@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 & 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.

METHODS: The isolates were identified using 16 S rRNA sequencing, morphological analysis, physiological and biochemical characterization and PCR, and they were then subjected to whole genome sequencing (WGS) analysis.

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.

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.},
}

*Bacteroides fragilis/genetics/pathogenicity/isolation & purification
Humans
*Colorectal Neoplasms/microbiology/genetics/pathology
*Tumor Microenvironment
Genome, Bacterial
Adaptation, Physiological/genetics
Phylogeny
Genomics
Whole Genome Sequencing
Virulence/genetics
Enterotoxins/genetics/metabolism

@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 = {},
number = {},
pages = {},
doi = {10.1089/mdr.2024.0212},
pmid = {40100768},
issn = {1931-8448},
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 {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//Vetenskapsrådet (Swedish Research Council)/ ; 2018-05771//Vetenskapsrådet (Swedish Research Council)/ ; 2019-03482//Vetenskapsrådet (Swedish Research Council)/ ; 2022-00945//Vetenskapsrådet (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.},
}

*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

@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},
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},
doi = {10.4014/jmb.2411.11043},
pmid = {40081886},
issn = {1738-8872},
mesh = {*Acinetobacter/genetics/classification/isolation & 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.},
}

*Acinetobacter/genetics/classification/isolation & purification
*Gene Transfer, Horizontal
Genome, Bacterial
Genetic Variation
Phylogeny
Humans
Biodegradation, Environmental
Acinetobacter Infections/microbiology

@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 & 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.},
}

Humans
Cambodia/epidemiology
*beta-Lactamases/genetics
Animals
*Escherichia coli/genetics/isolation & 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

@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 {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},
doi = {10.1128/jvi.01715-24},
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.},
}

*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

@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/drug effects/metabolism ; *Extracellular Polymeric Substance Matrix/metabolism ; *Bacteria/genetics/drug effects/metabolism ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Wastewater/microbiology ; Drug Resistance, Bacterial/genetics ; },
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.},
}

*Microalgae/genetics/drug effects/metabolism
*Extracellular Polymeric Substance Matrix/metabolism
*Bacteria/genetics/drug effects/metabolism
Anti-Bacterial Agents/pharmacology
Genes, Bacterial
Drug Resistance, Microbial/genetics
Gene Transfer, Horizontal
Wastewater/microbiology
Drug Resistance, Bacterial/genetics

@article {pmid39874760,
year = {2025},
author = {Liu, Y and Shan, X and Liu, C and Chen, H},
title = {Microcosm experiments deciphered resistome coalescence, risks and source-sink relationship of antibiotic resistance in the soil irrigated with reclaimed water.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137398},
doi = {10.1016/j.jhazmat.2025.137398},
pmid = {39874760},
issn = {1873-3336},
mesh = {*Agricultural Irrigation ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Soil/chemistry ; Gene Transfer, Horizontal ; },
abstract = {Reclaimed water is widely used in agriculture irrigation to alleviate water scarcity, whereas the dissemination of antibiotic resistance genes (ARGs) in the soil it introduces has attracted widespread attention. Currently, few studies have systematically elucidated the coalescence of the resistome originating from reclaimed water with the soil's native community. Also, the effects and mechanisms of irrigation on the dissemination of ARGs in soils have yet to be demonstrated. To address this gap, microcosm experiments have been conducted in this study to decipher the resistome coalescence, risks and source-sink relationship of ARGs in soils irrigated with reclaimed water. The results show 237 ARGs, 55 mobile genetic elements (MGEs) and 28 virulence factors were identified in the irrigated soils. Irrigation increased the abundance and diversity of ARGs in the soil by introducing antibiotic-resistant bacteria, altering the microbial community and facilitating horizontal transfer of ARGs via MGEs, and ultimately exacerbated resistome risks in the environment. Relatively, a larger volume of irrigation water led to a more complex propagation network of the resistome. Source apportionment analysis suggested reclaimed water contributed less than 15 % of ARGs in the irrigated soils, whereas its contribution proportion increased with a larger volume of irrigation water.},
}

*Agricultural Irrigation
*Soil Microbiology
*Drug Resistance, Microbial/genetics
Bacteria/genetics/drug effects
Genes, Bacterial
Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial/genetics
Soil/chemistry
Gene Transfer, Horizontal

@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 Américas/ ; },
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.},
}

*Gene Transfer, Horizontal
*Phylogeny
*Ascomycota/genetics
Evolution, Molecular
Proteome/genetics

@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 {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.

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.

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.

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.},
}

Ghana
Humans
Animals
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Bacteria/genetics/drug effects
Genes, Bacterial

@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},
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.},
}

*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

@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 & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c10879},
pmid = {40071515},
issn = {1520-5851},
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.},
}

*Spodoptera/genetics
Animals
*Gene Transfer, Horizontal
*Evolution, Molecular
*Genome, Insect
Genetic Variation

@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.},
}

*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

@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 = {},
number = {},
pages = {e0165224},
doi = {10.1128/aem.01652-24},
pmid = {40066988},
issn = {1098-5336},
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.},
}

*Geminiviridae/genetics
*Recombination, Genetic
Software
Algorithms
Sequence Alignment
Genome, Viral
Evolution, Molecular
Computational Biology/methods
Phylogeny

@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.},
}

*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

@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 = {},
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 {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},
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},
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},
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},
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 & 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//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; fellowship 1D//Conselho Nacional de Pesquisa e Desenvolvimento Tecnológico/ ; },
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.},
}

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

@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 = {*Plasmids/genetics ; *beta-Lactamases/genetics/metabolism ; Humans ; *Carbapenems/pharmacology ; *Microbial Sensitivity Tests ; *Acinetobacter/genetics/drug effects/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Klebsiella pneumoniae/genetics/drug effects/isolation & purification ; Klebsiella/genetics/drug effects/enzymology ; Enterobacter/genetics/drug effects/isolation & purification/enzymology ; Bacterial Proteins/genetics/metabolism ; Conjugation, Genetic ; Serratia marcescens/genetics/drug effects/enzymology/isolation & purification ; Victoria ; DNA Transposable Elements ; Gene Transfer, Horizontal ; },
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.

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.

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 1.17×10[-2] to 5.02×10[-5], P < 0.001).

CONCLUSIONS: Clonal spread, Inc type, homologous region, and insertion sequences are important mobility factors in the dissemination and evolution of blaIMP-4 plasmids.},
}

*Plasmids/genetics
*beta-Lactamases/genetics/metabolism
Humans
*Carbapenems/pharmacology
*Microbial Sensitivity Tests
*Acinetobacter/genetics/drug effects/isolation & purification
Anti-Bacterial Agents/pharmacology
Klebsiella pneumoniae/genetics/drug effects/isolation & purification
Klebsiella/genetics/drug effects/enzymology
Enterobacter/genetics/drug effects/isolation & purification/enzymology
Bacterial Proteins/genetics/metabolism
Conjugation, Genetic
Serratia marcescens/genetics/drug effects/enzymology/isolation & purification
Victoria
DNA Transposable Elements
Gene Transfer, Horizontal

@article {pmid39701446,
year = {2025},
author = {Long, X and Lin, F and Tang, B and Miao, F and Li, Z and Shen, Y and Yang, H and Ma, J},
title = {Acinetobacter indicus Coharboring Tet(X6) and blaNDM-1 Isolated From Slaughterhouse Waste.},
journal = {Journal of global antimicrobial resistance},
volume = {41},
number = {},
pages = {1-7},
doi = {10.1016/j.jgar.2024.12.004},
pmid = {39701446},
issn = {2213-7173},
mesh = {*beta-Lactamases/genetics ; *Acinetobacter/genetics/drug effects/isolation & purification ; *Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; *Abattoirs ; Animals ; Drug Resistance, Multiple, Bacterial/genetics ; Plasmids/genetics ; DNA Transposable Elements ; Whole Genome Sequencing ; Acinetobacter Infections/microbiology ; Gene Transfer, Horizontal ; },
abstract = {OBJECTIVES: Acinetobacter indicus is an important pathogen of nosocomial infection. The purpose of this study was to analyze the resistance and transmission of A. indicus strain AIBD14 isolated from slaughterhouse environment.

METHODS: A total of 96 environmental samples were collected from slaughterhouse. The antimicrobial susceptibility test was carried out by microbroth dilution method and E-test. Whole genome sequencing and bioinformatics analysis of the AIBD14 were performed, then S1-PFGE and southern blot verified the location of blaNDM-1 and tet(X6).

RESULTS: The AIBD14 is resistant to meropenem but susceptibility to tigecycline, and coharboring blaNDM-1 and tet(X6). The blaNDM-1 is located on the pAIBD14-NDM-1 that cannot be transferred by conjugation. Specifically, blaNDM-1 is located on the transposon Tn125, and blaNDM-1 can be transferred to other species with the help of transposon. The genetic background of blaNDM-1 is "ISAba125-blaNDM-1-bleMEL-dsbD-cutA-groES-groEL-insE-ISAba125". pAIBD14-NDM-1 is classified into the GR31 plasmid based on the homology of the repB. Meanwhile, there are two XerC/D-like binding sites on the plasmid, which can mediate the transfer of resistance genes. The tet(X6) gene is located on the chromosome of AIBD14, its downstream is accompanied by the neglected macrolide resistance gene estT, and there is a single copy of the insertion element ISCR2 around tet(X6) as the genetic background "ISAba4-IS3-hp-hp-tet(X6)-estT-guaA-ISCR2".

CONCLUSIONS: This is the first report of the coexistence of tet(X6) and blaNDM-1 in the A. indicus, and it has the risk of horizontal transfer across multiple species. So strict monitoring the multiple-resistant bacteria in the industrial chain is necessary based on the "One Heath".},
}

*beta-Lactamases/genetics
*Acinetobacter/genetics/drug effects/isolation & purification
*Microbial Sensitivity Tests
*Anti-Bacterial Agents/pharmacology
*Abattoirs
Animals
Drug Resistance, Multiple, Bacterial/genetics
Plasmids/genetics
DNA Transposable Elements
Whole Genome Sequencing
Acinetobacter Infections/microbiology
Gene Transfer, Horizontal

@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},
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 = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c11580},
pmid = {40045656},
issn = {1520-5118},
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},
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.

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.

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.

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.},
}

*Plasmids/genetics
*Nontuberculous Mycobacteria/genetics
*Genome, Bacterial
*Genomics/methods
Humans
Phylogeny
Mycobacterium Infections, Nontuberculous/microbiology

@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 & 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.},
}

*Salmonella typhimurium/genetics/pathogenicity
*Bacterial Proteins/metabolism/genetics
*Polynucleotide Adenylyltransferase/metabolism/genetics
*Sigma Factor/metabolism/genetics
*RNA Stability
*RNA, Messenger/metabolism/genetics
*Biofilms/growth & development
*Gene Expression Regulation, Bacterial
RNA-Binding Proteins/metabolism/genetics
3' Untranslated Regions/genetics
Polyadenylation

@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},
doi = {10.1073/pnas.2421910122},
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.},
}

Antarctic Regions
*Gene Transfer, Horizontal
*Freezing
Animals
*Rotifera/genetics
Genes, Bacterial
Antifreeze Proteins/genetics/metabolism

@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 = {},
number = {},
pages = {e0094824},
doi = {10.1128/msphere.00948-24},
pmid = {40035521},
issn = {2379-5042},
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.},
}

*Gene Transfer, Horizontal
*Extracellular Vesicles/metabolism
*Ecosystem
Seawater/microbiology/virology
Interspersed Repetitive Sequences
Viruses/genetics/metabolism

@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 = {},
number = {},
pages = {125952},
doi = {10.1016/j.envpol.2025.125952},
pmid = {40032228},
issn = {1873-6424},
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.},
}

*Gene Transfer, Horizontal
*Microbiota/genetics
Bacteria/genetics
Models, Theoretical
Microbial Interactions/genetics
Interspersed Repetitive Sequences/genetics
Ecosystem

@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.

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.

CODE AVAILABILITY: CASTLES-Pro is implemented inside the software package ASTER, available at https://github.com/chaoszhang/ASTER .

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 = {},
doi = {10.1101/2025.02.14.638328},
pmid = {40027631},
issn = {2692-8205},
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.

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.

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 & 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.},
}

*Haemophilus influenzae/drug effects
Humans
*Anti-Bacterial Agents/pharmacology
*Haemophilus Infections/drug therapy/microbiology
*Drug Resistance, Bacterial/genetics
Animals

@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},
doi = {10.3201/eid3103.241493},
pmid = {40023817},
issn = {1080-6059},
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.},
}

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

@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 = {},
number = {},
pages = {e2502193},
doi = {10.1002/advs.202502193},
pmid = {40019366},
issn = {2198-3844},
support = {2021YFD1400600//National Key R & 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/ ; },
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 = {},
number = {},
pages = {e0230624},
doi = {10.1128/aem.02306-24},
pmid = {40013789},
issn = {1098-5336},
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.

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 {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},
doi = {10.1128/spectrum.01347-24},
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 & 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.

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.},
}

*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 & purification

@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},
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},
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 & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c07248},
pmid = {40008406},
issn = {1520-5851},
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},
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 {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.},
}

Animals
*DNA, Mitochondrial/genetics
*Cardiidae/genetics
*Phylogeny
*Gene Transfer, Horizontal
Neoplasms/genetics
Washington

@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 = {*Aeromonas/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Polymyxins/pharmacology ; *Gram-Negative Bacterial Infections/microbiology/drug therapy ; *Colistin/pharmacology ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Gram-Negative Bacteria/drug effects/genetics ; Phylogeny ; Drug Resistance, Multiple, Bacterial/genetics ; Bacterial Proteins/genetics ; Gene Transfer, Horizontal ; Escherichia coli Proteins/genetics ; 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.},
}

*Aeromonas/genetics/drug effects
*Anti-Bacterial Agents/pharmacology
Humans
*Polymyxins/pharmacology
*Gram-Negative Bacterial Infections/microbiology/drug therapy
*Colistin/pharmacology
Drug Resistance, Bacterial/genetics
Microbial Sensitivity Tests
Gram-Negative Bacteria/drug effects/genetics
Phylogeny
Drug Resistance, Multiple, Bacterial/genetics
Bacterial Proteins/genetics
Gene Transfer, Horizontal
Escherichia coli Proteins/genetics
Transferases (Other Substituted Phosphate Groups)

@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 {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 .

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 {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.},
}

*Genome, Mitochondrial/genetics
*Genome, Chloroplast/genetics
*Phylogeny
*Genomics/methods
Codon Usage
Evolution, Molecular
Gene Transfer, Horizontal
RNA, Transfer/genetics

@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.

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.

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.

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.

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.

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.

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.},
}

*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

@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 = {},
number = {},
pages = {e0358824},
doi = {10.1128/mbio.03588-24},
pmid = {39998220},
issn = {2150-7511},
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 = {},
number = {},
pages = {132288},
doi = {10.1016/j.biortech.2025.132288},
pmid = {39993662},
issn = {1873-2976},
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, it concurrently enriched ARGs in MBR sludge, particularly for the largest-size particle sludge (>150 μm). A decreasing trend in the relative abundance of ARGs was observed along with the decreasing sludge particle size, and larger particle sludge (>106 μm) formed a relatively stable composition of ARGs, while ARGs on smaller 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. Larger-size particle sludge (>106 μm) showed higher HGT frequency with Proteobacteria as the dominant hosts undergoing HGT.},
}

@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 = {},
doi = {10.1101/2025.02.14.637881},
pmid = {39990427},
issn = {2692-8205},
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},
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 = {},
number = {},
pages = {},
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.

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.

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 µg/mL. Genomic analysis revealed 34 antibiotic resistance genes, including mcr-8.2 and multiple β-lactamase genes, alongside plasmid types IncFIB and IncFII. Chromosomal mutations in phoP, phoQ, and lpxM were also implicated in colistin resistance.

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},
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},
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 {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.},
}

*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

@article {pmid39976429,
year = {2025},
author = {Smith, EP and Valdivia, RH},
title = {Chlamydia trachomatis: a model for intracellular bacterial parasitism.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0036124},
doi = {10.1128/jb.00361-24},
pmid = {39976429},
issn = {1098-5530},
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 Tn9 16 in the Bacillus subtilis chromosome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39975115},
issn = {2692-8205},
abstract = {Integrative and conjugative elements (ICEs) are found in many bacterial species and are mediators of horizontal gene transfer. Tn 916 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, Tn 916 can integrate into many sites in the host chromosome. The consensus integration motif for Tn 916 , 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 Tn 916 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, Tn 916 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 Tn 916 .},
}

@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.

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},
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.},
}

*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

@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 = {},
doi = {10.1093/ismejo/wraf009},
pmid = {39869787},
issn = {1751-7370},
support = {2021-DST-004//Ningbo S&T project/ ; 2022S117//Ningbo Public Welfare project/ ; 42090063//National Natural Science Foundation of China/ ; },
mesh = {*Conjugation, Genetic ; *Plasmids/genetics ; *Acanthamoeba castellanii/microbiology/genetics ; *Soil Microbiology ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Bacteria/genetics/drug effects ; Metagenomics ; Cercozoa/genetics ; },
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.},
}

*Conjugation, Genetic
*Plasmids/genetics
*Acanthamoeba castellanii/microbiology/genetics
*Soil Microbiology
Drug Resistance, Microbial/genetics
Gene Transfer, Horizontal
Bacteria/genetics/drug effects
Metagenomics
Cercozoa/genetics

@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.},
}

*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

@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},
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.

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.

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.},
}

Animals
*Lepidoptera/genetics
*Evolution, Molecular
*Phylogeny
*Gene Duplication
*Multigene Family
Gene Transfer, Horizontal
Insect Proteins/genetics

@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.},
}

*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

@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},
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&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&MRGs, while ConsortiumLIN contained 57 ARGs and 32 BRGs&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&MRGs), Cupriavidus (2 ARGs, 10 BRGs&MRGs), and Bacillus (14 ARGs, 21 BRGs&MRGs). Chloramphenicol exposure significantly enriched genes linked to phenicol resistance (floR, capO) and co-expressed ARGs and BRGs&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},
doi = {10.1371/journal.pgen.1011606},
pmid = {39965000},
issn = {1553-7404},
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 = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf075},
pmid = {39960880},
issn = {1367-4811},
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 exists 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 (BHR) plasmids. Without adequate well-annotated training samples, learning models can fail to extract discriminative feature representations for plasmid host prediction.

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 NCBI RefSeq plasmid database, PLSDB 2025 database, plasmids with experimentally determined host labels, Hi-C dataset and DoriC dataset. The benchmark results against other plasmid host range prediction tools demonstrated that MOSTPLAS recognized more host labels while keeping a high precision.

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 10.5281/zenodo.14708999.

Please contact: yannisun@cityu.edu.hk. Supplementary data are available at Bioinformatics online.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf028},
pmid = {39960859},
issn = {1759-6653},
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 (HGT). Here, we provide support for an HGT-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, non-bilaterian metazoans and other basal eukaryotes suggests that an ancestral msp130 gene underwent an HGT 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 & 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.},
}

*Morganella morganii/virology/genetics
*Bacteriophages/genetics/classification/isolation & purification
*Genome, Viral
*Phylogeny
*Genomics
Host Specificity
Base Composition
Humans

@article {pmid39954947,
year = {2025},
author = {Saraiva, HCAS and Panzenhagen, P and Santos, AMPD and Portes, AB and Ferreira, JFDS and Junior, CAC},
title = {Unravelling the advances of CRISPR-Cas9 as a precise antimicrobial therapy: a systematic review.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.02.002},
pmid = {39954947},
issn = {2213-7173},
abstract = {Antimicrobial resistance (AMR) 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. This review explores the potential of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology and Cas9 nucleases in combating AMR. The literature review followed the PRISMA guidelines using PubMed, Embase, and Scopus databases until July 2023. The Enterobacterales family, particularly Escherichia coli, was the main focus. The resistance genes targeted were mainly associated with β-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%. 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.},
}