@article {pmid39343406,
year = {2024},
author = {Lin, L and Sun, M and Pan, X and Zhang, W and Yang, Y and Yang, Y},
title = {Absence of synergistic effects between microplastics and copper ions on the spread of antibiotic resistance genes within aquatic bacteria at the community level.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {176591},
doi = {10.1016/j.scitotenv.2024.176591},
pmid = {39343406},
issn = {1879-1026},
abstract = {Microplastics and copper ions (Cu[2+]) are favorable in accelerating the propagation of antibiotic resistance genes (ARGs) in the plastisphere, however, their combined effects on the ARG spread within the bacterial community of the natural environment were less understood. The influence of microplastic types and Cu[2+] concentrations on the horizontal gene transfer (HGT) of ARGs mediated by RP4 plasmid within natural bacterial communities in aquatic environments was investigated. Both biodegradable polybutylene succinate (PBS) and non-biodegradable polyvinyl chloride (PVC) microplastics significantly enhanced the transfer of ARGs, with PBS showing a significant higher effect compared to PVC. Cu[2+] also increased transconjugation rates at environmentally relevant concentrations (5 μg L[-1]), but higher levels (50 μg L[-1]) lead to decreased rates due to severe bacterial cell membrane damage. The transconjugation rates in the presence of both microplastics and Cu[2+] were lower than the sum of their individual effects, indicating no synergistic effects between them on transconjugation. Proteobacteria dominated the composition of transconjugates for all the treatment. Transmission electron microscope images and reactive oxygen species production in bacterial cells indicated that the increased contact frequency due to extracellular polymeric substances, combined with enhanced membrane permeability induced by microplastics and Cu[2+], accounted for the increasing transconjugation rates. The study provides valuable insight into the potential effects of microplastics and heavy metals on the spread of ARGs from donors to bacterial communities in natural environments.},
}

@article {pmid39343112,
year = {2024},
author = {Tao, Y and Zeng, Z and Deng, Y and Zhang, M and Wang, F and Wang, Y},
title = {Phylogeny and evolution of dissimilatory sulfite reduction in prokaryotes.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108208},
doi = {10.1016/j.ympev.2024.108208},
pmid = {39343112},
issn = {1095-9513},
abstract = {Sulfate is the second most common nonmetallic ion in modern oceans, as its concentration dramatically increased alongside tectonic activity and atmospheric oxidation in the Proterozoic. Microbial sulfate/sulfite metabolism, involving organic carbon or hydrogen oxidation, is linked to sulfur and carbon biogeochemical cycles. However, the coevolution of microbial sulfate/sulfite metabolism and Earth's history remains unclear. Here, we conducted a comprehensive phylogenetic analysis to explore the evolutionary history of the dissimilatory sulfite reduction (Dsr) pathway. The phylogenies of the Dsr-related genes presented similar branching patterns but also some incongruencies, indicating the complex origin and evolution of Dsr. Among these genes, dsrAB is the hallmark of sulfur-metabolizing prokaryotes. Our detailed analyses suggested that the evolution of dsrAB was shaped by vertical inheritance and multiple horizontal gene transfer events and that selection pressure varied across distinct lineages. Dated phylogenetic trees indicated that key evolutionary events of dissimilatory sulfur-metabolizing prokaryotes were related to the Great Oxygenation Event (2.4-2.0 Ga) and several geological events in the "Boring Billion" (1.8-0.8 Ga), including the fragmentation of the Columbia supercontinent (approximately 1.6 Ga), the rapid increase in marine sulfate (1.3-1.2 Ga), and the Neoproterozoic glaciation event (approximately 1.0 Ga). We also proposed that the voluminous iron formations (approximately 1.88 Ga) might have induced the metabolic innovation of iron reduction. In summary, our study provides new insights into Dsr evolution and a systematic view of the coevolution of dissimilatory sulfur-metabolizing prokaryotes and the Earth's environment.},
}

@article {pmid39343029,
year = {2024},
author = {Fernie, AR and de Vries, S and de Vries, J},
title = {Evolution of plant metabolism: the state-of-the-art.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1914},
pages = {20230347},
doi = {10.1098/rstb.2023.0347},
pmid = {39343029},
issn = {1471-2970},
mesh = {*Plants/metabolism/genetics ; Biological Evolution ; Metabolic Networks and Pathways/genetics ; Evolution, Molecular ; },
abstract = {Immense chemical diversity is one of the hallmark features of plants. This chemo-diversity is mainly underpinned by a highly complex and biodiverse biochemical machinery. Plant metabolic enzymes originated and were inherited from their eukaryotic and prokaryotic ancestors and further diversified by the unprecedentedly high rates of gene duplication and functionalization experienced in land plants. Unlike prokaryotic microbes, which display frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO2 and have experienced relatively few gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner using existing networks as a starting point and under various evolutionary constraints. That said, until recently, the evolution of only a handful of metabolic traits had been extensively investigated and as such, the evolution of metabolism has received a fraction of the attention of, the evolution of development, for example. Advances in metabolomics and next-generation sequencing have, however, recently led to a deeper understanding of how a wide range of plant primary and specialized (secondary) metabolic pathways have evolved both as a consequence of natural selection and of domestication and crop improvement processes. This article is part of the theme issue 'The evolution of plant metabolism'.},
}

*Plants/metabolism/genetics
Biological Evolution
Metabolic Networks and Pathways/genetics
Evolution, Molecular

@article {pmid39339889,
year = {2024},
author = {Arhab, Y and Pestova, TV and Hellen, CUT},
title = {Translation of Overlapping Open Reading Frames Promoted by Type 2 IRESs in Avian Calicivirus Genomes.},
journal = {Viruses},
volume = {16},
number = {9},
pages = {},
pmid = {39339889},
issn = {1999-4915},
support = {5 R01 GM097014//NIH (NIGMS)/ ; 5 R35 GM122602//NIH (NIGMS)/ ; },
mesh = {*Open Reading Frames ; *Genome, Viral ; Animals ; *Internal Ribosome Entry Sites/genetics ; *Caliciviridae/genetics ; *Protein Biosynthesis ; RNA, Viral/genetics ; 5' Untranslated Regions/genetics ; Ribosomes/metabolism/genetics ; },
abstract = {Caliciviruses have positive-sense RNA genomes, typically with short 5'-untranslated regions (5'UTRs) that precede the long open reading frame 1 (ORF1). Exceptionally, some avian caliciviruses have long 5'UTRs containing a picornavirus-like internal ribosomal entry site (IRES), which was likely acquired by horizontal gene transfer. Here, we identified numerous additional avian calicivirus genomes with IRESs, predominantly type 2, and determined that many of these genomes contain a ~200-300 codon-long ORF (designated ORF1*) that overlaps the 5'-terminal region of ORF1. The activity of representative type 2 IRESs from grey teal calicivirus (GTCV) and Caliciviridae sp. isolate yc-13 (RaCV1) was confirmed by in vitro translation. Toeprinting showed that in cell-free extracts and in vitro reconstituted reactions, ribosomal initiation complexes assembled on the ORF1* initiation codon and at one or two AUG codons in ORF1 at the 3'-border and/or downstream of the IRES. Initiation at all three sites required eIF4A and eIF4G, which bound to a conserved region of the IRES; initiation on the ORF1* and principal ORF1 initiation codons involved eIF1/eIF1A-dependent scanning from the IRES's 3'-border. Initiation on these IRESs was enhanced by the IRES trans-acting factors (ITAFs) Ebp1/ITAF45, which bound to the apical subdomain Id of the IRES, and PTB (GTCV) or PCBP2 (RaCV1).},
}

*Open Reading Frames
*Genome, Viral
Animals
*Internal Ribosome Entry Sites/genetics
*Caliciviridae/genetics
*Protein Biosynthesis
RNA, Viral/genetics
5' Untranslated Regions/genetics
Ribosomes/metabolism/genetics

@article {pmid39086116,
year = {2024},
author = {Yang, Q and Li, L and Zhao, G and Cui, Q and Gong, X and Ying, L and Yang, T and Fu, M and Shen, Z},
title = {Characterization of a multiresistance optrA- and lsa(E)-harbouring unconventional circularizable structure in Streptococcus suis.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {79},
number = {10},
pages = {2528-2533},
doi = {10.1093/jac/dkae250},
pmid = {39086116},
issn = {1460-2091},
support = {2022YFC2303900//National Key Research and Development Program of China/ ; 32141001//National Natural Science Foundation of China/ ; },
mesh = {*Streptococcus suis/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Microbial Sensitivity Tests ; *Multigene Family ; *Conjugation, Genetic/genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genomic Islands/genetics ; Lincosamides/pharmacology ; Pleuromutilins ; Diterpenes/pharmacology ; Polycyclic Compounds ; Streptococcal Infections/microbiology ; Genes, Bacterial ; Streptogramin A/pharmacology ; },
abstract = {OBJECTIVES: To identify novel genetic elements facilitating the horizontal transfer of the oxazolidinone/phenicol resistance gene optrA and the pleuromutilin-lincosamide-streptogramin A resistance gene lsa(E) in Streptococcus suis.

METHODS: The complete genomes of S. suis HB18 and two transconjugants were obtained using both the Illumina and Nanopore platforms. MICs were determined by broth microdilution. Inverse PCR was performed to identify circular forms of the novel unconventional circularizable structure (UCS), genomic island (GI) and integrative and conjugative element (ICE). Conjugation experiments assessed the transferability of optrA and lsa(E) genes in S. suis.

RESULTS: S. suis HB18 carried a multiresistance gene cluster optrA-lsa(E)-lnu(B)-aphA-aadE-spw. This gene cluster, flanked by intact and truncated erm(B) in the same orientation, resided on a novel ICESsuHB18. Inverse PCR revealed the existence of a novel UCS, named UCS-optrA + lsa(E), which could excise the gene cluster optrA-lsa(E)-lnu(B)-aphA-aadE-spw and one copy of erm(B) from ICESsuHB18. Two transconjugants with different characteristics were obtained. In transconjugant T-JH-GI, UCS-optrA + lsa(E) excised from ICESsuHB18 inserted into the erm(B)-positive GI, designated GISsuHB18, generating the novel GISsuHB18-1. Meanwhile, in T-JH-ICE, genetic rearrangement events occurred in ICESsuHB18 and GISsuHB18, forming the novel ICESsuHB18-1.

CONCLUSIONS: This is the first report demonstrating the functionally active UCS-optrA + lsa(E) excising from ICESsuHB18 and inserting into the erm(B)-positive GISsuHB18 during the conjugation process. The location of optrA and lsa(E) on a multiresistance UCS enhances its persistence and dissemination.},
}

*Streptococcus suis/genetics/drug effects
*Anti-Bacterial Agents/pharmacology
*Drug Resistance, Multiple, Bacterial/genetics
*Microbial Sensitivity Tests
*Multigene Family
*Conjugation, Genetic/genetics
*Gene Transfer, Horizontal
Genome, Bacterial
Genomic Islands/genetics
Lincosamides/pharmacology
Pleuromutilins
Diterpenes/pharmacology
Polycyclic Compounds
Streptococcal Infections/microbiology
Genes, Bacterial
Streptogramin A/pharmacology

@article {pmid39073766,
year = {2024},
author = {González-Pinto, L and Alonso-García, I and Blanco-Martín, T and Camacho-Zamora, P and Fraile-Ribot, PA and Outeda-García, M and Lasarte-Monterrubio, C and Guijarro-Sánchez, P and Maceiras, R and Moya, B and Juan, C and Vázquez-Ucha, JC and Beceiro, A and Oliver, A and Bou, G and Arca-Suárez, J},
title = {Impact of chromosomally encoded resistance mechanisms and transferable β-lactamases on the activity of cefiderocol and innovative β-lactam/β-lactamase inhibitor combinations against Pseudomonas aeruginosa.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {79},
number = {10},
pages = {2591-2597},
doi = {10.1093/jac/dkae263},
pmid = {39073766},
issn = {1460-2091},
support = {//European Union/ ; //Merck Sharp & Dohme/ ; //Investigator Initiated Studies Program/ ; CB21/13/00055//Centro de Investigación Biomédica en Red de Enfermedades Infecciosas/ ; //Spanish Network of Research in Infectious Diseases/ ; //National Plan for Scientific Research, Development and Technological Innovation 2013-2016/ ; //ISCIII-General Subdirection of Assessment and Promotion of the Research-European Regional Development Fund/ ; //Axencia Galega de Innovación/ ; IN607D2021/12//Consellería de Innovación, Consellería de Economía, Emprego e Industria/ ; PI21/00704//ISCIII/ ; CM21/00076//Río Hortega program/ ; IN606B-2022/009//Xunta de Galicia/ ; JR21/00026//Juan Rodés program/ ; },
mesh = {*Pseudomonas aeruginosa/drug effects/genetics/enzymology ; *Cephalosporins/pharmacology ; *Microbial Sensitivity Tests ; *beta-Lactamase Inhibitors/pharmacology ; *beta-Lactamases/genetics/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Azabicyclo Compounds/pharmacology ; *Drug Combinations ; *Cefiderocol ; Cyclooctanes/pharmacology ; Tazobactam/pharmacology ; beta-Lactams/pharmacology ; Humans ; beta-Lactam Resistance/genetics ; Ceftazidime/pharmacology ; Pseudomonas Infections/microbiology/drug therapy ; Gene Transfer, Horizontal ; Chromosomes, Bacterial/genetics ; },
abstract = {OBJECTIVES: We aimed to compare the stability of the newly developed β-lactams (cefiderocol) and β-lactam/β-lactamase inhibitor combinations (ceftazidime/avibactam, ceftolozane/tazobactam, aztreonam/avibactam, cefepime/taniborbactam, cefepime/zidebactam, imipenem/relebactam, meropenem/vaborbactam, meropenem/nacubactam and meropenem/xeruborbactam) against the most clinically relevant mechanisms of mutational and transferable β-lactam resistance in Pseudomonas aeruginosa.

METHODS: We screened a collection of 61 P. aeruginosa PAO1 derivatives. Eighteen isolates displayed the most relevant mechanisms of mutational resistance to β-lactams. The other 43 constructs expressed transferable β-lactamases from genes cloned in pUCP-24. MICs were determined by reference broth microdilution.

RESULTS: Cefiderocol and imipenem/relebactam exhibited excellent in vitro activity against all of the mutational resistance mechanisms studied. Aztreonam/avibactam, cefepime/taniborbactam, cefepime/zidebactam, meropenem/vaborbactam, meropenem/nacubactam and meropenem/xeruborbactam proved to be more vulnerable to mutational events, especially to overexpression of efflux operons. The agents exhibiting the widest spectrum of activity against transferable β-lactamases were aztreonam/avibactam and cefepime/zidebactam, followed by cefepime/taniborbactam, cefiderocol, meropenem/xeruborbactam and meropenem/nacubactam. However, some MBLs, particularly NDM enzymes, may affect their activity. Combined production of certain enzymes (e.g. NDM-1) with increased MexAB-OprM-mediated efflux and OprD deficiency results in resistance to almost all agents tested, including last options such as aztreonam/avibactam and cefiderocol.

CONCLUSIONS: Cefiderocol and new β-lactam/β-lactamase inhibitor combinations show promising and complementary in vitro activity against mutational and transferable P. aeruginosa β-lactam resistance. However, the combined effects of efflux pumps, OprD deficiency and efficient β-lactamases could still result in the loss of all therapeutic options. Resistance surveillance, judicious use of new agents and continued drug development efforts are encouraged.},
}

*Pseudomonas aeruginosa/drug effects/genetics/enzymology
*Cephalosporins/pharmacology
*Microbial Sensitivity Tests
*beta-Lactamase Inhibitors/pharmacology
*beta-Lactamases/genetics/metabolism
*Anti-Bacterial Agents/pharmacology
*Azabicyclo Compounds/pharmacology
*Drug Combinations
*Cefiderocol
Cyclooctanes/pharmacology
Tazobactam/pharmacology
beta-Lactams/pharmacology
Humans
beta-Lactam Resistance/genetics
Ceftazidime/pharmacology
Pseudomonas Infections/microbiology/drug therapy
Gene Transfer, Horizontal
Chromosomes, Bacterial/genetics

@article {pmid38867468,
year = {2024},
author = {Qi, L and Wang, W and Fang, L and Li, J and Qi, L and Wang, D and Liu, J and Xiao, Y and Zhou, W and Fang, X},
title = {DNA Molecular Glue Assisted Bacterial Conjugative Transfer.},
journal = {Chemistry (Weinheim an der Bergstrasse, Germany)},
volume = {30},
number = {52},
pages = {e202401399},
doi = {10.1002/chem.202401399},
pmid = {38867468},
issn = {1521-3765},
support = {2022YFA1304500,2022YFC3401003//the National Key Scientific Program of China/ ; Nos. 21735006//National Natural Science Foundation of China/ ; Nos.21890742//National Natural Science Foundation of China/ ; },
mesh = {*Escherichia coli/genetics ; *Conjugation, Genetic ; *DNA, Single-Stranded/chemistry ; Click Chemistry ; Gene Transfer, Horizontal ; Oligonucleotides/chemistry ; },
abstract = {Bacterial conjugation, a commonly used method to horizontally transfer functional genes from donor to recipient strains, plays an important role in the genetic manipulation of bacteria for basic research and industrial production. Successful conjugation depends on the donor-recipient cell recognition and a tight mating junction formation. However, the efficiency of conjugative transfer is usually very low. In this work, we developed a new technique that employed DNA molecule "glue" to increase the match frequency and the interaction stability between the donor and recipient cells. We used two E. coli strains, ETZ and BL21, as a model system, and modified them with the complementary ssDNA oligonucleotides by click chemistry. The conjugation efficiency of the modified bacteria was improved more than 4 times from 10 %-46 %. This technique is simple and generalizable as it only relies on the active amino groups on the bacterial surface. It is expected to have broad applications in constructing engineered bacteria.},
}

*Escherichia coli/genetics
*Conjugation, Genetic
*DNA, Single-Stranded/chemistry
Click Chemistry
Gene Transfer, Horizontal
Oligonucleotides/chemistry

@article {pmid39338985,
year = {2024},
author = {Sung, K and Nawaz, M and Park, M and Chon, J and Khan, SA and Alotaibi, K and Khan, AA},
title = {Comprehensive Genomic Analysis of Uropathogenic E. coli: Virulence Factors, Antimicrobial Resistance, and Mobile Genetic Elements.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {9},
pages = {},
pmid = {39338985},
issn = {2076-0817},
support = {E0770601//United States Food and Drug Administration/ ; },
abstract = {Our whole-genome sequencing analysis of sixteen uropathogenic E. coli isolates revealed a concerning picture of multidrug resistance and potentially virulent bacteria. All isolates belonged to four distinct clonal groups, with the highly prevalent ST131 lineage being associated with extensive antibiotic resistance and virulence factors. Notably, all isolates exhibited multidrug resistance, with some resistant to as many as 12 antibiotics. Fluoroquinolone resistance stemmed primarily from efflux pumps and mutations in gyrase and topoisomerase genes. Additionally, we identified genes encoding resistance to extended-spectrum cephalosporins, trimethoprim/sulfamethoxazole, and various heavy metals. The presence of diverse plasmids and phages suggests the potential for horizontal gene transfer and the dissemination of virulence factors. All isolates harbored genomic islands containing virulence factors associated with adhesion, biofilm formation, and invasion. Genes essential for iron acquisition, flagella biosynthesis, secretion systems, and toxin production were also prevalent. Adding further complexity to understanding the isolates' genetic makeup, we identified CRISPR-Cas systems. This study underscores the need for continued genomic surveillance in understanding the pathogenic mechanisms and resistance profiles of uropathogenic E. coli to aid in developing targeted therapeutic strategies.},
}

@article {pmid39338594,
year = {2024},
author = {Oliveira, M and Antunes, W and Mota, S and Madureira-Carvalho, Á and Dinis-Oliveira, RJ and Dias da Silva, D},
title = {An Overview of the Recent Advances in Antimicrobial Resistance.},
journal = {Microorganisms},
volume = {12},
number = {9},
pages = {},
pmid = {39338594},
issn = {2076-2607},
support = {UIDP/04378/2020, UIDB/04378/2020, LA/P/0140/2020, UIDB/50006//Fundação para a Ciência e Tecnologia/ ; },
abstract = {Antimicrobial resistance (AMR), frequently considered a major global public health threat, requires a comprehensive understanding of its emergence, mechanisms, advances, and implications. AMR's epidemiological landscape is characterized by its widespread prevalence and constantly evolving patterns, with multidrug-resistant organisms (MDROs) creating new challenges every day. The most common mechanisms underlying AMR (i.e., genetic mutations, horizontal gene transfer, and selective pressure) contribute to the emergence and dissemination of new resistant strains. Therefore, mitigation strategies (e.g., antibiotic stewardship programs-ASPs-and infection prevention and control strategies-IPCs) emphasize the importance of responsible antimicrobial use and surveillance. A One Health approach (i.e., the interconnectedness of human, animal, and environmental health) highlights the necessity for interdisciplinary collaboration and holistic strategies in combating AMR. Advancements in novel therapeutics (e.g., alternative antimicrobial agents and vaccines) offer promising avenues in addressing AMR challenges. Policy interventions at the international and national levels also promote ASPs aiming to regulate antimicrobial use. Despite all of the observed progress, AMR remains a pressing concern, demanding sustained efforts to address emerging threats and promote antimicrobial sustainability. Future research must prioritize innovative approaches and address the complex socioecological dynamics underlying AMR. This manuscript is a comprehensive resource for researchers, policymakers, and healthcare professionals seeking to navigate the complex AMR landscape and develop effective strategies for its mitigation.},
}

@article {pmid39338472,
year = {2024},
author = {Gonzalez, V and Abarca-Hurtado, J and Arancibia, A and Claverías, F and Guevara, MR and Orellana, R},
title = {Novel Insights on Extracellular Electron Transfer Networks in the Desulfovibrionaceae Family: Unveiling the Potential Significance of Horizontal Gene Transfer.},
journal = {Microorganisms},
volume = {12},
number = {9},
pages = {},
pmid = {39338472},
issn = {2076-2607},
support = {11190863//ANID/Fondecyt/ ; 1211977//ANID/Fondecyt/ ; PAI79170091//ANID/ ; FOVI 230154//ANID/ ; Milenio-NCN2023_054//ANID/ ; Scholarship 21231799/2023//ANID/ ; },
abstract = {Some sulfate-reducing bacteria (SRB), mainly belonging to the Desulfovibrionaceae family, have evolved the capability to conserve energy through microbial extracellular electron transfer (EET), suggesting that this process may be more widespread than previously believed. While previous evidence has shown that mobile genetic elements drive the plasticity and evolution of SRB and iron-reducing bacteria (FeRB), few have investigated the shared molecular mechanisms related to EET. To address this, we analyzed the prevalence and abundance of EET elements and how they contributed to their differentiation among 42 members of the Desulfovibrionaceae family and 23 and 59 members of Geobacteraceae and Shewanellaceae, respectively. Proteins involved in EET, such as the cytochromes PpcA and CymA, the outer membrane protein OmpJ, and the iron-sulfur cluster-binding CbcT, exhibited widespread distribution within Desulfovibrionaceae. Some of these showed modular diversification. Additional evidence revealed that horizontal gene transfer was involved in the acquiring and losing of critical genes, increasing the diversification and plasticity between the three families. The results suggest that specific EET genes were widely disseminated through horizontal transfer, where some changes reflected environmental adaptations. These findings enhance our comprehension of the evolution and distribution of proteins involved in EET processes, shedding light on their role in iron and sulfur biogeochemical cycling.},
}

@article {pmid39337307,
year = {2024},
author = {Zhang, J and Zhu, S and Sun, J and Liu, Y},
title = {Bisphenol S Promotes the Transfer of Antibiotic Resistance Genes via Transformation.},
journal = {International journal of molecular sciences},
volume = {25},
number = {18},
pages = {},
doi = {10.3390/ijms25189819},
pmid = {39337307},
issn = {1422-0067},
support = {BE2023332//Key R&D Program of Jiangsu Province (Modern Agriculture)/ ; ZDYF2024SHFZ050//Science and Technology special fund of Hainan Province/ ; },
mesh = {*Phenols ; *Escherichia coli/genetics/drug effects ; *Sulfones/pharmacology ; *Plasmids/genetics ; Reactive Oxygen Species/metabolism ; Transformation, Bacterial ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Benzhydryl Compounds ; Citric Acid Cycle/drug effects/genetics ; },
abstract = {The antibiotic resistance crisis has seriously jeopardized public health and human safety. As one of the ways of horizontal transfer, transformation enables bacteria to acquire exogenous genes naturally. Bisphenol compounds are now widely used in plastics, food, and beverage packaging, and have become a new environmental pollutant. However, their potential relationship with the spread of antibiotic resistance genes (ARGs) in the environment remains largely unexplored. In this study, we aimed to assess whether the ubiquitous bisphenol S (BPS) could promote the transformation of plasmid-borne ARGs. Using plasmid pUC19 carrying the ampicillin resistance gene as an extracellular ARG and model microorganism E. coli DH5α as the recipient, we established a transformation system. Transformation assays revealed that environmentally relevant concentrations of BPS (0.1-10 μg/mL) markedly enhanced the transformation frequency of plasmid-borne ARGs into E. coli DH5α up to 2.02-fold. Fluorescent probes and transcript-level analyses suggest that BPS stimulated increased reactive oxygen species (ROS) production, activated the SOS response, induced membrane damage, and increased membrane fluidity, which weakened the barrier for plasmid transfer, allowing foreign DNA to be more easily absorbed. Moreover, BPS stimulates ATP supply by activating the tricarboxylic acid (TCA) cycle, which promotes flagellar motility and expands the search for foreign DNA. Overall, these findings provide important insight into the role of bisphenol compounds in facilitating the horizontal spread of ARGs and emphasize the need to monitor the residues of these environmental contaminants.},
}

*Phenols
*Escherichia coli/genetics/drug effects
*Sulfones/pharmacology
*Plasmids/genetics
Reactive Oxygen Species/metabolism
Transformation, Bacterial
Drug Resistance, Microbial/genetics
Gene Transfer, Horizontal
Drug Resistance, Bacterial/genetics
Benzhydryl Compounds
Citric Acid Cycle/drug effects/genetics

@article {pmid39336804,
year = {2024},
author = {Opazo-Capurro, A and Xanthopoulou, K and Arazo Del Pino, R and González-Muñoz, P and Matus-Köhler, M and Amsteins-Romero, L and Jerez-Olate, C and Hormazábal, JC and Vera, R and Aguilera, F and Fuller, S and Higgins, PG and González-Rocha, G},
title = {Co-Occurrence of Two Plasmids Encoding Transferable blaNDM-1 and tet(Y) Genes in Carbapenem-Resistant Acinetobacter bereziniae.},
journal = {Genes},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/genes15091213},
pmid = {39336804},
issn = {2073-4425},
support = {FONDECYT 1220708//Agencia Nacional de Investigación y Desarrollo/ ; FONDECYT Iniciacion 11190602//Agencia Nacional de Investigación y Desarrollo/ ; FONDEQUIP EQM200056//Agencia Nacional de Investigación y Desarrollo/ ; },
mesh = {*Plasmids/genetics ; *Acinetobacter/genetics/drug effects ; *beta-Lactamases/genetics ; Humans ; *Carbapenems/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Acinetobacter Infections/microbiology/drug therapy/epidemiology ; Bacterial Proteins/genetics ; Whole Genome Sequencing ; COVID-19 ; },
abstract = {Acinetobacter bereziniae has emerged as a significant human pathogen, acquiring multiple antibiotic resistance genes, including carbapenemases. This study focuses on characterizing the plasmids harboring the blaNDM-1 and tet(Y) genes in two carbapenem-resistant A. bereziniae isolates (UCO-553 and UCO-554) obtained in Chile during the COVID-19 pandemic. Methods: Antibiotic susceptibility testing was conducted on UCO-553 and UCO-554. Both isolates underwent whole-genome sequencing to ascertain their sequence type (ST), core genome multilocus sequence-typing (cgMLST) profile, antibiotic resistance genes, plasmids, and mobile genetic elements. Conjugation experiments were performed for both isolates. Results: Both isolates exhibited broad resistance, including resistance to carbapenems, third-generation cephalosporins, fluoroquinolones, tetracycline, cotrimoxazole, and aminoglycosides. Both isolates belong to sequence type ST[PAS]1761, with a difference of 17 out of 2984 alleles. Each isolate carried a 47,274 bp plasmid with blaNDM-1 and aph(3')-VI genes and two highly similar plasmids: a 35,184 bp plasmid with tet(Y), sul2, aph(6)-Id, and aph(3″)-Ib genes, and a 6078 bp plasmid containing the ant(2″)-Ia gene. Quinolone-resistance mutations were identified in the gyrA and parC genes of both isolates. Importantly, blaNDM-1 was located within a Tn125 transposon, and tet(Y) was embedded in a Tn5393 transposon. Conjugation experiments successfully transferred blaNDM-1 and tet(Y) into the A. baumannii ATCC 19606 strain, indicating the potential for horizontal gene transfer. Conclusions: This study highlights the critical role of plasmids in disseminating resistance genes in A. bereziniae and underscores the need for the continued genomic surveillance of this emerging pathogen. The findings emphasize the importance of monitoring A. bereziniae for its potential to cause difficult-to-treat infections and its capacity to spread resistance determinants against clinically significant antibiotics.},
}

*Plasmids/genetics
*Acinetobacter/genetics/drug effects
*beta-Lactamases/genetics
Humans
*Carbapenems/pharmacology
*Anti-Bacterial Agents/pharmacology
Drug Resistance, Multiple, Bacterial/genetics
Microbial Sensitivity Tests
Acinetobacter Infections/microbiology/drug therapy/epidemiology
Bacterial Proteins/genetics
Whole Genome Sequencing
COVID-19

@article {pmid39335078,
year = {2024},
author = {Tarrah, A and Zhang, D and Darvishzadeh, P and LaPointe, G},
title = {The Contribution of Dairy Bedding and Silage to the Dissemination of Genes Coding for Antimicrobial Resistance: A Narrative Review.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/antibiotics13090905},
pmid = {39335078},
issn = {2079-6382},
abstract = {Antimicrobial resistance (AMR) is a concern in the dairy industry. Recent studies have indicated that bedding serves as a reservoir for antimicrobial-resistant bacteria and antimicrobial-resistance genes (ARGs), while silage has been proposed as another possible source. The impact of AMR in dairy farming can be significant, resulting in decreased productivity and economic losses for farmers. Several studies have highlighted the safety implications of AMR bacteria and genes in bedding and silage, emphasizing the need for further research on how housing, bedding, and silage management affect AMR in farm environments. Exposure to sub-lethal concentrations of antibiotics, such as those from contaminated bedding and silage, can prompt bacteria to develop resistance mechanisms. Thus, even if antimicrobial usage is diminished, ARGs may be maintained in the dairy farm environment. By implementing proactive measures to tackle AMR in dairy farming, we can take steps to preserve the health and productivity of dairy cattle while also protecting public health. This involves addressing the prudent use of antibiotics during production and promoting animal welfare, hygiene, and management practices in bedding and farm environments to minimize the risk of AMR development and spread. This narrative review compiles the growing research, positioning the contribution of bedding and silage to the prevalence and dissemination of AMR, which can elicit insights for researchers and policymakers.},
}

@article {pmid39334999,
year = {2024},
author = {Mitchell, TM and Ho, T and Salinas, L and VanderYacht, T and Walas, N and Trueba, G and Graham, JP},
title = {Analysis of Antibiotic Resistance Genes (ARGs) across Diverse Bacterial Species in Shrimp Aquaculture.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/antibiotics13090825},
pmid = {39334999},
issn = {2079-6382},
abstract = {There is little information available on antibiotic resistance (ABR) within shrimp aquaculture environments. The aim of this study was to investigate the presence of antibiotic resistance genes (ARGs) in shrimp farming operations in Atacames, Ecuador. Water samples (n = 162) and shrimp samples (n = 54) were collected from three shrimp farming operations. Samples were cultured and a subset of isolates that grew in the presence of ceftriaxone, a third-generation cephalosporin, were analyzed using whole-genome sequencing (WGS). Among the sequenced isolates (n = 44), 73% of the isolates contained at least one ARG and the average number of ARGs per isolate was two, with a median of 3.5 ARGs. Antibiotic resistance genes that confer resistance to the β-lactam class of antibiotics were observed in 65% of the sequenced isolates from water (20/31) and 54% of the isolates from shrimp (7/13). We identified 61 different ARGs across the 44 sequenced isolates, which conferred resistance to nine antibiotic classes. Over half of all sequenced isolates (59%, n = 26) carried ARGs that confer resistance to more than one class of antibiotics. ARGs for certain antibiotic classes were more common, including beta-lactams (26 ARGs); aminoglycosides (11 ARGs); chloramphenicol (three ARGs); and trimethoprim (four ARGs). Sequenced isolates consisted of a diverse array of bacterial orders and species, including Escherichia coli (48%), Klebsiella pneumoniae (7%), Aeromonadales (7%), Pseudomonadales (16%), Enterobacter cloacae (2%), and Citrobacter freundii (2%). Many ARGs were shared across diverse species, underscoring the risk of horizontal gene transfer in these environments. This study indicated the widespread presence of extended-spectrum β-lactamase (ESBL) genes in shrimp aquaculture, including blaCTX-M, blaSHV, and blaTEM genes. Increased antibiotic resistance surveillance of shrimp farms and identification of aquaculture operation-level risk factors, such as antibiotic use, will likely be important for mitigating the spread of ARGs of clinical significance.},
}

@article {pmid39334992,
year = {2024},
author = {Liu, L and Zou, X and Cheng, Y and Li, H and Zhang, X and Yuan, Q},
title = {Contrasting Dynamics of Intracellular and Extracellular Antibiotic Resistance Genes in Response to Nutrient Variations in Aquatic Environments.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/antibiotics13090817},
pmid = {39334992},
issn = {2079-6382},
support = {No. 42377436 and 42177348//National Natural Science Foundation of China/ ; 2022YFC3205400//China National Key R&D Program/ ; },
abstract = {The propagation of antibiotic resistance in environments, particularly aquatic environments that serve as primary pathways for antibiotic resistance genes (ARGs), poses significant health risks. The impact of nutrients, as key determinants of bacterial growth and metabolism, on the propagation of ARGs, particularly extracellular ARGs (eARGs), remains poorly understood. In this study, we collected microorganisms from the Yangtze River and established a series of microcosms to investigate how variations in nutrient levels and delivery frequency affect the relative abundance of intracellular ARGs (iARGs) and eARGs in bacterial communities. Our results show that the relative abundance of 7 out of 11 representative eARGs in water exceeds that of iARGs, while 8 iARGs dominate in biofilms. Notably, iARGs and eARGs consistently exhibited opposite responses to nutrient variation. When nutrient levels increased, iARGs in the water also increased, with the polluted group (COD = 333.3 mg/L, COD:N:P = 100:3:0.6, m/m) and the eutrophic group (COD = 100 mg/L, COD:N:P = 100:25:5, m/m) showing 1.2 and 3.2 times higher levels than the normal group (COD = 100 mg/L, COD:N:P = 100:10:2, m/m), respectively. In contrast, eARGs decreased by 6.7% and 8.4% in these groups. On the other hand, in biofilms, higher nutrient levels led to an increase in eARGs by 1.5 and 1.7 times, while iARGs decreased by 17.5% and 50.1% in the polluted and eutrophic groups compared to the normal group. Moreover, while increasing the frequency of nutrient delivery (from 1 time/10 d to 20 times/10 d) generally did not favor iARGs in either water or biofilm, it selectively enhanced eARGs in both. To further understand these dynamics, we developed an ARGs-nutrient model by integrating the Lotka-Volterra and Monod equations. The results highlight the complex interplay of bacterial growth, nutrient availability, and mechanisms such as horizontal gene transfer and secretion influencing ARGs' propagation, driving the opposite trend between these two forms of ARGs. This contrasting response between iARGs and eARGs contributes to a dynamic balance that stabilizes bacterial resistance levels amid nutrient fluctuations. This study offers helpful implications regarding the persistence of bacterial resistance in the environment.},
}

@article {pmid39329926,
year = {2024},
author = {Syed, K},
title = {Ferredoxins: Functions, Evolution, Potential Applications, and Challenges of Subtype Classification.},
journal = {Current issues in molecular biology},
volume = {46},
number = {9},
pages = {9659-9673},
pmid = {39329926},
issn = {1467-3045},
abstract = {Ferredoxins are proteins found in all biological kingdoms and are involved in essential biological processes including photosynthesis, lipid metabolism, and biogeochemical cycles. Ferredoxins are classified into different groups based on the iron-sulfur (Fe-S) clusters that they contain. A new subtype classification and nomenclature system, based on the spacing between amino acids in the Fe-S binding motif, has been proposed in order to better understand ferredoxins' biological diversity and evolutionary linkage across different organisms. This new classification system has revealed an unparalleled diversity between ferredoxins and has helped identify evolutionarily linked ferredoxins between species. The current review provides the latest insights into ferredoxin functions and evolution, and the new subtype classification, outlining their potential biotechnological applications and the future challenges in streamlining the process.},
}

@article {pmid39328914,
year = {2024},
author = {Yan, J and Doublet, B and Wiedemann, A},
title = {Trends in horizontal gene transfer research in Salmonella antimicrobial resistance: a bibliometric analysis.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1439664},
pmid = {39328914},
issn = {1664-302X},
abstract = {Horizontal gene transfer (HGT) favors the acquisition and spread of antimicrobial resistance (AMR) genes in Salmonella, making it a major public health concern. We performed a bibliometric analysis to provide the current landscape of HGT in research on Salmonella AMR and identify emerging trends and potential research directions for the future. Data were collected from the Web of Science Core Collection and limited to articles and reviews published between 1999 and 2024 in English. VOSviewer 1.6.19 and CiteSpace 6.2.R1 software were used to conduct bibliometric analysis and visualize co-occurring keywords. A total of 1,467 publications were retrieved for analysis. American researchers contributed the most articles (n = 310). In the meantime, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement have the highest citation/publication rate of 85.6. Recent studies have focused on the application of whole genome sequencing (WGS), Salmonella quinolone and colistin resistance, and the biocontrol of Salmonella AMR. These findings provide new insights into the role of HGT and help identify new targets for controlling the spread of AMR in Salmonella populations.},
}

@article {pmid39327210,
year = {2024},
author = {García-Lozano, M and Salem, H},
title = {Microbial bases of herbivory in beetles.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2024.08.004},
pmid = {39327210},
issn = {1878-4380},
abstract = {The ecological radiation of herbivorous beetles is among the most successful in the animal kingdom. It coincided with the rise and diversification of flowering plants, requiring beetles to adapt to a nutritionally imbalanced diet enriched in complex polysaccharides and toxic secondary metabolites. In this review, we explore how beetles overcame these challenges by coopting microbial genes, enzymes, and metabolites, through both horizontal gene transfer (HGT) and symbiosis. Recent efforts revealed the functional convergence governing both processes and the unique ways in which microbes continue to shape beetle digestion, development, and defense. The development of genetic and experimental tools across a diverse set of study systems has provided valuable mechanistic insights into how microbes spurred metabolic innovation and facilitated an herbivorous transition in beetles.},
}

@article {pmid39326418,
year = {2024},
author = {Liu, Y and Miao, B and Li, W and Hu, X and Bai, F and Abuduresule, Y and Liu, Y and Zheng, Z and Wang, W and Chen, Z and Zhu, S and Feng, X and Cao, P and Ping, W and Yang, R and Dai, Q and Liu, F and Tian, C and Yang, Y and Fu, Q},
title = {Bronze Age cheese reveals human-Lactobacillus interactions over evolutionary history.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.08.008},
pmid = {39326418},
issn = {1097-4172},
abstract = {Despite the long history of consumption of fermented dairy, little is known about how the fermented microbes were utilized and evolved over human history. Here, by retrieving ancient DNA of Bronze Age kefir cheese (∼3,500 years ago) from the Xiaohe cemetery, we explored past human-microbial interactions. Although it was previously suggested that kefir was spread from the Northern Caucasus to Europe and other regions, we found an additional spreading route of kefir from Xinjiang to inland East Asia. Over evolutionary history, the East Asian strains gained multiple gene clusters with defensive roles against environmental stressors, which can be a result of the adaptation of Lactobacillus strains to various environmental niches and human selection. Overall, our results highlight the role of past human activities in shaping the evolution of human-related microbes, and such insights can, in turn, provide a better understanding of past human behaviors.},
}

@article {pmid39324609,
year = {2024},
author = {Liu, QH and Yuan, L and Li, ZH and Leung, KMY and Sheng, GP},
title = {Natural Organic Matter Enhances Natural Transformation of Extracellular Antibiotic Resistance Genes in Sunlit Water.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c08211},
pmid = {39324609},
issn = {1520-5851},
abstract = {Antibiotic resistance genes (ARGs) as emerging environmental contaminants exacerbate the risk of spreading antibiotic resistance. Natural organic matter (NOM) is ubiquitous in aquatic environments and plays a crucial role in biogeochemical cycles. However, its impact on the dissemination of extracellular antibiotic resistance genes (eARGs) under sunlight exposure remains elusive. This study reveals that environmentally relevant levels of NOM (0.1-20 mg/L) can significantly enhance the natural transformation frequency of the model bacterium Acinetobacter baylyi ADP1 by up to 7.6-fold under simulated sunlight. Similarly, this enhancement was consistently observed in natural water and wastewater systems. Further mechanism analysis revealed that reactive oxygen species (ROS) generated by NOM under sunlight irradiation, primarily singlet oxygen and hydroxyl radicals, play a crucial role in this process. These ROS induce intracellular oxidative stress and elevated cellular membrane permeability, thereby indirectly boosting ATP production and enhancing cell competence of extracellular DNA uptake and integration. Our findings highlight a previously underestimated role of natural factors in the dissemination of eARGs within aquatic ecosystems and deepen our understanding of the complex interplay between NOM, sunlight, and microbes in environmental water bodies. This underscores the importance of developing comprehensive strategies to mitigate the spread of antibiotic resistance in aquatic environments.},
}

@article {pmid39322056,
year = {2024},
author = {Chen, J and Lin, Y and Zhu, Y and Zhang, Y and Qian, Q and Chen, C and Xie, S},
title = {Spatiotemporal profiles and underlying mechanisms of the antibiotic resistome in two water-diversion lakes.},
journal = {Environmental research},
volume = {263},
number = {Pt 1},
pages = {120051},
doi = {10.1016/j.envres.2024.120051},
pmid = {39322056},
issn = {1096-0953},
abstract = {Human-induced interventions have altered the local characteristics of the lake ecosystems through changes in hydraulic exchange, which in turn impacts the ecological processes of antibiotic resistance genes (ARGs) in the lakes. However, the current understanding of the spatiotemporal patterns and driving factors of ARGs in water-diversion lakes is still seriously insufficient. In the present study, we investigated antibiotic resistome in the main regulation and storage hubs, namely Nansi Lake and Dongping Lake, of the eastern part of the South-to-North Water Diversion project in Shandong Province (China) using a metagenomic-based approach. A total of 653 ARG subtypes belonging to 25 ARG types were detected with a total abundance of 0.125-0.390 copies/cell, with the dominance of bacitracin, multidrug, and macrolide-lincosamide streptogramin resistance genes. The ARG compositions were sensitive to seasonal variation and also interfered by artificial regulation structures along the way. Human pathogenic bacteria such as Acinetobacter calcoaceticus, Acinetobacter lwoffii, Klebsiella pneumoniae, along with the multidrug resistance genes they carried, were the focus of risk control in the two studied lakes, especially in summer. Plasmids were the key mobile genetic elements (MGEs) driving the horizontal gene transfer of ARGs, especially multidrug and sulfonamide resistance genes. The null model revealed that stochastic process was the main driver of ecological drift for ARGs in the lakes. The partial least squares structural equation model further determined that seasonal changes of pH and temperature drove a shift in the bacterial community, which in turn shaped the profile of ARGs by altering the composition of MGEs, antibacterial biocide- and metal-resistance genes (BMGs), and virulence factor genes (VFGs). Our results highlighted the importance of seasonal factors in determining the water transfer period. These findings can aid in a deeper understanding of the spatiotemporal variations of ARGs in lakes and their driving factors, offering a scientific basis for antibiotic resistance management.},
}

@article {pmid39321479,
year = {2024},
author = {Rong, L and Wu, L and Zong, L and Wang, W and Xiao, Y and Yang, C and Pan, H and Zou, X},
title = {Evolution of the Black solider fly larvae gut antibiotic resistome during kitchen waste disposal.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135878},
doi = {10.1016/j.jhazmat.2024.135878},
pmid = {39321479},
issn = {1873-3336},
abstract = {Kitchen waste (KW) is an important reservoir of antibiotic resistance genes (ARGs). Black solider fly larvae (BSFL) are extensively employed in KW disposal, closely linking to their robust gut microbes. However, antibiotic resistome in BSFL gut during the KW disposal processes and the mechanism remain unclear. In the present study, the antibiotic resistome in BSFL gut within the 12 days KW disposal processes were investigated. Results showed that, ARGs abundance initially increased and subsequently decreased, the five most prevalent core ARG classes were tetracycline, aminoglycoside, cephalosporin, lincosamide and multidrug. A total of 7 MGE types were observed and the horizontal gene transfer (HGT) of ARGs was predominantly mediated by plasmids. Host microbes were mainly categorized into Proteobacteria (98.12 %) and their assemblies were mainly classified into the deterministic processes. To elucidate the driving mechanisms, the mantel test and the structural equation model (SEM) were developed. Results indicated that microbial functions (0.912, p < 0.0001) and microbial community (1.014, p = 0.036), consistently showed very significant relationships with the patterns of ARGs, which presented higher direct effects than indirect effects. Overall, this study makes an initial contribution to a more deepgoing comprehension of the gut antibiotic resistome of BSFL during KW disposal.},
}

@article {pmid39319368,
year = {2024},
author = {Pierpont, CL and Baroch, JJ and Church, MJ and Miller, SR},
title = {Idiosyncratic genome evolution of the thermophilic cyanobacterium Synechococcus at the limits of phototrophy.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae184},
pmid = {39319368},
issn = {1751-7370},
abstract = {Thermophilic microorganisms are expected to have smaller cells and genomes compared with mesophiles, a higher proportion of horizontally acquired genes, and distinct nucleotide and amino acid composition signatures. Here, we took an integrative approach to investigate these apparent correlates of thermophily for Synechococcus A/B cyanobacteria, which include the most heat-tolerant phototrophs on the planet. Phylogenomics confirmed a unique origin of different thermotolerance ecotypes, with low levels of continued gene flow between ecologically divergent but overlapping populations, which has shaped the distribution of phenotypic traits along these geothermal gradients. More thermotolerant strains do have smaller genomes, but genome reduction is associated with a decrease in community richness and metabolic diversity, rather than with cell size. Horizontal gene transfer played only a limited role during Synechococcus evolution, but, the most thermotolerant strains have acquired a Thermus tRNA modification enzyme that may stabilize translation at high temperatures. Although nucleotide base composition was not associated with thermotolerance, we found a general replacement of aspartate with glutamate, as well as a dramatic remodeling of amino acid composition at the highest temperatures that substantially differed from previous predictions. We conclude that Synechococcus A/B genome diversification largely does not conform to the standard view of temperature adaptation. In addition, carbon fixation was more thermolabile than photosynthetic oxygen evolution for the most thermotolerant strains compared with less tolerant lineages. This suggests that increased flow of reducing power generated during the light reactions to an electron sink(s) beyond carbon dioxide has emerged during temperature adaptation of these bacteria.},
}

@article {pmid39316921,
year = {2024},
author = {Liu, Z and Feng, L and Li, B and Lü, C and Sun, J and Giannakis, S},
title = {Crouching bacteria, hidden tetA genes in natural waters: Intracellular damage via double persulfate activation (UVA/Fe[2+]/PDS) effectively alleviates the spread of antibiotic resistance.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135854},
doi = {10.1016/j.jhazmat.2024.135854},
pmid = {39316921},
issn = {1873-3336},
abstract = {In this study, we elucidated the chemical and biological inactivation mechanisms of peroxydisulfate (PDS) activated by UVA and Fe[2+] (UVA/Fe[2+]/PDS) in wild-type antibiotic-resistant bacteria (ARB) isolated from a river in Inner Mongolia. Among the screened wild-type ARB, the relative abundance of unidentified Enterobacteriaceae, Stenotrophomonas, and Ralstonia was high. A ratio of 1:1 for Fe[2+] and PDS under 18 W·m[-2] UVA radiation (sunny days) completely inactivated the environmental ARB isolates. In the macro view of the inactivation process, Fe[2+] first activates PDS rapidly, and later the UVA energy accumulated starts to activate PDS; HO• then becomes the main active species at a rate-limiting step. From a micro perspective, damage to the cell wall, intracellular proteins, inactivation of antioxidant enzymes, and genetic material degradation are the inactivation series of events by UVA/Fe[2+]/PDS, contributing to the 97.8 % inactivation of ARB at the initial stage. No regrowth of sublethal ARBs was observed. The transfer of tetracycline resistance genes from ARB to lab E. coli was evaluated by horizontal gene transfer (HGT), in which no HGT occurred when ARB was eliminated by UVA/Fe[2+]/PDS. Moreover, the sulfate and iron residuals in the effluents of treated water were lower than the drinking water standards. In summary, PDS, UVA, and Fe[2+] activation effectively inactivated wild ARB with a low concentration of reagents, while inhibiting their regrowth and spread of resistance due to the contribution of intracellular inactivation pathways.},
}

@article {pmid39213152,
year = {2024},
author = {Cordero, M and Jauffred, L},
title = {Following plasmid propagation in complex bacterial communities.},
journal = {Cell reports},
volume = {43},
number = {9},
pages = {114675},
doi = {10.1016/j.celrep.2024.114675},
pmid = {39213152},
issn = {2211-1247},
mesh = {*Plasmids/genetics/metabolism ; *Gene Transfer, Horizontal ; *Bacteria/genetics/metabolism ; Conjugation, Genetic ; },
abstract = {In this issue of Cell Reports, Ma et al.[1] identify causative regulatory links between self-organization in surface-attached bacterial colonies and the rate of horizontal gene transfers (conjugations) and subsequent selection of the newly arising population of recipient bacteria (transconjugants).},
}

*Plasmids/genetics/metabolism
*Gene Transfer, Horizontal
*Bacteria/genetics/metabolism
Conjugation, Genetic

@article {pmid39316269,
year = {2024},
author = {Wang, L and Yu, L and Cai, B},
title = {Characteristics of tetracycline antibiotic resistance gene enrichment and migration in soil-plant system.},
journal = {Environmental geochemistry and health},
volume = {46},
number = {11},
pages = {427},
pmid = {39316269},
issn = {1573-2983},
support = {LH2023C088//the Natural Science Foundation of Heilongjiang Province of China/ ; LH2023C088//the Natural Science Foundation of Heilongjiang Province of China/ ; LH2023C088//the Natural Science Foundation of Heilongjiang Province of China/ ; HST2022TR002//the Scientific Research Project on Ecological Environmental Protection in Heilongjiang Province/ ; HST2022TR002//the Scientific Research Project on Ecological Environmental Protection in Heilongjiang Province/ ; HST2022TR002//the Scientific Research Project on Ecological Environmental Protection in Heilongjiang Province/ ; 2023SYSJJ15//2023 Open Fund Subjects of the Key Laboratory of Agro-ecological Safety in Hebei Province Project/ ; 2023SYSJJ15//2023 Open Fund Subjects of the Key Laboratory of Agro-ecological Safety in Hebei Province Project/ ; 2023SYSJJ15//2023 Open Fund Subjects of the Key Laboratory of Agro-ecological Safety in Hebei Province Project/ ; },
mesh = {*Soil Microbiology ; *Soil Pollutants ; *Tetracycline Resistance/genetics ; *Gene Transfer, Horizontal ; Plants/microbiology ; Humans ; Bacteria/genetics/drug effects ; Soil/chemistry ; Tetracycline/pharmacology ; },
abstract = {Tetracycline Resistance Genes (TRGs) have received widespread attention in recent years, as they are a novel environmental pollutant that can rapidly accumulate and migrate in soil plant systems through horizontal gene transfer (HGT), posing a potential threat to food safety and public health. This article systematically reviews the pollution sources, enrichment, and migration characteristics of TRGs in soil. The main sources of TRGs include livestock manure and contaminated wastewater, especially in intensive farming environments where TRGs pollution is more severe. In soil, TRGs diffuse horizontally between bacteria and migrate to plant tissues through mechanisms such as plasmid conjugation, integron mediation, and phage transduction. The migration of TRGs is not limited to the soil interior, and increasing evidence suggests that they can also enter the plant system through plant root absorption and the HGT pathway of endophytic bacteria, ultimately accumulating in plant roots, stems, leaves, fruits, and other parts. This process has a direct impact on human health, especially when TRGs are found in crops such as vegetables, which may be transmitted to the human body through the food chain. In addition, this article also deeply analyzed various factors that affect the migration of TRGs, including the residual level of tetracycline in soil, the type and concentration of microorganisms, heavy metal pollution, and the presence of new pollutants such as microplastics. These factors significantly affect the enrichment rate and migration mode of TRGs in soil. In addition, two technologies that can effectively eliminate TRGs in livestock breeding environments were introduced, providing reference for healthy agricultural production. The article concludes by summarizing the shortcomings of current research on TRGs, particularly the limited understanding of TRG migration pathways and their impact mechanisms. Future research should focus on revealing the migration mechanisms of TRGs in soil plant systems and developing effective control and governance measures to reduce the environmental transmission risks of TRGs and ensure the safety of ecosystems and human health.},
}

*Soil Microbiology
*Soil Pollutants
*Tetracycline Resistance/genetics
*Gene Transfer, Horizontal
Plants/microbiology
Humans
Bacteria/genetics/drug effects
Soil/chemistry
Tetracycline/pharmacology

@article {pmid39312572,
year = {2024},
author = {Gonçalves, C and Harrison, MC and Steenwyk, JL and Opulente, DA and LaBella, AL and Wolters, JF and Zhou, X and Shen, XX and Groenewald, M and Hittinger, CT and Rokas, A},
title = {Diverse signatures of convergent evolution in cactus-associated yeasts.},
journal = {PLoS biology},
volume = {22},
number = {9},
pages = {e3002832},
doi = {10.1371/journal.pbio.3002832},
pmid = {39312572},
issn = {1545-7885},
abstract = {Many distantly related organisms have convergently evolved traits and lifestyles that enable them to live in similar ecological environments. However, the extent of phenotypic convergence evolving through the same or distinct genetic trajectories remains an open question. Here, we leverage a comprehensive dataset of genomic and phenotypic data from 1,049 yeast species in the subphylum Saccharomycotina (Kingdom Fungi, Phylum Ascomycota) to explore signatures of convergent evolution in cactophilic yeasts, ecological specialists associated with cacti. We inferred that the ecological association of yeasts with cacti arose independently approximately 17 times. Using a machine learning-based approach, we further found that cactophily can be predicted with 76% accuracy from both functional genomic and phenotypic data. The most informative feature for predicting cactophily was thermotolerance, which we found to be likely associated with altered evolutionary rates of genes impacting the cell envelope in several cactophilic lineages. We also identified horizontal gene transfer and duplication events of plant cell wall-degrading enzymes in distantly related cactophilic clades, suggesting that putatively adaptive traits evolved independently through disparate molecular mechanisms. Notably, we found that multiple cactophilic species and their close relatives have been reported as emerging human opportunistic pathogens, suggesting that the cactophilic lifestyle-and perhaps more generally lifestyles favoring thermotolerance-might preadapt yeasts to cause human disease. This work underscores the potential of a multifaceted approach involving high-throughput genomic and phenotypic data to shed light onto ecological adaptation and highlights how convergent evolution to wild environments could facilitate the transition to human pathogenicity.},
}

@article {pmid39309771,
year = {2024},
author = {Westerström, P and Gabrielsen Ås, C and Bak Dragsted, U},
title = {Characterising virulence in a nontoxigenic non-O1/non-O139 Vibrio cholerae isolate imported from Vietnam.},
journal = {Heliyon},
volume = {10},
number = {18},
pages = {e37205},
pmid = {39309771},
issn = {2405-8440},
abstract = {Vibrio cholerae is a major human pathogen that can cause life-threatening acute diarrhea. V. cholerae are classified according to O-antigen polysaccharide outer membrane properties, where the serotypes O1 and O139 are strains that cause pandemics and epidemics while non-O1/non-O139 usually cause mild disease. The dynamic evolution of V. cholerae involves acquisition of new virulence factors through horizontal gene transfer and formerly nontoxigenic serogroups are increasingly being reported to cause severe forms of human disease. In this study we have serotyped one isolate (ST588-CPH) of imported V. cholerae from Vietnam to Denmark and performed whole genome sequencing to identify known virulence genes and furthermore studied the pattern of virulence in closely related pathogenic strains of V. cholerae. ST558-CPH was found to be a non-O1/non-O139 strain. Initial analysis from the whole genome sequencing gave a 96,6 % match to the O139-specific wbfZ gene, but in a second analysis with a higher identification threshold, the wbfZ gene was absent. We suggest a "de novo" display of a database misannotation, which explains the conflicting results. The MLST analysis revealed that the isolate belongs to the nontoxigenic non-O1/non-O139 sequence type ST558. ST558 has recently been reported as a sequence type forming a cluster of ST's that should be monitored, as it has shown to have virulence causing moderate to severe illness. Our analysis of virulence genes identified MakA, a recently discovered toxin, which seems to be generally present in both toxigenic and nontoxigenic strains.},
}

@article {pmid39236811,
year = {2024},
author = {Sun, Z and Hong, W and Xue, C and Dong, N},
title = {A comprehensive review of antibiotic resistance gene contamination in agriculture: Challenges and AI-driven solutions.},
journal = {The Science of the total environment},
volume = {953},
number = {},
pages = {175971},
doi = {10.1016/j.scitotenv.2024.175971},
pmid = {39236811},
issn = {1879-1026},
mesh = {*Agriculture/methods ; *Drug Resistance, Microbial/genetics ; Artificial Intelligence ; Anti-Bacterial Agents ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Wastewater/microbiology ; Animals ; },
abstract = {Since their discovery, the prolonged and widespread use of antibiotics in veterinary and agricultural production has led to numerous problems, particularly the emergence and spread of antibiotic-resistant bacteria (ARB). In addition, other anthropogenic factors accelerate the horizontal transfer of antibiotic resistance genes (ARGs) and amplify their impact. In agricultural environments, animals, manure, and wastewater are the vectors of ARGs that facilitate their spread to the environment and humans via animal products, water, and other environmental pathways. Therefore, this review comprehensively analyzed the current status, removal methods, and future directions of ARGs on farms. This article 1) investigates the origins of ARGs on farms, the pathways and mechanisms of their spread to surrounding environments, and various strategies to mitigate their spread; 2) determines the multiple factors influencing the abundance of ARGs on farms, the pathways through which ARGs spread from farms to the environment, and the effects and mechanisms of non-antibiotic factors on the spread of ARGs; 3) explores methods for controlling ARGs in farm wastes; and 4) provides a comprehensive summary and integration of research across various fields, proposing that in modern smart farms, emerging technologies can be integrated through artificial intelligence to control or even eliminate ARGs. Moreover, challenges and future research directions for controlling ARGs on farms are suggested.},
}

*Agriculture/methods
*Drug Resistance, Microbial/genetics
Artificial Intelligence
Anti-Bacterial Agents
Gene Transfer, Horizontal
Drug Resistance, Bacterial/genetics
Wastewater/microbiology
Animals

@article {pmid39308980,
year = {2024},
author = {Mendoza, H and Lamb, EA and Thomas, J and Tavares, DG and Schroeder, LA and Müller, C and Agrawal, N and Schirawski, J and Perlin, MH},
title = {Comparative mitogenomic analysis of Sporisorium reilianum f. sp. zeae suggests recombination events during its evolutionary history.},
journal = {Frontiers in physiology},
volume = {15},
number = {},
pages = {1264359},
pmid = {39308980},
issn = {1664-042X},
abstract = {INTRODUCTION: Modern understanding of the concept of genetic diversity must include the study of both nuclear and organellar DNA, which differ greatly in terms of their structure, organization, gene content and distribution. This study comprises an analysis of the genetic diversity of the smut fungus Sporisorium reilianum f. sp. zeae from a mitochondrial perspective.

METHODS: Whole-genome sequencing data was generated from biological samples of S. reilianum collected from different geographical regions. Multiple sequence alignment and gene synteny analysis were performed to further characterize genetic diversity in the context of mitogenomic polymorphisms.

RESULTS: Mitochondria of strains collected in China contained unique sequences. The largest unique sequence stretch encompassed a portion of cox1, a mitochondrial gene encoding one of the subunits that make up complex IV of the mitochondrial electron transport chain. This unique sequence had high percent identity to the mitogenome of the related species Sporisorium scitamineum and Ustilago bromivora.

DISCUSSION: The results of this study hint at potential horizontal gene transfer or mitochondrial genome recombination events during the evolutionary history of basidiomycetes. Additionally, the distinct polymorphic region detected in the Chinese mitogenome provides the ideal foundation to develop a diagnostic method to discern between mitotypes and enhance knowledge on the genetic diversity of this organism.},
}

@article {pmid39305601,
year = {2024},
author = {Wang, F and Hu, Z and Wang, W and Wang, J and Xiao, Y and Shi, J and Wang, C and Mai, W and Li, G and An, T},
title = {Selective enrichment of high-risk antibiotic resistance genes and priority pathogens in freshwater plastisphere: Unique role of biodegradable microplastics.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135901},
doi = {10.1016/j.jhazmat.2024.135901},
pmid = {39305601},
issn = {1873-3336},
abstract = {Microplastics (MPs) has been concerned as emerging vectors for spreading antibiotic resistance and pathogenicity in aquatic environments, but the role of biodegradable MPs remains largely unknown. Herein, field in-situ incubation method combined with metagenomic sequencing were employed to reveal the dispersal characteristics of microbial community, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factors (VFs) enriched by MPs biofilms. Results showed that planktonic microbes were more prone to enrich on biodegradable MPs (i.e., polyhydroxyalkanoate and polylactic acid) than non-biodegradable MPs (i.e., polystyrene, polypropylene and polyethylene). Distinctive microbial communities were assembled on biodegradable MPs, and the abundances of ARGs, MGEs, and VFs on biofilms of biodegradable MPs were much higher than that of non-biodegradable MPs. Notably, network analysis showed that the biodegradable MPs selectively enriched pathogens carrying ARGs, VFs and MGEs concurrently, suggesting a strong potential risks of co-spreading antibiotic resistance and pathogenicity through horizontal gene transfer. According to WHO priority list of Antibiotic Resistant Pathogens (ARPs) and ARGs health risk assessment framework, the highest abundances of Priority 1 ARPs and Rank I risk ARGs were found on polylactic acid and polyhydroxyalkanoate, respectively. These findings elucidate the unique and critical role of biodegradable MPs for selective enrichment of high-risk ARGs and priority pathogens in freshwater environments.},
}

@article {pmid39304531,
year = {2024},
author = {Umar, M and Merlin, TS and Puthiyedathu, ST},
title = {Genomic insights into symbiosis and host adaptation of sponge-associated novel bacterium, Rossellomorea orangium sp. nov.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnae074},
pmid = {39304531},
issn = {1574-6968},
abstract = {Sponge-associated microorganisms play vital roles in marine sponge ecology. This study presents a genomic investigation of Rossellomorea sp. MCCB 382, isolated from Stelletta sp., reveals insights into its adaptations and symbiotic roles. Phylogenomic study and Overall Genomic Relatedness Index (OGRI) classify MCCB 382 as a novel species, Rossellomorea orangium sp. nov. The genome encodes numerous carbohydrate metabolism enzymes (CAZymes), likely aiding nutrient cycling in the sponge host. Unique eukaryotic-like protein domains hint at potential mechanisms of symbiosis. Defense mechanisms include CRISPR, restriction modification systems, DNA phosphorothioation, toxin-antitoxin systems, and heavy metal and multidrug resistance genes, indicating adaptation to challenging marine environments. Unlike obligate mutualists, MCCB 382 shows no genome reduction. Furthermore, the presence of mobile genetic elements, horizontal gene transfer, and prophages suggest genetic versatility, implying flexible metabolic potential and capacity for rapid adaptation and symbiosis shifts. MCCB 382 possesses six biosynthetic gene clusters for secondary metabolites, including both type II and III polyketide synthases (PKS), terpenes, (NRPS), NRPS-independent-siderophore, and lassopeptide. Further genome mining using BiGScape revealed four distinct gene cluster families, T2PKS, NRPS-independent-siderophore, lasso peptide, and terpene, presenting opportunities for novel compound elucidation. Our study reveals a symbiotic lifestyle of MCCB 382 with the host sponge, highlighting symbiont factors that aid in establishing and sustaining this relationship. This is the pioneering genomic characterisation of a novel Rossellomorea sp. within the sponge Stelletta sp. holobiont.},
}

@article {pmid39304387,
year = {2024},
author = {Vos, M and Buckling, A and Kuijper, B and Eyre-Walker, A and Bontemps, C and Leblond, P and Dimitriu, T},
title = {Why do mobile genetic elements transfer DNA of their hosts?.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2024.07.008},
pmid = {39304387},
issn = {0168-9525},
abstract = {The prokaryote world is replete with mobile genetic elements (MGEs) - self-replicating entities that can move within and between their hosts. Many MGEs not only transfer their own DNA to new hosts but also transfer host DNA located elsewhere on the chromosome in the process. This could potentially lead to indirect benefits to the host when the resulting increase in chromosomal variation results in more efficient natural selection. We review the diverse ways in which MGEs promote the transfer of host DNA and explore the benefits and costs to MGEs and hosts. In many cases, MGE-mediated transfer of host DNA might not be selected for because of a sex function, but evidence of MGE domestication suggests that there may be host benefits of MGE-mediated sex.},
}

@article {pmid39304140,
year = {2024},
author = {Qi, Q and Ghaly, TM and Rajabal, V and Russell, DH and Gillings, MR and Tetu, SG},
title = {Vegetable phylloplane microbiomes harbour class 1 integrons in novel bacterial hosts and drive the spread of chlorite resistance.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {176348},
doi = {10.1016/j.scitotenv.2024.176348},
pmid = {39304140},
issn = {1879-1026},
abstract = {Bacterial hosts in vegetable phylloplanes carry mobile genetic elements such as plasmids and transposons that are associated with integrons. These mobile genetic elements and their cargo genes can enter human microbiomes via consumption of fresh agricultural produce, including uncooked vegetables. This presents a risk of acquiring antimicrobial resistance genes from uncooked vegetables. To better understand horizontal gene transfer of class 1 integrons in these compartments, we applied epicPCR, a single-cell fusion-PCR surveillance technique, to link the class 1 integron integrase (intI1) gene with phylogenetic markers of their bacterial hosts. Ready-to-eat salads carried class 1 integrons from the phyla Bacteroidota and Pseudomonadota, including four novel genera that were previously not known to be associated with intI1. We whole-genome sequenced Pseudomonas and Erwinia hosts of pre-clinical class 1 integrons that are embedded in Tn402-like transposons. The proximal gene cassette in these integrons was identified as a chlorite dismutase gene cassette, which we showed experimentally to confer chlorite resistance. Chlorine-derived compounds such as acidified sodium chlorite and chloride dioxide are used to disinfectant raw vegetables in food processing facilities, suggesting selection for chlorite resistance in phylloplane integrons. The spread of integrons conferring chlorite resistance has the potential to exacerbate integron-mediated antimicrobial resistance (AMR) via co-selection of chlorite resistance and AMR, thus highlighting the importance of monitoring chlorite residues in agricultural produce. These results demonstrate the strength of combining epicPCR and culture-based isolation approaches for identifying hosts and dissecting the molecular ecology of class 1 integrons.},
}

@article {pmid39303860,
year = {2024},
author = {Yong, Y and Hu, S and Zhong, M and Wen, Y and Zhou, Y and Ma, R and Jiang, X and Zhang, Q},
title = {Horizontal gene transfer from chloroplast to mitochondria of seagrasses in the yellow-Bohai seas.},
journal = {Genomics},
volume = {116},
number = {5},
pages = {110940},
doi = {10.1016/j.ygeno.2024.110940},
pmid = {39303860},
issn = {1089-8646},
abstract = {Seagrasses are ideal for studying plant adaptation to marine environments. In this study, the mitochondrial (mt) and chloroplast (cp) genomes of Ruppia sinensis were sequenced. The results showed an extensive gene loss in seagrasses, including a complete loss of cp-rpl19 genes in Zosteraceae, most cp-ndh genes in Hydrocharitaceae, and mt-rpl and mt-rps genes in all seagrasses, except for the mt-rpl16 gene in Phyllospadix iwatensis. Notably, most ribosomal protein genes were lost in the mt and cp genomes. The deleted cp genes were not transferred to the mt genomes through horizontal gene transfer. Additionally, a significant DNA transfer between seagrass organelles was found, with the mt genomes of Zostera containing numerous sequences from the cp genome. Rearrangement analyses revealed an unreported inversion of the cp genome in R. sinensis. Moreover, four positively selected genes (atp8, nad5, atp4, and ccmFn) and five variable regions (matR, atp4, atp8, rps7, and ccmFn) were identified.},
}

@article {pmid39303615,
year = {2024},
author = {Li, X and Cai, S and Xu, M},
title = {Nanoscale zero-valent iron alleviated horizontal transfer of antibiotic resistance genes in soil: The important role of extracellular polymeric substances.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135902},
doi = {10.1016/j.jhazmat.2024.135902},
pmid = {39303615},
issn = {1873-3336},
abstract = {Extracellular polymeric substances (EPS) are tightly related to the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs), but often neglected in soil. In this study, nanoscale zero-valent iron (nZVI) was utilized for attenuation of ARGs in contaminated soil, with an emphasis on its effects on EPS secretion and HGT. Results showed during soil microbe cultivation exposed to tetracycline, more EPS was secreted and significant increase of tet was observed due to facilitated HGT. Notably, copies of EPS-tet accounted for 71.39 % of the total tet, implying vital effects of EPS on ARGs proliferation. When co-exposed to nZVI, EPS secretion was decreased by 38.36-71.46 %, for that nZVI could alleviate the microbial oxidative stress exerted by tetracycline resulting in downregulation of genes expression related to the c-di-GMP signaling system. Meanwhile, the abundance of EPS-tet was obviously reduced from 7.04 to 5.12-6.47 log unit, directly causing decrease of total tet from 7.19 to 5.68-6.69 log unit. For the reduced tet, it was mainly due to decreased EPS secretion induced by nZVI resulting in inhibition of HGT especially transformation of the EPS-tet. This work gives an inspiration for attenuation of ARGs dissemination in soil through an EPS regulation strategy.},
}

@article {pmid39301187,
year = {2024},
author = {Xu, M and Ke, H and Zang, Y and Gou, H and Yang, D and Shi, K and Zhang, K and Li, Y and Jiang, Z and Chu, P and Zhai, S and Li, C},
title = {Outer membrane vesicles secreted from Actinobacillus pleuropneumoniae isolate disseminating the floR resistance gene to Enterobacteriaceae.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1467847},
pmid = {39301187},
issn = {1664-302X},
abstract = {Actinobacillus pleuropneumoniae, a significant respiratory pig pathogen, is causing substantial losses in the global swine industry. The resistance spectrum of A. pleuropneumoniae is expanding, and multidrug resistance is a severe issue. Horizontal gene transfer (HGT) plays a crucial role in the development of the bacterial genome by facilitating the dissemination of resistance determinants. However, the horizontal transfer of resistance genes via A. pleuropneumoniae-derived outer membrane vesicles (OMVs) has not been previously reported. In this study, we used Illumina NovaSeq and PacBio SequeI sequencing platforms to determine the whole genome sequence of A. pleuropneumoniae GD2107, a multidrug-resistant (MDR) isolate from China. We detected a plasmid in the isolate named pGD2107-1; the plasmid was 5,027 bp in size with 7 putative open reading frames (ORF) and included the floR resistance genes. The carriage of resistance genes in A. pleuropneumoniae OMVs was identified using a polymerase chain reaction (PCR) assay, and then we thoroughly evaluated the influence of OMVs on the horizontal transfer of drug-resistant plasmids. The transfer of the plasmid to recipient bacteria via OMVs was confirmed by PCR. In growth competition experiments, all recipients carrying the pGD2107-1 plasmid exhibited a fitness cost compared to the corresponding original recipients. This study revealed that OMVs could mediate interspecific horizontal transfer of the resistance plasmid pGD2107-1 into Escherichia coli recipient strains and significantly enhance the resistance of the transformants. In summary, A. pleuropneumoniae-OMVs play the pivotal role of vectors for dissemination of the floR gene spread and may contribute to more antimicrobial resistance gene transfer in other Enterobacteriaceae.},
}

@article {pmid39299886,
year = {2024},
author = {Urquhart, A and Vogan, AA and Gluck-Thaler, E},
title = {Starships: a new frontier for fungal biology.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2024.08.006},
pmid = {39299886},
issn = {0168-9525},
abstract = {Transposable elements (TEs) are semiautonomous genetic entities that proliferate in genomes. We recently discovered the Starships, a previously hidden superfamily of giant TEs found in a diverse subphylum of filamentous fungi, the Pezizomycotina. Starships are unlike other eukaryotic TEs because they have evolved mechanisms for both mobilizing entire genes, including those encoding conditionally beneficial phenotypes, and for horizontally transferring between individuals. We argue that Starships have unrivaled capacity to engage their fungal hosts as genetic parasites and mutualists, revealing unexplored terrain for investigating the ecoevolutionary dynamics of TE-eukaryote interactions. We build on existing models of fungal genome evolution by conceptualizing Starships as a distinct genomic compartment whose dynamics profoundly shape fungal biology.},
}

@article {pmid39296779,
year = {2024},
author = {Thomy, J and Sanchez, F and Prioux, C and Yau, S and Xu, Y and Mak, J and Sun, R and Piganeau, G and Yung, CCM},
title = {Unveiling Prasinovirus diversity and host specificity through targeted enrichment in the South China Sea.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae109},
pmid = {39296779},
issn = {2730-6151},
abstract = {Unicellular green picophytoplankton from the Mamiellales order are pervasive in marine ecosystems and susceptible to infections by prasinoviruses, large double-stranded DNA viruses within the Nucleocytoviricota phylum. We developed a double-stranded DNA virus enrichment and shotgun sequencing method, and successfully assembled 80 prasinovirus genomes from 43 samples in the South China Sea. Our research delivered the first direct estimation of 94% accuracy in correlating genome similarity to host range. Stirkingly, our analyses uncovered unexpected host-switching across diverse algal lineages, challenging the existing paradigms of host-virus co-speciation and revealing the dynamic nature of viral evolution. We also detected six instances of horizontal gene transfer between prasinoviruses and their hosts, including a novel alternative oxidase. Additionally, diversifying selection on a major capsid protein suggests an ongoing co-evolutionary arms race. These insights not only expand our understanding of prasinovirus genomic diversity but also highlight the intricate evolutionary mechanisms driving their ecological success and shaping broader virus-host interactions in marine environments.},
}

@article {pmid39255666,
year = {2024},
author = {Li, Y and Zheng, Q and Lu, Y and Qiao, Y and Guo, H and Ma, Q and Zhou, J and Li, H and Wang, T},
title = {Water temperature disturbance alters the conjugate transfer of antibiotic resistance genes via affecting ROS content and intercellular aggregation.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135762},
doi = {10.1016/j.jhazmat.2024.135762},
pmid = {39255666},
issn = {1873-3336},
mesh = {*Reactive Oxygen Species/metabolism ; *Temperature ; *Plasmids/genetics ; Drug Resistance, Microbial/genetics ; Water/chemistry ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Gene Transfer, Horizontal ; Escherichia coli/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; Cell Membrane Permeability/drug effects ; Water Microbiology ; },
abstract = {Spread of antibiotic resistance genes (ARGs) in aquatic ecosystems poses a significant global challenge to public health. The potential effects of water temperature perturbation induced by specific water environment changes on ARGs transmission are still unclear. The conjugate transfer of plasmid-mediated ARGs under water temperature perturbation was investigated in this study. The conjugate transfer frequency (CTF) was only 7.16 × 10[-7] at a constant water temperature of 5 °C, and it reached 2.18 × 10[-5] at 30 °C. Interestingly, compared to the constant 5 °C, the water temperature perturbations (cooling and warming models between 5-30 °C) significantly promoted the CTF. Intracellular reactive oxygen species was a dominant factor, which not only directly affected the CTF of ARGs, but also functioned indirectly via influencing the cell membrane permeability and cell adhesion. Compared to the constant 5 °C, water temperature perturbations significantly elevated the gene expression associated with intercellular contact, cell membrane permeability, oxidative stress responses, and energy driven force for CTF. Furthermore, based on the mathematical model predictions, the stabilization times of acquiring plasmid maintenance were shortened to 184 h and 190 h under cooling and warming model, respectively, thus the water temperature perturbations promoted the ARGs transmission in natural conditions compared with the constant low temperature conditions.},
}

*Reactive Oxygen Species/metabolism
*Temperature
*Plasmids/genetics
Drug Resistance, Microbial/genetics
Water/chemistry
Anti-Bacterial Agents/pharmacology
Genes, Bacterial
Gene Transfer, Horizontal
Escherichia coli/genetics/drug effects
Drug Resistance, Bacterial/genetics
Cell Membrane Permeability/drug effects
Water Microbiology

@article {pmid39191006,
year = {2024},
author = {Zhao, H and Sun, Y and Cao, X and Waigi, MG and Liu, J},
title = {Effects and mechanisms of chlormequat on horizontal transfer of antibiotic resistance genes through plasmid-mediated conjugation in agro-ecosystems.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135639},
doi = {10.1016/j.jhazmat.2024.135639},
pmid = {39191006},
issn = {1873-3336},
mesh = {*Plasmids/genetics ; *Oryza/microbiology/growth & development/drug effects/genetics ; *Gene Transfer, Horizontal ; *Conjugation, Genetic ; *Escherichia coli/genetics/drug effects ; *Pseudomonas/genetics/drug effects/metabolism ; Pseudomonas putida/genetics/drug effects/metabolism ; Genes, Bacterial/drug effects ; Anti-Bacterial Agents/pharmacology ; Agriculture ; Drug Resistance, Bacterial/genetics/drug effects ; Drug Resistance, Microbial/genetics ; },
abstract = {Chlormequat (CCC) is widely used in agricultural production to increase the crop yield. However, the effects of CCC on transfer of ARGs in agricultural system are still unclear. In this study, using E.coli DH5α (carrying RP4 plasmid with Amp[R], Tet[R], Kan[R]) as the donor bacterium, E.coli HB101, endophytic Pseudomonas sp. Ph6 or rhizosphere Pseudomonas putida KT2440 as the recipient strain, three conjugative systems were designed to investigate the effects of CCC on ARG transfer. Meanwhile, hydroponics experiments were designed to study the ARG spread in the rice-nutrient solution system after CCC application. The results showed that CCC significantly promoted the RP4 conjugation by expanding cell membrane permeability and improving the relative transcription levels of trfAp, trbBp, traA and traL genes in RP4. Furthermore, the conjugation frequency between E. coli and Pseudomonas was much higher than that between E. coli cells. Compared with spraying foliage with 2500 mg·L[-1] of CCC, soaking seeds with 250 mg·L[-1] of CCC was more beneficial to the colonization of ARB in rice, and also increased the abundance of ARGs in rice cultivation system. These results remind that the use of CCC in agricultural production might promote the ARG transmission in agro-ecosystems; however, foliage spraying with 2500 mg·L[-1] of CCC could control its spread.},
}

*Plasmids/genetics
*Oryza/microbiology/growth & development/drug effects/genetics
*Gene Transfer, Horizontal
*Conjugation, Genetic
*Escherichia coli/genetics/drug effects
*Pseudomonas/genetics/drug effects/metabolism
Pseudomonas putida/genetics/drug effects/metabolism
Genes, Bacterial/drug effects
Anti-Bacterial Agents/pharmacology
Agriculture
Drug Resistance, Bacterial/genetics/drug effects
Drug Resistance, Microbial/genetics

@article {pmid39295911,
year = {2023},
author = {Panwar, S and Kumari, S and Verma, J and Bakshi, S and Narendrakumar, L and Paul, D and Das, B},
title = {Toxin-linked mobile genetic elements in major enteric bacterial pathogens.},
journal = {Gut microbiome (Cambridge, England)},
volume = {4},
number = {},
pages = {e5},
pmid = {39295911},
issn = {2632-2897},
abstract = {One of the fascinating outcomes of human microbiome studies adopting multi-omics technology is its ability to decipher millions of microbial encoded functions in the most complex and crowded microbial ecosystem, including the human gastrointestinal (GI) tract without cultivating the microbes. It is well established that several functions that modulate the human metabolism, nutrient assimilation, immunity, infections, disease severity and therapeutic efficacy of drugs are mostly of microbial origins. In addition, these microbial functions are dynamic and can disseminate between microbial taxa residing in the same ecosystem or other microbial ecosystems through horizontal gene transfer. For clinicians and researchers alike, understanding the toxins, virulence factors and drug resistance traits encoded by the microbes associated with the human body is of utmost importance. Nevertheless, when such traits are genetically linked with mobile genetic elements (MGEs) that make them transmissible, it creates an additional burden to public health. This review mainly focuses on the functions of gut commensals and the dynamics and crosstalk between commensal and pathogenic bacteria in the gut. Also, the review summarises the plethora of MGEs linked with virulence genes present in the genomes of various enteric bacterial pathogens, which are transmissible among other pathogens and commensals.},
}

@article {pmid39294579,
year = {2024},
author = {Shabbir, MAB and Shamim, M and Tahir, AH and Sattar, A and Qin, W and Ahmad, W and Ahmad, W and Khan, FA and Ashraf, MA},
title = {Potential of ZnO nanoparticles for multi-drug resistant Escherichia coli having CRISPR-Cas from poultry market in Lahore.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {355},
pmid = {39294579},
issn = {1471-2180},
mesh = {*Zinc Oxide/pharmacology ; Animals ; *Escherichia coli/genetics/drug effects ; *Drug Resistance, Multiple, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *CRISPR-Cas Systems ; *Microbial Sensitivity Tests ; *Poultry/microbiology ; *Escherichia coli Infections/microbiology/veterinary ; *Poultry Diseases/microbiology ; Nanoparticles ; },
abstract = {BACKGROUND AND OBJECTIVES: Apart from known factors such as irrational use of antibiotics and horizontal gene transfer, it is now reported that clustered regularly interspaced short palindromic repeats (CRISPR) are also associated with increased antimicrobial resistance. Hence, it is critical to explore alternatives to antibiotics to control economic losses. Therefore, the present study aimed to determine not only the association of CRISPR-Cas system with antibiotic resistance but also the potential of Zinc Oxide nanoparticles (ZnO-NPs) for avian pathogenic Escherichia coli (APEC) isolated from poultry market Lahore.

MATERIALS AND METHODS: Samples (n = 100) were collected from live bird markets of Lahore, and isolates were confirmed as Escherichia coli (E. coli) using the Remel One fast kit, and APEC was identified using PCR. The antibiotic resistance pattern in APEC was determined using the minimum inhibitory concentration (MIC), followed by genotypic confirmation of antibiotic-resistant genes using the PCR. The CRISPR-Cas system was also identified in multidrug-resistant (MDR) isolates, and its association with antibiotics was determined using qRT-PCR. The potential of ZnO-NPs was evaluated for multidrug-resistant (MDR) isolates by MIC.

RESULTS: All isolates of APEC were resistant to nalidixic acid, whereas 95% were resistant to chloramphenicol and 89% were resistant to streptomycin. Nineteen MDR APEC were found in the present study and the CRISPR-Cas system was detected in all of these MDR isolates. In addition, an increased expression of CRISPR-related genes was observed in the standard strain and MDR isolates of APEC. ZnO-NPs inhibited the growth of resistant isolates.

CONCLUSIONS: The findings showed the presence of the CRISPR-Cas system in MDR strains of APEC, along with the potential of ZnO-NPs for a possible solution to proceed. This highlights the importance of regulating antimicrobial resistance in poultry to reduce potential health consequences.},
}

*Zinc Oxide/pharmacology
Animals
*Escherichia coli/genetics/drug effects
*Drug Resistance, Multiple, Bacterial/genetics
*Anti-Bacterial Agents/pharmacology
*CRISPR-Cas Systems
*Microbial Sensitivity Tests
*Poultry/microbiology
*Escherichia coli Infections/microbiology/veterinary
*Poultry Diseases/microbiology
Nanoparticles

@article {pmid39293438,
year = {2024},
author = {Zhang, ZJ and Cole, CG and Coyne, MJ and Lin, H and Dylla, N and Smith, RC and Pappas, TE and Townson, SA and Laliwala, N and Waligurski, E and Ramaswamy, R and Woodson, C and Burgo, V and Little, JC and Moran, D and Rose, A and McMillin, M and McSpadden, E and Sundararajan, A and Sidebottom, AM and Pamer, EG and Comstock, LE},
title = {Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species- and strain-level diversity and evolution.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2024.08.016},
pmid = {39293438},
issn = {1934-6069},
abstract = {Species of the Bacteroidales order are among the most abundant and stable bacterial members of the human gut microbiome, with diverse impacts on human health. We cultured and sequenced the genomes of 408 Bacteroidales isolates from healthy human donors representing nine genera and 35 species and performed comparative genomic, gene-specific, metabolomic, and horizontal gene transfer analyses. Families, genera, and species could be grouped based on many distinctive features. We also observed extensive DNA transfer between diverse families, allowing for shared traits and strain evolution. Inter- and intra-species diversity is also apparent in the metabolomic profiling studies. This highly characterized and diverse Bacteroidales culture collection with strain-resolved genomic and metabolomic analyses represents a valuable resource to facilitate informed selection of strains for microbiome reconstitution.},
}

@article {pmid39288183,
year = {2024},
author = {Tuffet, R and Carvalho, G and Godeux, AS and Mazzamurro, F and Rocha, EPC and Laaberki, MH and Venner, S and Charpentier, X},
title = {Manipulation of natural transformation by AbaR-type islands promotes fixation of antibiotic resistance in Acinetobacter baumannii.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {39},
pages = {e2409843121},
doi = {10.1073/pnas.2409843121},
pmid = {39288183},
issn = {1091-6490},
support = {ANR-20-CE12-0004//Agence Nationale de la Recherche (ANR)/ ; ANR-11-LABX-0048//Agence Nationale de la Recherche (ANR)/ ; PhD grant//VetAgro Sup (VetAgro-Sup)/ ; 80|PRIME//Centre National de la Recherche Scientifique (CNRS)/ ; },
mesh = {*Acinetobacter baumannii/genetics/drug effects ; *Genomic Islands ; Drug Resistance, Multiple, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Transformation, Bacterial ; Polymorphism, Single Nucleotide ; Bacterial Proteins/genetics/metabolism ; },
abstract = {The opportunistic pathogen Acinetobacter baumannii, carries variants of A. baumannii resistance islands (AbaR)-type genomic islands conferring multidrug resistance. Their pervasiveness in the species has remained enigmatic. The dissemination of AbaRs is intricately linked to their horizontal transfer via natural transformation, a process through which bacteria can import and recombine exogenous DNA, effecting allelic recombination, genetic acquisition, and deletion. In experimental populations of the closely related pathogenic Acinetobacter nosocomialis, we quantified the rates at which these natural transformation events occur between individuals. When integrated into a model of population dynamics, they lead to the swift removal of AbaRs from the population, contrasting with the high prevalence of AbaRs in genomes. Yet, genomic analyses show that nearly all AbaRs specifically disrupt comM, a gene encoding a helicase critical for natural transformation. We found that such disruption impedes gene acquisition, and deletion, while moderately impacting acquisition of single nucleotide polymorphism. A mathematical evolutionary model demonstrates that AbaRs inserted into comM gain a selective advantage over AbaRs inserted in sites that do not inhibit or completely inhibit transformation, in line with the genomic observations. The persistence of AbaRs can be ascribed to their integration into a specific gene, diminishing the likelihood of their removal from the bacterial genome. This integration preserves the acquisition and elimination of alleles, enabling the host bacterium-and thus its AbaR-to adapt to unpredictable environments and persist over the long term. This work underscores how manipulation of natural transformation by mobile genetic elements can drive the prevalence of multidrug resistance.},
}

*Acinetobacter baumannii/genetics/drug effects
*Genomic Islands
Drug Resistance, Multiple, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Gene Transfer, Horizontal
Transformation, Bacterial
Polymorphism, Single Nucleotide
Bacterial Proteins/genetics/metabolism

@article {pmid39287446,
year = {2024},
author = {Contarin, R and Drapeau, A and François, P and Madec, J-Y and Haenni, M and Dordet-Frisoni, E},
title = {The interplay between mobilome and resistome in Staphylococcus aureus.},
journal = {mBio},
volume = {},
number = {},
pages = {e0242824},
doi = {10.1128/mbio.02428-24},
pmid = {39287446},
issn = {2150-7511},
abstract = {Antibiotic resistance genes (ARGs) in Staphylococcus aureus can disseminate vertically through successful clones, but also horizontally through the transfer of genes conveyed by mobile genetic elements (MGEs). Even though underexplored, MGE/ARG associations in S. aureus favor the emergence of multidrug-resistant clones, which are challenging therapeutic success in both human and animal health. This study investigated the interplay between the mobilome and the resistome of more than 10,000 S. aureus genomes from human and animal origin. The analysis revealed a remarkable diversity of MGEs and ARGs, with plasmids and transposons being the main carriers of ARGs. Numerous MGE/ARG associations were identified, suggesting that MGEs play a critical role in the dissemination of resistance. A high degree of similarity was observed in MGE/ARG associations between human and animal isolates, highlighting the potential for unrestricted spread of ARGs between hosts. Our results showed that in parallel to clonal expansion, MGEs and their associated ARGs can spread across different strain types sequence types (STs), favoring the evolution of these clones and their adaptation in selective environments. The high variability of MGE/ARG associations within individual STs and their spread across several STs highlight the crucial role of MGEs in shaping the S. aureus resistome. Overall, this study provides valuable insights into the complex interplay between MGEs and ARGs in S. aureus, emphasizing the need to elucidate the mechanisms governing the epidemic success of MGEs, particularly those implicated in ARG transfer.IMPORTANCEThe research presented in this article highlights the importance of understanding the interactions between mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs) carried by Staphylococcus aureus, a versatile bacterium that can be both a harmless commensal and a dangerous pathogen for humans and animals. S. aureus has a great capacity to acquire and disseminate ARGs, enabling efficient adaption to various environmental or clinical conditions. By analyzing a large data set of S. aureus genomes, we highlighted the substantial role of MGEs, particularly plasmids and transposons, in disseminating ARGs within and between S. aureus populations, bypassing host barriers. Given that multidrug-resistant S. aureus strains are classified as a high-priority pathogen by global health organizations, this knowledge is crucial for understanding the complex dynamics of transmission of antibiotic resistance in this species.},
}

@article {pmid39287432,
year = {2024},
author = {Nwokocha, GC and Ghosh, A and Grove, A},
title = {Regulation of bacterial virulence genes by PecS family transcription factors.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0030224},
doi = {10.1128/jb.00302-24},
pmid = {39287432},
issn = {1098-5530},
abstract = {Bacterial plant pathogens adjust their gene expression programs in response to environmental signals and host-derived compounds. This ensures that virulence genes or genes encoding proteins, which promote bacterial fitness in a host environment, are expressed only when needed. Such regulation is in the purview of transcription factors, many of which belong to the ubiquitous multiple antibiotic resistance regulator (MarR) protein family. PecS proteins constitute a subset of this large protein family. PecS has likely been distributed by horizontal gene transfer, along with the divergently encoded efflux pump PecM, suggesting its integration into existing gene regulatory networks. Here, we discuss the roles of PecS in the regulation of genes associated with virulence and fitness of bacterial plant pathogens. A comparison of phenotypes and differential gene expression associated with the disruption of pecS shows that functional consequences of PecS integration into existing transcriptional networks are highly variable, resulting in distinct PecS regulons. Although PecS universally binds to the pecS-pecM intergenic region to repress the expression of both genes, binding modes differ. A particularly relaxed sequence preference appears to apply for Dickeya dadantii PecS, perhaps to optimize its integration as a global regulator and regulate genes ancestral to the acquisition of pecS-pecM. Even inducing ligands for PecS are not universally conserved. It appears that PecS function has been optimized to match the unique regulatory needs of individual bacterial species and that its roles must be appreciated in the context of the regulatory networks into which it was recruited.},
}

@article {pmid39287139,
year = {2024},
author = {Pu, L and Shamir, R},
title = {4CAC: 4-class classifier of metagenome contigs using machine learning and assembly graphs.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae799},
pmid = {39287139},
issn = {1362-4962},
support = {1339/18//Israel Science Foundation/ ; //Edmond J. Safra Center for Bioinformatics at Tel-Aviv University/ ; //Planning & Budgeting Committee/ ; //Council for Higher Education/ ; },
abstract = {Microbial communities usually harbor a mix of bacteria, archaea, plasmids, viruses and microeukaryotes. Within these communities, viruses, plasmids, and microeukaryotes coexist in relatively low abundance, yet they engage in intricate interactions with bacteria. Moreover, viruses and plasmids, as mobile genetic elements, play important roles in horizontal gene transfer and the development of antibiotic resistance within microbial populations. However, due to the difficulty of identifying viruses, plasmids, and microeukaryotes in microbial communities, our understanding of these minor classes lags behind that of bacteria and archaea. Recently, several classifiers have been developed to separate one or more minor classes from bacteria and archaea in metagenome assemblies. However, these classifiers often overlook the issue of class imbalance, leading to low precision in identifying the minor classes. Here, we developed a classifier called 4CAC that is able to identify viruses, plasmids, microeukaryotes, and prokaryotes simultaneously from metagenome assemblies. 4CAC generates an initial four-way classification using several sequence length-adjusted XGBoost models and further improves the classification using the assembly graph. Evaluation on simulated and real metagenome datasets demonstrates that 4CAC substantially outperforms existing classifiers and combinations thereof on short reads. On long reads, it also shows an advantage unless the abundance of the minor classes is very low. 4CAC runs 1-2 orders of magnitude faster than the other classifiers. The 4CAC software is available at https://github.com/Shamir-Lab/4CAC.},
}

@article {pmid39189727,
year = {2024},
author = {Xu, Y and Liu, B and Jiao, N and Liu, J and Chen, F},
title = {New evidence supports the prophage origin of RcGTA.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {9},
pages = {e0043424},
doi = {10.1128/aem.00434-24},
pmid = {39189727},
issn = {1098-5336},
support = {2020ZLYS04//Department of Science and Technology of Shandong Province ()/ ; 2018YFA0605800//Ministry of Science and Technology of the People's Republic of China (MOST)/ ; },
mesh = {*Prophages/genetics ; Rhodobacter capsulatus/virology/genetics ; Gene Transfer, Horizontal ; Genome, Viral ; Phylogeny ; Evolution, Molecular ; Methylobacterium/virology/genetics ; },
abstract = {Gene transfer agents (GTAs) are phage-like entities that package and transfer random host genome fragments between prokaryotes. RcGTA, produced by Rhodobacter capsulatus, is hypothesized to originate from a prophage ancestor. Most of the evidence supporting this hypothesis came from the finding of RcGTA-like genes in phages. More than 75% of the RcGTA genes have a phage homolog. However, only a few RcGTA homologs have been identified in a (pro)phage genome, leaving the hypothesis that GTAs evolved from prophages through gene loss with only weak evidence. We herein report the discovery of an inducible prophage (vB_MseS-P1) from a Mesorhizobium sediminum strain that contains the largest number (12) of RcGTA homologs found in a phage genome to date. We also identified three putative prophages and two prophage remnants harboring 12-14 RcGTA homologs in a Methylobacterium nodulans strain. The protein remote homology detection also revealed more RcGTA homologs from other phages than we previously thought. Moreover, the head-tail gene architecture of these newly discovered prophage-related elements closely resembles that of RcGTA. Furthermore, vB_MseS-P1 virions have structural proteins similar to RcGTA particles. Close phylogenetic relationships between certain prophage genes and RcGTA-like genes in Alphaproteobacteria further support the shared ancestry between RcGTA and prophages. Our findings provide new relatively direct evidence of the origin of RcGTA from a prophage progenitor.IMPORTANCEGTAs are important genetic elements in certain groups of bacteria and contribute to the genetic diversification, evolution, and ecological adaptation of bacteria. RcGTA, a common type of GTA, is known to package and transfer random fragments of the bacterial genome to recipient cells. However, the origin of RcGTA is still elusive. It has been hypothesized that RcGTA evolved from a prophage ancestor through gene loss. However, the few RcGTA homologs identified in a (pro)phage genome leave the hypothesis lacking direct evidence. This study uncovers the presence of a large number of RcGTA homologs in an inducible prophage and several putative prophages. The similar head-tail gene architecture and structural protein compositions of these newly discovered prophage-related elements and RcGTA further demonstrate an unprecedentedly observed close evolutionary relationship between prophages and RcGTA. Together, our findings provide more direct evidence supporting the origin of RcGTA from prophage.},
}

*Prophages/genetics
Rhodobacter capsulatus/virology/genetics
Gene Transfer, Horizontal
Genome, Viral
Phylogeny
Evolution, Molecular
Methylobacterium/virology/genetics

@article {pmid39158311,
year = {2024},
author = {Liu, H and Zheng, L and Fan, H and Pang, J},
title = {Genomic analysis of antibiotic resistance genes and mobile genetic elements in eight strains of nontyphoid Salmonella.},
journal = {mSystems},
volume = {9},
number = {9},
pages = {e0058624},
pmid = {39158311},
issn = {2379-5077},
support = {2022-JSYZ-13//The Second Phase of Jinshan Medical Personnel Training Program/ ; KFQM-27//Rehabilitation Medicine Talent Leading Program/ ; },
mesh = {Humans ; *Salmonella/genetics/drug effects/isolation & purification ; *Interspersed Repetitive Sequences/genetics ; *Salmonella Infections/microbiology/epidemiology ; Anti-Bacterial Agents/pharmacology ; China/epidemiology ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Plasmids/genetics ; Genomics ; Feces/microbiology ; },
abstract = {UNLABELLED: Nontyphoidal Salmonella (NTS) is the main etiological agent of human nontyphoidal salmonellosis. The aim of this study was to analyze the epidemiological characteristics and horizontal transfer mechanisms of antimicrobial resistance (AMR) genes from eight strains of NTS detected in Zhenjiang City, Jiangsu Province, China. Fecal samples from outpatients with food-borne diarrhea were collected in 2022. The NTS isolates were identified, and their susceptibility was tested with the Vitek 2 Compact system. The genomes of the NTS isolates were sequenced with the Illumina NovaSeq platform and Oxford Nanopore Technologies platform. The AMR genes and mobile genetic elements (MGEs) were predicted with the relevant open access resources. Eight strains of NTS were isolated from 153 specimens, and Salmonella Typhimurium ST19 was the most prevalent serotype. The AMR gene with the highest detection rate was AAC(6')-Iaa (10.5%) followed by TEM-1 (7.9%), sul2 (6.6%), and tet(A) (5.3%). Eleven MGEs carrying 34 AMR genes were identified on the chromosomes of 3 of the 8 NTS, including 3 resistance islands, 6 composite transposons (Tns), and 2 integrons. Eighteen plasmids carrying 40 AMR genes were detected in the 8 NTS strains, including 6 mobilizable plasmids, 3 conjugative plasmids, and 9 nontransferable plasmids, 7 of which carried 10 composite Tns and 3 integrons. This study provided a theoretical basis, from a genetic perspective, for the prevention and control of NTS resistance in Zhenjiang City.

IMPORTANCE: Human nontyphoidal salmonellosis is one of the common causes of bacterial food-borne illnesses, with significant social and economic impacts, especially those caused by invasive multidrug-resistant nontyphoidal Salmonella, which entails high morbidity and mortality. Antimicrobial resistance is mainly mediated by drug resistance genes, and mobile genetic elements play key roles in the capture, accumulation, and dissemination of antimicrobial resistance genes. Therefore, it is necessary to study the epidemiological characteristics and horizontal transfer mechanisms of antimicrobial resistance genes of nontyphoidal Salmonella to prevent the spread of multidrug-resistant nontyphoidal Salmonella.},
}

Humans
*Salmonella/genetics/drug effects/isolation & purification
*Interspersed Repetitive Sequences/genetics
*Salmonella Infections/microbiology/epidemiology
Anti-Bacterial Agents/pharmacology
China/epidemiology
Drug Resistance, Bacterial/genetics
Microbial Sensitivity Tests
Gene Transfer, Horizontal
Genome, Bacterial/genetics
Plasmids/genetics
Genomics
Feces/microbiology

@article {pmid39282498,
year = {2024},
author = {Jiang, C and Yang, J and Xiao, G and Xiao, N and Hu, J and Yang, Y and Sun, Z and Li, Y},
title = {The ISVsa3-ORF2-abh-tet(X4) circular intermediate-mediated transmission of tigecycline resistance in Escherichia coli isolates from duck farms.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1444031},
pmid = {39282498},
issn = {2235-2988},
mesh = {*Ducks/microbiology ; *Tigecycline/pharmacology ; Animals ; *Escherichia coli/genetics/drug effects/isolation & purification ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; China ; *Plasmids/genetics ; *Farms ; *Escherichia coli Infections/veterinary/microbiology ; *Whole Genome Sequencing ; Feces/microbiology ; Multilocus Sequence Typing ; Drug Resistance, Multiple, Bacterial/genetics ; Genotype ; Poultry Diseases/microbiology ; Escherichia coli Proteins/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; },
abstract = {Tigecycline is a last-resort drug used to treat serious infections caused by multidrug-resistant bacteria. tet(X4) is a recently discovered plasmid-mediated tigecycline resistance gene that confers high-level resistance to tigecycline and other tetracyclines. Since the first discovery of tet(X4) in 2019, it has spread rapidly worldwide, and as a consequence, tigecycline has become increasingly ineffective in the clinical treatment of multidrug-resistant infections. In this study, we identified and analyzed tet(X4)-positive Escherichia coli isolates from duck farms in Hunan Province, China. In total, 976 samples were collected from nine duck farms. Antimicrobial susceptibility testing and whole-genome sequencing (WGS) were performed to establish the phenotypes and genotypes of tet(X4)-positive isolates. In addition, the genomic characteristics and transferability of tet(X4) were determined based on bioinformatics analysis and conjugation. We accordingly detected an E. coli strain harboring tet(X4) and seven other resistance genes in duck feces. Multi-locus sequence typing analysis revealed that this isolate belonged to a new clone, and subsequent genetic analysis indicated that tet(X4) was carried in a 4608-bp circular intermediate, flanked by ISVsa3-ORF2-abh elements. Moreover, it exhibited transferability to E. coli C600 with a frequency of 10[-5]. The detection of tet(X4)-harboring E, coli strains on duck farms enhances our understanding of tigecycline resistance dynamics. The transferable nature of the circular intermediate of tet(X4) contributing to the spread of tigecycline resistance genes poses a substantial threat to healthcare. Consequently, vigilant monitoring and proactive measures are necessary to prevent their spread.},
}

*Ducks/microbiology
*Tigecycline/pharmacology
Animals
*Escherichia coli/genetics/drug effects/isolation & purification
*Anti-Bacterial Agents/pharmacology
*Microbial Sensitivity Tests
China
*Plasmids/genetics
*Farms
*Escherichia coli Infections/veterinary/microbiology
*Whole Genome Sequencing
Feces/microbiology
Multilocus Sequence Typing
Drug Resistance, Multiple, Bacterial/genetics
Genotype
Poultry Diseases/microbiology
Escherichia coli Proteins/genetics
Gene Transfer, Horizontal
Drug Resistance, Bacterial/genetics

@article {pmid39278585,
year = {2024},
author = {Yang, B and Sun, J and Zhu, S and Wang, Z and Liu, Y},
title = {Exposure to bisphenol compounds accelerates the conjugative transfer of antibiotic resistance plasmid.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120002},
doi = {10.1016/j.envres.2024.120002},
pmid = {39278585},
issn = {1096-0953},
abstract = {Antimicrobial resistance poses the most formidable challenge to public health, with plasmid-mediated horizontal gene transfer playing a pivotal role in its global spread. Bisphenol compounds (BPs), a group of environmental contaminants with endocrine-disrupting properties, are extensively used in various plastic products and can be transmitted to food. However, the impact of BPs on the plasmid-mediated horizontal transfer of antibiotic resistance genes (ARGs) has not yet been elucidated. Herein, we demonstrate that BPs could promote the conjugative transfer frequency of RP4-7 and clinically multidrug-resistant plasmids. Furthermore, the promoting effect of BPs on the plasmid transfer was also confirmed in a murine model. Microbial diversity analysis of transconjugants indicated an increase in α diversity in the BPAF-treated group, along with the declined richness of some beneficial bacteria and elevated richness of Faecalibaculum rodentium, which might serve as an intermediate repository for resistance plasmids. The underlying mechanisms driving the enhanced conjugative transfer upon BPAF treatment include exacerbated oxidative stress, disrupted membrane homeostasis, augmented energy metabolism, and the increased expression of conjugation-related genes. Collectively, our findings highlight the potential risk associated with the exacerbated dissemination of AMR both in vitro and in vivo caused by BPs exposure.},
}

@article {pmid39277355,
year = {2024},
author = {Gao, Y and Guo, Y and Wang, L and Guo, L and Shi, B and Zhu, L and Wang, J and Kim, YM and Wang, J},
title = {Tebuconazole exacerbates co-occurrence and horizontal transfer of antibiotic resistance genes.},
journal = {Pesticide biochemistry and physiology},
volume = {204},
number = {},
pages = {106026},
doi = {10.1016/j.pestbp.2024.106026},
pmid = {39277355},
issn = {1095-9939},
mesh = {*Triazoles/toxicity/pharmacology ; *Gene Transfer, Horizontal ; *Fungicides, Industrial/toxicity/pharmacology ; *Biofilms/drug effects ; Drug Resistance, Microbial/genetics ; Plasmids/genetics ; Genes, Bacterial ; },
abstract = {As one of the most widely used pesticides in the global fungicide market, tebuconazole has become heavily embedded in soil along with antibiotic resistance genes (ARGs). However, it remains unclear whether the selective pressure produced by tebuconazole affects ARGs and their horizontal transfer. In this experiment, we simulated a tebuconazole-contaminated soil ecosystem and observed changes in the abundance of ARGs and mobile genetic element (MGEs) due to tebuconazole exposure. We also established a plasmid RP4-mediated conjugative transfer system to investigate in depth the impact of tebuconazole on the horizontal transfer of ARGs and its mechanism of action. The results showed that under tebuconazole treatment at concentrations ranging from 0 to 10 mg/L, there was a gradual increase in the frequency of plasmid conjugative transfer, peaking at 10 mg/L which was 7.93 times higher than that of the control group, significantly promoting horizontal transfer of ARGs. Further analysis revealed that the conjugative transfer system under tebuconazole stress exhibited strong ability to form biofilm, and the conjugative transfer frequency ratio of biofilm to planktonic bacteria varied with the growth cycle of biofilm. Additionally, scanning electron microscopy and flow cytometry demonstrated increased cell membrane permeability in both donor and recipient bacteria under tebuconazole stress, accompanied by upregulation of ompA gene expression controlling cell membrane permeability. Furthermore, enzyme activity assays indicated significant increases in CAT, SOD activity, and GSH content in recipient bacteria under tebuconazole stress. Moreover, expression levels of transmembrane transporter gene trfAp as well as genes involved in oxidative stress and SOS response were found to be correlated with the frequency of plasmid conjugative transfer.},
}

*Triazoles/toxicity/pharmacology
*Gene Transfer, Horizontal
*Fungicides, Industrial/toxicity/pharmacology
*Biofilms/drug effects
Drug Resistance, Microbial/genetics
Plasmids/genetics
Genes, Bacterial

@article {pmid39276831,
year = {2024},
author = {Li, C and Zhang, Y and Shi, W and Peng, Y and Han, Y and Jiang, S and Dong, X and Zhang, R},
title = {Viral diversity within marine biofilms and interactions with corrosive microbes.},
journal = {Environmental research},
volume = {},
number = {},
pages = {119991},
doi = {10.1016/j.envres.2024.119991},
pmid = {39276831},
issn = {1096-0953},
abstract = {In marine environments, a wide variety of microbes like bacteria, and archaea influence on the corrosion of materials. Viruses are widely distributed in biofilms among these microbes and may affect the corrosion process through interactions with key corrosive prokaryotes. However, understanding of the viral communities within biofilms and their interactions with corrosive microbes remains is limited. To improve this knowledge gap, 53 metagenomes were utilized to investigate the diversity of viruses within biofilms on 8 different materials and their interactions with corrosive microbes. Notably, the viruses within biofilms predominantly belonged to Caudoviricetes, and phylogenetic analysis of Caudoviricetes and protein-sharing networks with other environments revealed the presence of numerous novel viral clades in biofilms. The virus‒host linkages revealed a close association between viruses and corrosive microbes in biofilms. This mean that viruses may modulate host corrosion-related metabolism through auxiliary metabolic genes. It was observed that the virus could enhance host resistance to metals and antibiotics via horizontal gene transfer. Interestingly, viruses could protect themselves from host antiviral systems through anti-defense systems. This study illustrates the diversity of viruses within biofilms formed on materials and the intricate interactions between viruses and corrosive microbes, showing the potential roles of viruses in corrosive biofilms.},
}

@article {pmid39270765,
year = {2024},
author = {Bjornson, S and Verbruggen, H and Upham, NS and Steenwyk, JL},
title = {Reticulate evolution: Detection and utility in the phylogenomics era.},
journal = {Molecular phylogenetics and evolution},
volume = {201},
number = {},
pages = {108197},
doi = {10.1016/j.ympev.2024.108197},
pmid = {39270765},
issn = {1095-9513},
abstract = {Phylogenomics has enriched our understanding that the Tree of Life can have network-like or reticulate structures among some taxa and genes. Two non-vertical modes of evolution - hybridization/introgression and horizontal gene transfer - deviate from a strictly bifurcating tree model, causing non-treelike patterns. However, these reticulate processes can produce similar patterns to incomplete lineage sorting or recombination, potentially leading to ambiguity. Here, we present a brief overview of a phylogenomic workflow for inferring organismal histories and compare methods for distinguishing modes of reticulate evolution. We discuss how the timing of coalescent events can help disentangle introgression from incomplete lineage sorting and how horizontal gene transfer events can help determine the relative timing of speciation events. In doing so, we identify pitfalls of certain methods and discuss how to extend their utility across the Tree of Life. Workflows, methods, and future directions discussed herein underscore the need to embrace reticulate evolutionary patterns for understanding the timing and rates of evolutionary events, providing a clearer view of life's history.},
}

@article {pmid39270668,
year = {2024},
author = {Aserse, AA and Nimusiima, J and Tumuhairwe, JB and Yli-Halla, M and Lindström, K},
title = {Phylogenetic diversity of Rhizobium species recovered from nodules of common beans (Phaseolus vulgaris L.) in fields in Uganda: R. phaseoli, R. etli, and R. hidalgonense.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae120},
pmid = {39270668},
issn = {1574-6941},
abstract = {A total of 75 bacterial isolates were obtained from nodules of beans cultivated across 10 sites in six agro-ecological zones in Uganda. Using recA gene sequence analysis, 66 isolates were identified as members of the genus Rhizobium, while nine were related to Agrobacterium species. In the recA gene tree, most Rhizobium strains were classified into five recognized species. Phylogenetic analysis based on six concatenated sequences (recA-rpoB-dnaK-glnII-gyrB-atpD) placed 32 representative strains into five distinct Rhizobium species, consistent with the species groups observed in the recA gene tree: R. phaseoli, R. etli, R. hidalgonense, R. ecuadorense, and R. sophoriradicis, with the first three being the predominant. The rhizobial strains grouped into three nodC subclades within the symbiovar phaseoli clade, encompassing strains from distinct phylogenetic groups. This pattern reflects the conservation of symbiotic genes, likely acquired through horizontal gene transfer among diverse rhizobial species. The 32 representative strains formed symbiotic relationships with host beans, while the Agrobacterium strains did not form nodules and lacked symbiotic genes. Multivariate analysis revealed that species distribution was influenced by the environmental factors of the sampling sites, emphasizing the need to consider these factors in future effectiveness studies to identify effective nitrogen-fixing strains for specific locations.},
}

@article {pmid39269515,
year = {2024},
author = {Amara, Y and Mahjoubi, M and Souissi, Y and Cherif, H and Naili, I and ElHidri, D and Kadidi, I and Mosbah, A and Masmoudi, AS and Cherif, A},
title = {Tapping into haloalkaliphilic bacteria for sustainable agriculture in treated wastewater: insights into genomic fitness and environmental adaptation.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {1},
pages = {1},
pmid = {39269515},
issn = {1572-9699},
support = {No 688320//European Union's Horizon 2020, MADFORWATER/ ; No 688320//European Union's Horizon 2020, MADFORWATER/ ; No 688320//European Union's Horizon 2020, MADFORWATER/ ; No 688320//European Union's Horizon 2020, MADFORWATER/ ; },
mesh = {*Wastewater/microbiology ; *Phylogeny ; *Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; Salinity ; Rhizosphere ; Bacteria/genetics/classification/isolation & purification/metabolism ; Agriculture/methods ; Tunisia ; Adaptation, Physiological ; Olea/microbiology ; Genome, Bacterial ; },
abstract = {The increasing salinity and alkalinity of soils pose a global challenge, particularly in arid regions such as Tunisia, where about 50% of lands are sensitive to soil salinization. Anthropogenic activities, including the use of treated wastewater (TWW) for irrigation, exacerbate these issues. Haloalkaliphilic bacteria, adapted to TWW conditions and exhibiting plant-growth promotion (PGP) and biocontrol traits, could offer solutions. In this study, 24 haloalkaliphilic bacterial strains were isolated from rhizosphere sample of olive tree irrigated with TWW for more than 20 years. The bacterial identification using 16S rRNA gene sequencing showed that the haloalkaliphilic isolates, capable of thriving in high salinity and alkaline pH, were primarily affiliated to Bacillota (Oceanobacillus and Staphylococcus). Notably, these strains exhibited biofertilization and enzyme production under both normal and saline conditions. Traits such as phosphate solubilization, and the production of exopolysaccharide, siderophore, ammonia, and hydrogen cyanide were observed. The strains also demonstrated enzymatic activities, including protease, amylase, and esterase. Four selected haloalkaliphilic PGPR strains displayed antifungal activity against Alternaria terricola, with three showing tolerances to heavy metals and pesticides. The strain Oceanobacillus picturea M4W.A2 was selected for genome sequencing. Phylogenomic analyses indicated that the extreme environmental conditions probably influenced the development of specific adaptations in M4W.A2 strain, differentiating it from other Oceanobacillus picturae strains. The presence of the key genes associated with plant growth promotion, osmotic and oxidative stress tolerance, antibiotic and heavy metals resistance hinted the functional capabilities might help the strain M4W.A2 to thrive in TWW-irrigated soils. By demonstrating this connection, we aim to improve our understanding of genomic fitness to stressed environments. Moreover, the identification of gene duplication and horizontal gene transfer events through mobile genetic elements allow the comprehension of these adaptation dynamics. This study reveals that haloalkaliphilc bacteria from TWW-irrigated rhizosphere exhibit plant-growth promotion and biocontrol traits, with genomic adaptations enabling their survival in high salinity and alkaline conditions, offering potential solutions for soil salinization issues.},
}

*Wastewater/microbiology
*Phylogeny
*Soil Microbiology
*RNA, Ribosomal, 16S/genetics
Salinity
Rhizosphere
Bacteria/genetics/classification/isolation & purification/metabolism
Agriculture/methods
Tunisia
Adaptation, Physiological
Olea/microbiology
Genome, Bacterial

@article {pmid39268957,
year = {2024},
author = {Yang, P and Li, J and Lv, M and He, P and Song, G and Shan, B and Yang, X},
title = {Molecular Epidemiology and Horizontal Transfer Mechanism of optrA-Carrying Linezolid-Resistant Enterococcus faecalis.},
journal = {Polish journal of microbiology},
volume = {73},
number = {3},
pages = {349-362},
pmid = {39268957},
issn = {2544-4646},
mesh = {*Enterococcus faecalis/genetics/drug effects ; *Linezolid/pharmacology ; *Gene Transfer, Horizontal ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Gram-Positive Bacterial Infections/microbiology/epidemiology ; China/epidemiology ; Bacterial Proteins/genetics/metabolism ; Molecular Epidemiology ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Drug Resistance, Multiple, Bacterial/genetics ; Whole Genome Sequencing ; Conjugation, Genetic ; },
abstract = {The aim of this work was to provide a theoretical and scientific basis for the treatment, prevention, and control of clinical drug-resistant bacterial infections by studying the molecular epidemiology and horizontal transfer mechanism of optrA-carrying linezolid-resistant Enterococcus faecalis strains (LREfs) that were clinically isolated in a tertiary hospital in Kunming, China. Non-repetitive LREfs retained in a tertiary A hospital in Kunming, China. The strains were identified by Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The transferability and horizontal transfer mechanism of optrA gene were analyzed using polymerase chain reaction (PCR), whole-genome sequencing (WGS), and conjugation experiments. A total of 39 LREfs strains were collected, and all of them were multi-drug resistant. There were 30 LREfs strains (76.9%) carrying the optrA gene, The cfr, poxtA genes and mutations in the 23S rRNA gene were not detected. The conjugation experiments showed that only three of 10 randomly selected optrA-carrying LREfs were successfully conjugated with JH2-2. Further analysis of one successfully conjugated strain revealed that the optrA gene, located in the donor bacterium, formed the IS1216E-erm(A)-optrA-fexA-IS1216E transferable fragment under the mediation of the mobile genetic element (MGE) IS1216E, which was then transferred to the recipient bacterium via horizontal plasmid transfer. Carrying the optrA gene is the primary resistance mechanism of LREfs strains. The optrA gene could carry the erm(A) and fexA genes to co-transfer among E. faecalis. MGEs such as insertion sequence IS1216E play an important role in the horizontal transfer of the optrA gene.},
}

*Enterococcus faecalis/genetics/drug effects
*Linezolid/pharmacology
*Gene Transfer, Horizontal
*Anti-Bacterial Agents/pharmacology
Humans
*Gram-Positive Bacterial Infections/microbiology/epidemiology
China/epidemiology
Bacterial Proteins/genetics/metabolism
Molecular Epidemiology
Drug Resistance, Bacterial/genetics
Microbial Sensitivity Tests
Drug Resistance, Multiple, Bacterial/genetics
Whole Genome Sequencing
Conjugation, Genetic

@article {pmid39268528,
year = {2024},
author = {Riva, F and Dechesne, A and Eckert, EM and Riva, V and Borin, S and Mapelli, F and Smets, BF and Crotti, E},
title = {Conjugal plasmid transfer in the plant rhizosphere in the One Health context.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1457854},
pmid = {39268528},
issn = {1664-302X},
abstract = {INTRODUCTION: Horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) is one of the primary routes of antimicrobial resistance (AMR) dissemination. In the One Health context, tracking the spread of mobile genetic elements (MGEs) carrying ARGs in agri-food ecosystems is pivotal in understanding AMR diffusion and estimating potential risks for human health. So far, little attention has been devoted to plant niches; hence, this study aimed to evaluate the conjugal transfer of ARGs to the bacterial community associated with the plant rhizosphere, a hotspot for microbial abundance and activity in the soil. We simulated a source of AMR determinants that could enter the food chain via plants through irrigation.

METHODS: Among the bacterial strains isolated from treated wastewater, the strain Klebsiella variicola EEF15 was selected as an ARG donor because of the relevance of Enterobacteriaceae in the AMR context and the One Health framework. The strain ability to recolonize lettuce, chosen as a model for vegetables that were consumed raw, was assessed by a rifampicin resistant mutant. K. variicola EEF15 was genetically manipulated to track the conjugal transfer of the broad host range plasmid pKJK5 containing a fluorescent marker gene to the natural rhizosphere microbiome obtained from lettuce plants. Transconjugants were sorted by fluorescent protein expression and identified through 16S rRNA gene amplicon sequencing.

RESULTS AND DISCUSSION: K. variicola EEF15 was able to colonize the lettuce rhizosphere and inhabit its leaf endosphere 7 days past bacterial administration. Fluorescence stereomicroscopy revealed plasmid transfer at a frequency of 10[-3]; cell sorting allowed the selection of the transconjugants. The conjugation rates and the strain's ability to colonize the plant rhizosphere and leaf endosphere make strain EEF15::lacI[q]-pLpp-mCherry-gm[R] with pKJK5::Plac::gfp an interesting candidate to study ARG spread in the agri-food ecosystem. Future studies taking advantage of additional environmental donor strains could provide a comprehensive snapshot of AMR spread in the One Health context.},
}

@article {pmid39266980,
year = {2024},
author = {Wu, H and Dongchen, W and Li, Y and Brown, SE and Wei, S and Lin, C and Mao, Z and Liu, Z},
title = {Mitogenomes comparison of 3 species of Asparagus L shedding light on their functions due to domestication and adaptative evolution.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {857},
pmid = {39266980},
issn = {1471-2164},
support = {202305A0350012//Yunnan Basic Research Program/ ; 202305A0350012//Yunnan Basic Research Program/ ; 202305A0350012//Yunnan Basic Research Program/ ; 202305A0350012//Yunnan Basic Research Program/ ; 202305A0350012//Yunnan Basic Research Program/ ; 32360089//National Natural Science Foundation of China/ ; 32360089//National Natural Science Foundation of China/ ; 202101BD070001-027//Yunnan Agricultural joint Fund-key project/ ; },
mesh = {*Asparagus Plant/genetics ; *Genome, Mitochondrial ; *Phylogeny ; *Domestication ; *Evolution, Molecular ; RNA Editing ; Gene Transfer, Horizontal ; Genome, Chloroplast ; },
abstract = {BACKGROUND: Asparagus L., widely distributed in the old world is a genus under Asparagaceae, Asparagales. The species of the genus were mainly used as vegetables, traditional medicines as well as ornamental plants. However, the evolution and functions of mitochondrial (Mt) genomes (mitogenomes) remains largely unknown. In this study, the typical herbal medicine A. taliensis and ornamental plant A. setaceus were used to assemble and annotate the mitogenomes, and the resulting mitogenomes were further compared with published mitogenome of A. officinalis for the analysis of their functions in the context of domestication and adaptative evolution.

RESULTS: The mitochondrial genomes of both A. taliensis and A. setaceus were assembled as complete circular ones. The phylogenetic trees based on conserved protein-coding genes of Mt genomes and whole chloroplast (Cp) genomes showed that, the phylogenetic relationship of the sampled 13 species of Asparagus L. were not exactly consistent. The collinear analyses between the nuclear (Nu) and Mt genomes confirmed the existence of mutual horizontal genes transfers (HGTs) between Nu and Mt genomes within these species. Based on RNAseq data, the Mt RNA editing were predicted and atp1 and ccmB RNA editing of A. taliensis were further confirmed by DNA sequencing. Simultaneously homologous search found 5 Nu coding gene families including pentatricopeptide-repeats (PPRs) involved in Mt RNA editing. Finally, the Mt genome variations, gene expressions and mutual HGTs between Nu and Mt were detected with correlation to the growth and developmental phenotypes respectively. The results suggest that, both Mt and Nu genomes co-evolved and maintained the Mt organella replication and energy production through TCA and oxidative phosphorylation .

CONCLUSION: The assembled and annotated complete mitogenomes of both A. taliensis and A. setaceus provide valuable information for their phylogeny and concerted action of Nu and Mt genomes to maintain the energy production system of Asparagus L. in the context of domestication and adaptation to environmental niches.},
}

*Asparagus Plant/genetics
*Genome, Mitochondrial
*Phylogeny
*Domestication
*Evolution, Molecular
RNA Editing
Gene Transfer, Horizontal
Genome, Chloroplast

@article {pmid39266188,
year = {2024},
author = {Ali, N and Vora, C and Mathuria, A and Kataria, N and Mani, I},
title = {Advances in CRISPR-Cas systems for gut microbiome.},
journal = {Progress in molecular biology and translational science},
volume = {208},
number = {},
pages = {59-81},
doi = {10.1016/bs.pmbts.2024.07.008},
pmid = {39266188},
issn = {1878-0814},
mesh = {*CRISPR-Cas Systems/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; Animals ; Gene Editing ; Probiotics/therapeutic use ; },
abstract = {CRISPR-Cas technology has revolutionized microbiome research by enabling precise genetic manipulation of microbial communities. This review explores its diverse applications in gut microbiome studies, probiotic development, microbiome diagnostics, pathogen targeting, and microbial community engineering. Engineered bacteriophages and conjugative probiotics exemplify CRISPR-Cas's capability for targeted bacterial manipulation, offering promising strategies against antibiotic-resistant infections and other gut-related disorders. CRISPR-Cas systems also enhance probiotic efficacy by improving stress tolerance and colonization in the gastrointestinal tract. CRISPR-based techniques in diagnostics enable early intervention by enabling fast and sensitive pathogen identification. Furthermore, CRISPR-mediated gene editing allows tailored modification of microbial populations, mitigating risks associated with horizontal gene transfer and enhancing environmental and health outcomes. Despite its transformative potential, ethical and regulatory challenges loom large, demanding robust frameworks to guide its responsible application. This chapter highlights CRISPR-Cas's pivotal role in advancing microbiome research toward personalized medicine and microbial therapeutics while emphasizing the imperative of balanced ethical deliberations and comprehensive regulatory oversight.},
}

*CRISPR-Cas Systems/genetics
Humans
*Gastrointestinal Microbiome/genetics
Animals
Gene Editing
Probiotics/therapeutic use

@article {pmid39138294,
year = {2024},
author = {York, A},
title = {Targeting the spread of antimicrobial resistance plasmids.},
journal = {Nature reviews. Microbiology},
volume = {22},
number = {10},
pages = {595},
pmid = {39138294},
issn = {1740-1534},
mesh = {*Plasmids/genetics ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Bacteria/drug effects/genetics ; Gene Transfer, Horizontal ; },
}

*Plasmids/genetics
Humans
*Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Bacteria/drug effects/genetics
Gene Transfer, Horizontal

@article {pmid39103039,
year = {2024},
author = {Zhang, H and Xu, L and Hou, X and Li, Y and Niu, L and Zhang, J and Wang, X},
title = {Ketoprofen promotes the conjugative transfer of antibiotic resistance among antibiotic resistant bacteria in natural aqueous environments.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {360},
number = {},
pages = {124676},
doi = {10.1016/j.envpol.2024.124676},
pmid = {39103039},
issn = {1873-6424},
mesh = {*Ketoprofen/pharmacology ; *Gene Transfer, Horizontal ; Conjugation, Genetic ; Escherichia coli/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Water Pollutants, Chemical/toxicity ; Anti-Inflammatory Agents, Non-Steroidal/pharmacology ; },
abstract = {The emergence and spread of antibiotic resistance in the environment pose a serious threat to global public health. It is acknowledged that non-antibiotic stresses, including disinfectants, pharmaceuticals and organic pollutants, play a crucial role in horizontal transmission of antibiotic resistance genes (ARGs). Despite the widespread presence of non-steroidal anti-inflammatory drugs (NSAIDs), notably in surface water, their contributions to the transfer of ARGs have not been systematically explored. Furthermore, previous studies have primarily concentrated on model strains to investigate whether contaminants promote the conjugative transfer of ARGs, leaving the mechanisms of ARG transmission among antibiotic resistant bacteria in natural aqueous environments under the selective pressures of non-antibiotic contaminants remains unclear. In this study, the Escherichia coli (E. coli) K12 carrying RP4 plasmid was used as the donor strain, indigenous strain Aeromonas veronii containing rifampicin resistance genes in Taihu Lake, and E. coli HB101 were used as receptor strains to establish inter-genus and intra-genus conjugative transfer systems, examining the conjugative transfer frequency under the stress of ketoprofen. The results indicated that ketoprofen accelerated the environmental spread of ARGs through several mechanisms. Ketoprofen promoted cell-to-cell contact by increasing cell surface hydrophobicity and reducing cell surface charge, thereby mitigating cell-to-cell repulsion. Furthermore, ketoprofen induced increased levels of reactive oxygen species (ROS) production, activated the DNA damage-induced response (SOS), and enhanced cell membrane permeability, facilitating ARG transmission in intra-genus and inter-genus systems. The upregulation of outer membrane proteins, oxidative stress, SOS response, mating pair formation (Mpf) system, and DNA transfer and replication (Dtr) system related genes, as well as the inhibition of global regulatory genes, all contributed to higher transfer efficiency under ketoprofen treatment. These findings served as an early warning for a comprehensive assessment of the roles of NSAIDs in the spread of antibiotic resistance in natural aqueous environments.},
}

*Ketoprofen/pharmacology
*Gene Transfer, Horizontal
Conjugation, Genetic
Escherichia coli/genetics/drug effects
Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial/genetics
Drug Resistance, Microbial/genetics
Water Pollutants, Chemical/toxicity
Anti-Inflammatory Agents, Non-Steroidal/pharmacology

@article {pmid39266183,
year = {2024},
author = {Mathuria, A and Vora, C and Ali, N and Mani, I},
title = {Advances in CRISPR-Cas systems for human bacterial disease.},
journal = {Progress in molecular biology and translational science},
volume = {208},
number = {},
pages = {19-41},
doi = {10.1016/bs.pmbts.2024.07.013},
pmid = {39266183},
issn = {1878-0814},
mesh = {*CRISPR-Cas Systems/genetics ; Humans ; *Bacterial Infections/microbiology/genetics ; Gene Editing ; Bacteria/genetics ; },
abstract = {Prokaryotic adaptive immune systems called CRISPR-Cas systems have transformed genome editing by allowing for precise genetic alterations through targeted DNA cleavage. This system comprises CRISPR-associated genes and repeat-spacer arrays, which generate RNA molecules that guide the cleavage of invading genetic material. CRISPR-Cas is classified into Class 1 (multi-subunit effectors) and Class 2 (single multi-domain effectors). Its applications span combating antimicrobial resistance (AMR), targeting antibiotic resistance genes (ARGs), resensitizing bacteria to antibiotics, and preventing horizontal gene transfer (HGT). CRISPR-Cas3, for example, effectively degrades plasmids carrying resistance genes, providing a precise method to disarm bacteria. In the context of ESKAPE pathogens, CRISPR technology can resensitize bacteria to antibiotics by targeting specific resistance genes. Furthermore, in tuberculosis (TB) research, CRISPR-based tools enhance diagnostic accuracy and facilitate precise genetic modifications for studying Mycobacterium tuberculosis. CRISPR-based diagnostics, leveraging Cas endonucleases' collateral cleavage activity, offer highly sensitive pathogen detection. These advancements underscore CRISPR's transformative potential in addressing AMR and enhancing infectious disease management.},
}

*CRISPR-Cas Systems/genetics
Humans
*Bacterial Infections/microbiology/genetics
Gene Editing
Bacteria/genetics

@article {pmid39264185,
year = {2024},
author = {Magar, S and Kolte, V and Sharma, G and Govindarajan, S},
title = {Exploring pangenomic diversity and CRISPR-Cas evasion potential in jumbo phages: a comparative genomics study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0420023},
doi = {10.1128/spectrum.04200-23},
pmid = {39264185},
issn = {2165-0497},
abstract = {UNLABELLED: Jumbo phages are characterized by their remarkably large-sized genome and unique life cycles. Jumbo phages belonging to Chimalliviridae family protect the replicating phage DNA from host immune systems like CRISPR-Cas and restriction-modification system through a phage nucleus structure. Several recent studies have provided new insights into jumbo phage infection biology, but the pan-genome diversity of jumbo phages and their relationship with CRISPR-Cas targeting beyond Chimalliviridae are not well understood. In this study, we used pan-genome analysis to identify orthologous gene families shared among 331 jumbo phages with complete genomes. We show that jumbo phages lack a universally conserved set of core genes but identified seven "soft-core genes" conserved in over 50% of these phages. These genes primarily govern DNA-related activities, such as replication, repair, or nucleotide synthesis. Jumbo phages exhibit a wide array of accessory and unique genes, underscoring their genetic diversity. Phylogenetic analyses of the soft-core genes revealed frequent horizontal gene transfer events between jumbo phages, non-jumbo phages, and occasionally even giant eukaryotic viruses, indicating a polyphyletic evolutionary nature. We categorized jumbo phages into 11 major viral clusters (VCs) spanning 130 sub-clusters, with the majority being multi-genus jumbo phage clusters. Moreover, through the analysis of hallmark genes related to CRISPR-Cas targeting, we predict that many jumbo phages can evade host immune systems using both known and yet-to-be-identified mechanisms. In summary, our study enhances our understanding of jumbo phages, shedding light on their pan-genome diversity and remarkable genome protection capabilities.

IMPORTANCE: Jumbo phages are large bacterial viruses known for more than 50 years. However, only in recent years, a significant number of complete genome sequences of jumbo phages have become available. In this study, we employed comparative genomic approaches to investigate the genomic diversity and genome protection capabilities of the 331 jumbo phages. Our findings revealed that jumbo phages exhibit high genetic diversity, with only a few genes being relatively conserved across jumbo phages. Interestingly, our data suggest that jumbo phages employ yet-to-be-identified strategies to protect their DNA from the host immune system, such as CRISPR-Cas.},
}

@article {pmid39258299,
year = {2024},
author = {Song, W and Li, C and Lu, Y and Shen, D and Jia, Y and Huo, Y and Piao, W and Jin, H},
title = {Chlomito: a novel tool for precise elimination of organelle genome contamination from nuclear genome assembly.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1430443},
pmid = {39258299},
issn = {1664-462X},
abstract = {INTRODUCTION: Accurate reference genomes are fundamental to understanding biological evolution, biodiversity, hereditary phenomena and diseases. However, many assembled nuclear chromosomes are often contaminated by organelle genomes, which will mislead bioinformatic analysis, and genomic and transcriptomic data interpretation.

METHODS: To address this issue, we developed a tool named Chlomito, aiming at precise identification and elimination of organelle genome contamination from nuclear genome assembly. Compared to conventional approaches, Chlomito utilized new metrics, alignment length coverage ratio (ALCR) and sequencing depth ratio (SDR), thereby effectively distinguishing true organelle genome sequences from those transferred into nuclear genomes via horizontal gene transfer (HGT).

RESULTS: The accuracy of Chlomito was tested using sequencing data from Plum, Mango and Arabidopsis. The results confirmed that Chlomito can accurately detect contigs originating from the organelle genomes, and the identified contigs covered most regions of the organelle reference genomes, demonstrating efficiency and precision of Chlomito. Considering user convenience, we further packaged this method into a Docker image, simplified the data processing workflow.

DISCUSSION: Overall, Chlomito provides an efficient, accurate and convenient method for identifying and removing contigs derived from organelle genomes in genomic assembly data, contributing to the improvement of genome assembly quality.},
}

@article {pmid39253440,
year = {2024},
author = {Frail, S and Steele-Ogus, M and Doenier, J and Moulin, SLY and Braukmann, T and Xu, S and Yeh, E},
title = {Genomes of nitrogen-fixing eukaryotes reveal a non-canonical model of organellogenesis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39253440},
issn = {2692-8205},
support = {S10 OD030441/OD/NIH HHS/United States ; T32 AI007328/AI/NIAID NIH HHS/United States ; T32 GM007276/GM/NIGMS NIH HHS/United States ; },
abstract = {Endosymbiont gene transfer and import of host-encoded proteins are considered hallmarks of organelles necessary for stable integration of two cells. However, newer endosymbiotic models have challenged the origin and timing of such genetic integration during organellogenesis. Epithemia diatoms contain diazoplasts, closely related to recently-described nitrogen-fixing organelles, that are also stably integrated and co-speciating with their host algae. We report genomic analyses of two species, freshwater E.clementina and marine E.pelagica, which are highly divergent but share a common endosymbiotic origin. We found minimal evidence of genetic integration: nonfunctional diazoplast-to-nuclear DNA transfers in the E.clementina genome and 6 host-encoded proteins of unknown function in the E.clementina diazoplast proteome, far fewer than in other recently-acquired organelles. Epithemia diazoplasts are a valuable counterpoint to existing organellogenesis models, demonstrating that endosymbionts can be stably integrated and inherited absent significant genetic integration. The minimal genetic integration makes diazoplasts valuable blueprints for bioengineering endosymbiotic compartments de novo.},
}

@article {pmid39254330,
year = {2024},
author = {Lee, E and Priutt, E and Woods, S and Quick, A and King, S and McLellan, LK and Shields, RC},
title = {Genomic analysis of conjugative and chromosomally integrated mobile genetic elements in oral streptococci.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0136024},
doi = {10.1128/aem.01360-24},
pmid = {39254330},
issn = {1098-5336},
abstract = {This study aimed to investigate the diversity of conjugative and chromosomally integrated mobile genetic elements (cciMGEs) within six oral streptococci species. cciMGEs, including integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs), are stably maintained on the host cell chromosome; however, under certain conditions, they are able to excise, form extrachromosomal circles, and transfer via a conjugation apparatus. Many cciMGEs encode "cargo" functions that aid survival in new niches and evolve new antimicrobial resistance or virulence properties, whereas others have been shown to influence host bacterial physiology. Here, using a workflow employing preexisting bioinformatics tools, we analyzed 551 genomes for the presence of cciMGEs across six common health- and disease-associated oral streptococci. We identified 486 cciMGEs, 173 of which were ICEs and 233 of which were IMEs. The cciMGEs were diverse in size, cargo genes, and relaxase types. We identified several novel relaxase proteins and a widespread IME carrying a small multidrug resistance transporter. Additionally, we provide evidence that several of the bioinformatically predicted cciMGEs encoded within various Streptococcus mutans strains are capable of excision and circularization, a critical step for cciMGE conjugative transfer. These findings highlight the significance and potential impact of MGEs in shaping the genetic landscape, pathogenicity, and antimicrobial resistance profiles of the oral microbiota.IMPORTANCEOral streptococci are important players in the oral microbiome, influencing both health and disease states within dental bacterial communities. Evolutionary adaptation, shaped in a major part by the horizontal transfer of genes, is essential for their survival in the oral cavity and within new environments. Conjugation is a significant driver of horizontal gene transfer; however, there is limited information regarding this process in oral bacteria. This study utilizes publicly available genome sequences to identify conjugative and chromosomally integrated mobile genetic elements (cciMGEs) across several species of oral streptococci and presents the preliminary characterization of these elements. Our findings significantly enhance our understanding of the mobile genomic landscape of oral streptococci critical for human health, with valuable insights into how cciMGEs might influence the survival and pathogenesis of these bacteria in the oral microbiome.},
}

@article {pmid39249569,
year = {2024},
author = {Ruhal, R and Sahu, A and Koujalagi, T and Das, A and Prasanth, H and Kataria, R},
title = {Biofilm-specific determinants of enterococci pathogen.},
journal = {Archives of microbiology},
volume = {206},
number = {10},
pages = {397},
pmid = {39249569},
issn = {1432-072X},
support = {NA//VIT University/ ; NA//VIT University/ ; NA//VIT University/ ; NA//VIT University/ ; NA//VIT University/ ; NA//VIT University/ ; },
mesh = {*Enterococcus/genetics/metabolism ; *Biofilms ; Gene Expression Regulation, Bacterial ; *Gram-Positive Bacterial Infections/epidemiology/microbiology/physiopathology ; Bacterial Adhesion/genetics ; Adhesins, Bacterial/genetics/metabolism ; Polysaccharides, Bacterial/metabolism ; Gene Transfer, Horizontal ; },
abstract = {Amongst all Enterococcus spp., E. faecalis and E. faecium are most known notorious pathogen and their biofilm formation has been associated with endocarditis, oral, urinary tract, and wound infections. Biofilm formation involves a pattern of initial adhesion, microcolony formation, and mature biofilms. The initial adhesion and microcolony formation involve numerous surface adhesins e.g. pili Ebp and polysaccharide Epa. The mature biofilms are maintained by eDNA, It's worth noting that phage-mediated dispersal plays a prominent role. Further, the involvement of peptide pheromones in regulating biofilm maintenance sets it apart from other pathogens and facilitating the horizontal transfer of resistance genes. The role of fsr based regulation by regulating gelE expression is also discussed. Thus, we provide a concise overview of the significant determinants at each stage of Enterococcus spp. biofilm formation. These elements could serve as promising targets for antibiofilm strategies.},
}

*Enterococcus/genetics/metabolism
*Biofilms
Gene Expression Regulation, Bacterial
*Gram-Positive Bacterial Infections/epidemiology/microbiology/physiopathology
Bacterial Adhesion/genetics
Adhesins, Bacterial/genetics/metabolism
Polysaccharides, Bacterial/metabolism
Gene Transfer, Horizontal

@article {pmid39248479,
year = {2024},
author = {Glen, KA and Lamont, IL},
title = {Characterization of acquired β-lactamases in Pseudomonas aeruginosa and quantification of their contributions to resistance.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0069424},
doi = {10.1128/spectrum.00694-24},
pmid = {39248479},
issn = {2165-0497},
abstract = {Pseudomonas aeruginosa is a highly problematic opportunistic pathogen that causes a range of different infections. Infections are commonly treated with β-lactam antibiotics, including cephalosporins, monobactams, penicillins, and carbapenems, with carbapenems regarded as antibiotics of last resort. Isolates of P. aeruginosa can contain horizontally acquired bla genes encoding β-lactamase enzymes, but the extent to which these contribute to β-lactam resistance in this species has not been systematically quantified. The overall aim of this research was to address this knowledge gap by quantifying the frequency of β-lactamase-encoding genes in P. aeruginosa and by determining the effects of β-lactamases on susceptibility of P. aeruginosa to β-lactams. Genome analysis showed that β-lactamase-encoding genes are present in 3% of P. aeruginosa but are enriched in carbapenem-resistant isolates (35%). To determine the substrate antibiotics, 10 β-lactamases were expressed from an integrative plasmid in the chromosome of P. aeruginosa reference strain PAO1. The β-lactamases reduced susceptibility to a variety of clinically used antibiotics, including carbapenems (meropenem, imipenem), penicillins (ticarcillin, piperacillin), cephalosporins (ceftazidime, cefepime), and a monobactam (aztreonam). Different enzymes acted on different β-lactams. β-lactamases encoded by the genomes of P. aeruginosa clinical isolates had similar effects to the enzymes expressed in strain PAO1. Genome engineering was used to delete β-lactamase-encoding genes from three carbapenem-resistant clinical isolates and increased susceptibility to substrate β-lactams. Our findings demonstrate that acquired β-lactamases play an important role in β-lactam resistance in P. aeruginosa, identifying substrate antibiotics for a range of enzymes and quantifying their contributions to resistance.IMPORTANCEPseudomonas aeruginosa is an extremely problematic pathogen, with isolates that are resistant to the carbapenem class of β-lactam antibiotics being in critical need of new therapies. Genes encoding β-lactamase enzymes that degrade β-lactam antibiotics can be present in P. aeruginosa, including carbapenem-resistant isolates. Here, we show that β-lactamase genes are over-represented in carbapenem-resistant isolates, indicating their key role in resistance. We also show that different β-lactamases alter susceptibility of P. aeruginosa to different β-lactam antibiotics and quantify the effects of selected enzymes on β-lactam susceptibility. This research significantly advances the understanding of the contributions of acquired β-lactamases to antibiotic resistance, including carbapenem resistance, in P. aeruginosa and by implication in other species. It has potential to expedite development of methods that use whole genome sequencing of infecting bacteria to inform antibiotic treatment, allowing more effective use of antibiotics, and facilitate the development of new antibiotics.},
}

@article {pmid38723713,
year = {2024},
author = {Na, IY and Seo, J and Jin, Y and Ko, KS},
title = {Whole-plasmid analysis of NDM-1-producing Acinetobacter seifertii isolate and its fitness in several Acinetobacter species.},
journal = {Journal of global antimicrobial resistance},
volume = {38},
number = {},
pages = {223-226},
doi = {10.1016/j.jgar.2024.05.003},
pmid = {38723713},
issn = {2213-7173},
mesh = {*Acinetobacter/genetics/drug effects/isolation & purification/enzymology ; *beta-Lactamases/genetics ; *Plasmids/genetics ; Humans ; *Microbial Sensitivity Tests ; Republic of Korea ; *Anti-Bacterial Agents/pharmacology ; *Acinetobacter Infections/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Genotype ; Carbapenems/pharmacology ; Conjugation, Genetic ; },
abstract = {OBJECTIVES: The aim of this study was to characterize an NDM-1-producing Acinetobacter seifertii isolates from a patient in South Korea.

METHODS: Antibiotic susceptibility testing and genotyping using multigene sequencing were performed and whole plasmid sequences were determined.

RESULTS: The genotype of A. seifertii was ST1899 and was resistant to ceftazidime, trimethoprim-sulfamethoxazole, and piperacillin-tazobactam, in addition to carbapenem. blaNDM-1 was surrounded by the ISAba125 insertion sequence within the structure of Tn125 in the 47 kb-sized plasmid. The plasmid exhibited a structure similar to that of other plasmids of diverse Acinetobacter sp. found worldwide. Transconjugation and the growth curve indicated that the plasmid was adapted to A. seifertii rather than other closely related Acinetobacter sp.

CONCLUSIONS: Acquisition of carbapenem resistance by horizontal transfer of the blaNDM-1-carrying plasmid from another Acinetobacter species was found with no growth defect.},
}

*Acinetobacter/genetics/drug effects/isolation & purification/enzymology
*beta-Lactamases/genetics
*Plasmids/genetics
Humans
*Microbial Sensitivity Tests
Republic of Korea
*Anti-Bacterial Agents/pharmacology
*Acinetobacter Infections/microbiology
Drug Resistance, Multiple, Bacterial/genetics
Gene Transfer, Horizontal
Genotype
Carbapenems/pharmacology
Conjugation, Genetic

@article {pmid39243547,
year = {2024},
author = {Hu, RG and Yang, L and Wang, LY and Yang, YL and Li, HJ and Yang, BT and Kang, YH and Liang, ZL and Cong, W},
title = {Unveiling the pathogenic and multidrug-resistant profiles of Vibrio alfacsensis: A potential identified threat in turbot (Scophthalmus maximus) aquaculture.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135729},
doi = {10.1016/j.jhazmat.2024.135729},
pmid = {39243547},
issn = {1873-3336},
abstract = {Vibrio alfacsensis is traditionally seen as an environmental symbiont within its genus, with no detailedly documented pathogenicity in marine aquaculture to date. This study delves into the largely unexplored pathogenic potential and emerging antibiotic resistance of V. alfacsensis. The VA-1 strain, isolated from recirculating aquaculture system (RAS) effluent of cultured turbot (Scophthalmus maximus), underwent comprehensive analysis including biochemical identification, antibiotic susceptibility testing and reinfection trials. The results confirmed VA-1's pathogenicity and significant multiple antibiotic resistance. VA-1 could induce systemic infection in turbot, with symptoms like kidney enlargement, exhibiting virulence comparable to known Vibrio pathogens, with an LD50 around 2.36 × 10[6] CFU/fish. VA-1's remarkable resistance phenotype (14/22) suggested potential for genetic exchange and resistance factor acquisition in aquaculture environments. Phylogenetic analysis based on 16S rDNA sequences and whole-genome sequencing has firmly placed VA-1 within the V. alfacsensis clade, while genome-wide analysis highlights its similarity and diversity in relation to strains from across the globe. VA-1 contained numerous replicons, indicating the possibility for the spread of resistance and virulence genes. This study suggests V. alfacsensis may acquire and transfer pathogenic and resistant traits through horizontal gene transfer, a likelihood intensified by changing environmental and aquaculture conditions, highlighting the need for vigilant pathogen monitoring and new non-antibiotic treatments.},
}

@article {pmid39243538,
year = {2024},
author = {Lin, L and Li, L and Yang, X and Hou, L and Wu, D and Wang, B and Ma, B and Liao, X and Yan, X and Gad, M and Su, J and Liu, Y and Liu, K and Hu, A},
title = {Unnoticed antimicrobial resistance risk in Tibetan cities unveiled by sewage metagenomic surveillance: Compared to the eastern Chinese cities.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135730},
doi = {10.1016/j.jhazmat.2024.135730},
pmid = {39243538},
issn = {1873-3336},
abstract = {Sewage surveillance is a cost-effective tool for assessing antimicrobial resistance (AMR) in urban populations. However, research on sewage AMR in remote areas is still limited. Here, we used shotgun metagenomic sequencing to profile antibiotic resistance genes (ARGs) and ARG-carrying pathogens (APs) across 15 cities in Tibetan Plateau (TP) and the major cities in eastern China. Notable regional disparities in sewage ARG composition were found, with a significantly higher ARG abundance in TP (2.97 copies/cell). A total of 542 and 545 APs were identified in sewage from TP and the East, respectively, while more than 40 % carried mobile genetic elements (MGEs). Moreover, 65 MGEs-carrying APs were identified as World Health Organization (WHO) priority-like bacterial and fungal pathogens. Notably, a fungal zoonotic pathogen, Enterocytozoon bieneusi, was found for the first time to carry a nitroimidazole resistance gene (nimJ). Although distinct in AP compositions, the relative abundances of APs were comparable in these two regions. Furthermore, sewage in TP was found to be comparable to the cities in eastern China in terms of ARG mobility and AMR risks. These findings provide insights into ARGs and APs distribution in Chinese sewage and stress the importance of AMR surveillance and management strategies in remote regions.},
}

@article {pmid39208359,
year = {2024},
author = {Ares-Arroyo, M and Coluzzi, C and Moura de Sousa, JA and Rocha, EPC},
title = {Hijackers, hitchhikers, or co-drivers? The mysteries of mobilizable genetic elements.},
journal = {PLoS biology},
volume = {22},
number = {8},
pages = {e3002796},
doi = {10.1371/journal.pbio.3002796},
pmid = {39208359},
issn = {1545-7885},
mesh = {*Gene Transfer, Horizontal ; Interspersed Repetitive Sequences/genetics ; Bacteria/genetics ; Evolution, Molecular ; Genomic Islands ; Symbiosis/genetics ; Genome, Bacterial ; },
abstract = {Mobile genetic elements shape microbial gene repertoires and populations. Recent results reveal that many, possibly most, microbial mobile genetic elements require helpers to transfer between genomes, which we refer to as Hitcher Genetic Elements (hitchers or HGEs). They may be a large fraction of pathogenicity and resistance genomic islands, whose mechanisms of transfer have remained enigmatic for decades. Together with their helper elements and their bacterial hosts, hitchers form tripartite networks of interactions that evolve rapidly within a parasitism-mutualism continuum. In this emerging view of microbial genomes as communities of mobile genetic elements many questions arise. Which elements are being moved, by whom, and how? How often are hitchers costly hyper-parasites or beneficial mutualists? What is the evolutionary origin of hitchers? Are there key advantages associated with hitchers' lifestyle that justify their unexpected abundance? And why are hitchers systematically smaller than their helpers? In this essay, we start answering these questions and point ways ahead for understanding the principles, origin, mechanisms, and impact of hitchers in bacterial ecology and evolution.},
}

*Gene Transfer, Horizontal
Interspersed Repetitive Sequences/genetics
Bacteria/genetics
Evolution, Molecular
Genomic Islands
Symbiosis/genetics
Genome, Bacterial

@article {pmid39242818,
year = {2024},
author = {Porras, MÁG and Assié, A and Tietjen, M and Violette, M and Kleiner, M and Gruber-Vodicka, H and Dubilier, N and Leisch, N},
title = {An intranuclear bacterial parasite of deep-sea mussels expresses apoptosis inhibitors acquired from its host.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39242818},
issn = {2058-5276},
support = {340535//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; 340535//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; 340535//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; 340535//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; Gottfried Wilhelm Leibniz Prize//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Heisenberggrant GR 5028/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; OIA 1934844//National Science Foundation (NSF)/ ; IOS 2003107//National Science Foundation (NSF)/ ; },
abstract = {A limited number of bacteria are able to colonize the nuclei of eukaryotes. 'Candidatus Endonucleobacter' infects the nuclei of deep-sea mussels, where it replicates to ≥80,000 bacteria per nucleus and causes nuclei to swell to 50 times their original size. How these parasites are able to replicate and avoid apoptosis is not known. Dual RNA-sequencing transcriptomes of infected nuclei isolated using laser-capture microdissection revealed that 'Candidatus Endonucleobacter' does not obtain most of its nutrition from nuclear DNA or RNA. Instead, 'Candidatus Endonucleobacter' upregulates genes for importing and digesting sugars, lipids, amino acids and possibly mucin from its host. It likely prevents apoptosis of host cells by upregulating 7-13 inhibitors of apoptosis, proteins not previously seen in bacteria. Comparative phylogenetic analyses revealed that 'Ca. Endonucleobacter' acquired inhibitors of apoptosis through horizontal gene transfer from their hosts. Horizontal gene transfer from eukaryotes to bacteria is assumed to be rare, but may be more common than currently recognized.},
}

@article {pmid39236533,
year = {2024},
author = {Yuan, Q and Li, W and Goh, SG and Chen, SL and Ng, OT and He, Y and Gin, KY},
title = {Genetic traits and transmission of antimicrobial resistance characteristics of cephalosporin resistant Escherichia coli in tropical aquatic environments.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135707},
doi = {10.1016/j.jhazmat.2024.135707},
pmid = {39236533},
issn = {1873-3336},
abstract = {This study investigates the genetic traits and transmission mechanisms of cephalosporin-resistant Escherichia coli in tropical aquatic environments in Singapore. From 2016 to 2020, monthly samples were collected from wastewater treatment plants, marine niches, community sewage, beaches, reservoirs, aquaculture farms, and hospitals, yielding 557 isolates that were analyzed for antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) using genomic methods. Findings reveal significant genotypic similarities between environmental and hospital-derived strains, particularly the pandemic E. coli ST131. Environmental strains exhibited high levels of intrinsic resistance mechanisms, including mutations in porins and efflux pumps, with key ARGs such as CMY-2 and NDM-9 predominantly carried by MGEs, which facilitate horizontal gene transfer. Notably, pathogenic EPEC and EHEC strains were detected in community sewage and aquaculture farms, posing substantial public health risks. This underscores the critical role of these environments as reservoirs for multidrug-resistant pathogens and emphasizes the interconnectedness of human activities and environmental health.},
}

@article {pmid39236354,
year = {2024},
author = {Brdová, D and Ruml, T and Viktorová, J},
title = {Mechanism of staphylococcal resistance to clinically relevant antibiotics.},
journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy},
volume = {77},
number = {},
pages = {101147},
doi = {10.1016/j.drup.2024.101147},
pmid = {39236354},
issn = {1532-2084},
abstract = {Staphylococcus aureus, a notorious pathogen with versatile virulence, poses a significant challenge to current antibiotic treatments due to its ability to develop resistance mechanisms against a variety of clinically relevant antibiotics. In this comprehensive review, we carefully dissect the resistance mechanisms employed by S. aureus against various antibiotics commonly used in clinical settings. The article navigates through intricate molecular pathways, elucidating the mechanisms by which S. aureus evades the therapeutic efficacy of antibiotics, such as β-lactams, vancomycin, daptomycin, linezolid, etc. Each antibiotic is scrutinised for its mechanism of action, impact on bacterial physiology, and the corresponding resistance strategies adopted by S. aureus. By synthesising the knowledge surrounding these resistance mechanisms, this review aims to serve as a comprehensive resource that provides a foundation for the development of innovative therapeutic strategies and alternative treatments for S. aureus infections. Understanding the evolving landscape of antibiotic resistance is imperative for devising effective countermeasures in the battle against this formidable pathogen.},
}

@article {pmid39235659,
year = {2024},
author = {Fu, Y and Fu, Z and Yu, J and Wang, H and Zhang, Y and Liu, M and Wang, X and Yu, W and Han, F},
title = {Biochemical Characterization of Hyaluronate Lyase CpHly8 from an Intestinal Microorganism Clostridium perfringens G1121.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {39235659},
issn = {1559-0291},
support = {2022QNLM030003-1//Qingdao Marine Science and Technology Center/ ; ZR2019ZD18//Natural Science Foundation of Shandong Province/ ; 2018YFC0311105//Shandong Province Technology Innovation Guidance Program/ ; 22-3-6-gjxm-5-gx//Science & Technology Development Project of Qingdao/ ; 21-1-6-gjxm-27-gx//Science & Technology Development Project of Qingdao/ ; 20-11-6-64-gx//Science & Technology Development Project of Qingdao/ ; },
abstract = {Hyaluronic acid (HA) is an important component of extracellular matrices (ECM) and a linear polysaccharide involved in various physiological and pathological processes within the biological system. Several pathogens exploit HA degradation within the extracellular matrix to facilitate infection. While many intestinal microorganisms play significant roles in HA utilization in the human body, there remains a scarcity of related studies. This paper addressed this gap by screening intestinal microorganisms capable of degrading HA, resulting in the isolation of Clostridium perfringens G1121, which had been demonstrated the ability to degrade HA. Subsequent genome sequencing and analysis of C. perfringens G1121 revealed its utilization of the polysaccharide utilization loci of HA (PULHA), which was obtained by horizontal gene transfer. The PULHA contains a sequence encoding a hyaluronic acid-specific degradation enzyme designated CpHly8, belonging to polysaccharide lyase family 8. The specific activity of CpHly8 towards HA was 142.98 U/mg, with the optimum reaction temperature and pH observed at 50℃ and 6.0, respectively. The final product of HA degradation by CpHly8 was unsaturated hyaluronic acid disaccharide. Moreover, subcutaneous diffusion experiments with trypan blue in mice revealed that CpHly8 effectively promoted subcutaneous diffusion and sustained its effects long-term, suggesting its potential application as an adjunct in drug delivery. Overall, our study enriches our understanding of intestinal microbial degradation of HA, provides new evidence for horizontal gene transfer among intestinal microorganisms, and confirms that CpHly8 is a promising candidate for intestinal microbial hyaluronidase.},
}

@article {pmid39235644,
year = {2024},
author = {Jaswal, R and Dubey, H and Kiran, K and Rawal, H and Kumar, G and Rajarammohan, S and Deshmukh, R and Sonah, H and Prasad, P and Bhardwaj, SC and Gupta, N and Sharma, TR},
title = {Identification and functional characterization of the npc-2-like domain containing rust effector protein that suppresses cell death in plants.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {962},
pmid = {39235644},
issn = {1573-4978},
mesh = {*Plant Diseases/microbiology ; *Phylogeny ; *Cell Death ; *Fungal Proteins/metabolism/genetics ; Nicotiana/microbiology/metabolism/genetics ; Basidiomycota/pathogenicity/metabolism/genetics ; Puccinia/pathogenicity/metabolism ; Protein Domains ; Molecular Docking Simulation ; Onions/microbiology/metabolism/genetics ; },
abstract = {The MD-2-related lipid-recognition (ML/Md-2) domain is a lipid/sterol-binding domain that are involved in sterol transfer and innate immunity in eukaryotes. Here we report a genome-wide survey of this family, identifying 84 genes in 30 fungi including plant pathogens. All the studied species were found to have varied ML numbers, and expansion of the family was observed in Rhizophagus irregularis (RI) with 33 genes. The molecular docking studies of these proteins with cholesterol derivatives indicate lipid-binding functional conservation across the animal and fungi kingdom. The phylogenetic studies among eukaryotic ML proteins showed that Puccinia ML members are more closely associated with animal (insect) npc2 proteins than other fungal ML members. One of the candidates from leaf rust fungus Puccinia triticina, Pt5643 was PCR amplified and further characterized using various studies such as qRT-PCR, subcellular localization studies, yeast functional complementation, signal peptide validation, and expression studies. The Pt5643 exhibits the highest expression on the 5th day post-infection (dpi). The confocal microscopy of Pt5643 in onion epidermal cells and N. benthamiana shows its location in the cytoplasm and nucleus. The functional complementation studies of Pt5643 in npc2 mutant yeast showed its functional similarity to the eukaryotic/yeast npc2 gene. Furthermore, the overexpression of Pt5643 also suppressed the BAX, NEP1, and H2O2-induced program cell death in Nicotiana species and yeast. Altogether the present study reports the novel function of ML domain proteins in plant fungal pathogens and their possible role as effector molecules in host defense manipulation.},
}

*Plant Diseases/microbiology
*Phylogeny
*Cell Death
*Fungal Proteins/metabolism/genetics
Nicotiana/microbiology/metabolism/genetics
Basidiomycota/pathogenicity/metabolism/genetics
Puccinia/pathogenicity/metabolism
Protein Domains
Molecular Docking Simulation
Onions/microbiology/metabolism/genetics

@article {pmid39235595,
year = {2024},
author = {Xu, R and Huang, C and Yang, B and Wang, S and Zhong, T and Ma, L and Shang, Q and Zhang, M and Chu, Z and Liu, X},
title = {Influence of Two-Dimensional Black Phosphorus on the Horizontal Transfer of Plasmid-Mediated Antibiotic Resistance Genes: Promotion or Inhibition?.},
journal = {Current microbiology},
volume = {81},
number = {10},
pages = {344},
pmid = {39235595},
issn = {1432-0991},
support = {52070063//National Natural Science Foundation of China/ ; 2308085Y38//Science Fund for Distinguished Young Scholars of Anhui Province/ ; 21-22RC30//Hefei University/ ; },
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Phosphorus/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Conjugation, Genetic ; Escherichia coli/genetics/drug effects ; Nanostructures ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial/drug effects ; Bacteria/genetics/drug effects ; },
abstract = {The problem of bacterial resistance caused by antibiotic abuse is seriously detrimental to global human health and ecosystem security. The two-dimensional nanomaterial (2D) such as black phosphorus (BP) is recently expected to become a new bacterial inhibitor and has been widely used in the antibacterial field due to its specific physicochemical properties. Nevertheless, the effects of 2D-BP on the propagation of antibiotic resistance genes (ARGs) in environments and the relevant mechanisms are not clear. Herein, we observed that the sub-inhibitory concentrations of 2D-BP dramatically increased the conjugative transfer of ARGs mediated by the RP4 plasmid up to 2.6-fold at the 125 mg/L exposure level compared with the untreated bacterial cells. Nevertheless, 2D-BP with the inhibitory concentration caused a dramatic decrease in the conjugative frequency. The phenotypic changes revealed that the increase of the conjugative transfer caused by 2D-BP exposure were attributed to the excessive reactive oxygen species and oxidative stress, and increased bacterial cell membrane permeability. The genotypic evidence demonstrated that 2D-BP affecting the horizontal gene transfer of ARGs was probably through the upregulation of mating pair formation genes (trbBp and traF) and DNA transfer and replication genes (trfAp and traJ), as well as the downregulation of global regulatory gene expression (korA, korB, and trbA). In summary, the changes in the functional and regulatory genes in the conjugative transfer contributed to the stimulation of conjugative transfer. This research aims to broaden our comprehension of how nanomaterials influence the dissemination of ARGs by elucidating their effects and mechanisms.},
}

*Plasmids/genetics
*Gene Transfer, Horizontal
*Phosphorus/metabolism
*Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Conjugation, Genetic
Escherichia coli/genetics/drug effects
Nanostructures
Bacterial Proteins/genetics/metabolism
Gene Expression Regulation, Bacterial/drug effects
Bacteria/genetics/drug effects

@article {pmid39233522,
year = {2024},
author = {Lee, JH and Tareen, AR and Kim, NH and Jeong, C and Kang, B and Lee, G and Kim, DW and Zahra, R and Lee, SH},
title = {Comparative Genomic Analyses of E. coli ST2178 Strains Originated from Wild Birds in Pakistan.},
journal = {Journal of microbiology and biotechnology},
volume = {34},
number = {10},
pages = {1-8},
doi = {10.4014/jmb.2407.07026},
pmid = {39233522},
issn = {1738-8872},
abstract = {The emergence and spread of multidrug-resistance (MDR) pathogenic Escherichia coli due to horizontal gene transfer of antibiotic resistance genes (ARGs) and virulence factors (VFs) is a global health concern, particularly in developing countries. While numerous studies have focused on major sequence types (STs), the implication of minor STs in ARG dissemination and their pathogenicity remains crucial. In this study, two E. coli strains (PEC1011 and PEC1012) were isolated from wild bird feces in Pakistan and identified as ST2178 based on their complete genome sequences. To understand this minor ST, 204 genome assemblies of ST2178 were comparatively analyzed with the isolates' genomes. The phylogenetic analyses revealed five subclades of ST2178. Subclade E strains were predominantly isolated from human specimens, whereas subclades A and B strains including strains PEC1011 and PEC1012, respectively, were frequently isolated from animal. Mobile genetic elements (MGEs) exhibited the positive correlation with ARGs but not with VFs in this ST. Plasmid-borne ARGs exhibited higher correlation with plasmid-borne MGEs, indicating the role of diverse mobile plasmid structures in ARG transmission. Subclade E exhibited diverse plasmid-borne ARG repertoires correlated with MGEs, marking it as a critical surveillance target. In the case of VFs, they exhibited phylogeny-dependent profiles. Strain PEC1012 harbored various plasmid-borne ARGs, which are similar with conserved ARG repertoires in subclade A. The presence of unique ARG insertion in pPEC1012 highlights the importance of subclade A in ARG dissemination. This study comprehensively elucidates the landscape of ST2178, identifying critical phylogenetic subclades and their characteristics in ARG and VF occurrence.},
}

@article {pmid39233087,
year = {2024},
author = {Kong, F and Qi, Z and Tong, H and Ren, N and You, S},
title = {Case study on the relationship between transmission of antibiotic resistance genes and microbial community under freeze-thaw cycle on cold-region dairy farm.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {175989},
doi = {10.1016/j.scitotenv.2024.175989},
pmid = {39233087},
issn = {1879-1026},
abstract = {Freeze-thaw cycle (FTC) is a naturally occurring phenomenon in high-latitude terrestrial ecosystems, which may exert influence on distribution and evolution of microbial community in the soil. The relationship between transmission of antibiotic resistance genes (ARGs) and microbial community was investigated upon the case study on the soil of cold-region dairy farm under seasonal FTC. The results demonstrated that 37 ARGs underwent decrease in the abundance of blaTEM from 80.4 % for frozen soil to 71.7 % for thawed soil, and that sul2 from 8.8 % for frozen soil to 6.5 % for thawed soil, respectively. Antibiotic deactivation was identified to be closely related to the highest relative abundance of blaTEM, and the spread of sulfonamide resistance genes (SRGs) occurred mainly via target modification. Firmicutes in frozen soil were responsible for dominating the abundance of ARGs by suppressing the native bacteria under starvation effect in cold regions, and then underwent horizontal gene transfer (HGT) among native bacteria through mobile genetic elements (MGEs). The TRB-C (32.6-49.1 %) and tnpA-06 (0.27-7.5 %) were significantly increased in frozen soil, while Int3 (0.67-10.6 %) and tnpA-04 (11.1-19.4 %) were up-regulated in thawed soil. Moreover, the ARGs in frozen soil primarily underwent HGT through MGEs, i.e. TRB-C and tnpA-06, with increased number of Firmicutes serving as carrier. The case study not only demonstrated relationship between transmission of ARGs and microbial community in the soil under practically relevant FTC condition, but also emphasized the importance for formulating better strategies for preventing FTC-induced ARGs in dairy farm in cold regions.},
}

@article {pmid39226958,
year = {2024},
author = {Muñoz, JSC and Aransiola, SA and Reddy, KV and Ranjit, P and Victor-Ekwebelem, MO and Oyedele, OJ and Pérez-Almeida, IB and Maddela, NR and Díaz, JMR},
title = {Antibiotic resistant bacteria and antibiotic resistance genes as contaminants of emerging concern: Occurrences, impacts, mitigations and future guidelines.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {175906},
doi = {10.1016/j.scitotenv.2024.175906},
pmid = {39226958},
issn = {1879-1026},
abstract = {Antibiotic resistance, driven by the proliferation of antibiotic resistance genes (ARGs) and antibiotic resistance bacteria (ARBs), has emerged as a pressing global health concern. Antimicrobial resistance is exacerbated by the widespread use of antibiotics in agriculture, aquaculture, and human medicine, leading to their accumulation in various environmental compartments such as soil, water, and sediments. The presence of ARGs in the environment, particularly in municipal water, animal husbandry, and hospital environments, poses significant risks to human health, as they can be transferred to potential human pathogens. Current remediation strategies, including the use of pyroligneous acid, coagulants, advanced oxidation, and bioelectrochemical systems, have shown promising results in reducing ARGs and ARBs from soil and water. However, these methods come with their own set of challenges, such as the need for elevated base levels in UV-activated persulfate and the long residence period required for photocatalysts. The future of combating antibiotic resistance lies in the development of standardized monitoring techniques, global collaboration, and the exploration of innovative remediation methods. Emphasis on combination therapies, advanced oxidation processes, and monitoring horizontal gene transfer can pave the way for a comprehensive approach to mitigate the spread of antibiotic resistance in the environment.},
}

@article {pmid39224035,
year = {2024},
author = {Chopra, A and Bhuvanagiri, G and Natu, K and Chopra, A},
title = {Role of CRISPR-Cas systems in periodontal disease pathogenesis and potential for periodontal therapy: A review.},
journal = {Molecular oral microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/omi.12483},
pmid = {39224035},
issn = {2041-1014},
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPRs) are DNA sequences capable of editing a host genome sequence. CRISPR and its specific CRISPR-associated (Cas) protein complexes have been adapted for various applications. These include activating or inhibiting specific genetic sequences or acting as molecular scissors to cut and modify the host DNA precisely. CRISPR-Cas systems are also naturally present in many oral bacteria, where they aid in nutrition, biofilm formation, inter- and intraspecies communication (quorum sensing), horizontal gene transfer, virulence, inflammation modulation, coinfection, and immune response evasion. It even functions as an adaptive immune system, defending microbes against invading viruses and foreign genetic elements from other bacteria by targeting and degrading their DNA. Recently, CRISPR-Cas systems have been tested as molecular editing tools to manipulate specific genes linked with periodontal disease (such as periodontitis) and as novel methods of delivering antimicrobial agents to overcome antimicrobial resistance. With the rapidly increasing role of CRISPR in treating inflammatory diseases, its application in periodontal disease is also becoming popular. Therefore, this review aims to discuss the different types of CRISPR-Cas in oral microbes and their role in periodontal disease pathogenesis and precision periodontal therapy.},
}

@article {pmid39223450,
year = {2024},
author = {Valerio, F and Martel, C and Stefanescu, C and van Nouhuys, S and Kankare, M and Duplouy, A},
title = {Wolbachia strain diversity in a complex group of sympatric cryptic parasitoid wasp species.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {319},
pmid = {39223450},
issn = {1471-2180},
mesh = {Animals ; *Wolbachia/genetics/classification/isolation & purification ; *Wasps/microbiology ; *Symbiosis ; *Phylogeny ; Sympatry ; Gene Transfer, Horizontal ; Genetic Variation ; Lepidoptera/microbiology/parasitology ; },
abstract = {BACKGROUND: Maternally-inherited symbionts can induce pre-mating and/or post-mating reproductive isolation between sympatric host lineages, and speciation, by modifying host reproductive phenotypes. The large parasitoid wasp genus Cotesia (Braconidae) includes a diversity of cryptic species, each specialized in parasitizing one to few related Lepidoptera host species. Here, we characterized the infection status of an assemblage of 21 Cotesia species from 15 countries by several microbial symbionts, as a first step toward investigating whether symbionts may provide a barrier to gene flow between these parasitoid host lineages.

RESULTS: The symbiotic microbes Arsenophonus, Cardinium, Microsporidium and Spiroplasma were not detected in the Cotesia wasps. However, the endosymbiotic bacterium Wolbachia was present in at least eight Cotesia species, and hence we concentrated on it upon screening additional DNA extracts and SRAs from NCBI. Some of the closely related Cotesia species carry similar Wolbachia strains, but most Wolbachia strains showed patterns of horizontal transfer between phylogenetically distant host lineages.

CONCLUSIONS: The lack of co-phylogenetic signal between Wolbachia and Cotesia suggests that the symbiont and hosts have not coevolved to an extent that would drive species divergence between the Cotesia host lineages. However, as the most common facultative symbiont of Cotesia species, Wolbachia may still function as a key-player in the biology of the parasitoid wasps. Its precise role in the evolution of this complex clade of cryptic species remains to be experimentally investigated.},
}

Animals
*Wolbachia/genetics/classification/isolation & purification
*Wasps/microbiology
*Symbiosis
*Phylogeny
Sympatry
Gene Transfer, Horizontal
Genetic Variation
Lepidoptera/microbiology/parasitology

@article {pmid39222343,
year = {2024},
author = {Lyulina, AS and Liu, Z and Good, BH},
title = {Linkage equilibrium between rare mutations.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyae145},
pmid = {39222343},
issn = {1943-2631},
abstract = {Recombination breaks down genetic linkage by reshuffling existing variants onto new genetic backgrounds. These dynamics are traditionally quantified by examining the correlations between alleles, and how they decay as a function of the recombination rate. However, the magnitudes of these correlations are strongly influenced by other evolutionary forces like natural selection and genetic drift, making it difficult to tease out the effects of recombination. Here we introduce a theoretical framework for analyzing an alternative family of statistics that measure the homoplasy produced by recombination. We derive analytical expressions that predict how these statistics depend on the rates of recombination and recurrent mutation, the strength of negative selection and genetic drift, and the present-day frequencies of the mutant alleles. We find that the degree of homoplasy can strongly depend on this frequency scale, which reflects the underlying timescales over which these mutations occurred. We show how these scaling properties can be used to isolate the effects of recombination, and discuss their implications for the rates of horizontal gene transfer in bacteria.},
}

@article {pmid39221153,
year = {2024},
author = {Belay, WY and Getachew, M and Tegegne, BA and Teffera, ZH and Dagne, A and Zeleke, TK and Abebe, RB and Gedif, AA and Fenta, A and Yirdaw, G and Tilahun, A and Aschale, Y},
title = {Mechanism of antibacterial resistance, strategies and next-generation antimicrobials to contain antimicrobial resistance: a review.},
journal = {Frontiers in pharmacology},
volume = {15},
number = {},
pages = {1444781},
pmid = {39221153},
issn = {1663-9812},
abstract = {Antibacterial drug resistance poses a significant challenge to modern healthcare systems, threatening our ability to effectively treat bacterial infections. This review aims to provide a comprehensive overview of the types and mechanisms of antibacterial drug resistance. To achieve this aim, a thorough literature search was conducted to identify key studies and reviews on antibacterial resistance mechanisms, strategies and next-generation antimicrobials to contain antimicrobial resistance. In this review, types of resistance and major mechanisms of antibacterial resistance with examples including target site modifications, decreased influx, increased efflux pumps, and enzymatic inactivation of antibacterials has been discussed. Moreover, biofilm formation, and horizontal gene transfer methods has also been included. Furthermore, measures (interventions) taken to control antimicrobial resistance and next-generation antimicrobials have been discussed in detail. Overall, this review provides valuable insights into the diverse mechanisms employed by bacteria to resist the effects of antibacterial drugs, with the aim of informing future research and guiding antimicrobial stewardship efforts.},
}

@article {pmid39221073,
year = {2024},
author = {Xie, X and Deng, X and Chen, L and Yuan, J and Chen, H and Wei, C and Liu, X and Wuertz, S and Qiu, G},
title = {Integrated genomics provides insights into the evolution of the polyphosphate accumulation trait of Ca. Accumulibacter.},
journal = {Environmental science and ecotechnology},
volume = {20},
number = {},
pages = {100353},
pmid = {39221073},
issn = {2666-4984},
abstract = {Candidatus Accumulibacter, a prominent polyphosphate-accumulating organism (PAO) in wastewater treatment, plays a crucial role in enhanced biological phosphorus removal (EBPR). The genetic underpinnings of its polyphosphate accumulation capabilities, however, remain largely unknown. Here, we conducted a comprehensive genomic analysis of Ca. Accumulibacter-PAOs and their relatives within the Rhodocyclaceae family, identifying 124 core genes acquired via horizontal gene transfer (HGT) at its least common ancestor. Metatranscriptomic analysis of an enrichment culture of Ca. Accumulibacter revealed active transcription of 44 of these genes during an EBPR cycle, notably including the polyphosphate kinase 2 (PPK2) gene instead of the commonly recognized polyphosphate kinase 1 (PPK1) gene. Intriguingly, the phosphate regulon (Pho) genes showed minimal transcriptions, pointing to a distinctive fact of Pho dysregulation, where PhoU, the phosphate signaling complex protein, was not regulating the high-affinity phosphate transport (Pst) system, resulting in continuous phosphate uptake. To prevent phosphate toxicity, Ca. Accumulibacter utilized the laterally acquired PPK2 to condense phosphate into polyphosphate, resulting in the polyphosphate-accumulating feature. This study provides novel insights into the evolutionary emergence of the polyphosphate-accumulating trait in Ca. Accumulibacter, offering potential advancements in understanding the PAO phenotype in the EBPR process.},
}

@article {pmid39219575,
year = {2024},
author = {He, XY and Chen, JM and Li, ZZ},
title = {Complete organelle genomes of the threatened aquatic species Scheuchzeria palustris (Scheuchzeriaceae): Insights into adaptation and phylogenomic placement.},
journal = {Ecology and evolution},
volume = {14},
number = {9},
pages = {e70248},
pmid = {39219575},
issn = {2045-7758},
abstract = {Scheuchzeria palustris, the only species in the Scheuchzeriaceae family, plays a crucial role in methane production and transportation, influencing the global carbon cycle and maintaining ecosystem stability. However, it is now threatened by human activities and global warming. In this study, we generated new organelle genomes for S. palustris, with the plastome (pt) measuring 158,573 bp and the mitogenome (mt) measuring 420,724 bp. We predicted 296 RNA editing sites in mt protein-coding genes (PCGs) and 142 in pt-PCGs. Notably, abundant RNA editing sites in pt-PCGs likely originated from horizontal gene transfer between the plastome and mitogenome. Additionally, we identified positive selection signals in four mt-PCGs (atp4, ccmB, nad3, and sdh4) and one pt-PCG (rps7), which may contribute to the adaptation of S. palustris to low-temperature and high-altitude environments. Furthermore, we identified 35 mitochondrial plastid DNA (MTPT) segments totaling 58,479 bp, attributed to dispersed repeats near most MTPT. Phylogenetic trees reconstructed from mt- and pt-PCGs showed topologies consistent with the APG IV system. However, the conflicting position of S. palustris can be explained by significant differences in the substitution rates of its mt- and pt-PCGs (p < .001). In conclusion, our study provides vital genomic resources to support future conservation efforts and explores the adaptation mechanisms of S. palustris.},
}

@article {pmid39216666,
year = {2024},
author = {Qiu, T and Shen, L and Guo, Y and Gao, M and Gao, H and Li, Y and Zhao, G and Wang, X},
title = {Impact of aeration rate on the transfer range of antibiotic-resistant plasmids during manure composting.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {124851},
doi = {10.1016/j.envpol.2024.124851},
pmid = {39216666},
issn = {1873-6424},
abstract = {Conjugative plasmids are important vectors of mobile antibiotic resvistance genes (ARGs), facilitating their horizontal transfer within the environment. While composting is recognized as an effective method to reduce antibiotics and ARGs in animal manure, its impact on the bacterial host communities containing antibiotic-resistant plasmids remains unclear. In this study, we investigated the permissiveness of bacterial community during composting when challenged with multidrug-resistant conjugative RP4 plasmids, employing Pseudomonas putida as the donor strain. Ultimately, this represents the first exploration of the effects of aeration rates on the range of RP4 plasmid transfer hosts. Transconjugants were analyzed through fluorescent reporter gene-based fluorescence-activated cell sorting and Illumina sequencing. Overall, aeration rates were found to influence various physicochemical parameters of compost, including temperature, pH, total organic matter, total nitrogen, and potassium. Regarding RP4 plasmid host bacteria, the dominant phylum was determined to shift from Bacteroidetes in the raw material to Proteobacteria in the compost. Notably, a moderate-intensity aeration rate (0.05 L/min/L) was found to be more effective in reducing the diversity and richness of the RP4 plasmid host bacterial community. Following composting, the total percentage of dominant transconjugant-related genera decreased by 66.15-76.62%. Ultimately, this study determined that the aeration rate negatively impacts RP4 plasmid host abundance primarily through alterations to the environmental factors during composting. In summary, these findings enhance our understanding of plasmid host bacterial communities under varying composting aeration rates and offer novel insights into preventing the dissemination of ARGs from animal manure to farmland.},
}

@article {pmid39216410,
year = {2024},
author = {Vissapragada, M and Addala, S and Aggunna, M and Sodasani, M and Grandhi, AVKS and Yedidi, RS},
title = {Leveraging the potential of bacterial lateral gene transfer in boosting the efficacy of an edible probiotic prototype yogurt vaccine for COVID-19.},
journal = {Biochemical and biophysical research communications},
volume = {734},
number = {},
pages = {150622},
doi = {10.1016/j.bbrc.2024.150622},
pmid = {39216410},
issn = {1090-2104},
abstract = {Administration of coronavirus disease-2019 (COVID-19) vaccines with appropriate booster doses through painful injections under clinical supervision was challenging during the recent COVID-19 pandemic. As an alternative solution, we designed a safer, edible probiotic yogurt vaccine prototype (YoVac) that can be orally consumed by circumventing painful injections and clinical supervision. We hypothesized that YoVac prepared using Lactobacillus carrying an antigen coding gene (donor) can transfer the same to other bacteria (recipients) in the human gut microbiome (hgMb) through lateral gene transfer (LGT) for boosted antigen levels potentially triggering a robust immune response. In this study we confirmed the in vitro LGT efficiency of a plasmid (pRBD-Amp[r]) containing severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) spike protein-receptor binding domain (RBD) coding gene along with an ampicillin-resistance gene (selection marker) from the probiotic Lactobacillus (donor) cultured from homemade yogurt to E. coli and Helicobacter pylori (recipients). Both the donor and recipient bacteria not only exhibited ampicillin-resistance from pRBD-Amp[r] but also expressed RBD protein. Furthermore, Lactobacillus isolated from YoVac consistently showed the expression of RBD protein over a period of one month confirming the shelf life of our prototype stored at 4 °C. Taken together, our in vitro results provide a preliminary basis for the potential in vivo transfer of RBD coding gene from YoVac to other bacterial species in the hgMb through LGT and may potentially boost the vaccine dosage by delegating them.},
}

@article {pmid39216330,
year = {2024},
author = {Fernández-Arévalo, U and Fuchs, J and Boll, M and Díaz, E},
title = {Transcriptional regulation of the anaerobic 3-hydroxybenzoate degradation pathway in Aromatoleum sp. CIB.},
journal = {Microbiological research},
volume = {288},
number = {},
pages = {127882},
doi = {10.1016/j.micres.2024.127882},
pmid = {39216330},
issn = {1618-0623},
abstract = {Phenolic compounds are commonly found in anoxic environments, where they serve as both carbon and energy sources for certain anaerobic bacteria. The anaerobic breakdown of m-cresol, catechol, and certain lignin-derived compounds yields the central intermediate 3-hydroxybenzoate/3-hydroxybenzoyl-CoA. In this study, we have characterized the transcription and regulation of the hbd genes responsible for the anaerobic degradation of 3-hydroxybenzoate in the β-proteobacterium Aromatoleum sp. CIB. The hbd cluster is organized in three catabolic operons and a regulatory hbdR gene that encodes a dimeric transcriptional regulator belonging to the TetR family. HbdR suppresses the activity of the three catabolic promoters (PhbdN, PhbdE and PhbdH) by binding to a conserved palindromic operator box (ATGAATGAN4TCATTCAT). 3-Hydroxybenzoyl-CoA, the initial intermediate of the 3-hydroxybenzoate degradation pathway, along with benzoyl-CoA, serve as effector molecules that bind to HbdR inducing the expression of the hbd genes. Moreover, the hbd genes are subject to additional regulation influenced by the presence of non-aromatic carbon sources (carbon catabolite repression), and their expression is induced in oxygen-deprived conditions by the AcpR transcriptional activator. The prevalence of the hbd cluster among members of the Aromatoleum/Thauera bacterial group, coupled with its association with mobile genetic elements, suggests acquisition through horizontal gene transfer. These findings significantly enhance our understanding of the regulatory mechanisms governing the hbd gene cluster in bacteria, paving the way for further exploration into the anaerobic utilization/valorization of phenolic compounds derived from lignin.},
}

@article {pmid39214976,
year = {2024},
author = {Yi, X and Liang, JL and Wen, P and Jia, P and Feng, SW and Liu, SY and Zhuang, YY and Guo, YQ and Lu, JL and Zhong, SJ and Liao, B and Wang, Z and Shu, WS and Li, JT},
title = {Giant viruses as reservoirs of antibiotic resistance genes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7536},
pmid = {39214976},
issn = {2041-1723},
mesh = {*Phylogeny ; *Giant Viruses/genetics ; *Genome, Viral/genetics ; Drug Resistance, Microbial/genetics ; Bacteriophages/genetics/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Metagenome/genetics ; Gene Transfer, Horizontal ; Trimethoprim/pharmacology ; Drug Resistance, Bacterial/genetics ; },
abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs; also called giant viruses), constituting the phylum Nucleocytoviricota, can infect a wide range of eukaryotes and exchange genetic material with not only their hosts but also prokaryotes and phages. A few NCLDVs were reported to encode genes conferring resistance to beta‑lactam, trimethoprim, or pyrimethamine, suggesting that they are potential vehicles for the transmission of antibiotic resistance genes (ARGs) in the biome. However, the incidence of ARGs across the phylum Nucleocytoviricota, their evolutionary characteristics, their dissemination potential, and their association with virulence factors remain unexplored. Here, we systematically investigated ARGs of 1416 NCLDV genomes including those of almost all currently available cultured isolates and high-quality metagenome-assembled genomes from diverse habitats across the globe. We reveal that 39.5% of them carry ARGs, which is approximately 37 times higher than that for phage genomes. A total of 12 ARG types are encoded by NCLDVs. Phylogenies of the three most abundant NCLDV-encoded ARGs hint that NCLDVs acquire ARGs from not only eukaryotes but also prokaryotes and phages. Two NCLDV-encoded trimethoprim resistance genes are demonstrated to confer trimethoprim resistance in Escherichia coli. The presence of ARGs in NCLDV genomes is significantly correlated with mobile genetic elements and virulence factors.},
}

*Phylogeny
*Giant Viruses/genetics
*Genome, Viral/genetics
Drug Resistance, Microbial/genetics
Bacteriophages/genetics/isolation & purification
Anti-Bacterial Agents/pharmacology
Metagenome/genetics
Gene Transfer, Horizontal
Trimethoprim/pharmacology
Drug Resistance, Bacterial/genetics

@article {pmid39047887,
year = {2024},
author = {Wu, X and Jia, W and Fang, Z and Sun, H and Wang, G and Liu, L and Zheng, M and Chen, G},
title = {Cyanobacteria mediate the dissemination of bacterial antibiotic resistance through conjugal transfer.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {359},
number = {},
pages = {124592},
doi = {10.1016/j.envpol.2024.124592},
pmid = {39047887},
issn = {1873-6424},
mesh = {*Drug Resistance, Bacterial/genetics ; *Microcystis/genetics ; *Gene Transfer, Horizontal ; *Cyanobacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Genes, Bacterial ; Bacteria/genetics/drug effects ; },
abstract = {Cyanobacterial blooms are expanding world-wide in freshwater and marine environments, and can cause serious ecological and environmental issues, which also contribute to the spread of antibiotic resistance genes (ARGs). However, the mechanistic understanding of cyanobacteria-mediated resistance dynamics is not fully elucidated yet. We selected Microcystis aeruginosa as a model cyanobacteria to illustrate how cyanobacteria mediate the evolution and transfer processes of bacterial antibiotic resistance. The results show that the presence of cyanobacteria significantly decreased the abundance of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) by 3%-99% and 2%-18%, respectively. In addition, it clearly altered bacterial community structure, with the dominant genera evolving from Acinetobacter (27%) and Enterobacter (42%) to Porphyrobacter (59%). The abundance of ARGs positively correlated with Proteobacteria and Firmicutes, rather than Cyanobacteria, and Bacteroidetes. In the presence of cyanobacteria, the transfer events of bacterial resistance genes via conjugation were found to decrease by 10%-89% (p < 0.05). Surprisingly, we found an extradentary high transfer frequency (about 0.1) for the ARGs via plasmid conjugation from the bacteria into M. aeruginosa population. It confirmed the role of cyanobacterial population as the competent hosts to facilitate ARGs spreading. Our findings provide valuable information on the risk evaluation of ARGs caused by cyanobacterial blooms in aquatic environments, key for the protection and assessment of aquatic environmental quality.},
}

*Drug Resistance, Bacterial/genetics
*Microcystis/genetics
*Gene Transfer, Horizontal
*Cyanobacteria/genetics
Anti-Bacterial Agents/pharmacology
Conjugation, Genetic
Genes, Bacterial
Bacteria/genetics/drug effects

@article {pmid39214865,
year = {2024},
author = {Fonseca, DR and Day, LA and Crone, KK and Costa, KC},
title = {An Extracellular, Ca[2+]-Activated Nuclease (EcnA) Mediates Transformation in a Naturally Competent Archaeon.},
journal = {Molecular microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mmi.15311},
pmid = {39214865},
issn = {1365-2958},
support = {MCB-2148165//National Science Foundation/ ; },
abstract = {Transformation, the uptake of DNA directly from the environment, is a major driver of gene flow in microbial populations. In bacteria, DNA uptake requires a nuclease that processes dsDNA to ssDNA, which is subsequently transferred into the cell and incorporated into the genome. However, the process of DNA uptake in archaea is still unknown. Previously, we cataloged genes essential to natural transformation in Methanococcus maripaludis, but few homologs of bacterial transformation-associated genes were identified. Here, we characterize one gene, MMJJ_16440 (named here as ecnA), to be an extracellular nuclease. We show that EcnA is Ca[2+]-activated, present on the cell surface, and essential for transformation. While EcnA can degrade several forms of DNA, the highest activity was observed with ssDNA as a substrate. Activity was also observed with circular dsDNA, suggesting that EcnA is an endonuclease. This is the first biochemical characterization of a transformation-associated protein in a member of the archaeal domain and suggests that both archaeal and bacterial transformation initiate in an analogous fashion.},
}

@article {pmid39214042,
year = {2024},
author = {Li, G and Long, TF and Zhou, SY and Xia, LJ and Gao, A and Wan, L and Diao, XY and He, YZ and Sun, RY and Yang, JT and Tang, SQ and Ren, H and Fang, LX and Liao, XP and Liu, YH and Chen, L and Sun, J},
title = {CRISPR-AMRtracker: A novel toolkit to monitor the antimicrobial resistance gene transfer in fecal microbiota.},
journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy},
volume = {77},
number = {},
pages = {101142},
doi = {10.1016/j.drup.2024.101142},
pmid = {39214042},
issn = {1532-2084},
abstract = {The spread of antibiotic resistance genes (ARGs), particularly those carried on plasmids, poses a major risk to global health. However, the extent and frequency of ARGs transfer in microbial communities among human, animal, and environmental sectors is not well understood due to a lack of effective tracking tools. We have developed a novel fluorescent tracing tool, CRISPR-AMRtracker, to study ARG transfer. It combines CRISPR/Cas9 fluorescence tagging, fluorescence-activated cell sorting, 16S rRNA gene sequencing, and microbial community analysis. CRISPR-AMRtracker integrates a fluorescent tag immediately downstream of ARGs, enabling the tracking of ARG transfer without compromising the host cell's antibiotic susceptibility, fitness, conjugation, and transposition. Notably, our experiments demonstrate that sfGFP-tagged plasmid-borne mcr-1 can transfer across diverse bacterial species within fecal samples. This innovative approach holds the potential to illuminate the dynamics of ARG dissemination and provide valuable insights to shape effective strategies in mitigating the escalating threat of antibiotic resistance.},
}

@article {pmid39213533,
year = {2024},
author = {Zeng, Q and Wu, X and Song, M and Jiang, L and Zeng, Q and Qiu, R and Luo, C},
title = {Opposite Effects of Planting on Antibiotic Resistomes in Rhizosphere Soil with Different Sulfamethoxazole Levels.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c04258},
pmid = {39213533},
issn = {1520-5118},
abstract = {Achieving consensus about the rhizosphere effect on soil antibiotic resistomes is challenging due to the variability in antibiotic concentrations, sources, and the elusory underlying mechanisms. Here, we characterized the antibiotic resistomes in both the rhizosphere and bulk soils of soybean plants grown in environments with varying levels of antibiotic contamination, using sulfamethoxazole (SMX) as a model compound. We also investigated the factors influencing resistome profiles. Soybean cultivation altered the structure of antibiotic-resistant genes (ARGs) and increased their absolute abundance. However, the rhizosphere effect on the relative abundance of ARGs was dependent on SMX concentrations. At low SMX levels, the rhizosphere effect was characterized by the inhibition of antibiotic-resistant bacteria (ARBs) and the promotion of sensitive bacteria. In contrast, at high SMX levels, the rhizosphere promoted the growth of ARBs and facilitated horizontal gene transfer of ARGs. This novel mechanism provides new insights into accurately assessing the rhizosphere effect on soil antibiotic resistomes.},
}

@article {pmid39213158,
year = {2024},
author = {Ma, Y and Kan, A and Johnson, DR},
title = {Metabolic interactions control the transfer and spread of plasmid-encoded antibiotic resistance during surface-associated microbial growth.},
journal = {Cell reports},
volume = {43},
number = {9},
pages = {114653},
doi = {10.1016/j.celrep.2024.114653},
pmid = {39213158},
issn = {2211-1247},
abstract = {Surface-associated microbial systems are hotspots for the spread of plasmid-encoded antibiotic resistance, but how surface association affects plasmid transfer and proliferation remains unclear. Surface association enables prolonged spatial proximities between different populations, which promotes plasmid transfer between them. However, surface association also fosters strong metabolic interactions between different populations, which can direct their spatial self-organization with consequences for plasmid transfer and proliferation. Here, we hypothesize that metabolic interactions direct the spatial self-organization of different populations and, in turn, regulate the spread of plasmid-encoded antibiotic resistance. We show that resource competition causes populations to spatially segregate, which represses plasmid transfer. In contrast, resource cross-feeding causes populations to spatially intermix, which promotes plasmid transfer. We further show that the spatial positionings that emerge from metabolic interactions determine the proliferation of plasmid recipients. Our results demonstrate that metabolic interactions are important regulators of both the transfer and proliferation of plasmid-encoded antibiotic resistance.},
}

@article {pmid39211246,
year = {2024},
author = {Hughes Lago, C and Blackburn, D and Kinder Pavlicek, M and Threadgill, DS},
title = {Comparative Genomic Analysis of Campylobacter rectus and Closely Related Species.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.07.26.605372},
pmid = {39211246},
issn = {2692-8205},
abstract = {Campylobacter rectus is a gram-negative, anaerobic bacterium strongly associated with periodontitis. It also causes various extraoral infections and is linked to adverse pregnancy outcomes in humans and murine models. C. rectus and related oral Campylobacters have been termed "emerging Campylobacter species" because infections by these organisms are likely underreported. Previously, no comparative methods have been used to analyze more than single C. rectus strains and until recently, very few C. rectus genomes have been publicly available. More sequenced genomes and comparative analyses are needed to study the genomic features and pathogenicity of this species. We sequenced eight new C. rectus strains and used comparative methods to identify regions of interest. An emphasis was put on the type III flagellar secretion system (T3SS), type IV secretion system (T4SS), and type VI secretion system (T6SS) because these protein complexes are important for pathogenesis in other Campylobacter species. RAST, BV-BRC, and other bioinformatics tools were used to assemble, annotate, and compare these regions in the genomes. The pan-genome of C. rectus consists of 2670 genes with core and accessory genomes of 1429 and 1241 genes, respectively. All isolates analyzed in this study have T3SS and T6SS hallmark proteins, while five of the isolates are missing a T4SS system. Twenty-one prophage clusters were identified across the panel of isolates, including four that appear intact. Overall, significant genomic islands were found, suggesting regions in the genomes that underwent horizontal gene transfer. Additionally, the high frequency of CRISPR arrays and other repetitive elements has led to genome rearrangements across the strains, including in areas adjacent to secretion system gene clusters. This study describes the substantial diversity present among C. rectus isolates and highlights tools/assays that have been developed to permit functional genomic studies. Additionally, we have expanded the studies on C. showae T4SS since we have two new C. showae genomes to report. We also demonstrate that unlike C. rectus , C showae does not demonstrate evidence of intact T6SS except for the strain CAM. The only strain of sequenced C. massilensis has neither T4SS or T6SS.},
}

@article {pmid39211212,
year = {2024},
author = {Marcarian, HQ and Sivakoses, A and Arias, AM and Ihedioha, OC and Lee, BR and Bishop, MC and Bothwell, ALM},
title = {Renal cancer cells acquire immune surface protein through trogocytosis and horizontal gene transfer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.08.07.607036},
pmid = {39211212},
issn = {2692-8205},
abstract = {UNLABELLED: Trogocytosis is an underappreciated phenomenon that shapes the immune microenvironment surrounding many types of solid tumors. The consequences of membrane-bound proteins being deposited from a donor immune cell to a recipient cancer cell via trogocytosis are still unclear. Here, we report that human clear cell renal carcinoma tumors stably express the lymphoid markers CD45, CD56, CD14, and CD16. Flow cytometry performed on fresh kidney tumors revealed consistent CD45 expression on tumor cells, as well as varying levels of the other markers mentioned previously. These results were consistent with our immunofluorescent analysis, which also revealed colocalization of lymphoid markers with carbonic anhydrase 9 (CAIX), a standard kidney tumor marker. RNA analysis showed a significant upregulation of genes typically associated with immune cells in tumor cells following trogocytosis. Finally, we show evidence of chromosomal DNA being transferred from immune cells to tumor cells during trogocytosis. This horizontal gene transfer has transcriptional consequences in the recipient tumor cell, resulting in a fusion phenotype that expressed both immune and cancer specific proteins. This work demonstrates a novel mechanism by which tumor cell protein expression is altered through the acquisition of surface membrane fragments and genomic DNA from infiltrating lymphocytes. These results alter the way in which we understand tumor-immune cell interactions and may reveal new insights into the mechanisms by which tumors develop. Additionally, further studies into trogocytosis will help push the field towards the next generation of immunotherapies and biomarkers for treating renal cell carcinoma and other types of cancers.

SIGNIFICANCE STATEMENT: We have identified trogocytosis as a mechanism by which human clear cell renal carcinoma tumors acquire lymphocyte surface protein expression from tumor infiltrating immune cells. In addition to the transfer of membrane fragments, we have provided evidence to show that genomic DNA is transferred from a normal immune cell to a tumor cell during trogocytosis. This process alters the transcriptome of cancer cells such that they express significantly more mRNA for immune proteins such as the lymphocyte marker CD45 compared to tumor cells that have not undergone trogocytosis. This study provides an in-depth analysis of the interactions between cancer cells and tumor infiltrating lymphocytes, and how these interactions alter the development of human tumors.},
}