}
@article {pmid36641904,
year = {2023},
author = {Alnahhas, RN and Dunlop, MJ},
title = {Advances in linking single-cell bacterial stress response to population-level survival.},
journal = {Current opinion in biotechnology},
volume = {79},
number = {},
pages = {102885},
pmid = {36641904},
issn = {1879-0429},
support = {R01 AI102922/AI/NIAID NIH HHS/United States ; },
mesh = {*Anti-Bacterial Agents ; *Bacteria/genetics ; Phenotype ; },
abstract = {Stress response mechanisms can allow bacteria to survive a myriad of challenges, including nutrient changes, antibiotic encounters, and antagonistic interactions with other microbes. Expression of these stress response pathways, in addition to other cell features such as growth rate and metabolic state, can be heterogeneous across cells and over time. Collectively, these single-cell-level phenotypes contribute to an overall population-level response to stress. These include diversifying actions, which can be used to enable bet-hedging, and coordinated actions, such as biofilm production, horizontal gene transfer, and cross-feeding. Here, we highlight recent results and emerging technologies focused on both single-cell and population-level responses to stressors, and we draw connections about the combined impact of these effects on survival of bacterial communities.},
}
@article {pmid36639816,
year = {2023},
author = {Zhu, J and Yang, F and Du, K and Wei, ZL and Wu, QF and Chen, Y and Li, WF and Li, Q and Zhou, CZ},
title = {Phylogenomics of five Pseudanabaena cyanophages and evolutionary traces of horizontal gene transfer.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {3},
pmid = {36639816},
issn = {2524-6372},
support = {No. 202104i07020004//Key Research and Development Projects of Anhui Province/ ; No. WK2070000195 and WK9100000015//Fundamental Research Funds for the Central Universities/ ; No. U19A2020//National Natural Science Foundation of China/ ; No. 2018YFA0903100//Ministry of Science and Technology of the People's Republic of China/ ; },
abstract = {BACKGROUND: Along with the fast development and urbanization in developing countries, the waterbodies aside the growing cities become heavily polluted and highly eutrophic, thus leading to the seasonal outbreak of cyanobacterial bloom. Systematic isolation and characterization of freshwater cyanophages might provide a biological solution to control the awful blooms. However, genomic sequences and related investigations on the freshwater cyanophages remain very limited to date.<br><br>RESULTS: Following our recently reported five cyanophages Pam1~Pam5 from Lake Chaohu in China, here we isolated another five cyanophages, termed Pan1~Pan5, which infect the cyanobacterium Pseudanabaena sp. Chao 1811. Whole-genome sequencing showed that they all contain a double-stranded DNA genome of 37.2 to 72.0&#xa0;kb in length, with less than half of the putative open reading frames annotated with known functions. Remarkably, the siphophage Pan1 encodes an auxiliary metabolic gene phoH and constitutes, together with the host, a complete queuosine modification pathway. Proteomic analyses revealed that although Pan1~Pan5 are distinct from each other in evolution, Pan1 and Pan3 are somewhat similar to our previously identified cyanophages Pam3 and Pam1 at the genomic level, respectively. Moreover, phylogenetic analyses suggested that Pan1 resembles the &#x3b1;-proteobacterial phage vB_DshS-R5C, revealing direct evidence for phage-mediated horizontal gene transfer between cyanobacteria and &#x3b1;-proteobacteria.<br><br>CONCLUSION: In addition to the previous reports of Pam1~Pam5, the present findings on Pan1~Pan5 largely enrich the library of reference freshwater cyanophages. The abundant genomic information provides a pool to identify novel genes and proteins of unknown function. Moreover, we found for the first time the evolutionary traces in the cyanophage that horizontal gene transfer might occur at the level of not only inter-species, but even inter-phylum. It indicates that the bacteriophage or cyanophage could be developed as a powerful tool for gene manipulation among various species or phyla.},
}
@article {pmid36638983,
year = {2023},
author = {Yang, K and Chen, ML and Zhu, D},
title = {Exposure to benzalkonium chloride disinfectants promotes antibiotic resistance in sewage sludge microbiomes.},
journal = {The Science of the total environment},
volume = {867},
number = {},
pages = {161527},
pmid = {36638983},
issn = {1879-1026},
mesh = {Humans ; Sewage/microbiology ; Benzalkonium Compounds/pharmacology ; Genes, Bacterial ; *Disinfectants ; *COVID-19 ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; *Microbiota ; },
abstract = {Disinfectants are routinely used in human environments to control and prevent the transmission of microbial disease, and this is particularly true during the current COVID-19 crisis. However, it remains unclear whether the increased disinfectant loadings to wastewater treatment plants facilitate the dissemination of antibiotic resistance genes (ARGs) in sewage sludge microbiomes. Here, we investigated the impacts of benzalkonium chlorides (BACs), widely used disinfectants, on ARGs profiles and microbial community structures in sewage sludge by using high-throughput quantitative PCR and Illumina sequencing. A total of 147 unique ARGs and 39 mobile genetic elements (MGEs) were detected in all sewage sludge samples. Our results show that exposure to BACs disinfectants at environmentally relevant concentrations significantly promotes both the diversity and absolute abundance of ARGs in sludge microbiomes, indicating the co-selection of ARGs by BACs disinfectants. The enrichment of ARGs abundance varied from 2.15-fold to 3.63-fold compared to controls. In addition, BACs exposure significantly alters bacterial and protistan communities, resulting in dysbiosis of the sludge microbiota. The Mantel test and Procrustes analysis confirm that bacterial communities are significantly correlated with ARGs profiles under BACs treatments. The structural equation model explains 83.8 % of the total ARGs variation and further illustrates that the absolute abundance of MGEs exerts greater impacts on the variation of absolute abundance of ARGs than microbial communities under BACs exposure, suggesting BACs may promote antibiotic resistance by enhancing the horizontal gene transfer of ARGs across sludge microbiomes. Collectively, our results provide new insights into the proliferation of antibiotic resistance through disinfectant usage during the pandemic and highlight the necessity to minimize the environmental release of disinfectants into the non-target environment for combating antibiotic resistance.},
}
@article {pmid36638546,
year = {2023},
author = {Gibson, PS and Veening, JW},
title = {Gaps in the wall: understanding cell wall biology to tackle amoxicillin resistance in Streptococcus pneumoniae.},
journal = {Current opinion in microbiology},
volume = {72},
number = {},
pages = {102261},
doi = {10.1016/j.mib.2022.102261},
pmid = {36638546},
issn = {1879-0364},
mesh = {Child ; Humans ; *Amoxicillin/pharmacology ; Streptococcus pneumoniae/genetics ; *Respiratory Tract Infections/microbiology ; Peptidoglycan ; Biology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Streptococcus pneumoniae is the most common cause of community-acquired pneumonia, and one of the main pathogens responsible for otitis media infections in children. Amoxicillin (AMX) is a broad-spectrum β-lactam antibiotic, used frequently for the treatment of bacterial respiratory tract infections. Here, we discuss the pneumococcal response to AMX, including the mode of action of AMX, the effects on autolysin regulation, and the evolution of resistance through natural transformation. We discuss current knowledge gaps in the synthesis and translocation of peptidoglycan and teichoic acids, major constituents of the pneumococcal cell wall and critical to AMX activity. Furthermore, an outlook of AMX resistance research is presented, including the development of natural competence inhibitors to block evolution via horizontal gene transfer, and the use of high-throughput essentiality screens for the discovery of novel cotherapeutics.},
}
@article {pmid36634159,
year = {2024},
author = {Ryan, MP and Carraro, N and Slattery, S and Pembroke, JT},
title = {Integrative Conjugative Elements (ICEs) of the SXT/R391 family drive adaptation and evolution in γ-Proteobacteria.},
journal = {Critical reviews in microbiology},
volume = {50},
number = {1},
pages = {105-126},
doi = {10.1080/1040841X.2022.2161870},
pmid = {36634159},
issn = {1549-7828},
mesh = {*Gammaproteobacteria/genetics ; DNA Transposable Elements ; Conjugation, Genetic ; Anti-Bacterial Agents ; },
abstract = {Integrative Conjugative Elements (ICEs) are mosaics containing functional modules allowing maintenance by site-specific integration and excision into and from the host genome and conjugative transfer to a specific host range. Many ICEs encode a range of adaptive functions that aid bacterial survival and evolution in a range of niches. ICEs from the SXT/R391 family are found in γ-Proteobacteria. Over 100 members have undergone epidemiological and molecular characterization allowing insight into their diversity and function. Comparative analysis of SXT/R391 elements from a wide geographic distribution has revealed conservation of key functions, and the accumulation and evolution of adaptive genes. This evolution is associated with gene acquisition in conserved hotspots and variable regions within the SXT/R391 ICEs catalysed via element-encoded recombinases. The elements can carry IS elements and transposons, and a mutagenic DNA polymerase, PolV, which are associated with their evolution. SXT/R391 ICEs isolated from different niches appear to have retained adaptive functions related to that specific niche; phage resistance determinants in ICEs carried by wastewater bacteria, antibiotic resistance determinants in clinical isolates and metal resistance determinants in bacteria recovered from polluted environments/ocean sediments. Many genes found in the element hotspots are undetermined and have few homologs in the nucleotide databases.},
}
@article {pmid36629415,
year = {2023},
author = {Finks, SS and Martiny, JBH},
title = {Plasmid-Encoded Traits Vary across Environments.},
journal = {mBio},
volume = {14},
number = {1},
pages = {e0319122},
pmid = {36629415},
issn = {2150-7511},
mesh = {Humans ; *Ecosystem ; Plasmids/genetics ; *Bacteria/genetics ; Anti-Bacterial Agents ; Gene Transfer, Horizontal ; },
abstract = {Plasmids are key mobile genetic elements in bacterial evolution and ecology as they allow the rapid adaptation of bacteria under selective environmental changes. However, the genetic information associated with plasmids is usually considered separately from information about their environmental origin. To broadly understand what kinds of traits may become mobilized by plasmids in different environments, we analyzed the properties and accessory traits of 9,725 unique plasmid sequences from a publicly available database with known bacterial hosts and isolation sources. Although most plasmid research focuses on resistance traits, such genes made up <1% of the total genetic information carried by plasmids. Similar to traits encoded on the bacterial chromosome, plasmid accessory trait compositions (including general Clusters of Orthologous Genes [COG] functions, resistance genes, and carbon and nitrogen genes) varied across seven broadly defined environment types (human, animal, wastewater, plant, soil, marine, and freshwater). Despite their potential for horizontal gene transfer, plasmid traits strongly varied with their host's taxonomic assignment. However, the trait differences across environments of broad COG categories could not be entirely explained by plasmid host taxonomy, suggesting that environmental selection acts on the plasmid traits themselves. Finally, some plasmid traits and environments (e.g., resistance genes in human-related environments) were more often associated with mobilizable plasmids (those having at least one detected relaxase) than others. Overall, these findings underscore the high level of diversity of traits encoded by plasmids and provide a baseline to investigate the potential of plasmids to serve as reservoirs of adaptive traits for microbial communities. IMPORTANCE Plasmids are well known for their role in the transmission of antibiotic resistance-conferring genes. Beyond human and clinical settings, however, they disseminate many other types of genes, including those that contribute to microbially driven ecosystem processes. In this study, we identified the distribution of traits genetically encoded by plasmids isolated from seven broadly categorized environments. We find that plasmid trait content varied with both bacterial host taxonomy and environment and that, on average, half of the plasmids were potentially mobilizable. As anthropogenic activities impact ecosystems and the climate, investigating and identifying the mechanisms of how microbial communities can adapt will be imperative for predicting the impacts on ecosystem functioning.},
}
@article {pmid36626782,
year = {2022},
author = {Sundarraj, S and Sudarmani, DNP and Samuel, P and Sevarkodiyone, SP},
title = {Bioremediation of hexavalent chromium by transformation of Escherichia coli DH5α with chromate reductase (ChrR) genes of Pseudomonas putida isolated from tannery effluent.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxac019},
pmid = {36626782},
issn = {1365-2672},
abstract = {AIMS: Hexavalent chromium (Cr(VI)), a toxic heavy metal, is a serious pollutant from tannery effluent, and its accumulation in soil and water causes severe environmental concerns and increasing public health issues. The present study focuses on the isolation and identification of chromium-reducing bacteria collected from the tannery industry in Dindigul, Tamil Nadu. Chromium-reducing bacteria Pseudomonas putida were identified by 16S rRNA sequencing followed by BLAST search. The plasmid with Cr(VI) reductase gene was isolated from Ps. putida and transferred to Escherichia coli DH5α for further studies.<br><br>METHODS AND RESULTS: The bacterial cultures were kept under controlled conditions for 72&#xa0;h to observe the growth rates and bacterial resistance to chromium. When strains wild-type and transformant E. coli DH5&#x3b1; were grown in chromium-supplemented media, they revealed significant growth, but strains cured type Ps. putida and E. coli DH5&#x3b1; recorded minimum growth. The Cr(VI) reduction employed by transformant E. coli DH5&#x3b1; and wild Ps. putida was 42.52&#xa0;&#xb1;&#xa0;1.48% and 44.46&#xa0;&#xb1;&#xa0;0.55%, respectively. The culture supernatant of the wild Ps. putida and transformant E. coli DH5&#x3b1; showed an increased reduction of Cr(VI) compared with cell extract supernatant and cell debris due to the extracellular activity of chromium reductase being responsible for Cr(VI) reduction. Besides, the chromium reductase gene was confirmed in the isolated Ps. putida and transformant E. coli DH5&#x3b1;.<br><br>CONCLUSIONS: Transformant bacteria could employ an alternative method for heavy metal detoxification in contaminated environments like tannery effluent and mining processes.<br><br>High Cr(VI) concentration resistance and high Cr(VI) reducing the strain's ability make it suitable for bioremediation. These possible horizontal gene transfer events indicated in this study may have enabled transformant E. coli DH5&#x3b1; as a good candidate for reducing the heavy metal pollution.},
}
@article {pmid36623672,
year = {2023},
author = {Sazykin, IS and Sazykina, MA},
title = {The role of oxidative stress in genome destabilization and adaptive evolution of bacteria.},
journal = {Gene},
volume = {857},
number = {},
pages = {147170},
doi = {10.1016/j.gene.2023.147170},
pmid = {36623672},
issn = {1879-0038},
mesh = {*Oxidative Stress/genetics ; *Bacteria/genetics ; Mutagenesis ; Genome, Bacterial ; },
abstract = {The review is devoted to bacterial genome destabilization by oxidative stress. The article discusses the main groups of substances causing such stress. Stress regulons involved in destabilization of genetic material and mechanisms enhancing mutagenesis, bacterial genome rearrangements, and horizontal gene transfer, induced by oxidative damage to cell components are also considered. Based on the analysis of publications, it can be claimed that rapid development of new food substrates and ecological niches by microorganisms occurs due to acceleration of genetic changes induced by oxidative stress, mediated by several stress regulons (SOS, RpoS and RpoE) and under selective pressure. The authors conclude that non-lethal oxidative stress is probably-one of the fundamental processes that guide evolution of prokaryotes and a powerful universal trigger for adaptive destabilization of bacterial genome under changing environmental conditions.},
}
@article {pmid36623656,
year = {2023},
author = {Wang, C and Jia, Y and Li, J and Wang, Y and Niu, H and Qiu, H and Li, X and Fang, W and Qiu, Z},
title = {Effect of bioaugmentation on tetracyclines influenced chicken manure composting and antibiotics resistance.},
journal = {The Science of the total environment},
volume = {867},
number = {},
pages = {161457},
doi = {10.1016/j.scitotenv.2023.161457},
pmid = {36623656},
issn = {1879-1026},
mesh = {Animals ; *Composting ; Manure ; Chickens ; Tetracyclines ; Genes, Bacterial ; Anti-Bacterial Agents ; },
abstract = {Antibiotic residue in husbandry waste has become a serious concern. In this study, contaminated chicken manure composting was conducted to reveal the bioaugmentation effect on tetracyclines residue and antibiotics resistance genes (ARGs). The bioaugmented composting removed most of the antibiotics in 7 days. Under bioaugmentation, 96.88 % of tetracycline and 92.31 % of oxytetracycline were removed, 6.32 % and 20.93 % higher than the control (P < 0.05). The high-temperature period was the most effective phase for eliminating antibiotics. The treatment showed a long high-temperature period (7 days), while no high-temperature period was in control. After composting, the treatment showed 13.87 % higher TN (26.51 g/kg) and 13.42 % higher NO3[-]-N (2.45 g/kg) than control (23.28 and 2.16 g/kg, respectively) but 12.72 % lower C/N, indicating fast decomposition and less nutrient loss. Exogenous microorganisms from bioaugmentation significantly reshaped the microbial community structure and facilitated the enrichment of genera such as Truepera and Fermentimonas, whose abundance increased by 71.10 % and 75.37 % than the control, respectively. Remarkably, ARGs, including tetC, tetG, and tetW, were enhanced by 198.77 %, 846.77 %, and 62.63 % compared with the control, while the integron gene (intl1) was elevated by 700.26 %, indicating horizontal gene transfer of ARGs. Eventually, bioaugmentation was efficient in regulating microbial metabolism, relieving antibiotic stress, and eliminating antibiotics in composting. However, the ability to remove ARGs should be further investigated. Such an approach should be further considered for treating pollutants-influenced organic waste to eliminate environmental concerns.},
}
@article {pmid36622346,
year = {2023},
author = {Nieves, C and Vincent, AT and Zarantonelli, L and Picardeau, M and Veyrier, FJ and Buschiazzo, A},
title = {Horizontal transfer of the rfb cluster in Leptospira is a genetic determinant of serovar identity.},
journal = {Life science alliance},
volume = {6},
number = {2},
pages = {},
pmid = {36622346},
issn = {2575-1077},
mesh = {Humans ; *Leptospira/genetics ; Serogroup ; Lipopolysaccharides ; Phenotype ; },
abstract = {Leptospira bacteria comprise numerous species, several of which cause serious disease to a broad range of hosts including humans. These spirochetes exhibit large intraspecific variation, resulting in complex tabulations of serogroups/serovars that crisscross the species classification. Serovar identity, linked to biological/clinical phenotypes, depends on the structure of surface-exposed LPS. Many LPS biosynthesis-encoding genes reside within the chromosomic rfb gene cluster. However, the genetic basis of intraspecies variability is not fully understood, constraining diagnostics/typing methods to cumbersome serologic procedures. We now show that the gene content of the rfb cluster strongly correlates with Leptospira serovar designation. Whole-genome sequencing of pathogenic L. noguchii, including strains of different serogroups, reveals that the rfb cluster undergoes extensive horizontal gene transfer. The rfb clusters from several Leptospira species disclose a univocal correspondence between gene composition and serovar identity. This work paves the way to genetic typing of Leptospira serovars, and to pinpointing specific genes within the distinct rfb clusters, encoding host-specific virulence traits. Further research shall unveil the molecular mechanism of rfb transfer among Leptospira strains and species.},
}
@article {pmid36622251,
year = {2023},
author = {Lindqvist, LL and Jarmusch, SA and Sonnenschein, EC and Strube, ML and Kim, J and Nielsen, MW and Kempen, PJ and Schoof, EM and Zhang, SD and Gram, L},
title = {Tropodithietic Acid, a Multifunctional Antimicrobial, Facilitates Adaption and Colonization of the Producer, Phaeobacter piscinae.},
journal = {mSphere},
volume = {8},
number = {1},
pages = {e0051722},
pmid = {36622251},
issn = {2379-5042},
mesh = {*Type IV Secretion Systems/metabolism ; *Rhodobacteraceae/genetics ; Anti-Bacterial Agents/metabolism ; },
abstract = {In the marine environment, surface-associated bacteria often produce an array of antimicrobial secondary metabolites, which have predominantly been perceived as competition molecules. However, they may also affect other hallmarks of surface-associated living, such as motility and biofilm formation. Here, we investigate the ecological significance of an antibiotic secondary metabolite, tropodithietic acid (TDA), in the producing bacterium, Phaeobacter piscinae S26. We constructed a markerless in-frame deletion mutant deficient in TDA biosynthesis, S26ΔtdaB. Molecular networking demonstrated that other chemical sulfur-containing features, likely related to TDA, were also altered in the secondary metabolome. We found several changes in the physiology of the TDA-deficient mutant, ΔtdaB, compared to the wild type. Growth of the two strains was similar; however, ΔtdaB cells were shorter and more motile. Transcriptome and proteome profiling revealed an increase in gene expression and protein abundance related to a type IV secretion system, and to a prophage, and a gene transfer agent in ΔtdaB. All these systems may contribute to horizontal gene transfer (HGT), which may facilitate adaptation to novel niches. We speculate that once a TDA-producing population has been established in a new niche, the accumulation of TDA acts as a signal of successful colonization, prompting a switch to a sessile lifestyle. This would lead to a decrease in motility and the rate of HGT, while filamentous cells could form the base of a biofilm. In addition, the antibiotic properties of TDA may inhibit invading competing microorganisms. This points to a role of TDA in coordinating colonization and adaptation. IMPORTANCE Despite the broad clinical usage of microbial secondary metabolites with antibiotic activity, little is known about their role in natural microbiomes. Here, we studied the effect of production of the antibiotic tropodithietic acid (TDA) on the producing strain, Phaeobacter piscinae S26, a member of the Roseobacter group. We show that TDA affects several phenotypes of the producing strain, including motility, cell morphology, metal metabolism, and three horizontal gene transfer systems: a prophage, a type IV secretion system, and a gene transfer agent. Together, this indicates that TDA participates in coordinating the colonization process of the producer. TDA is thus an example of a multifunctional secondary metabolite that can mediate complex interactions in microbial communities. This work broadens our understanding of the ecological role that secondary metabolites have in microbial community dynamics.},
}
@article {pmid36620013,
year = {2022},
author = {Lieberman, LA},
title = {Outer membrane vesicles: A bacterial-derived vaccination system.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1029146},
pmid = {36620013},
issn = {1664-302X},
abstract = {Outer membrane vesicles (OMVs) are non-living spherical nanostructures that derive from the cell envelope of Gram-negative bacteria. OMVs are important in bacterial pathogenesis, cell-to-cell communication, horizontal gene transfer, quorum sensing, and in maintaining bacterial fitness. These structures can be modified to express antigens of interest using glycoengineering and genetic or chemical modification. The resulting OMVs can be used to immunize individuals against the expressed homo- or heterologous antigens. Additionally, cargo can be loaded into OMVs and they could be used as a drug delivery system. OMVs are inherently immunogenic due to proteins and glycans found on Gram negative bacterial outer membranes. This review focuses on OMV manipulation to increase vesiculation and decrease antigenicity, their utility as vaccines, and novel engineering approaches to extend their application.},
}
@article {pmid36611105,
year = {2023},
author = {Aldaihani, R and Heath, LS},
title = {Connecting genomic islands across prokaryotic and phage genomes via protein families.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {344},
pmid = {36611105},
issn = {2045-2322},
mesh = {*Genomic Islands/genetics ; *Bacteriophages/genetics ; Prokaryotic Cells ; Proteins/genetics ; Bacteria/genetics ; Computational Biology/methods ; Gene Transfer, Horizontal ; Genome, Bacterial ; },
abstract = {Prokaryotic genomes evolve via horizontal gene transfer (HGT), mutations, and rearrangements. A noteworthy part of the HGT process is facilitated by genomic islands (GIs). While previous computational biology research has focused on developing tools to detect GIs in prokaryotic genomes, there has been little research investigating GI patterns and biological connections across species. We have pursued the novel idea of connecting GIs across prokaryotic and phage genomes via patterns of protein families. Such patterns are sequences of protein families frequently present in the genomes of multiple species. We combined the large data set from the IslandViewer4 database with protein families from Pfam while implementing a comprehensive strategy to identify patterns making use of HMMER, BLAST, and MUSCLE. we also implemented Python programs that link the analysis into a single pipeline. Research results demonstrated that related GIs often exist in species that are evolutionarily unrelated and in multiple bacterial phyla. Analysis of the discovered patterns led to the identification of biological connections among prokaryotes and phages. These connections suggest broad HGT connections across the bacterial kingdom and its associated phages. The discovered patterns and connections could provide the basis for additional analysis on HGT breadth and the patterns in pathogenic GIs.},
}
@article {pmid36610752,
year = {2023},
author = {Botelho, J and Cazares, A and Schulenburg, H},
title = {The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements.},
journal = {Nucleic acids research},
volume = {51},
number = {1},
pages = {236-252},
pmid = {36610752},
issn = {1362-4962},
mesh = {Humans ; *Interspersed Repetitive Sequences/genetics ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Plasmids/genetics ; Gene Transfer, Horizontal/genetics ; Prophages/genetics ; },
abstract = {Mobile genetic elements (MGEs) mediate the shuffling of genes among organisms. They contribute to the spread of virulence and antibiotic resistance (AMR) genes in human pathogens, such as the particularly problematic group of ESKAPE pathogens. Here, we performed the first systematic analysis of MGEs, including plasmids, prophages, and integrative and conjugative/mobilizable elements (ICEs/IMEs), across all ESKAPE pathogens. We found that different MGE types are asymmetrically distributed across these pathogens, and that most horizontal gene transfer (HGT) events are restricted by phylum or genus. We show that the MGEs proteome is involved in diverse functional processes and distinguish widespread proteins within the ESKAPE context. Moreover, anti-CRISPRs and AMR genes are overrepresented in the ESKAPE mobilome. Our results also underscore species-specific trends shaping the number of MGEs, AMR, and virulence genes across pairs of conspecific ESKAPE genomes with and without CRISPR-Cas systems. Finally, we observed that CRISPR spacers found on prophages, ICEs/IMEs, and plasmids have different targeting biases: while plasmid and prophage CRISPRs almost exclusively target other plasmids and prophages, respectively, ICEs/IMEs CRISPRs preferentially target prophages. Overall, our study highlights the general importance of the ESKAPE mobilome in contributing to the spread of AMR and mediating conflict among MGEs.},
}
@article {pmid36608829,
year = {2023},
author = {Tan, Y and Cao, X and Chen, S and Ao, X and Li, J and Hu, K and Liu, S and Penttinen, P and Yang, Y and Yu, X and Liu, A and Liu, C and Zhao, K and Zou, L},
title = {Antibiotic and heavy metal resistance genes in sewage sludge survive during aerobic composting.},
journal = {The Science of the total environment},
volume = {866},
number = {},
pages = {161386},
doi = {10.1016/j.scitotenv.2023.161386},
pmid = {36608829},
issn = {1879-1026},
mesh = {Anti-Bacterial Agents ; Sewage/microbiology ; Genes, Bacterial ; *Composting ; *Metals, Heavy ; Bacteria/genetics ; Manure ; },
abstract = {Municipal sewage sludge has been generated in increasing amounts with the acceleration of urbanization and economic development. The nutrient rich sewage sludge can be recycled by composting that has a great potential to produce stabilized organic fertilizer and substrate for plant cultivation. However, little is known about the metals, pathogens and antibiotic resistance transfer risks involved in applying the composted sludge in agriculture. We studied changes in and relationships between heavy metal contents, microbial communities, and antibiotic resistance genes (ARGs), heavy metal resistance genes (HMRGs) and mobile genetic elements (MGEs) in aerobic composting of sewage sludge. The contents of most of the analyzed heavy metals were not lower after composting. The bacterial α-diversity was lower, and the community composition was different after composting. Firmicutes were enriched, and Proteobacteria and potential pathogens in the genera Arcobacter and Acinetobacter were depleted in the composted sludge. The differences in bacteria were possibly due to the high temperature phase during the composting which was likely to affect temperature-sensitive bacteria. The number of detected ARGs, HMRGs and MGEs was lower, and the relative abundances of several resistance genes were lower after composting. However, the abundance of seven ARGs and six HMRGs remained on the same level after composting. Co-occurrence analysis of bacterial taxa and the genes suggested that the ARGs may spread via horizontal gene transfer during composting. In summary, even though aerobic composting is effective for managing sewage sludge and to decrease the relative abundance of potential pathogens, ARGs and HMRGs, it might include a potential risk for the dissemination of ARGs in the environment.},
}
@article {pmid36608658,
year = {2023},
author = {Utter, DR and Orphan, VJ},
title = {Gifts hidden in shadowy genome islands.},
journal = {Cell},
volume = {186},
number = {1},
pages = {5-7},
doi = {10.1016/j.cell.2022.12.001},
pmid = {36608658},
issn = {1097-4172},
mesh = {Archaea/genetics ; *Bacteria/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Interspersed Repetitive Sequences ; },
abstract = {Despite being typically perceived as "clonal" organisms, bacteria and archaea possess numerous mechanisms to share and co-opt genetic material from other lineages. Several mechanisms for horizontal gene transfer have been discovered, but the high mosaicity observed in many bacterial genomes outscales that explained by known mechanisms, hinting at yet undiscovered processes. In this issue of Cell, Hackl et al. introduce a new category of mobile genetic elements called tycheposons, providing a novel mechanism that contributes to the prodigious genomic diversity within microbial populations. The discovery and characterization of tycheposons prompts a reevaluation of microbial diversification in complex environments.},
}
@article {pmid36608657,
year = {2023},
author = {Hackl, T and Laurenceau, R and Ankenbrand, MJ and Bliem, C and Cariani, Z and Thomas, E and Dooley, KD and Arellano, AA and Hogle, SL and Berube, P and Leventhal, GE and Luo, E and Eppley, JM and Zayed, AA and Beaulaurier, J and Stepanauskas, R and Sullivan, MB and DeLong, EF and Biller, SJ and Chisholm, SW},
title = {Novel integrative elements and genomic plasticity in ocean ecosystems.},
journal = {Cell},
volume = {186},
number = {1},
pages = {47-62.e16},
doi = {10.1016/j.cell.2022.12.006},
pmid = {36608657},
issn = {1097-4172},
mesh = {*Ecosystem ; *Genome, Bacterial/genetics ; Phylogeny ; Oceans and Seas ; Genomics ; },
abstract = {Horizontal gene transfer accelerates microbial evolution. The marine picocyanobacterium Prochlorococcus exhibits high genomic plasticity, yet the underlying mechanisms are elusive. Here, we report a novel family of DNA transposons-"tycheposons"-some of which are viral satellites while others carry cargo, such as nutrient-acquisition genes, which shape the genetic variability in this globally abundant genus. Tycheposons share distinctive mobile-lifecycle-linked hallmark genes, including a deep-branching site-specific tyrosine recombinase. Their excision and integration at tRNA genes appear to drive the remodeling of genomic islands-key reservoirs for flexible genes in bacteria. In a selection experiment, tycheposons harboring a nitrate assimilation cassette were dynamically gained and lost, thereby promoting chromosomal rearrangements and host adaptation. Vesicles and phage particles harvested from seawater are enriched in tycheposons, providing a means for their dispersal in the wild. Similar elements are found in microbes co-occurring with Prochlorococcus, suggesting a common mechanism for microbial diversification in the vast oligotrophic oceans.},
}
@article {pmid36602323,
year = {2023},
author = {Regmi, A and Tague, JG and Boas Lichty, KE and Boyd, EF},
title = {A Class IV Adenylate Cyclase, CyaB, Is Required for Capsule Polysaccharide Production and Biofilm Formation in Vibrio parahaemolyticus.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {1},
pages = {e0187422},
pmid = {36602323},
issn = {1098-5336},
mesh = {*Adenylyl Cyclases/genetics/metabolism ; *Vibrio parahaemolyticus/genetics/metabolism ; Escherichia coli/genetics/metabolism ; Phylogeny ; Cyclic AMP/metabolism ; Bacterial Proteins/genetics/metabolism ; Cyclic AMP Receptor Protein/genetics/metabolism ; Biofilms ; Polysaccharides ; },
abstract = {Cyclic AMP (cAMP) receptor protein (CRP), encoded by crp, is a global regulator that is activated by cAMP, a second messenger synthesized by a class I adenylate cyclase (AC-I) encoded by cyaA in Escherichia coli. cAMP-CRP is required for growth on nonpreferred carbon sources and is a global regulator. We constructed in-frame nonpolar deletions of the crp and cyaA homologs in Vibrio parahaemolyticus and found that the Δcrp mutant did not grow in minimal media supplemented with nonpreferred carbon sources, but the ΔcyaA mutant grew similarly to the wild type. Bioinformatics analysis of the V. parahaemolyticus genome identified a 181-amino-acid protein annotated as a class IV adenylate cyclase (AC-IV) named CyaB, a member of the CYTH protein superfamily. AC-IV phylogeny showed that CyaB was present in Gammaproteobacteria and Alphaproteobacteria as well as Planctomycetes and Archaea. Only the bacterial CyaB proteins contained an N-terminal motif, HFxxxxExExK, indicative of adenylyl cyclase activity. Both V. parahaemolyticus cyaA and cyaB genes functionally complemented an E. coli ΔcyaA mutant. The Δcrp and ΔcyaB ΔcyaA mutants showed defects in growth on nonpreferred carbon sources and in swimming and swarming motility, indicating that cAMP-CRP is an activator. The ΔcyaA and ΔcyaB single mutants had no defects in these phenotypes, indicating that AC-IV complements AC-I. Capsule polysaccharide and biofilm production assays showed significant defects in the Δcrp, ΔcyaBΔcyaA, and ΔcyaB mutants, whereas the ΔcyaA strain behaved similarly to the wild type. This is consistent with a role of cAMP-CRP as an activator of these phenotypes and establishes a cellular role for AC-IV in capsule and biofilm formation, which to date has been unestablished. IMPORTANCE Here, we characterized the roles of CRP and CyaA in V. parahaemolyticus, showing that cAMP-CRP is an activator of metabolism, motility, capsule production, and biofilm formation. These results are in contrast to cAMP-CRP in V. cholerae, which represses capsule and biofilm formation. Previously, only an AC-I CyaA had been identified in Vibrio species. Our data showed that an AC-IV CyaB homolog is present in V. parahaemolyticus and is required for optimal growth. The data demonstrated that CyaB is essential for capsule production and biofilm formation, uncovering a physiological role of AC-IV in bacteria. The data showed that the cyaB gene was widespread among Vibrionaceae species and several other Gammaproteobacteria, but in general, its phylogenetic distribution was limited. Our phylogenetic analysis also demonstrated that in some species the cyaB gene was acquired by horizontal gene transfer.},
}
@article {pmid36599855,
year = {2023},
author = {Cho, CH and Park, SI and Huang, TY and Lee, Y and Ciniglia, C and Yadavalli, HC and Yang, SW and Bhattacharya, D and Yoon, HS},
title = {Genome-wide signatures of adaptation to extreme environments in red algae.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {10},
pmid = {36599855},
issn = {2041-1723},
mesh = {*Rhodophyta/genetics ; Genome/genetics ; Acclimatization ; *Hot Springs ; *Metals, Heavy ; Phylogeny ; },
abstract = {The high temperature, acidity, and heavy metal-rich environments associated with hot springs have a major impact on biological processes in resident cells. One group of photosynthetic eukaryotes, the Cyanidiophyceae (Rhodophyta), has successfully thrived in hot springs and associated sites worldwide for more than 1 billion years. Here, we analyze chromosome-level assemblies from three representative Cyanidiophyceae species to study environmental adaptation at the genomic level. We find that subtelomeric gene duplication of functional genes and loss of canonical eukaryotic traits played a major role in environmental adaptation, in addition to horizontal gene transfer events. Shared responses to environmental stress exist in Cyanidiales and Galdieriales, however, most of the adaptive genes (e.g., for arsenic detoxification) evolved independently in these lineages. Our results underline the power of local selection to shape eukaryotic genomes that may face vastly different stresses in adjacent, extreme microhabitats.},
}
@article {pmid36598481,
year = {2023},
author = {O'Leary, ML and Burbank, LP},
title = {Natural Recombination among Type I Restriction-Modification Systems Creates Diverse Genomic Methylation Patterns among Xylella fastidiosa Strains.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {1},
pages = {e0187322},
pmid = {36598481},
issn = {1098-5336},
mesh = {Crops, Agricultural ; DNA Methylation ; Gene Transfer, Horizontal ; Genomics ; *Plant Diseases/genetics/microbiology ; *Xylella/genetics/pathogenicity ; },
abstract = {Xylella fastidiosa is an important bacterial plant pathogen causing high-consequence diseases in agricultural crops around the world. Although as a species X. fastidiosa can infect many host plants, there is significant variability between strains regarding virulence on specific host plant species and other traits. Natural competence and horizontal gene transfer are believed to occur frequently in X. fastidiosa and likely influence the evolution of this pathogen. However, some X. fastidiosa strains are difficult to manipulate genetically using standard transformation techniques. Several type I restriction-modification (R-M) systems are encoded in the X. fastidiosa genome, which may influence horizontal gene transfer and recombination. Type I R-M systems themselves may undergo recombination, exchanging target recognition domains (TRDs) between specificity subunits (hsdS) to generate novel alleles with new target specificities. In this study, several conserved type I R-M systems were compared across 129 X. fastidiosa genome assemblies representing all known subspecies and 32 sequence types. Forty-four unique TRDs were identified among 50 hsdS alleles, which are arrayed in 31 allele profiles that are generally conserved within a monophyletic cluster of strains. Inactivating mutations were identified in type I R-M systems of specific strains, showing heterogeneity in the complements of functional type I R-M systems across X. fastidiosa. Genomic DNA methylation patterns were characterized in 20 X. fastidiosa strains and associated with type I R-M system allele profiles. Overall, these data suggest hsdS genes recombine among Xylella strains and/or unknown donors, and the resulting TRD reassortment establishes differential epigenetic modifications across Xylella lineages. IMPORTANCE Economic impacts on agricultural production due to X. fastidiosa have been severe in the Americas, Europe, and parts of Asia. Despite a long history of research on this pathogen, certain fundamental questions regarding the biology, pathogenicity, and evolution of X. fastidiosa have still not been answered. Wide-scale whole-genome sequencing has begun to provide more insight into X. fastidiosa genetic diversity and horizontal gene transfer, but the mechanics of genomic recombination in natural settings and the extent to which this directly influences bacterial phenotypes such as plant host range are not well understood. Genome methylation is an important factor in horizontal gene transfer and bacterial recombination that has not been comprehensively studied in X. fastidiosa. This study characterizes methylation associated with type I restriction-modification systems across a wide range of X. fastidiosa strains and lays the groundwork for a better understanding of X. fastidiosa biology and evolution through epigenetics.},
}
@article {pmid36598279,
year = {2023},
author = {Xu, C and Rao, J and Xie, Y and Lu, J and Li, Z and Dong, C and Wang, L and Jiang, J and Chen, C and Chen, S},
title = {The DNA Phosphorothioation Restriction-Modification System Influences the Antimicrobial Resistance of Pathogenic Bacteria.},
journal = {Microbiology spectrum},
volume = {11},
number = {1},
pages = {e0350922},
pmid = {36598279},
issn = {2165-0497},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; DNA Restriction-Modification Enzymes/genetics ; DNA ; Gene Transfer, Horizontal ; },
abstract = {Bacterial defense barriers, such as DNA methylation-associated restriction-modification (R-M) and the CRISPR-Cas system, play an important role in bacterial antimicrobial resistance (AMR). Recently, a novel R-M system based on DNA phosphorothioate (PT) modification has been shown to be widespread in the kingdom of Bacteria as well as Archaea. However, the potential role of the PT R-M system in bacterial AMR remains unclear. In this study, we explored the role of PT R-Ms in AMR with a series of common clinical pathogenic bacteria. By analyzing the distribution of AMR genes related to mobile genetic elements (MGEs), it was shown that the presence of PT R-M effectively reduced the distribution of horizontal gene transfer (HGT)-derived AMR genes in the genome, even in the bacteria that did not tend to acquire AMR genes by HGT. In addition, unique gene variation analysis based on pangenome analysis and MGE prediction revealed that the presence of PT R-M could suppress HGT frequency. Thus, this is the first report showing that the PT R-M system has the potential to repress HGT-derived AMR gene acquisition by reducing the HGT frequency. IMPORTANCE In this study, we demonstrated the effect of DNA PT modification-based R-M systems on horizontal gene transfer of AMR genes in pathogenic bacteria. We show that there is no apparent association between the genetic background of the strains harboring PT R-Ms and the number of AMR genes or the kinds of gene families. The strains equipped with PT R-M harbor fewer plasmid-derived, prophage-derived, or integrating mobile genetic element (iMGE)-related AMR genes and have a lower HGT frequency, but the degree of inhibition varies among different bacteria. In addition, compared with Salmonella enterica and Escherichia coli, Klebsiella pneumoniae prefers to acquire MGE-derived AMR genes, and there is no coevolution between PT R-M clusters and bacterial core genes.},
}
@article {pmid36597348,
year = {2023},
author = {Lai, CK and Lee, YC and Ke, HM and Lu, MR and Liu, WA and Lee, HH and Liu, YC and Yoshiga, T and Kikuchi, T and Chen, PJ and Tsai, IJ},
title = {The Aphelenchoides genomes reveal substantial horizontal gene transfers in the last common ancestor of free-living and major plant-parasitic nematodes.},
journal = {Molecular ecology resources},
volume = {23},
number = {4},
pages = {905-919},
doi = {10.1111/1755-0998.13752},
pmid = {36597348},
issn = {1755-0998},
support = {AS-CDA-107-L01//Academia Sinica/ ; },
mesh = {Animals ; *Gene Transfer, Horizontal ; *Nematoda/genetics ; Phylogeny ; Plants/genetics/parasitology ; },
abstract = {Aphelenchoides besseyi is a plant-parasitic nematode (PPN) in the family Aphelenchoididae capable of infecting more than 200 plant species. A. besseyi is also a species complex with strains exhibiting varying pathogenicity to plants. We present the genome and annotations of six Aphelenchoides species, four of which belonged to the A. besseyi species complex. Most Aphelenchoides genomes have a size of 44.7-47.4 Mb and are among the smallest in clade IV, with the exception of A. fujianensis, which has a size of 143.8 Mb and is one of the largest. Phylogenomic analysis successfully delimited the species complex into A. oryzae and A. pseudobesseyi and revealed a reduction of transposon elements in the last common ancestor of Aphelenchoides. Synteny analyses between reference genomes indicated that three chromosomes in A. besseyi were derived from fission and fusion events. A systematic identification of horizontal gene transfer (HGT) genes across 27 representative nematodes allowed us to identify two major episodes of acquisition corresponding to the last common ancestor of clade IV or major PPNs, respectively. These genes were mostly lost and differentially retained between clades or strains. Most HGT events were acquired from bacteria, followed by fungi, and also from plants; plant HGT was especially prevalent in Bursaphelenchus mucronatus. Our results comprehensively improve the understanding of HGT in nematodes.},
}
@article {pmid36592614,
year = {2023},
author = {Liu, Y and Chen, J and Raj, K and Baerg, L and Nathan, N and Philpott, DJ and Mahadevan, R},
title = {A Universal Strategy to Promote Secretion of G+/G- Bacterial Extracellular Vesicles and Its Application in Host Innate Immune Responses.},
journal = {ACS synthetic biology},
volume = {12},
number = {1},
pages = {319-328},
doi = {10.1021/acssynbio.2c00583},
pmid = {36592614},
issn = {2161-5063},
mesh = {Humans ; *Escherichia coli/genetics ; Anti-Bacterial Agents/pharmacology ; HEK293 Cells ; Gram-Positive Bacteria ; Gram-Negative Bacteria ; Bacteria ; Immunity, Innate ; *Extracellular Vesicles ; },
abstract = {Both Gram-positive and Gram-negative bacteria release nanosized extracellular vesicles called membrane vesicles (MVs, 20-400 nm), which have great potential in various biomedical applications due to their abilities to deliver effector molecules and induce therapeutic responses. To fully utilize bacterial MVs for therapeutic purposes, regulated and enhanced production of MVs would be highly advantageous. In this study, we developed a universal method to enhance MV yields in both G+/G- bacteria through an autonomous controlled peptidoglycan hydrolase (PGase) expression system. A significant increase (9.37-fold) of MV concentration was observed in engineered E. coli Nissle 1917 compared to the wild-type. With the help of this autonomous system, for the first time we experimentally confirmed horizontal gene transfer and nutrient acquisition in a cocultured bacterial consortium. Furthermore, the engineered probiotic E. coli strains with high yield of MVs showed higher activation of the innate immune responses in human embryonic kidney 293T (HEK293T) and human colorectal carcinoma cells (HCT116), thereby demonstrating the great potential of engineering probiotics in immunology and further living therapeutics in humans.},
}
@article {pmid36588930,
year = {2022},
author = {Martinez-Vaz, BM and Dodge, AG and Lucero, RM and Stockbridge, RB and Robinson, AA and Tassoulas, LJ and Wackett, LP},
title = {Wastewater bacteria remediating the pharmaceutical metformin: Genomes, plasmids and products.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {10},
number = {},
pages = {1086261},
pmid = {36588930},
issn = {2296-4185},
support = {R35 GM128768/GM/NIGMS NIH HHS/United States ; },
abstract = {Metformin is used globally to treat type II diabetes, has demonstrated anti-ageing and COVID mitigation effects and is a major anthropogenic pollutant to be bioremediated by wastewater treatment plants (WWTPs). Metformin is not adsorbed well by activated carbon and toxic N-chloro derivatives can form in chlorinated water. Most earlier studies on metformin biodegradation have used wastewater consortia and details of the genomes, relevant genes, metabolic products, and potential for horizontal gene transfer are lacking. Here, two metformin-biodegrading bacteria from a WWTP were isolated and their biodegradation characterized. Aminobacter sp. MET metabolized metformin stoichiometrically to guanylurea, an intermediate known to accumulate in some environments including WWTPs. Pseudomonas mendocina MET completely metabolized metformin and utilized all the nitrogen atoms for growth. Pseudomonas mendocina MET also metabolized metformin breakdown products sometimes observed in WWTPs: 1-N-methylbiguanide, biguanide, guanylurea, and guanidine. The genome of each bacterium was obtained. Genes involved in the transport of guanylurea in Aminobacter sp. MET were expressed heterologously and shown to serve as an antiporter to expel the toxic guanidinium compound. A novel guanylurea hydrolase enzyme was identified in Pseudomonas mendocina MET, purified, and characterized. The Aminobacter and Pseudomonas each contained one plasmid of 160 kb and 90 kb, respectively. In total, these studies are significant for the bioremediation of a major pollutant in WWTPs today.},
}
@article {pmid36587809,
year = {2023},
author = {Trissi, N and Troczka, BJ and Ozsanlav-Harris, L and Singh, KS and Mallott, M and Aishwarya, V and O'Reilly, A and Bass, C and Wilding, CS},
title = {Differential regulation of the Tor gene homolog drives the red/green pigmentation phenotype in the aphid Myzuspersicae.},
journal = {Insect biochemistry and molecular biology},
volume = {153},
number = {},
pages = {103896},
doi = {10.1016/j.ibmb.2022.103896},
pmid = {36587809},
issn = {1879-0240},
mesh = {Animals ; *Aphids/physiology ; Lycopene/metabolism ; Pigmentation/genetics ; Carotenoids/metabolism ; },
abstract = {In some aphid species, intraspecific variation in body colour is caused by differential carotenoid content: whilst green aphids contain only yellow carotenoids (β-, γ-, and β,γ-carotenes), red aphids additionally possess red carotenoids (torulene and 3,4-didehydrolycopene). Unusually, within animals who typically obtain carotenoids from their diet, ancestral horizontal gene transfer of carotenoid biosynthetic genes from fungi (followed by gene duplication), have imbued aphids with the intrinsic gene repertoire necessary to biosynthesise carotenoids. In the pea aphid, Acyrthosiphon pisum a lycopene (phytoene) desaturase gene (Tor) underpins the red/green phenotype, with this locus present in heterozygous form in red individuals but absent in green aphids, resulting in them being unable to convert lycopene into the red compounds 3,4-didehydrolycopene and torulene. The green peach aphid, Myzus persicae, separated from the pea aphid for ≈45MY also exists as distinct colour variable morphs, with both red and green individuals present. Here, we examined genomic data for both red and green morphs of M. persicae and identified an enlarged (compared to A. pisum) repertoire of 16 carotenoid biosynthetic genes (11 carotenoid desaturases and five carotenoid cyclase/synthase genes). From these, we identify the homolog of A. pisum Tor (here called carotene desaturase 2 or CDE-2) and show through 3D modelling that this homolog can accommodate the torulene precursor lycopene and, through RNA knockdown feeding experiments, demonstrate that disabling CDE-2 expression in red M. persicae clones results in green-coloured offspring. Unlike in A. pisum, we show that functional CDE-2 is present in the genomes of both red and green aphids. However, expression differences between the two colour morphs (350-700 fold CDE-2 overexpression in red clones), potentially driven by variants identified in upstream putative regulatory elements, underpin this phenotype. Thus, whilst aphids have a common origin of their carotenoid biosynthetic pathway, two aphid species separated for over 40MY have evolved very different drivers of intraspecific colour variation.},
}
@article {pmid36586689,
year = {2023},
author = {Shi, H and Hu, X and Xu, J and Hu, B and Ma, L and Lou, L},
title = {Conjugation-mediated transfer of antibiotic resistance genes influenced by primary soil components and underlying mechanisms.},
journal = {The Science of the total environment},
volume = {865},
number = {},
pages = {161232},
doi = {10.1016/j.scitotenv.2022.161232},
pmid = {36586689},
issn = {1879-1026},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Soil ; Bentonite ; Kaolin ; Quartz/pharmacology ; Gene Transfer, Horizontal ; Drug Resistance, Microbial/genetics ; Escherichia coli/genetics ; Genes, Bacterial ; Bacteria/genetics ; Plasmids ; },
abstract = {Soil is the main natural reservoir of antibiotic resistant bacteria and antibiotic resistance genes (ARGs). Their dissemination and proliferation were largely motivated by conjugative transfer, while the influence of soil components on bacterial conjugative transfer and the underlying mechanisms remain poorly understood. In the present study, two Escherichia coli strains were exposed to soil minerals (quartz, kaolinite and montmorillonite) and organic matters (humic acid, biochar and soot) respectively to investigate their impact on ARGs conjugation. The results showed that quartz had no significant effect on conjugation; montmorillonite promoted the growth of the donor, but inhibited the recipient and conjugant; kaolinite and three organic matters significantly promoted the production of conjugant, while biochar promoted and then inhibited it with time prolong. Within the range of bacterial concentration involved in this study, the concentration of conjugant increased with the ratio of the concentration of donor and recipient (RD/R), indicating that the variation of conjugant production was mainly mediated by changing RD/R. Further observation of biochar treatment group showed that the bacterial responses such as cell membrane permeability, cell surface hydrophobicity and biofilm formation ability shifted with the exposure time, which might be a potential factor affecting conjugative transfer. Collectively, our findings suggest that the type and exposure time of soil components jointly affected conjugation, while the change of RD/R and related bacterial responses are the main underlying mechanisms.},
}
@article {pmid36586329,
year = {2023},
author = {Nnorom, MA and Saroj, D and Avery, L and Hough, R and Guo, B},
title = {A review of the impact of conductive materials on antibiotic resistance genes during the anaerobic digestion of sewage sludge and animal manure.},
journal = {Journal of hazardous materials},
volume = {446},
number = {},
pages = {130628},
doi = {10.1016/j.jhazmat.2022.130628},
pmid = {36586329},
issn = {1873-3336},
mesh = {Animals ; Humans ; *Sewage/microbiology ; *Genes, Bacterial ; Manure/microbiology ; Anti-Bacterial Agents/pharmacology ; Anaerobiosis ; Drug Resistance, Microbial/genetics ; },
abstract = {The urgent need to reduce the environmental burden of antibiotic resistance genes (ARGs) has become even more apparent as concerted efforts are made globally to tackle the dissemination of antimicrobial resistance. Concerning levels of ARGs abound in sewage sludge and animal manure, and their inadequate attenuation during conventional anaerobic digestion (AD) compromises the safety of the digestate, a nutrient-rich by-product of AD commonly recycled to agricultural land for improvement of soil quality. Exogenous ARGs introduced into the natural environment via the land application of digestate can be transferred from innocuous environmental bacteria to clinically relevant bacteria by horizontal gene transfer (HGT) and may eventually reach humans through food, water, and air. This review, therefore, discusses the prospects of using carbon- and iron-based conductive materials (CMs) as additives to mitigate the proliferation of ARGs during the AD of sewage sludge and animal manure. The review spotlights the core mechanisms underpinning the influence of CMs on the resistome profile, the steps to maximize ARG attenuation using CMs, and the current knowledge gaps. Data and information gathered indicate that CMs can profoundly reduce the abundance of ARGs in the digestate by easing selective pressure on ARGs, altering microbial community structure, and diminishing HGT.},
}
@article {pmid36583227,
year = {2023},
author = {Sloan, DB and Warren, JM and Williams, AM and Kuster, SA and Forsythe, ES},
title = {Incompatibility and Interchangeability in Molecular Evolution.},
journal = {Genome biology and evolution},
volume = {15},
number = {1},
pages = {},
pmid = {36583227},
issn = {1759-6653},
support = {R01 GM118046/GM/NIGMS NIH HHS/United States ; T32 GM132057/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {*Hybridization, Genetic ; *Evolution, Molecular ; },
abstract = {There is remarkable variation in the rate at which genetic incompatibilities in molecular interactions accumulate. In some cases, minor changes-even single-nucleotide substitutions-create major incompatibilities when hybridization forces new variants to function in a novel genetic background from an isolated population. In other cases, genes or even entire functional pathways can be horizontally transferred between anciently divergent evolutionary lineages that span the tree of life with little evidence of incompatibilities. In this review, we explore whether there are general principles that can explain why certain genes are prone to incompatibilities while others maintain interchangeability. We summarize evidence pointing to four genetic features that may contribute to greater resistance to functional replacement: (1) function in multisubunit enzyme complexes and protein-protein interactions, (2) sensitivity to changes in gene dosage, (3) rapid rate of sequence evolution, and (4) overall importance to cell viability, which creates sensitivity to small perturbations in molecular function. We discuss the relative levels of support for these different hypotheses and lay out future directions that may help explain the striking contrasts in patterns of incompatibility and interchangeability throughout the history of molecular evolution.},
}
@article {pmid36582150,
year = {2024},
author = {Manaia, CM and Aga, DS and Cytryn, E and Gaze, WH and Graham, DW and Guo, J and Leonard, AFC and Li, L and Murray, AK and Nunes, OC and Rodriguez-Mozaz, S and Topp, E and Zhang, T},
title = {The Complex Interplay Between Antibiotic Resistance and Pharmaceutical and Personal Care Products in the Environment.},
journal = {Environmental toxicology and chemistry},
volume = {43},
number = {3},
pages = {637-652},
doi = {10.1002/etc.5555},
pmid = {36582150},
issn = {1552-8618},
support = {MR/P028195/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; *Genes, Bacterial ; Bacteria ; Angiotensin Receptor Antagonists/pharmacology ; Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Drug Resistance, Microbial/genetics ; *Cosmetics ; Pharmaceutical Preparations ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are important environmental contaminants. Nonetheless, what drives the evolution, spread, and transmission of antibiotic resistance dissemination is still poorly understood. The abundance of ARB and ARGs is often elevated in human-impacted areas, especially in environments receiving fecal wastes, or in the presence of complex mixtures of chemical contaminants, such as pharmaceuticals and personal care products. Self-replication, mutation, horizontal gene transfer, and adaptation to different environmental conditions contribute to the persistence and proliferation of ARB in habitats under strong anthropogenic influence. Our review discusses the interplay between chemical contaminants and ARB and their respective genes, specifically in reference to co-occurrence, potential biostimulation, and selective pressure effects, and gives an overview of mitigation by existing man-made and natural barriers. Evidence and strategies to improve the assessment of human health risks due to environmental antibiotic resistance are also discussed. Environ Toxicol Chem 2024;43:637-652. © 2022 SETAC.},
}
@article {pmid36575565,
year = {2023},
author = {Chen, H and Tao, S and Li, N and Zhu, Q and Liu, L and Fang, Y and Xu, Y and Liang, W},
title = {Anti-restriction protein ArdA promotes clinical Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae spread and its molecular mechanism.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {78},
number = {2},
pages = {521-530},
doi = {10.1093/jac/dkac423},
pmid = {36575565},
issn = {1460-2091},
mesh = {Humans ; *Klebsiella pneumoniae ; Klebsiella/genetics ; *Klebsiella Infections/microbiology ; Molecular Epidemiology ; Bacterial Proteins/genetics ; beta-Lactamases/genetics/metabolism ; Plasmids ; },
abstract = {BACKGROUND: Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae (KPC-KP) has spread worldwide and has become a major threat to public health. The restriction modification system provides an innate defence of bacteria against plasmids or transposons, while many different types of plasmid encoding the anti-restriction protein ArdA can specifically affect the restriction activity in bacteria.<br><br>OBJECTIVES: To detect the codistribution of ArdA and blaKPC-2 plasmids in KPC-KP and explore the molecular mechanism of ArdA promoting KPC-KP spread.<br><br>METHODS: We collected 65 clinical CRKP isolates from Ningbo, China, and 68 cases of plasmid complete sequences in GenBank to determine the prevalence of ArdA gene on the K. pneumoniae blaKPC-2 plasmid. The anti-restriction function of ArdA in promoting horizontal gene transfer (HGT) was verified by transformation, conjugation and transduction methods, and the pull-down experiment was used to investigate the molecular mechanism of ArdA protein in vitro.<br><br>RESULTS: We found that ArdA was widely distributed in KPC-KP in 100% of cases, which was detected in 0% of drug susceptible K. pneumoniae, and the plasmids containing the ArdA gene in 90% of the 30 cases randomly retrieved from the database. We also verified that ArdA has a good anti-restriction function (P&#x200a;<&#x200a;0.05) through two aspects of HGT (transformation, transduction), and explored the non-occurrence interaction of ArdA and the hsdM subunit protein of EcoKI enzyme from the perspective of protein molecules.<br><br>CONCLUSIONS: These findings suggest that the coexistence advantage of ArdA with the blaKPC-2 plasmids may provide KPC-producing K. pneumoniae with a very efficient evasion of the restriction of type I systems, which not only favours ArdA-containing mobile genetic elements in the same species HGT between bacteria also facilitates HGT between other bacterial species.},
}
@article {pmid36573357,
year = {2023},
author = {Bethke, JH and Ma, HR and Tsoi, R and Cheng, L and Xiao, M and You, L},
title = {Vertical and horizontal gene transfer tradeoffs direct plasmid fitness.},
journal = {Molecular systems biology},
volume = {19},
number = {2},
pages = {e11300},
pmid = {36573357},
issn = {1744-4292},
support = {R01 AI125604/AI/NIAID NIH HHS/United States ; R01 GM098642/GM/NIGMS NIH HHS/United States ; R01 EB031869/EB/NIBIB NIH HHS/United States ; },
mesh = {*Gene Transfer, Horizontal ; *Escherichia coli/genetics ; Plasmids/genetics ; Drug Resistance, Microbial ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Plasmid fitness is directed by two orthogonal processes-vertical transfer through cell division and horizontal transfer through conjugation. When considered individually, improvements in either mode of transfer can promote how well a plasmid spreads and persists. Together, however, the metabolic cost of conjugation could create a tradeoff that constrains plasmid evolution. Here, we present evidence for the presence, consequences, and molecular basis of a conjugation-growth tradeoff across 40 plasmids derived from clinical Escherichia coli pathogens. We discover that most plasmids operate below a conjugation efficiency threshold for major growth effects, indicating strong natural selection for vertical transfer. Below this threshold, E. coli demonstrates a remarkable growth tolerance to over four orders of magnitude change in conjugation efficiency. This tolerance fades as nutrients become scarce and horizontal transfer attracts a greater share of host resources. Our results provide insight into evolutionary constraints directing plasmid fitness and strategies to combat the spread of antibiotic resistance.},
}
@article {pmid36572269,
year = {2023},
author = {Beltrán de Heredia, I and Garbisu, C and Alkorta, I and Urra, J and González-Gaya, B and Ruiz-Romera, E},
title = {Spatio-seasonal patterns of the impact of wastewater treatment plant effluents on antibiotic resistance in river sediments.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {319},
number = {},
pages = {120883},
doi = {10.1016/j.envpol.2022.120883},
pmid = {36572269},
issn = {1873-6424},
mesh = {*Genes, Bacterial ; Seasons ; *Ecosystem ; Wastewater ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/analysis ; Water ; },
abstract = {There is a growing concern about the risk of antibiotic resistance emergence and dissemination in the environment. Here, we evaluated the spatio-seasonal patterns of the impact of wastewater treatment plant (WWTP) effluents on antibiotic resistance in river sediments. To this purpose, sediment samples were collected in three river basins affected by WWTP effluents in wet (high-water period) and dry (low-water period) hydrological conditions at three locations: (i) upstream the WWTPs; (ii) WWTP effluent discharge points (effluent outfall); and (iii) downstream the WWTPs (500 m downriver from the effluent outfall). The absolute and relative abundances of 9 antibiotic resistance genes (ARGs), 3 mobile genetic element (MGE) genes, and 4 metal resistance genes (MRGs) were quantified in sediment samples, as well as a variety of physicochemical parameters, metal contents, and antibiotic concentrations in both sediment and water samples. In sediments, significantly higher relative abundances of most genes were observed in downstream vs. upstream sampling points. Seasonal changes (higher values in low-water vs. high-water period) were observed for both ARG absolute and relative abundances in sediment samples. Chemical data revealed the contribution of effluents from WWTPs as a source of antibiotic and metal contamination in river ecosystems. The observed positive correlations between ARG and MGE genes relative abundances point out to the role of horizontal gene transfer in antibiotic resistance dissemination. Monitoring plans that take into consideration spatio-temporal patterns must be implemented to properly assess the environmental fate of WWTP-related emerging contaminants in river ecosystems.},
}
@article {pmid36571993,
year = {2023},
author = {Su, Z and Wen, D and Gu, AZ and Zheng, Y and Tang, Y and Chen, L},
title = {Industrial effluents boosted antibiotic resistome risk in coastal environments.},
journal = {Environment international},
volume = {171},
number = {},
pages = {107714},
doi = {10.1016/j.envint.2022.107714},
pmid = {36571993},
issn = {1873-6750},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Wastewater ; Bacteria/genetics ; Genes, Bacterial ; Sewage ; },
abstract = {Wastewater treatment plants (WWTPs) have been regarded as an important source of antibiotic resistance genes (ARGs) in environment, but out of municipal domestic WWTPs, few evidences show how environment is affected by industrial WWTPs. Here we chose Hangzhou Bay (HZB), China as our study area, where land-based municipal and industrial WWTPs discharged their effluent into the bay for decades. We adopted high-throughput metagenomic sequencing to examine the antibiotic resistome of the WWTP effluent and coastal sediment samples. And we proposed a conceptual framework for the assessment of antibiotic resistome risk, and a new bioinformatic pipeline for the evaluation of the potential horizontal gene transfer (HGT) frequency. Our results revealed that the diversity and abundance of ARGs in the WWTP's effluent were significantly higher than those in the sediment. Furthermore, the antibiotic resistome in the effluent-receiving area (ERA) showed significant difference from that in HZB. For the first time, we identified that industrial WWTP effluent boosted antibiotic resistome risk in coastal sediment. The crucial evidences included: 1) the proportion of ARGs derived from WWTP activated sludge (WA) was higher (14.3 %) and two high-risky polymyxin resistance genes (mcr-4 and mcr-5) were enriched in the industrial effluent receiving area; 2) the HGT potential was higher between resistant microbiome of the industrial effluent and its ERA sediment; and 3) the highest resistome risk was determined in the industrial effluent, and some biocide resistance genes located on high-risky contigs were related to long-term stress of industrial chemicals. These findings highlight the important effects of industrial activities on the development of environmental antimicrobial resistance.},
}
@article {pmid36571495,
year = {2023},
author = {Sun, M and Yuan, S and Xia, R and Ye, M and Balcázar, JL},
title = {Underexplored viral auxiliary metabolic genes in soil: Diversity and eco-evolutionary significance.},
journal = {Environmental microbiology},
volume = {25},
number = {4},
pages = {800-810},
doi = {10.1111/1462-2920.16329},
pmid = {36571495},
issn = {1462-2920},
mesh = {Genes, Viral ; *Bacteriophages/genetics ; Biological Evolution ; Bacteria/metabolism ; *Microbiota/genetics ; Soil ; },
abstract = {Bacterial viruses are the most abundant biological entities in soil ecosystems. Owing to the advent of metagenomics and viromics approaches, an ever-increasing diversity of virus-encoded auxiliary metabolic genes (AMGs) have been identified in soils, including those involved in the transformation of carbon, phosphorus, and sulfur, degradation of organic pollutants, and antibiotic resistance, among other processes. These viral AMGs can alter soil biogeochemical processes and metabolic activities by interfering with bacterial host metabolism. It is recognized that viral AMGs compensate for host bacterial metabolism outputs by encoding accessory functional genes and are favourable for the hosts' adaptation to stressed soil environments. The eco-evolutionary mechanisms behind this fascinating diversity of viral AMGs in soil microbiomes have begun to emerge, such as horizontal gene transfer, lytic-lysogenic conversion, and single-nucleotide polymorphisms. In this mini-review, we summarize recent advances in the diversity and function of virus-encoded AMGs in the soil environment, especially focusing on the evolutionary significance of AMGs involved in virus-host interactions. This mini-review also sheds light on the existing gaps and future perspectives that could have major significance for viral AMGs research in soils.},
}
@article {pmid36568361,
year = {2022},
author = {Nayar, G and Terrizzano, I and Seabolt, E and Agarwal, A and Boucher, C and Ruiz, J and Slizovskiy, IB and Kaufman, JH and Noyes, NR},
title = {ggMOB: Elucidation of genomic conjugative features and associated cargo genes across bacterial genera using genus-genus mobilization networks.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {1024577},
pmid = {36568361},
issn = {1664-8021},
abstract = {Horizontal gene transfer mediated by conjugation is considered an important evolutionary mechanism of bacteria. It allows organisms to quickly evolve new phenotypic properties including antimicrobial resistance (AMR) and virulence. The frequency of conjugation-mediated cargo gene exchange has not yet been comprehensively studied within and between bacterial taxa. We developed a frequency-based network of genus-genus conjugation features and candidate cargo genes from whole-genome sequence data of over 180,000 bacterial genomes, representing 1,345 genera. Using our method, which we refer to as ggMOB, we revealed that over half of the bacterial genomes contained one or more known conjugation features that matched exactly to at least one other genome. Moreover, the proportion of genomes containing these conjugation features varied substantially by genus and conjugation feature. These results and the genus-level network structure can be viewed interactively in the ggMOB interface, which allows for user-defined filtering of conjugation features and candidate cargo genes. Using the network data, we observed that the ratio of AMR gene representation in conjugative versus non-conjugative genomes exceeded 5:1, confirming that conjugation is a critical force for AMR spread across genera. Finally, we demonstrated that clustering genomes by conjugation profile sometimes correlated well with classical phylogenetic structuring; but that in some cases the clustering was highly discordant, suggesting that the importance of the accessory genome in driving bacterial evolution may be highly variable across both time and taxonomy. These results can advance scientific understanding of bacterial evolution, and can be used as a starting point for probing genus-genus gene exchange within complex microbial communities that include unculturable bacteria. ggMOB is publicly available under the GNU licence at https://ruiz-hci-lab.github.io/ggMOB/.},
}
@article {pmid36567403,
year = {2023},
author = {Feng, R and Duan, L and Shen, S and Cheng, Y and Wang, Y and Wang, W and Yang, S},
title = {Temporal dynamic of antibiotic resistance genes in the Zaohe-Weihe hyporheic zone: driven by oxygen and bacterial community.},
journal = {Ecotoxicology (London, England)},
volume = {32},
number = {1},
pages = {57-72},
doi = {10.1007/s10646-022-02616-5},
pmid = {36567403},
issn = {1573-3017},
mesh = {*Genes, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Sulfanilamide ; },
abstract = {The widespread spread of antibiotic resistance genes (ARGs) in hyporheic zone (HZ) has become an emerging environmental problem due to their potentially harmful nature. In this research, three different oxygen treatment systems were set up to study the effects of oxygen changes on the abundance of ARGs in the HZ. In addition, the effects of temperature and salinity on ARGs were investigated under aerobic and anaerobic systems, respectively. The bacterial community composition of sediment samples and the relationship with ARGs were analyzed. The explanation ratio and causality of the driving factors affecting ARGs were analyzed using variation partitioning analysis (VPA) and structural equation model (SEM). The relative abundance of ARGs and mobile genetic elements (MGEs) in the anaerobic system increased significantly, which was higher than that in the aerobic system and the aerobic-anaerobic interaction system. The experiment of salinity and temperature also further proved this result. There were many bacterial communities that affected tetracycline and sulfonamide ARGs in sediments, and these host bacteria are mainly concentrated in Proteobacteria, Firmicutes and Bacteroidetes. VPA and SEM further revealed that the abundance of ARGs was mainly influenced by changes in bacterial communities and oxygen conditions, and horizontal gene transfer (HGT) of MGEs also had a positive effect on the spread of ARGs. Those findings suggest that complex oxygen conditions in the HZ alter bacterial communities and promote MGEs-mediated horizontal transfer, which together lead to the spread of ARGs. This study has value as a reference for formulating effective strategies to minimize the propagation of ARGs in underground environment.},
}
@article {pmid36563663,
year = {2022},
author = {Vatanen, T and Jabbar, KS and Ruohtula, T and Honkanen, J and Avila-Pacheco, J and Siljander, H and Stražar, M and Oikarinen, S and Hyöty, H and Ilonen, J and Mitchell, CM and Yassour, M and Virtanen, SM and Clish, CB and Plichta, DR and Vlamakis, H and Knip, M and Xavier, RJ},
title = {Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism.},
journal = {Cell},
volume = {185},
number = {26},
pages = {4921-4936.e15},
pmid = {36563663},
issn = {1097-4172},
support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; },
mesh = {Female ; Humans ; Infant ; Pregnancy ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; Mothers ; Breast Feeding ; Feces ; Interspersed Repetitive Sequences ; },
abstract = {The perinatal period represents a critical window for cognitive and immune system development, promoted by maternal and infant gut microbiomes and their metabolites. Here, we tracked the co-development of microbiomes and metabolomes from late pregnancy to 1 year of age using longitudinal multi-omics data from a cohort of 70 mother-infant dyads. We discovered large-scale mother-to-infant interspecies transfer of mobile genetic elements, frequently involving genes associated with diet-related adaptations. Infant gut metabolomes were less diverse than maternal but featured hundreds of unique metabolites and microbe-metabolite associations not detected in mothers. Metabolomes and serum cytokine signatures of infants who received regular-but not extensively hydrolyzed-formula were distinct from those of exclusively breastfed infants. Taken together, our integrative analysis expands the concept of vertical transmission of the gut microbiome and provides original insights into the development of maternal and infant microbiomes and metabolomes during late pregnancy and early life.},
}
@article {pmid36561977,
year = {2022},
author = {González-Villarreal, JA and González-Lozano, KJ and Aréchiga-Carvajal, ET and Morlett-Chávez, JA and Luévanos-Escareño, MP and Balagurusamy, N and Salinas-Santander, MA},
title = {Molecular mechanisms of multidrug resistance in clinically relevant enteropathogenic bacteria (Review).},
journal = {Experimental and therapeutic medicine},
volume = {24},
number = {6},
pages = {753},
pmid = {36561977},
issn = {1792-1015},
abstract = {Multidrug resistant (MDR) enteropathogenic bacteria are a growing problem within the clinical environment due to their acquired tolerance to a wide range of antibiotics, thus causing severe illnesses and a tremendous economic impact in the healthcare sector. Due to its difficult treatment, knowledge and understanding of the molecular mechanisms that confer this resistance are needed. The aim of the present review is to describe the mechanisms of antibiotic resistance from a genomic perspective observed in bacteria, including naturally acquired resistance. The present review also discusses common pharmacological and alternative treatments used in cases of infection caused by MDR bacteria, thus covering necessary information for the development of novel antimicrobials and adjuvant molecules inhibiting bacterial proliferation.},
}
@article {pmid36560776,
year = {2022},
author = {Nale, JY and Thanki, AM and Rashid, SJ and Shan, J and Vinner, GK and Dowah, ASA and Cheng, JKJ and Sicheritz-Pontén, T and Clokie, MRJ},
title = {Diversity, Dynamics and Therapeutic Application of Clostridioides difficile Bacteriophages.},
journal = {Viruses},
volume = {14},
number = {12},
pages = {},
pmid = {36560776},
issn = {1999-4915},
support = {RM38G0140/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Humans ; *Bacteriophages/genetics ; *Clostridioides difficile ; Clostridioides ; Prophages/genetics ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {Clostridioides difficile causes antibiotic-induced diarrhoea and pseudomembranous colitis in humans and animals. Current conventional treatment relies solely on antibiotics, but C. difficile infection (CDI) cases remain persistently high with concomitant increased recurrence often due to the emergence of antibiotic-resistant strains. Antibiotics used in treatment also induce gut microbial imbalance; therefore, novel therapeutics with improved target specificity are being investigated. Bacteriophages (phages) kill bacteria with precision, hence are alternative therapeutics for the targeted eradication of the pathogen. Here, we review current progress in C. difficile phage research. We discuss tested strategies of isolating C. difficile phages directly, and via enrichment methods from various sample types and through antibiotic induction to mediate prophage release. We also summarise phenotypic phage data that reveal their morphological, genetic diversity, and various ways they impact their host physiology and pathogenicity during infection and lysogeny. Furthermore, we describe the therapeutic development of phages through efficacy testing in different in vitro, ex vivo and in vivo infection models. We also discuss genetic modification of phages to prevent horizontal gene transfer and improve lysis efficacy and formulation to enhance stability and delivery of the phages. The goal of this review is to provide a more in-depth understanding of C. difficile phages and theoretical and practical knowledge on pre-clinical, therapeutic evaluation of the safety and effectiveness of phage therapy for CDI.},
}
@article {pmid36560636,
year = {2022},
author = {Ács, N and Holohan, R and Dunne, LJ and Fernandes, AR and Clooney, AG and Draper, LA and Ross, RP and Hill, C},
title = {Comparing In Vitro Faecal Fermentation Methods as Surrogates for Phage Therapy Application.},
journal = {Viruses},
volume = {14},
number = {12},
pages = {},
pmid = {36560636},
issn = {1999-4915},
mesh = {Humans ; Fermentation ; *Phage Therapy ; Feces ; Gastrointestinal Tract ; *Bacteriophages/genetics ; },
abstract = {The human microbiome and its importance in health and disease have been the subject of numerous research articles. Most microbes reside in the digestive tract, with up to 10[12] cells per gram of faecal material found in the colon. In terms of gene number, it has been estimated that the gut microbiome harbours >100 times more genes than the human genome. Several human intestinal diseases are strongly associated with disruptions in gut microbiome composition. Less studied components of the gut microbiome are the bacterial viruses called bacteriophages that may be present in numbers equal to or greater than the prokaryotes. Their potential to lyse their bacterial hosts, or to act as agents of horizontal gene transfer makes them important research targets. In this study in vitro faecal fermentation systems were developed and compared for their ability to act as surrogates for the human colon. Changes in bacterial and viral composition occurred after introducing a high-titre single phage preparation both with and without a known bacterial host during the 24 h-long fermentation. We also show that during this timeframe 50 mL plastic tubes can provide data similar to that generated in a sophisticated faecal fermenter system. This knowledge can guide us to a better understanding of the short-term impact of bacteriophage transplants on the bacteriomes and viromes of human recipients.},
}
@article {pmid36558750,
year = {2022},
author = {de Brito, FAE and de Freitas, APP and Nascimento, MS},
title = {Multidrug-Resistant Biofilms (MDR): Main Mechanisms of Tolerance and Resistance in the Food Supply Chain.},
journal = {Pathogens (Basel, Switzerland)},
volume = {11},
number = {12},
pages = {},
pmid = {36558750},
issn = {2076-0817},
support = {001//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; 403925/2021-5//National Council for Scientific and Technological Development/ ; },
abstract = {Biofilms are mono- or multispecies microbial communities enclosed in an extracellular matrix (EPS). They have high potential for dissemination and are difficult to remove. In addition, biofilms formed by multidrug-resistant strains (MDRs) are even more aggravated if we consider antimicrobial resistance (AMR) as an important public health issue. Quorum sensing (QS) and horizontal gene transfer (HGT) are mechanisms that significantly contribute to the recalcitrance (resistance and tolerance) of biofilms, making them more robust and resistant to conventional sanitation methods. These mechanisms coordinate different strategies involved in AMR, such as activation of a quiescent state of the cells, moderate increase in the expression of the efflux pump, decrease in the membrane potential, antimicrobial inactivation, and modification of the antimicrobial target and the architecture of the EPS matrix itself. There are few studies investigating the impact of the use of inhibitors on the mechanisms of recalcitrance and its impact on the microbiome. Therefore, more studies to elucidate the effect and applications of these methods in the food production chain and the possible combination with antimicrobials to establish new strategies to control MDR biofilms are needed.},
}
@article {pmid36555178,
year = {2022},
author = {Janczarek, M},
title = {The Ros/MucR Zinc-Finger Protein Family in Bacteria: Structure and Functions.},
journal = {International journal of molecular sciences},
volume = {23},
number = {24},
pages = {},
pmid = {36555178},
issn = {1422-0067},
support = {2018/31/B/NZ9/00663//National Science Center/ ; },
mesh = {Phylogeny ; Amino Acid Sequence ; *Bacterial Proteins/metabolism ; *Zinc Fingers/genetics ; Transcription Factors/genetics ; Bacteria/metabolism ; Zinc/metabolism ; },
abstract = {Ros/MucR is a widespread family of bacterial zinc-finger-containing proteins that integrate multiple functions, such as symbiosis, virulence, transcription regulation, motility, production of surface components, and various other physiological processes in cells. This regulatory protein family is conserved in bacteria and is characterized by its zinc-finger motif, which has been proposed as the ancestral domain from which the eukaryotic C2H2 zinc-finger structure has evolved. The first prokaryotic zinc-finger domain found in the transcription regulator Ros was identified in Agrobacterium tumefaciens. In the past decades, a large body of evidence revealed Ros/MucR as pleiotropic transcriptional regulators that mainly act as repressors through oligomerization and binding to AT-rich target promoters. The N-terminal domain and the zinc-finger-bearing C-terminal region of these regulatory proteins are engaged in oligomerization and DNA binding, respectively. These properties of the Ros/MucR proteins are similar to those of xenogeneic silencers, such as H-NS, MvaT, and Lsr2, which are mainly found in other lineages. In fact, a novel functional model recently proposed for this protein family suggests that they act as H-NS-'like' gene silencers. The prokaryotic zinc-finger domain exhibits interesting structural and functional features that are different from that of its eukaryotic counterpart (a βββα topology), as it folds in a significantly larger zinc-binding globular domain (a βββαα topology). Phylogenetic analysis of Ros/MucR homologs suggests an ancestral origin of this type of protein in α-Proteobacteria. Furthermore, multiple duplications and lateral gene transfer events contributing to the diversity and phyletic distribution of these regulatory proteins were found in bacterial genomes.},
}
@article {pmid36551459,
year = {2022},
author = {Lienen, T and Grobbel, M and Tenhagen, BA and Maurischat, S},
title = {Plasmid-Coded Linezolid Resistance in Methicillin-Resistant Staphylococcus aureus from Food and Livestock in Germany.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {11},
number = {12},
pages = {},
pmid = {36551459},
issn = {2079-6382},
support = {1322-769//Federal Institute for Risk Assessment/ ; },
abstract = {Resistance of methicillin-resistant Staphylococcus aureus (MRSA) from food and livestock to last resort antibiotics such as linezolid is highly concerning, since treatment options for infections in humans might be diminished. Known mechanisms of linezolid resistance include point mutations in the 23S rRNA gene and in the ribosomal proteins L3, L4 and L22 as well as an acquisition of the cfr, optrA or poxtA gene. The objective of our study was to characterize antimicrobial resistance (AMR) determinants and phylogenetic relationships among linezolid-resistant (LR-) MRSA from food and livestock. In total, from more than 4000 incoming isolates in the years 2012 to 2021, only two strains from 2015 originating from pig samples exhibited linezolid resistance in the antimicrobial susceptibility testing with MICs of ≥8 mg/L. These LR-MRSA were characterized in detail by whole-genome sequencing and phylogenetic analyses using cgMLST. The LR-MRSA strains showed resistances to ten and eight different antibiotics, respectively. Both strains harbored plasmid-coded cfr genes mediating the linezolid resistance. The cfr genes showed identical sequences in both strains. In addition to the cfr gene, genes for phenicol and clindamycin resistance were detected on the respective plasmids, opening the possibility for a co-selection. The LR-MRSA differed distantly in the phylogenetic analyses and also to other MRSA from pig samples in the year 2015. In conclusion, the occurrence of LR-MRSA in food and livestock seems to be very rare in Germany. However, carriage of plasmids with linezolid resistance determinants could lead to further linezolid-resistant strains by horizontal gene transfer.},
}
@article {pmid36549493,
year = {2023},
author = {Abudureheman, M and Ailijiang, N and Mamat, A and Feng, Y and He, C and Pu, M},
title = {Enhanced biodegradation of fluoroquinolones and the changes of bacterial communities and antibiotic-resistant genes under intermittent electrical stimulation.},
journal = {Environmental research},
volume = {219},
number = {},
pages = {115127},
doi = {10.1016/j.envres.2022.115127},
pmid = {36549493},
issn = {1096-0953},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Fluoroquinolones/pharmacology/analysis/metabolism ; Wastewater ; Bacteria/genetics/metabolism ; Electric Stimulation ; Genes, Bacterial ; },
abstract = {In this study, an anaerobic-aerobic coupling system under intermittent electrical stimulation was used to improve the biodegradation of synthetic wastewater containing fluoroquinolones (FQs). The effect of electrical stimulation on FQ removal performance is more pronounced with appropriate voltage and hydraulic retention time. In addition, the combination of anaerobic-anodic and aerobic-cathodic chambers is more conducive to improving the removal efficiency of FQs. Under 0.9 V, the removal efficiencies of ofloxacin, norfloxacin, ciprofloxacin, and enrofloxacin were significantly improved in the anaerobic-anodic and aerobic-cathodic system. The contribution of the anaerobic/aerobic anodic chambers to FQ removal was greater than that of the anaerobic/aerobic cathodic chambers. Electrical stimulation selectively enriched electroactive bacteria related to biodegradation (Desulfovibrio and Terrimonas), antibiotic-resistant bacteria (Atopobium and Neochlamydia), and nitrifying bacteria (SM1A02 and Reyranella). This study indicated the potential effectiveness of intermittent electrical stimulation in treating fluoroquinolone-containing wastewater in a biofilm reactor. However, electrical stimulation led to an increase in mobile genetic elements , induced horizontal gene transfer and enriched resistant bacteria, which accelerated the spread of antibiotic-resistant genes (ARGs) in the system, indicating that the diffusion of ARGs remains a challenge.},
}
@article {pmid36539881,
year = {2022},
author = {Kwun, MJ and Ion, AV and Cheng, HC and D'Aeth, JC and Dougan, S and Oggioni, MR and Goulding, DA and Bentley, SD and Croucher, NJ},
title = {Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA.},
journal = {Genome medicine},
volume = {14},
number = {1},
pages = {144},
pmid = {36539881},
issn = {1756-994X},
support = {102169/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; MR/T016434/1/MRC_/Medical Research Council/United Kingdom ; BB/N002903/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; 104169/Z/14/A/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; *Streptococcus pneumoniae/genetics ; Serogroup ; *Pneumococcal Infections/epidemiology/prevention &amp; control/microbiology ; Prophages/genetics ; Pneumococcal Vaccines ; Vaccines, Conjugate ; RNA, Untranslated/genetics/pharmacology ; },
abstract = {BACKGROUND: The respiratory pathogen Streptococcus pneumoniae (the pneumococcus) is a genetically diverse bacterium associated with over 101 immunologically distinct polysaccharide capsules (serotypes). Polysaccharide conjugate vaccines (PCVs) have successfully eliminated multiple targeted serotypes, yet the mucoid serotype 3 has persisted despite its inclusion in PCV13. This capsule type is predominantly associated with a single globally disseminated strain, GPSC12 (clonal complex 180).<br><br>METHODS: A genomic epidemiology study combined previous surveillance datasets of serotype 3 pneumococci to analyse the population structure, dynamics,&#xa0;and differences in rates of diversification within GPSC12 during the period of PCV introductions. Transcriptomic analyses, whole genome sequencing, mutagenesis, and electron microscopy were used to characterise the phenotypic impact of loci hypothesised to affect this strain's evolution.<br><br>RESULTS: GPSC12 was split into clades by a genomic analysis. Clade I, the most common, rarely underwent transformation, but was typically infected with the prophage &#x3d5;OXC141. Prior to the introduction of PCV13, this clade's composition shifted towards a &#x3d5;OXC141-negative subpopulation in a systematically sampled UK collection. In the post-PCV13 era, more rapidly recombining non-Clade I isolates, also &#x3d5;OXC141-negative, have risen in prevalence. The low in vitro transformation efficiency of a Clade I isolate could not be fully explained by the ~100-fold reduction attributable to the serotype 3 capsule. Accordingly, prophage &#x3d5;OXC141 was found to modify csRNA3, a non-coding RNA that inhibits the induction of transformation. This alteration was identified in ~30% of all pneumococci and was particularly common in the unusually clonal serotype 1 GPSC2 strain. RNA-seq and quantitative reverse transcriptase PCR experiments using a genetically tractable pneumococcus demonstrated the altered csRNA3 was more effective at inhibiting production of the competence-stimulating peptide pheromone. This resulted in a reduction in the induction of competence for transformation.<br><br>CONCLUSION: This interference with the quorum sensing needed to induce competence reduces the risk of the prophage being deleted by homologous recombination. Hence the selfish prophage-driven alteration of a regulatory RNA limits cell-cell communication and horizontal gene transfer, complicating the interpretation of post-vaccine population dynamics.},
}
@article {pmid36537743,
year = {2022},
author = {Lisboa, MP and Canal, D and Filgueiras, JPC and Turchetto-Zolet, AC},
title = {Molecular evolution and diversification of phytoene synthase (PSY) gene family.},
journal = {Genetics and molecular biology},
volume = {45},
number = {4},
pages = {e20210411},
pmid = {36537743},
issn = {1415-4757},
abstract = {Phytoene synthase (PSY) is a crucial enzyme required for carotenoid biosynthesis, encoded by a gene family conserved in carotenoid-producing organisms. This gene family is diversified in angiosperms through distinct duplication events. Understanding diversification patterns and the evolutionary history of the PSY gene family is important for explaining carotenogenesis in different plant tissues. This study identified 351 PSY genes in 166 species, including Viridiplantae, brown and red algae, cyanobacteria, fungi, arthropods, and bacteria. All PSY genes displayed conserved intron/exon organization. Fungi and arthropod PSY sequences were grouped with prokaryote PSY, suggesting the occurrence of horizontal gene transfer. Angiosperm PSY is split into five subgroups. One includes the putative ortholog of PSY3 (Subgroup E3) from eudicots, and the other four subgroups include PSY from both monocots and eudicots (subgroups E1, E2, M1, and M2). Expression profile analysis revealed that PSY genes are constitutively expressed across developmental stages and anatomical parts, except for the eudicot PSY3, with root-specific expression. This study elucidates the molecular evolution and diversification of the PSY gene family, furthering our understanding of variations in carotenogenesis.},
}
@article {pmid36536072,
year = {2023},
author = {Camargo, AP and de Souza, RSC and Jose, J and Gerhardt, IR and Dante, RA and Mukherjee, S and Huntemann, M and Kyrpides, NC and Carazzolle, MF and Arruda, P},
title = {Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot.},
journal = {The ISME journal},
volume = {17},
number = {3},
pages = {354-370},
pmid = {36536072},
issn = {1751-7370},
mesh = {*Ecosystem ; Brazil ; Soil Microbiology ; Biodiversity ; *Microbiota ; Bacteria/genetics/metabolism ; Plants/metabolism ; Soil/chemistry ; Phosphorus/metabolism ; Nitrogen/metabolism ; },
abstract = {The substrates of the Brazilian campos rupestres, a grassland ecosystem, have extremely low concentrations of phosphorus and nitrogen, imposing restrictions to plant growth. Despite that, this ecosystem harbors almost 15% of the Brazilian plant diversity, raising the question of how plants acquire nutrients in such a harsh environment. Here, we set out to uncover the taxonomic profile, the compositional and functional differences and similarities, and the nutrient turnover potential of microbial communities associated with two plant species of the campos rupestres-dominant family Velloziaceae that grow over distinct substrates (soil and rock). Using amplicon sequencing data, we show that, despite the pronounced composition differentiation, the plant-associated soil and rock communities share a core of highly efficient colonizers that tend to be highly abundant and is enriched in 21 bacterial families. Functional investigation of metagenomes and 522 metagenome-assembled genomes revealed that the microorganisms found associated to plant roots are enriched in genes involved in organic compound intake, and phosphorus and nitrogen turnover. We show that potential for phosphorus transport, mineralization, and solubilization are mostly found within bacterial families of the shared microbiome, such as Xanthobacteraceae and Bryobacteraceae. We also detected the full repertoire of nitrogen cycle-related genes and discovered a lineage of Isosphaeraceae that acquired nitrogen-fixing potential via horizontal gene transfer and might be also involved in nitrification via a metabolic handoff association with Binataceae. We highlight that plant-associated microbial populations in the campos rupestres harbor a genetic repertoire with potential to increase nutrient availability and that the microbiomes of biodiversity hotspots can reveal novel mechanisms of nutrient turnover.},
}
@article {pmid36532464,
year = {2022},
author = {Li, P and Luo, W and Xiang, TX and Jiang, Y and Liu, P and Wei, DD and Fan, L and Huang, S and Liao, W and Liu, Y and Zhang, W},
title = {Horizontal gene transfer via OMVs co-carrying virulence and antimicrobial-resistant genes is a novel way for the dissemination of carbapenem-resistant hypervirulent Klebsiella pneumoniae.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {945972},
pmid = {36532464},
issn = {1664-302X},
abstract = {INTRODUCTION: The rapidly increased isolation rate of CR-HvKP worldwide has brought great difficulties in controlling clinical infection. Moreover, it has been demonstrated that the transmission of drug-resistant genes among bacteria can be mediated by outer membrane vesicles (OMVs), which is a new way of horizontal gene transfer (HGT). The transmission of virulence genes among bacteria has also been well studied; however, it remains unclear whether virulence and drug-resistant genes can be co-transmitted simultaneously. Co-transmission of virulence and drug-resistant genes is essential for the formation and prevalence of CR-HvKP.<br><br>METHODS: First, we isolated OMVs from CR-HvKP by cushioned-density gradient ultracentrifugation (C-DGUC). TEM and DLS were used to examine the morphology and size of bacterial OMVs. OMV-mediated gene transfer in liquid cultures and the acquisition of the carbapenem gene and virulence gene was confirmed using colony-PCR. Antimicrobial susceptibility testing, mCIM and eCIM were conducted for the resistance of transformant. Serum killing assay, assessment of the anti-biofilm effect and galleria mellonella infection model, mucoviscosity assay, extraction and quantification of capsules were verified the virulence of transformant. Pulsed-field gel electrophoresis (PFGE), S1 nuclease-pulsed-field gel electrophoresis (S1-PFGE), Southern blotting hybridization confirmed the plasmid of transformant.<br><br>RESULTS: Firstly, OMVs were isolated from CR-HvKP NUHL30457 (K2, ST86). TEM and DLS analyses revealed the spherical morphology of the vesicles. Secondly, our study demonstrated that CR-HvKP delivered genetic material, incorporated DNA within the OMVs, and protected it from degradation by extracellular exonucleases. Thirdly, the vesicular lumen DNA was delivered to the recipient cells after determining the presence of virulence and carbapenem-resistant genes in the CR-HvKP OMVs. Importantly, S1-PFGE and Southern hybridization analysis of the 700603 transformant strain showed that the transformant contained both drug-resistant and virulence plasmids.<br><br>DISCUSSION: In the present study, we aimed to clarify the role of CRHvKP-OMVs in transmitting CR-HvKP among K. pneumoniae. Collectively, our findings provided valuable insights into the evolution of CR-HvKP.},
}
@article {pmid36532424,
year = {2022},
author = {Pillay, S and Calderón-Franco, D and Urhan, A and Abeel, T},
title = {Metagenomic-based surveillance systems for antibiotic resistance in non-clinical settings.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1066995},
pmid = {36532424},
issn = {1664-302X},
abstract = {The success of antibiotics as a therapeutic agent has led to their ineffectiveness. The continuous use and misuse in clinical and non-clinical areas have led to the emergence and spread of antibiotic-resistant bacteria and its genetic determinants. This is a multi-dimensional problem that has now become a global health crisis. Antibiotic resistance research has primarily focused on the clinical healthcare sectors while overlooking the non-clinical sectors. The increasing antibiotic usage in the environment - including animals, plants, soil, and water - are drivers of antibiotic resistance and function as a transmission route for antibiotic resistant pathogens and is a source for resistance genes. These natural compartments are interconnected with each other and humans, allowing the spread of antibiotic resistance via horizontal gene transfer between commensal and pathogenic bacteria. Identifying and understanding genetic exchange within and between natural compartments can provide insight into the transmission, dissemination, and emergence mechanisms. The development of high-throughput DNA sequencing technologies has made antibiotic resistance research more accessible and feasible. In particular, the combination of metagenomics and powerful bioinformatic tools and platforms have facilitated the identification of microbial communities and has allowed access to genomic data by bypassing the need for isolating and culturing microorganisms. This review aimed to reflect on the different sequencing techniques, metagenomic approaches, and bioinformatics tools and pipelines with their respective advantages and limitations for antibiotic resistance research. These approaches can provide insight into resistance mechanisms, the microbial population, emerging pathogens, resistance genes, and their dissemination. This information can influence policies, develop preventative measures and alleviate the burden caused by antibiotic resistance.},
}
@article {pmid36532220,
year = {2022},
author = {Boury, N and Van den Bogaard, MED and Wasendorf, C and Amon, J and Judson, S and Maroushek, SR and Peters, NT},
title = {The Use of a Multimodal Case Study To Illustrate Microbial Genetics, Metabolism, and Evolution: The Emergence of VRSA-1.},
journal = {Journal of microbiology &amp; biology education},
volume = {23},
number = {3},
pages = {},
pmid = {36532220},
issn = {1935-7877},
abstract = {Antibiotic Resistance (ABR) is a global concern and while many students are aware of this issue, many of them are unclear on the mechanisms by which ABR may emerge. The mechanism of horizontal gene transfer is something many students are not familiar with. In this curriculum contribution we present 2 versions of an 'interrupted case study' that is designed as an introduction to horizontal gene transfer for early major students and as a review case for advanced major students in biology and life sciences. The case is based on an authentic patient who developed infections with both methicillin resistant Staphylococcus aureus and vancomycin resistant S. aureus. The interrupted case study is appropriate for small and large groups and engages students while content is introduced in a highly structured way. This type of case study can be done by novice and seasoned instructors and lead to considerable learning gains in both introductory and intermediate microbiology courses.},
}
@article {pmid36528203,
year = {2023},
author = {Jaiswal, S and Singh, DK and Shukla, P},
title = {Degradation effectiveness of hexachlorohexane (ϒ-HCH) by bacterial isolate Bacillus cereus SJPS-2, its gene annotation for bioremediation and comparison with Pseudomonas putida KT2440.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {318},
number = {},
pages = {120867},
doi = {10.1016/j.envpol.2022.120867},
pmid = {36528203},
issn = {1873-6424},
mesh = {*Hexachlorocyclohexane/metabolism ; Biodegradation, Environmental ; *Pseudomonas putida/genetics ; Bacillus cereus/genetics ; Molecular Sequence Annotation ; },
abstract = {The contamination of Hexachlorohexane (Lindane) in soil and water has toxic effects due to its persistent nature. In our study, an indigenous HCH (gamma isomer) degrading bacterium viz Bacillus cereus SJPS-2 was isolated from Yamuna river water using enrichment culture method. The growth curve indicated that Bacillus cereus SJPS-2 was able to degrade ϒ-HCH effectively with 80.98% degradation. Further, process was improved by using immobilization using alginate beads which showed enhanced degradation (89.34%). Interestingly, in presence of fructose, the ϒ-HCH degradation was up to 79.24% with exponential growth curve whereas the degradation was only 5.61% in presence of glucose revealing diauxic growth curve. Furthermore, The FTIR results confirmed the potential lindane degradation capability of Bacillus cereus SJPS-2 and the bonds were recorded at wavelengths viz. 2900-2500 cm-[1], 3300-2800 cm-[1] and 785-540 cm-[1]. Similarity, the GC studies also reconfirmed the degradation potential with retention time (RT) of ethyl acetate and lindane was 2.12 and 11.0 respectively. Further, we studied the metabolic pathway involved for lindane utilization in Bacillus cereus using KEGG-KASS and functional gene annotation through Rapid Annotation using Subsystems Technology (RAST) resulted in the annotation of the lin genes (lin A, lin B, lin C, lin X, lin D, lin E) and respective encoding enzymes. The comparative ϒ-HCH degradation potential of B. cereus and P. putida KT2440 was also evaluated. The island viewer showed the different colors on circular genome indicate the coordinates of genomic islands resulted with some common genomic islands (GEIs) between both bacteria indicating the possibility of horizontal gene transfer at contaminated site or natural environment. These genomic islands (GEIs) contribute in the rearrangement genetic material or to evolve bacteria in stress conditions, as a result the metabolic pathways evolve by formation of catabolic genes. This study establishes the potential of Bacillus cereus SJPS-2 for effectual ϒ-HCH degradation.},
}
@article {pmid36527364,
year = {2023},
author = {Knoop, V},
title = {C-to-U and U-to-C: RNA editing in plant organelles and beyond.},
journal = {Journal of experimental botany},
volume = {74},
number = {7},
pages = {2273-2294},
doi = {10.1093/jxb/erac488},
pmid = {36527364},
issn = {1460-2431},
mesh = {*RNA Editing ; Uridine/genetics/metabolism ; *Organelles/genetics/metabolism ; Plants/genetics/metabolism ; Chloroplasts/metabolism ; RNA, Plant/genetics/metabolism ; Plant Proteins/metabolism ; },
abstract = {The genomes in the two energy-converting organelles of plant cells, chloroplasts and mitochondria, contain numerous 'errors' that are corrected at the level of RNA transcript copies. The genes encoded in the two endosymbiotic organelles would not function properly if their transcripts were not altered by site-specific cytidine-to-uridine (C-to-U) exchanges and by additional reverse U-to-C exchanges in hornworts, lycophytes, and ferns. These peculiar processes of plant RNA editing, re-establishing genetic information that could alternatively be present at the organelle genome level, has spurred much research over >30 years. Lately new studies have revealed numerous interesting insights, notably on the biochemical machinery identifying specific pyrimidine nucleobases for conversion from C to U and vice versa. Here, I will summarize prominent research findings that lately have contributed to our better understanding of these phenomena introducing an added layer of information processing in plant cells. Some of this recent progress is based on the successful functional expression of plant RNA editing factors in bacteria and mammalian cells. These research approaches have recapitulated natural processes of horizontal gene transfer through which some protist lineages seem to have acquired plant RNA editing factors and adapted them functionally for their own purposes.},
}
@article {pmid36525956,
year = {2022},
author = {Liu, HW and Roisné-Hamelin, F and Beckert, B and Li, Y and Myasnikov, A and Gruber, S},
title = {DNA-measuring Wadjet SMC ATPases restrict smaller circular plasmids by DNA cleavage.},
journal = {Molecular cell},
volume = {82},
number = {24},
pages = {4727-4740.e6},
doi = {10.1016/j.molcel.2022.11.015},
pmid = {36525956},
issn = {1097-4164},
mesh = {*Adenosine Triphosphatases/genetics/metabolism ; *DNA Cleavage ; Plasmids/genetics ; Chromosomes/metabolism ; DNA/genetics ; Cell Cycle Proteins/genetics ; Chromosomes, Bacterial/genetics/metabolism ; },
abstract = {Structural maintenance of chromosome (SMC) complexes fold DNA by loop extrusion to support chromosome segregation and genome maintenance. Wadjet systems (JetABCD/MksBEFG/EptABCD) are derivative SMC complexes with roles in bacterial immunity against selfish DNA. Here, we show that JetABCD restricts circular plasmids with an upper size limit of about 100 kb, whereas a linear plasmid evades restriction. Purified JetABCD complexes cleave circular DNA molecules, regardless of the DNA helical topology; cleavage is DNA sequence nonspecific and depends on the SMC ATPase. A cryo-EM structure reveals a distinct JetABC dimer-of-dimers geometry, with the two SMC dimers facing in opposite direction-rather than the same as observed with MukBEF. We hypothesize that JetABCD is a DNA-shape-specific endonuclease and propose the "total extrusion model" for DNA cleavage exclusively when extrusion of an entire plasmid has been completed by a JetABCD complex. Total extrusion cannot be achieved on the larger chromosome, explaining how self-DNA may evade processing.},
}
@article {pmid36525447,
year = {2022},
author = {Zou, X and Nguyen, M and Overbeek, J and Cao, B and Davis, JJ},
title = {Classification of bacterial plasmid and chromosome derived sequences using machine learning.},
journal = {PloS one},
volume = {17},
number = {12},
pages = {e0279280},
pmid = {36525447},
issn = {1932-6203},
mesh = {Plasmids/genetics ; *Genome, Bacterial ; *Chromosomes, Bacterial/genetics ; Bacteria/genetics ; Machine Learning ; Nucleotides ; },
abstract = {Plasmids are important genetic elements that facilitate horizonal gene transfer between bacteria and contribute to the spread of virulence and antimicrobial resistance. Most bacterial genome sequences in the public archives exist in draft form with many contigs, making it difficult to determine if a contig is of chromosomal or plasmid origin. Using a training set of contigs comprising 10,584 chromosomes and 10,654 plasmids from the PATRIC database, we evaluated several machine learning models including random forest, logistic regression, XGBoost, and a neural network for their ability to classify chromosomal and plasmid sequences using nucleotide k-mers as features. Based on the methods tested, a neural network model that used nucleotide 6-mers as features that was trained on randomly selected chromosomal and plasmid subsequences 5kb in length achieved the best performance, outperforming existing out-of-the-box methods, with an average accuracy of 89.38% ± 2.16% over a 10-fold cross validation. The model accuracy can be improved to 92.08% by using a voting strategy when classifying holdout sequences. In both plasmids and chromosomes, subsequences encoding functions involved in horizontal gene transfer-including hypothetical proteins, transporters, phage, mobile elements, and CRISPR elements-were most likely to be misclassified by the model. This study provides a straightforward approach for identifying plasmid-encoding sequences in short read assemblies without the need for sequence alignment-based tools.},
}
@article {pmid36523753,
year = {2022},
author = {Alam, M and Bano, N and Upadhyay, TK and Binsuwaidan, R and Alshammari, N and Sharangi, AB and Kaushal, RS and Saeed, M},
title = {Enzymatic Activity and Horizontal Gene Transfer of Heavy Metals and Antibiotic Resistant Proteus vulgaris from Hospital Wastewater: An Insight.},
journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale},
volume = {2022},
number = {},
pages = {3399137},
pmid = {36523753},
issn = {1712-9532},
abstract = {Globally, the issue of microbial resistance to medicines and heavy metals is getting worse. There are few reports or data available for Proteus vulgaris (P. vulgaris), particularly in India. This investigation intends to reveal the bacteria's ability to transmit genes and their level of resistance as well. The wastewater samples were taken from several hospitals in Lucknow City, India, and examined for the presence of Gram-negative bacteria that were resistant to antibiotics and heavy metals. The microbial population count in different hospital wastewaters decreases with increasing concentrations of metal and antibiotics. Among all the examined metals, Ni and Zn had the highest viable counts, whereas Hg, Cd, and Co had the lowest viable counts. Penicillin, ampicillin, and amoxicillin, among the antibiotics, demonstrated higher viable counts, whereas tetracycline and erythromycin exhibited lower viable counts. The MIC values for the P. vulgaris isolates tested ranged from 50 to 16,00 μg/ml for each metal tested. The multiple metal resistance (MMR) index, which ranged from 0.04 to 0.50, showed diverse heavy metal resistance patterns in all P. vulgaris isolates (in the case of 2-7 metals in various combinations). All of the tested isolates had methicillin resistance, whereas the least number of isolates had ofloxacin, gentamycin, or neomycin resistance. The P. vulgaris isolates displayed multidrug resistance patterns (2-12 drugs) in various antibiotic combinations. The MAR indexes were shown to be between (0.02-0.7). From the total isolates, 98%, 84%, and 80% had urease, gelatinase, and amylase activity, whereas 68% and 56% displayed protease and beta-lactamase activity. Plasmids were present in all the selected resistant isolates and varied in size from 42.5 to 57.0 kb and molecular weight from 27.2 to 37.0 MD. The transmission of the antibiotic/metal resistance genes was evaluated between a total of 7 pairs of isolates. A higher transfer frequency (4.4 × 10[-1]) was observed among antibiotics, although a lower transfer frequency (1.0 × 10[-2]) was observed against metals in both the media from the entire site tested. According to exponential decay, the population of hospital wastewater declined in the following order across all sites: Site II > Site IV > Site III > Site I for antibiotics and site IV > site II > site I >site III for metal. Different metal and antibiotic concentrations have varying effects on the population. The metal-tolerant P. vulgaris from hospital wastewater was studied in the current study had multiple distinct patterns of antibiotic resistance. It could provide cutting-edge methods for treating infectious diseases, which are essential for managing and assessing the risks associated with hospital wastewater, especially in the case of P. vulgaris.},
}
@article {pmid36522135,
year = {2023},
author = {Dorrell, RG and Kuo, A and Füssy, Z and Richardson, EH and Salamov, A and Zarevski, N and Freyria, NJ and Ibarbalz, FM and Jenkins, J and Pierella Karlusich, JJ and Stecca Steindorff, A and Edgar, RE and Handley, L and Lail, K